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Schön ME, Abarenkov K, Garnica S. Host generalists dominate fungal communities associated with alpine knotweed roots: a study of Sebacinales. PeerJ 2022; 10:e14047. [PMID: 36217381 PMCID: PMC9547586 DOI: 10.7717/peerj.14047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 08/22/2022] [Indexed: 01/19/2023] Open
Abstract
Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity and specificity from root tips of B. vivipara in two local mountain ecosystems as well as on a global scale. Sequences were generated by Sanger sequencing of the internal transcribed spacer (ITS) region followed by an analysis of accurately annotated nuclear segments including ITS1-5.8S-ITS2 sequences available from public databases. In total, 181 different UNITE species hypotheses (SHs) were detected to be fungi associated with B. vivipara, 73 of which occurred in the Bavarian Alps and nine in the Swabian Alps-with one SH shared among both mountains. In both sites as well as in additional public data, individuals of B. vivipara were found to contain phylogenetically diverse fungi, with the Basidiomycota, represented by the Thelephorales and Sebacinales, being the most dominant. A comparative analysis of the diversity of the Sebacinales associated with B. vivipara and other co-occurring plant genera showed that the highest number of sebacinoid SHs were associated with Quercus and Pinus, followed by Bistorta. A comparison of B. vivipara with plant families such as Ericaceae, Fagaceae, Orchidaceae, and Pinaceae showed a clear trend: Only a few species were specific to B. vivipara and a large number of SHs were shared with other co-occurring non-B. vivipara plant species. In Sebacinales, the majority of SHs associated with B. vivipara belonged to the ectomycorrhiza (ECM)-forming Sebacinaceae, with fewer SHs belonging to the Serendipitaceae encompassing diverse ericoid-orchid-ECM-endophytic associations. The large proportion of non-host-specific fungi able to form a symbiosis with other non-B. vivipara plants could suggest that the high fungal diversity in B. vivipara comes from an active recruitment of their associates from the co-occurring vegetation. The non-host-specificity suggests that this strategy may offer ecological advantages; specifically, linkages with generalist rather than specialist fungi. Proximity to co-occurring non-B. vivipara plants can maximise the fitness of B. vivipara, allowing more rapid and easy colonisation of the available habitats.
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Affiliation(s)
- Max Emil Schön
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Sigisfredo Garnica
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
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Wang X, Han Q. A Closer Examination of the 'Abundant-Center' for Ectomycorrhizal Fungal Community Associated With Picea crassifolia in China. FRONTIERS IN PLANT SCIENCE 2022; 13:759801. [PMID: 35283884 PMCID: PMC8908202 DOI: 10.3389/fpls.2022.759801] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
A long-standing hypothesis in biogeography predicts that a species' abundance is highest at the center of its geographical range and decreases toward its edges. In this study, we test the abundant-center hypothesis of ectomycorrhizal (ECM) fungal communities associated with Picea crassifolia, an endemic species widely distributed in northwest China. We analyzed the taxonomic richness and the relative abundance of ECM fungi in four main distribution areas, from center to edges. In total, 234 species of ECM fungi were detected, and of these, 137 species were shared among all four sites. Inocybe, Sebacina, Tomentella, and Cortinarius were the dominant genera. ECM fungal richness and biodiversity were highest at the central and lower at peripheral sites. Our results indicated that ECM fungal species richness was consistent with the abundant-center hypothesis, while the relative abundances of individual fungal genera shifted inconsistently across the plant's range.
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Affiliation(s)
- Xiaobing Wang
- School of Civil Engineering and Architecture, Xinxiang University, Xinxiang, China
| | - Qisheng Han
- Farmland Irrigation Research Institute, Chinese Academy of Agricultural Sciences, Xinxiang, China
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3
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Seed quantity affects the fungal community composition detected using metabarcoding. Sci Rep 2022; 12:3060. [PMID: 35197533 PMCID: PMC8866403 DOI: 10.1038/s41598-022-06997-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/10/2022] [Indexed: 11/08/2022] Open
Abstract
Pest introductions via trade in tree seed may result from a lack of adequate survey and validation protocols. Developing better diagnostic protocols to identify potentially harmful pests and pathogens in forest tree seed is of critical importance. High-throughput sequencing-based barcoding and metabarcoding provide effective tools for screening potentially harmful organisms in various plant materials, including seeds. However, the sample size needed to detect the total microorganism diversity of a community is a major challenge in microbiome studies. In this work, we examined how increasing sample size (ranging between 100 and 1000 seeds) influences diversity of fungal communities detected by high throughput sequencing in Pinus sylvestris seeds. Our results showed that as sample size increased, fungal alpha diversity also increased. Beta-diversity estimators detected significant differences between the mycobiota from different samples. However, taxonomic and functional diversity were not correlated with sample size. In addition, we found that increasing the number of PCR replicates resulted in a higher abundance of plant pathogens. We concluded that for the purpose of screening for potentially harmful pathogens using HTS, greater efforts should be made to increase the sample size and replicates when testing tree seed.
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Høyer AK, Hodkinson TR. Hidden Fungi: Combining Culture-Dependent and -Independent DNA Barcoding Reveals Inter-Plant Variation in Species Richness of Endophytic Root Fungi in Elymus repens. J Fungi (Basel) 2021; 7:jof7060466. [PMID: 34207673 PMCID: PMC8226481 DOI: 10.3390/jof7060466] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 05/27/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
The root endophyte community of the grass species Elymus repens was investigated using both a culture-dependent approach and a direct amplicon sequencing method across five sites and from individual plants. There was much heterogeneity across the five sites and among individual plants. Focusing on one site, 349 OTUs were identified by direct amplicon sequencing but only 66 OTUs were cultured. The two approaches shared ten OTUs and the majority of cultured endophytes do not overlap with the amplicon dataset. Media influenced the cultured species richness and without the inclusion of 2% MEA and full-strength MEA, approximately half of the unique OTUs would not have been isolated using only PDA. Combining both culture-dependent and -independent methods for the most accurate determination of root fungal species richness is therefore recommended. High inter-plant variation in fungal species richness was demonstrated, which highlights the need to rethink the scale at which we describe endophyte communities.
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5
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Arraiano-Castilho R, Bidartondo MI, Niskanen T, Clarkson JJ, Brunner I, Zimmermann S, Senn-Irlet B, Frey B, Peintner U, Mrak T, Suz LM. Habitat specialisation controls ectomycorrhizal fungi above the treeline in the European Alps. THE NEW PHYTOLOGIST 2021; 229:2901-2916. [PMID: 33107606 DOI: 10.1111/nph.17033] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Alpine habitats are one of the most vulnerable ecosystems to environmental change, however, little information is known about the drivers of plant-fungal interactions in these ecosystems and their resilience to climate change. We investigated the influence of the main drivers of ectomycorrhizal (EM) fungal communities along elevation and environmental gradients in the alpine zone of the European Alps and measured their degree of specialisation using network analysis. We sampled ectomycorrhizas of Dryas octopetala, Bistorta vivipara and Salix herbacea, and soil fungal communities at 28 locations across five countries, from the treeline to the nival zone. We found that: (1) EM fungal community composition, but not richness, changes along elevation, (2) there is no strong evidence of host specialisation, however, EM fungal networks in the alpine zone and within these, EM fungi associated with snowbed communities, are more specialised than in other alpine habitats, (3) plant host population structure does not influence EM fungal communities, and (4) most variability in EM fungal communities is explained by fine-scale changes in edaphic properties, like soil pH and total nitrogen. The higher specialisation and narrower ecological niches of these plant-fungal interactions in snowbed habitats make these habitats particularly vulnerable to environmental change in alpine ecosystems.
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Affiliation(s)
- Ricardo Arraiano-Castilho
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Martin I Bidartondo
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Tuula Niskanen
- Identification and Naming, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - James J Clarkson
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, 8903, Switzerland
| | - Stephan Zimmermann
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, 8903, Switzerland
| | - Beatrice Senn-Irlet
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, 8903, Switzerland
| | - Beat Frey
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, 8903, Switzerland
| | - Ursula Peintner
- Institute of Microbiology, University of Innsbruck, Technikerstraße 25d, Innsbruck, 6020, Austria
| | - Tanja Mrak
- Slovenian Forestry Institute, Večna pot 2, Ljubljana, 1000, Slovenia
| | - Laura M Suz
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK
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Aas AB, Andrew CJ, Blaalid R, Vik U, Kauserud H, Davey ML. Fine-scale diversity patterns in belowground microbial communities are consistent across kingdoms. FEMS Microbiol Ecol 2020; 95:5484836. [PMID: 31049552 DOI: 10.1093/femsec/fiz058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
The belowground environment is heterogeneous and complex at fine spatial scales. Physical structures, biotic components and abiotic conditions create a patchwork mosaic of potential niches for microbes. Questions remain about mechanisms and patterns of community assembly belowground, including: Do fungal and bacterial communities assemble differently? How do microbes reach the roots of host plants? Within a 4 m2 plot in alpine vegetation, high throughput sequencing of the 16S (bacteria) and ITS1 (fungal) ribosomal RNA genes was used to characterise microbial community composition in roots and adjacent soil of a viviparous host plant (Bistorta vivipara). At fine spatial scales, beta-diversity patterns in belowground bacterial and fungal communities were consistent, although compositional change was greater in bacteria than fungi. Spatial structure and distance-decay relationships were also similar for bacteria and fungi, with significant spatial structure detected at <50 cm among root- but not soil-associated microbes. Recruitment of root microbes from the soil community appeared limited at this sampling and sequencing depth. Possible explanations for this include recruitment from low-abundance populations of soil microbes, active recruitment from neighbouring plants and/or vertical transmission of symbionts to new clones, suggesting varied methods of microbial community assembly for viviparous plants. Our results suggest that even at relatively small spatial scales, deterministic processes play a significant role in belowground microbial community structure and assembly.
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Affiliation(s)
- Anders Bjørnsgaard Aas
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carrie J Andrew
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rakel Blaalid
- Norwegian Institute for Nature Research, Bergen, Norway
| | - Unni Vik
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Håvard Kauserud
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marie L Davey
- Section of Genetic and Evolution Department of Biosciences, University of Oslo, Oslo, Norway.,Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway
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7
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Gupta S, Chaturvedi P, Kulkarni MG, Van Staden J. A critical review on exploiting the pharmaceutical potential of plant endophytic fungi. Biotechnol Adv 2020; 39:107462. [DOI: 10.1016/j.biotechadv.2019.107462] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/22/2019] [Accepted: 10/22/2019] [Indexed: 02/08/2023]
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8
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Thoen E, Aas AB, Vik U, Brysting AK, Skrede I, Carlsen T, Kauserud H. A single ectomycorrhizal plant root system includes a diverse and spatially structured fungal community. MYCORRHIZA 2019; 29:167-180. [PMID: 30929039 DOI: 10.1007/s00572-019-00889-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 03/19/2019] [Indexed: 05/11/2023]
Abstract
Although only a relatively small proportion of plant species form ectomycorrhizae with fungi, it is crucial for growth and survival for a number of widespread woody plant species. Few studies have attempted to investigate the fine scale spatial structure of entire root systems of adult ectomycorrhizal (EcM) plants. Here, we use the herbaceous perennial Bistorta vivipara to map the entire root system of an adult EcM plant and investigate the spatial structure of its root-associated fungi. All EcM root tips were sampled, mapped and identified using a direct PCR approach and Sanger sequencing of the internal transcribed spacer region. A total of 32.1% of all sampled root tips (739 of 2302) were successfully sequenced and clustered into 41 operational taxonomic units (OTUs). We observed a clear spatial structuring of the root-associated fungi within the root system. Clusters of individual OTUs were observed in the younger parts of the root system, consistent with observations of priority effects in previous studies, but were absent from the older parts of the root system. This may suggest a succession and fragmentation of the root-associated fungi even at a very fine scale, where competition likely comes into play at different successional stages within the root system.
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Affiliation(s)
- Ella Thoen
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway.
| | - Anders B Aas
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
- Bymiljøetaten Oslo Kommune, PO box 636, Løren, 0507, Oslo, Norway
| | - Unni Vik
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Anne K Brysting
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
| | - Tor Carlsen
- The Natural History museum, University of Oslo, PO box 1172, Blindern, 0318, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, PO box 1066, Blindern, 0316, Oslo, Norway
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9
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Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE, Selbmann L. Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities. Life (Basel) 2018; 8:E19. [PMID: 29865244 PMCID: PMC6027399 DOI: 10.3390/life8020019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
- Italian National Antarctic Museum (MNA), Mycological Section, Genoa 16166, Italy.
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Sheldrake M, Rosenstock NP, Revillini D, Olsson PA, Mangan S, Sayer EJ, Wallander H, Turner BL, Tanner EVJ. Arbuscular mycorrhizal fungal community composition is altered by long-term litter removal but not litter addition in a lowland tropical forest. THE NEW PHYTOLOGIST 2017; 214:455-467. [PMID: 28042878 DOI: 10.1111/nph.14384] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
Tropical forest productivity is sustained by the cycling of nutrients through decomposing organic matter. Arbuscular mycorrhizal (AM) fungi play a key role in the nutrition of tropical trees, yet there has been little experimental investigation into the role of AM fungi in nutrient cycling via decomposing organic material in tropical forests. We evaluated the responses of AM fungi in a long-term leaf litter addition and removal experiment in a tropical forest in Panama. We described AM fungal communities using 454-pyrosequencing, quantified the proportion of root length colonised by AM fungi using microscopy, and estimated AM fungal biomass using a lipid biomarker. AM fungal community composition was altered by litter removal but not litter addition. Root colonisation was substantially greater in the superficial organic layer compared with the mineral soil. Overall colonisation was lower in the litter removal treatment, which lacked an organic layer. There was no effect of litter manipulation on the concentration of the AM fungal lipid biomarker in the mineral soil. We hypothesise that reductions in organic matter brought about by litter removal may lead to AM fungi obtaining nutrients from recalcitrant organic or mineral sources in the soil, besides increasing fungal competition for progressively limited resources.
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Affiliation(s)
- Merlin Sheldrake
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
| | - Nicholas P Rosenstock
- Center for Environmental and Climate Research, Lund University, Lund, 22362, Sweden
- Department of Biology, Lund University, Lund, 22362, Sweden
| | - Daniel Revillini
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
- Department of Biological Sciences, Northern Arizona University, PO BOX 5640, Flagstaff, AZ, 86011, USA
| | | | - Scott Mangan
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
- Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA
| | - Emma J Sayer
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | | | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama
| | - Edmund V J Tanner
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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11
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Davey ML, Skogen MJ, Heegaard E, Halvorsen R, Kauserud H, Ohlson M. Host and tissue variations overshadow the response of boreal moss-associated fungal communities to increased nitrogen load. Mol Ecol 2017; 26:571-588. [DOI: 10.1111/mec.13938] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/28/2016] [Accepted: 09/30/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Marie L. Davey
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
- Section for Genetics and Evolutionary Biology; Department of Biosciences; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Marte J. Skogen
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
| | - Einar Heegaard
- Norwegian Forest and Landscape Institute; Fanaflaten 4 NO-5244 Fana Norway
| | - Rune Halvorsen
- Department of Botany; Natural History Museum; University of Oslo; PO Box 1172 Blindern NO-0318 Oslo Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology; Department of Biosciences; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Mikael Ohlson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
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12
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Tahon G, Tytgat B, Willems A. Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica. Front Microbiol 2016; 7:2026. [PMID: 28066352 PMCID: PMC5165242 DOI: 10.3389/fmicb.2016.02026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/02/2016] [Indexed: 01/10/2023] Open
Abstract
Microbial life in exposed terrestrial surface layers in continental Antarctica is faced with extreme environmental conditions, including scarcity of organic matter. Bacteria in these exposed settings can therefore be expected to use alternative energy sources such as solar energy, abundant during the austral summer. Using Illumina MiSeq sequencing, we assessed the diversity and abundance of four conserved protein encoding genes involved in different key steps of light-harvesting pathways dependent on (bacterio)chlorophyll (pufM, bchL/chlL, and bchX genes) and rhodopsins (actinorhodopsin genes), in exposed soils from the Sør Rondane Mountains, East Antarctica. Analysis of pufM genes, encoding a subunit of the type 2 photochemical reaction center found in anoxygenic phototrophic bacteria, revealed a broad diversity, dominated by Roseobacter- and Loktanella-like sequences. The bchL and chlL, involved in (bacterio)chlorophyll synthesis, on the other hand, showed a high relative abundance of either cyanobacterial or green algal trebouxiophyceael chlL reads, depending on the sample, while most bchX sequences belonged mostly to previously unidentified phylotypes. Rhodopsin-containing phototrophic bacteria could not be detected in the samples. Our results, while suggesting that Cyanobacteria and green algae are the main phototrophic groups, show that light-harvesting bacteria are nevertheless very diverse in microbial communities in Antarctic soils.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University Ghent, Belgium
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Mundra S, Bahram M, Eidesen PB. Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard. MYCORRHIZA 2016; 26:809-818. [PMID: 27325524 DOI: 10.1007/s00572-016-0716-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023]
Abstract
Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.
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Affiliation(s)
- Sunil Mundra
- The University Centre in Svalbard, P.O. Box 156, Longyearbyen, NO-9171, Norway.
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, Oslo, NO-0316, Norway.
| | - Mohammad Bahram
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, SE 75236, Sweden
- Institute of Ecology and Earth Sciences, Tartu University, 14A Ravila, Tartu, 50411, Estonia
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Morgado LN, Semenova TA, Welker JM, Walker MD, Smets E, Geml J. Long-term increase in snow depth leads to compositional changes in arctic ectomycorrhizal fungal communities. GLOBAL CHANGE BIOLOGY 2016; 22:3080-3096. [PMID: 27004610 DOI: 10.1111/gcb.13294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/16/2016] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Many arctic ecological processes are regulated by soil temperature that is tightly interconnected with snow cover distribution and persistence. Recently, various climate-induced changes have been observed in arctic tundra ecosystems, e.g. shrub expansion, resulting in reduction in albedo and greater C fixation in aboveground vegetation as well as increased rates of soil C mobilization by microbes. Importantly, the net effects of these shifts are unknown, in part because our understanding of belowground processes is limited. Here, we focus on the effects of increased snow depth, and as a consequence, increased winter soil temperature on ectomycorrhizal (ECM) fungal communities in dry and moist tundra. We analyzed deep DNA sequence data from soil samples taken at a long-term snow fence experiment in Northern Alaska. Our results indicate that, in contrast with previously observed responses of plants to increased snow depth at the same experimental site, the ECM fungal community of the dry tundra was more affected by deeper snow than the moist tundra community. In the dry tundra, both community richness and composition were significantly altered while in the moist tundra, only community composition changed significantly while richness did not. We observed a decrease in richness of Tomentella, Inocybe and other taxa adapted to scavenge the soil for labile N forms. On the other hand, richness of Cortinarius, and species with the ability to scavenge the soil for recalcitrant N forms, did not change. We further link ECM fungal traits with C soil pools. If future warmer atmospheric conditions lead to greater winter snow fall, changes in the ECM fungal community will likely influence C emissions and C fixation through altering N plant availability, fungal biomass and soil-plant C-N dynamics, ultimately determining important future interactions between the tundra biosphere and atmosphere.
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Affiliation(s)
- Luis N Morgado
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Section for Genetics and Evolutionary Biology (Evogene), Department of Biosciences, University of Oslo, P.O. Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Tatiana A Semenova
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Jeffrey M Welker
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK, USA
| | | | - Erik Smets
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
- Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Box 2437, 3001, Leuven, Belgium
| | - József Geml
- Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands
- Faculty of Science, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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15
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Rosenstock NP, Berner C, Smits MM, Krám P, Wallander H. The role of phosphorus, magnesium and potassium availability in soil fungal exploration of mineral nutrient sources in Norway spruce forests. THE NEW PHYTOLOGIST 2016; 211:542-553. [PMID: 26996085 DOI: 10.1111/nph.13928] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 02/02/2016] [Indexed: 06/05/2023]
Abstract
We investigated fungal growth and community composition in buried meshbags, amended with apatite, biotite or hornblende, in Norway spruce (Picea abies) forests of varying nutrient status. Norway spruce needles and soil collected from forests overlying serpentinite had low levels of potassium and phosphorus, those from granite had low levels of magnesium, whereas those from amphibolite had comparably high levels of these nutrients. We assayed the fungal colonization of meshbags by measuring ergosterol content and fungal community with 454 sequencing of the internal transcribed spacer region. In addition, we measured fine root density. Fungal biomass was increased by apatite amendment across all plots and particularly on the K- and P-deficient serpentinite plots, whereas hornblende and biotite had no effect on fungal biomass on any plots. Fungal community (total fungal and ectomycorrhizal) composition was affected strongly by sampling location and soil depth, whereas mineral amendments had no effect on community composition. Fine root biomass was significantly correlated with fungal biomass. Ectomycorrhizal communities may respond to increased host-tree phosphorus demand by increased colonization of phosphorus-containing minerals, but this does not appear to translate to a shift in ectomycorrhizal community composition. This growth response to nutrient demand does not appear to exist for potassium or magnesium limitation.
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Affiliation(s)
- Nicholas P Rosenstock
- Center for Environmental and Climate Research, Lund University, SE-22362, Lund, Sweden
| | - Christoffer Berner
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, SE-39182, Kalmar, Sweden
| | - Mark M Smits
- Center for Environmental Sciences, Hasselt University, Building D, Agoralaan, Diepenbeek, 3590, Limburg, Belgium
| | - Pavel Krám
- Czech Geological Survey, Klárov 3, 118 21, Prague 1, Czech Republic
| | - Håkan Wallander
- MEMEG, Department of Biology, Lund University, SE-22362, Lund, Sweden
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16
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Yang T, Weisenhorn P, Gilbert JA, Ni Y, Sun R, Shi Y, Chu H. Carbon constrains fungal endophyte assemblages along the timberline. Environ Microbiol 2016; 18:2455-69. [DOI: 10.1111/1462-2920.13153] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 11/23/2015] [Accepted: 11/23/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences 71 East Beijing Road Nanjing 210008 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Pamela Weisenhorn
- Argonne National Laboratory Institute for Genomics and Systems Biology Argonne IL 60439 USA
| | - Jack A. Gilbert
- Argonne National Laboratory Institute for Genomics and Systems Biology Argonne IL 60439 USA
- Departments of Ecology and Evolution
- Surgery University of Chicago Chicago IL 60637 USA
- Marine Biological Laboratory 7 MBL Street Woods Hole MA 02543 USA
- College of Environmental and Resource Sciences Zhejiang University Hangzhou 310058 China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences 71 East Beijing Road Nanjing 210008 China
| | - Ruibo Sun
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences 71 East Beijing Road Nanjing 210008 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences 71 East Beijing Road Nanjing 210008 China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil Science Chinese Academy of Sciences 71 East Beijing Road Nanjing 210008 China
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17
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Reininger V, Martinez-Garcia LB, Sanderson L, Antunes PM. Composition of fungal soil communities varies with plant abundance and geographic origin. AOB PLANTS 2015; 7:plv110. [PMID: 26371291 PMCID: PMC4614812 DOI: 10.1093/aobpla/plv110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/30/2015] [Accepted: 09/01/2015] [Indexed: 06/05/2023]
Abstract
Interactions of belowground fungal communities with exotic and native plant species may be important drivers of plant community structure in invaded grasslands. However, field surveys linking plant community structure with belowground fungal communities are missing. We investigated whether a selected number of abundant and relatively rare plants, either native or exotic, from an old-field site associate with different fungal communities. We also assessed whether these plants showed different symbiotic relationships with soil biota through their roots. We characterized the plant community and collected roots to investigate fungal communities using 454 pyrosequencing and assessed arbuscular mycorrhizal colonization and enemy-induced lesions. Differences in fungal communities were considered based on the assessment of α- and β diversity depending on plant 'abundance' and 'origin'. Plant abundance and origin determined the fungal community. Fungal richness was higher for native abundant as opposed to relatively rare native plant species. However, this was not observed for exotics of contrasting abundance. Regardless of their origin, β diversity was higher for rare than for abundant species. Abundant exotics in the community, which happen to be grasses, were the least mycorrhizal whereas rare natives were most susceptible to enemy attack. Our results suggest that compared with exotics, the relative abundance of remnant native plant species in our old-field site is still linked to the structure of belowground fungal communities. In contrast, exotic species may act as a disturbing agent contributing towards the homogenization of soil fungal communities, potentially changing feedback interactions.
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Affiliation(s)
- Vanessa Reininger
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4 Canada Present address: Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, 8820 Wädenswil, Switzerland Present address: ETH Zurich, Institute of Integrative Biology, Forest Pathology and Dendrology, Universitätstrasse 16, 8092 Zurich, Switzerland
| | - Laura B Martinez-Garcia
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4 Canada Present address: Department of Soil Quality, Wageningen University, 6700 AA, Wageningen, The Netherlands
| | - Laura Sanderson
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4 Canada
| | - Pedro M Antunes
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4 Canada
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18
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Geml J, Morgado LN, Semenova TA, Welker JM, Walker MD, Smets E. Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi. FEMS Microbiol Ecol 2015; 91:fiv095. [PMID: 26253509 DOI: 10.1093/femsec/fiv095] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2015] [Indexed: 11/13/2022] Open
Abstract
Fungi, including symbionts, pathogens and decomposers, play crucial roles in community dynamics and nutrient cycling in terrestrial ecosystems. Despite their ecological importance, the response of most arctic fungi to climate warming is unknown, so are their potential roles in driving the observed and predicted changes in tundra communities. We carried out deep DNA sequencing of soil samples to study the long-term effects of experimental warming on fungal communities in dry heath and moist tussock tundra in Arctic Alaska. The data presented here indicate that fungal community composition responds strongly to warming in the moist tundra, but not in the dry tundra. While total fungal richness was not significantly affected by warming, there were clear correlations among operational taxonomic unit richness of various ecological and taxonomic groups and long-term warming. Richness of ectomycorrhizal, ericoid mycorrhizal and lichenized fungi generally decreased with warming, while richness of saprotrophic, plant and animal pathogenic, and root endophytic fungi tended to increase in the warmed plots. More importantly, various taxa within these functional guilds followed opposing trends that highlight the importance of species-specific responses to warming. We recommend that species-level ecological differences be taken into account in climate change and nutrient cycling studies that involve arctic fungi.
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Affiliation(s)
- József Geml
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands Faculty of Science, Leiden University, PO Box 9502, 2300 RA Leiden, the Netherlands
| | - Luis N Morgado
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands
| | - Tatiana A Semenova
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands Faculty of Science, Leiden University, PO Box 9502, 2300 RA Leiden, the Netherlands
| | - Jeffrey M Welker
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA
| | | | - Erik Smets
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA Leiden, the Netherlands Faculty of Science, Leiden University, PO Box 9502, 2300 RA Leiden, the Netherlands Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Box 2437, 3001 Leuven, Belgium
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19
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A conserved arbuscular mycorrhizal fungal core-species community colonizes potato roots in the Andes. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0328-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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González-Tortuero E, Rusek J, Petrusek A, Gießler S, Lyras D, Grath S, Castro-Monzón F, Wolinska J. The Quantification of Representative Sequences pipeline for amplicon sequencing: case study on within-population ITS1 sequence variation in a microparasite infecting Daphnia. Mol Ecol Resour 2015; 15:1385-95. [PMID: 25728529 DOI: 10.1111/1755-0998.12396] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 11/28/2022]
Abstract
Next generation sequencing (NGS) platforms are replacing traditional molecular biology protocols like cloning and Sanger sequencing. However, accuracy of NGS platforms has rarely been measured when quantifying relative frequencies of genotypes or taxa within populations. Here we developed a new bioinformatic pipeline (QRS) that pools similar sequence variants and estimates their frequencies in NGS data sets from populations or communities. We tested whether the estimated frequency of representative sequences, generated by 454 amplicon sequencing, differs significantly from that obtained by Sanger sequencing of cloned PCR products. This was performed by analysing sequence variation of the highly variable first internal transcribed spacer (ITS1) of the ichthyosporean Caullerya mesnili, a microparasite of cladocerans of the genus Daphnia. This analysis also serves as a case example of the usage of this pipeline to study within-population variation. Additionally, a public Illumina data set was used to validate the pipeline on community-level data. Overall, there was a good correspondence in absolute frequencies of C. mesnili ITS1 sequences obtained from Sanger and 454 platforms. Furthermore, analyses of molecular variance (amova) revealed that population structure of C. mesnili differs across lakes and years independently of the sequencing platform. Our results support not only the usefulness of amplicon sequencing data for studies of within-population structure but also the successful application of the QRS pipeline on Illumina-generated data. The QRS pipeline is freely available together with its documentation under GNU Public Licence version 3 at http://code.google.com/p/quantification-representative-sequences.
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Affiliation(s)
- E González-Tortuero
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany.,Berlin Centre for Genomics in Biodiversity Research (BeGenDiv), Königin-Luise-Straße 6-8, 14195, Berlin, Germany.,Department of Biology II, Ludwig Maximilians University, Großhaderner Straße 2, 82512, Planegg-Martinsried, Germany
| | - J Rusek
- Department of Biology II, Ludwig Maximilians University, Großhaderner Straße 2, 82512, Planegg-Martinsried, Germany
| | - A Petrusek
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague, Czech Republic
| | - S Gießler
- Department of Biology II, Ludwig Maximilians University, Großhaderner Straße 2, 82512, Planegg-Martinsried, Germany
| | - D Lyras
- Department of Biology II, Ludwig Maximilians University, Großhaderner Straße 2, 82512, Planegg-Martinsried, Germany
| | - S Grath
- Department of Biology II, Ludwig Maximilians University, Großhaderner Straße 2, 82512, Planegg-Martinsried, Germany
| | - F Castro-Monzón
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
| | - J Wolinska
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Müggelseedamm 301, 12587, Berlin, Germany
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21
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Davey M, Blaalid R, Vik U, Carlsen T, Kauserud H, Eidesen PB. Primary succession ofBistorta vivipara(L.) Delabre (Polygonaceae) root-associated fungi mirrors plant succession in two glacial chronosequences. Environ Microbiol 2015; 17:2777-90. [DOI: 10.1111/1462-2920.12770] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Marie Davey
- Department of Arctic Biology; The University Centre in Svalbard (UNIS); P.O. Box 156 Longyearbyen 9171 Norway
- Department of Biology; University of Oslo; P.O. Box 1066 Blindern Oslo N-0316 Norway
| | - Rakel Blaalid
- Department of Biology; University of Oslo; P.O. Box 1066 Blindern Oslo N-0316 Norway
| | - Unni Vik
- Department of Biology; University of Oslo; P.O. Box 1066 Blindern Oslo N-0316 Norway
| | - Tor Carlsen
- Department of Biology; University of Oslo; P.O. Box 1066 Blindern Oslo N-0316 Norway
| | - Håvard Kauserud
- Department of Biology; University of Oslo; P.O. Box 1066 Blindern Oslo N-0316 Norway
| | - Pernille B. Eidesen
- Department of Arctic Biology; The University Centre in Svalbard (UNIS); P.O. Box 156 Longyearbyen 9171 Norway
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22
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Mundra S, Halvorsen R, Kauserud H, Müller E, Vik U, Eidesen PB. Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation. THE NEW PHYTOLOGIST 2015; 205:1587-1597. [PMID: 25483568 DOI: 10.1111/nph.13216] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/07/2014] [Indexed: 06/04/2023]
Abstract
Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.
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Affiliation(s)
- Sunil Mundra
- The University Centre in Svalbard (UNIS), PO Box 156, N-9171, Longyearbyen (Svalbard), Norway
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Rune Halvorsen
- Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318, Oslo, Norway
| | - Håvard Kauserud
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Eike Müller
- The University Centre in Svalbard (UNIS), PO Box 156, N-9171, Longyearbyen (Svalbard), Norway
| | - Unni Vik
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Pernille B Eidesen
- The University Centre in Svalbard (UNIS), PO Box 156, N-9171, Longyearbyen (Svalbard), Norway
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23
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Martínez-García LB, Richardson SJ, Tylianakis JM, Peltzer DA, Dickie IA. Host identity is a dominant driver of mycorrhizal fungal community composition during ecosystem development. THE NEW PHYTOLOGIST 2015; 205:1565-1576. [PMID: 25640965 DOI: 10.1111/nph.13226] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/13/2014] [Indexed: 05/26/2023]
Abstract
Little is known about the response of arbuscular mycorrhizal fungal communities to ecosystem development. We use a long-term soil chronosequence that includes ecosystem progression and retrogression to quantify the importance of host plant identity as a factor driving fungal community composition during ecosystem development. We identified arbuscular mycorrhizal fungi and plant species from 50 individual roots from each of 10 sites spanning 5-120 000 yr of ecosystem age using terminal restriction fragment length polymorphism (T-RFLP), Sanger sequencing and pyrosequencing. Arbuscular mycorrhizal fungal communities were highly structured by ecosystem age. There was strong niche differentiation, with different groups of operational taxonomic units (OTUs) being characteristic of early succession, ecosystem progression and ecosystem retrogression. Fungal alpha diversity decreased with ecosystem age, whereas beta diversity was high at early stages and lower in subsequent stages. A total of 39% of the variance in fungal communities was explained by host plant and site age, 29% of which was attributed to host and the interaction between host and site (24% and 5%, respectively). The strong response of arbuscular mycorrhizal fungi to ecosystem development appears to be largely driven by plant host identity, supporting the concept that plant and fungal communities are tightly coupled rather than independently responding to habitat.
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Affiliation(s)
- Laura B Martínez-García
- Landcare Research, Box 69040, Lincoln, 7640, New Zealand
- Algoma University, 1520 Queen Street East, Sault Ste. Marie, P6A 2G4, ON, Canada
- Centre for Ecology, Evolution and Environmental Changes (Ce3C), Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | | | - Jason M Tylianakis
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK
| | | | - Ian A Dickie
- Landcare Research, Box 69040, Lincoln, 7640, New Zealand
- Bio-Protection Research Centre, Lincoln University, Box 85084, Lincoln, 7647, New Zealand
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24
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Morgado LN, Semenova TA, Welker JM, Walker MD, Smets E, Geml J. Summer temperature increase has distinct effects on the ectomycorrhizal fungal communities of moist tussock and dry tundra in Arctic Alaska. GLOBAL CHANGE BIOLOGY 2015; 21:959-72. [PMID: 25156129 PMCID: PMC4322476 DOI: 10.1111/gcb.12716] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/19/2014] [Accepted: 07/28/2014] [Indexed: 05/22/2023]
Abstract
Arctic regions are experiencing the greatest rates of climate warming on the planet and marked changes have already been observed in terrestrial arctic ecosystems. While most studies have focused on the effects of warming on arctic vegetation and nutrient cycling, little is known about how belowground communities, such as fungi root-associated, respond to warming. Here, we investigate how long-term summer warming affects ectomycorrhizal (ECM) fungal communities. We used Ion Torrent sequencing of the rDNA internal transcribed spacer 2 (ITS2) region to compare ECM fungal communities in plots with and without long-term experimental warming in both dry and moist tussock tundra. Cortinarius was the most OTU-rich genus in the moist tundra, while the most diverse genus in the dry tundra was Tomentella. On the diversity level, in the moist tundra we found significant differences in community composition, and a sharp decrease in the richness of ECM fungi due to warming. On the functional level, our results indicate that warming induces shifts in the extramatrical properties of the communities, where the species with medium-distance exploration type seem to be favored with potential implications for the mobilization of different nutrient pools in the soil. In the dry tundra, neither community richness nor community composition was significantly altered by warming, similar to what had been observed in ECM host plants. There was, however, a marginally significant increase in OTUs identified as ECM fungi with the medium-distance exploration type in the warmed plots. Linking our findings of decreasing richness with previous results of increasing ECM fungal biomass suggests that certain ECM species are favored by warming and may become more abundant, while many other species may go locally extinct due to direct or indirect effects of warming. Such compositional shifts in the community might affect nutrient cycling and soil organic C storage.
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Affiliation(s)
- Luis N Morgado
- Naturalis Biodiversity CenterP.O. Box 9517, Leiden, RA, 2300, The Netherlands
| | - Tatiana A Semenova
- Naturalis Biodiversity CenterP.O. Box 9517, Leiden, RA, 2300, The Netherlands
- Faculty of Science, Leiden UniversityP.O. Box 9502, Leiden, RA, 2300, The Netherlands
| | - Jeffrey M Welker
- Department of Biological Sciences, University of Alaska AnchorageAnchorage, USA
| | | | - Erik Smets
- Naturalis Biodiversity CenterP.O. Box 9517, Leiden, RA, 2300, The Netherlands
- Faculty of Science, Leiden UniversityP.O. Box 9502, Leiden, RA, 2300, The Netherlands
- Plant Conservation and Population Biology, KU LeuvenKasteelpark Arenberg 31, Box 2437, Leuven, 3001, Belgium
| | - József Geml
- Naturalis Biodiversity CenterP.O. Box 9517, Leiden, RA, 2300, The Netherlands
- Faculty of Science, Leiden UniversityP.O. Box 9502, Leiden, RA, 2300, The Netherlands
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25
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Zhan A, He S, Brown EA, Chain FJ, Therriault TW, Abbott CL, Heath DD, Cristescu ME, MacIsaac HJ. Reproducibility of pyrosequencing data for biodiversity assessment in complex communities. Methods Ecol Evol 2014. [DOI: 10.1111/2041-210x.12230] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aibin Zhan
- Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; 18 Shuangqing Road Haidian District Beijing 100085 China
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
| | - Song He
- Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; 18 Shuangqing Road Haidian District Beijing 100085 China
| | - Emily A. Brown
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - Frédéric J.J. Chain
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - Thomas W. Therriault
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Cathryn L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
| | - Melania E. Cristescu
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal QC H3A 1B1 Canada
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor ON N9B 3P4 Canada
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Williams-Newkirk AJ, Rowe LA, Mixson-Hayden TR, Dasch GA. Characterization of the bacterial communities of life stages of free living lone star ticks (Amblyomma americanum). PLoS One 2014; 9:e102130. [PMID: 25054227 PMCID: PMC4108322 DOI: 10.1371/journal.pone.0102130] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/15/2014] [Indexed: 11/23/2022] Open
Abstract
The lone star tick (Amblyomma americanum) is an abundant and aggressive biter of humans, domestic animals, and wildlife in the southeastern-central USA and an important vector of several known and suspected zoonotic bacterial pathogens. However, the biological drivers of bacterial community variation in this tick are still poorly defined. Knowing the community context in which tick-borne bacterial pathogens exist and evolve is required to fully understand the ecology and immunobiology of the ticks and to design effective public health and veterinary interventions. We performed a metagenomic survey of the bacterial communities of questing A. americanum and tested 131 individuals (66 nymphs, 24 males, and 41 females) from five sites in three states. Pyrosequencing was performed with barcoded eubacterial primers targeting variable 16S rRNA gene regions 5–3. The bacterial communities were dominated by Rickettsia (likely R. amblyommii) and an obligate Coxiella symbiont, together accounting for 6.7–100% of sequences per tick. DNAs from Midichloria, Borrelia, Wolbachia, Ehrlichia, Pseudomonas, or unidentified Bacillales, Enterobacteriaceae, or Rhizobiales groups were also detected frequently. Wolbachia and Midichloria significantly co-occurred in Georgia (p<0.00001), but not in other states. The significance of the Midichloria-Wolbachia co-occurrence is unknown. Among ticks collected in Georgia, nymphs differed from adults in both the composition (p = 0.002) and structure (p = 0.002) of their bacterial communities. Adults differed only in their community structure (p = 0.002) with males containing more Rickettsia and females containing more Coxiella. Comparisons among adult ticks collected in New York and North Carolina supported the findings from the Georgia collection despite differences in geography, collection date, and sample handling, implying that the differences detected are consistent attributes. The data also suggest that some members of the bacterial community change during the tick life cycle and that some sex-specific attributes may be detectable in nymphs.
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Affiliation(s)
- Amanda Jo Williams-Newkirk
- Department of Environmental Sciences, College of Arts and Sciences, Emory University, Atlanta, Georgia, United States of America
- Graduate Program in Population Biology, Ecology and Evolution, Emory University, Atlanta, Georgia, United States of America
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Lori A. Rowe
- Biotechnology Core Facility Branch, National Center for Emerging Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Tonya R. Mixson-Hayden
- Laboratory Branch, Division of Viral Hepatitis, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Gregory A. Dasch
- Rickettsial Zoonoses Branch, Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
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27
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The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands. PLoS One 2014; 9:e99852. [PMID: 24937200 PMCID: PMC4061046 DOI: 10.1371/journal.pone.0099852] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/17/2014] [Indexed: 11/19/2022] Open
Abstract
Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.
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Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing. PLoS One 2014; 9:e96928. [PMID: 24800821 PMCID: PMC4011962 DOI: 10.1371/journal.pone.0096928] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 04/12/2014] [Indexed: 11/19/2022] Open
Abstract
Large-scale high-throughput sequencing techniques are rapidly becoming popular methods to profile complex communities and have generated deep insights into community biodiversity. However, several technical problems, especially sequencing artifacts such as nucleotide calling errors, could artificially inflate biodiversity estimates. Sequence filtering for artifact removal is a conventional method for deleting error-prone sequences from high-throughput sequencing data. As rare species represented by low-abundance sequences in datasets may be sensitive to artifact removal process, the influence of artifact removal on rare species recovery has not been well evaluated in natural complex communities. Here we employed both internal (reliable operational taxonomic units selected from communities themselves) and external (indicator species spiked into communities) references to evaluate the influence of artifact removal on rare species recovery using 454 pyrosequencing of complex plankton communities collected from both freshwater and marine habitats. Multiple analyses revealed three clear patterns: 1) rare species were eliminated during sequence filtering process at all tested filtering stringencies, 2) more rare taxa were eliminated as filtering stringencies increased, and 3) elimination of rare species intensified as biomass of a species in a community was reduced. Our results suggest that cautions be applied when processing high-throughput sequencing data, especially for rare taxa detection for conservation of species at risk and for rapid response programs targeting non-indigenous species. Establishment of both internal and external references proposed here provides a practical strategy to evaluate artifact removal process.
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29
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Kim M, Yu Z. Variations in 16S rRNA-based microbiome profiling between pyrosequencing runs and between pyrosequencing facilities. J Microbiol 2014; 52:355-65. [PMID: 24723104 DOI: 10.1007/s12275-014-3443-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 12/13/2022]
Abstract
Pyrosequencing of 16S rRNA gene amplicons on the 454 FLX Titanium platform has been widely used to analyze microbiomes in various environments. However, different results may stem from variations among sequencing runs or among sequencing facilities. This study aimed to evaluate these variations between different pyrosequencing runs by sequencing 16S rRNA gene amplicon libraries generated from three sets of rumen samples twice each on the 454 FLX Titanium system at two independent sequencing facilities. Similar relative abundances were found for predominant taxa represented by large numbers of sequence reads but not for minor taxa represented by small numbers of sequence reads. The two sequencing facilities revealed different bacterial profiles with respect to both predominant taxa and minor taxa, including the most predominant genus Prevotella, the family Lachnospiraceae, and the phylum Proteobacteria. Differences in primers used to generate amplicon libraries may be a major source of variations in microbiome profiling. Because different primers and regions of 16S rRNA genes are often used by different researchers, significant variations likely exist among studies. Quantitative interpretation for relative abundance of taxa, especially minor taxa, from prevalence of sequence reads and comparisons of results from different studies should be done with caution.
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Affiliation(s)
- Minseok Kim
- Department of Animal Sciences, The Ohio State University, Columbus, OH, USA
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30
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Botnen S, Vik U, Carlsen T, Eidesen PB, Davey ML, Kauserud H. Low host specificity of root-associated fungi at an Arctic site. Mol Ecol 2014; 23:975-85. [DOI: 10.1111/mec.12646] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 12/10/2013] [Accepted: 12/23/2013] [Indexed: 10/25/2022]
Affiliation(s)
- Synnøve Botnen
- Department of Biosciences; Section for Genetics and Evolutionary Biology (EVOGENE); University of Oslo; PO box 1066 Blindern NO-0316 Oslo Norway
- The University Centre in Svalbard; PO box 156 NO-9171 Longyearbyen Norway
| | - Unni Vik
- Department of Biosciences; Section for Genetics and Evolutionary Biology (EVOGENE); University of Oslo; PO box 1066 Blindern NO-0316 Oslo Norway
| | - Tor Carlsen
- Department of Biosciences; Section for Genetics and Evolutionary Biology (EVOGENE); University of Oslo; PO box 1066 Blindern NO-0316 Oslo Norway
| | | | - Marie L. Davey
- The University Centre in Svalbard; PO box 156 NO-9171 Longyearbyen Norway
| | - Håvard Kauserud
- Department of Biosciences; Section for Genetics and Evolutionary Biology (EVOGENE); University of Oslo; PO box 1066 Blindern NO-0316 Oslo Norway
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Blaalid R, Davey ML, Kauserud H, Carlsen T, Halvorsen R, Høiland K, Eidesen PB. Arctic root-associated fungal community composition reflects environmental filtering. Mol Ecol 2014; 23:649-59. [DOI: 10.1111/mec.12622] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 11/19/2013] [Accepted: 12/04/2013] [Indexed: 12/01/2022]
Affiliation(s)
- Rakel Blaalid
- Department of Biology; Microbial Evolution Research Group (MERG); University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Marie L. Davey
- The University Centre in Svalbard; PO Box 156 NO-9171 Longyearbyen Norway
| | - Håvard Kauserud
- Department of Biology; Microbial Evolution Research Group (MERG); University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Tor Carlsen
- Department of Biology; Microbial Evolution Research Group (MERG); University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Rune Halvorsen
- Natural History Museum; University of Oslo; PO Box 1172 Blindern NO-0318 Oslo Norway
| | - Klaus Høiland
- Department of Biology; Microbial Evolution Research Group (MERG); University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
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32
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Multiple ITS Haplotypes in the Genome of the Lichenized Basidiomycete Cora inversa (Hygrophoraceae): Fact or Artifact? J Mol Evol 2013; 78:148-62. [DOI: 10.1007/s00239-013-9603-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
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Vik U, Logares R, Blaalid R, Halvorsen R, Carlsen T, Bakke I, Kolstø AB, Økstad OA, Kauserud H. Different bacterial communities in ectomycorrhizae and surrounding soil. Sci Rep 2013; 3:3471. [PMID: 24326907 PMCID: PMC3858787 DOI: 10.1038/srep03471] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/25/2013] [Indexed: 02/01/2023] Open
Abstract
Several eukaryotic symbioses have shown to host a rich diversity of prokaryotes that interact with their hosts. Here, we study bacterial communities associated with ectomycorrhizal root systems of Bistorta vivipara compared to bacterial communities in bulk soil using pyrosequencing of 16S rRNA amplicons. A high richness of Operational Taxonomic Units (OTUs) was found in plant roots (3,571 OTUs) and surrounding soil (3,476 OTUs). The community composition differed markedly between these two environments. Actinobacteria, Armatimonadetes, Chloroflexi and OTUs unclassified at phylum level were significantly more abundant in plant roots than in soil. A large proportion of the OTUs, especially those in plant roots, presented low similarity to Sanger 16S rRNA reference sequences, suggesting novel bacterial diversity in ectomycorrhizae. Furthermore, the bacterial communities of the plant roots were spatially structured up to a distance of 60 cm, which may be explained by bacteria using fungal hyphae as a transport vector. The analyzed ectomycorrhizae presents a distinct microbiome, which likely influence the functioning of the plant-fungus symbiosis.
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Affiliation(s)
- Unni Vik
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Ramiro Logares
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain
| | - Rakel Blaalid
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Rune Halvorsen
- Natural History Museum, Department of research and collections, University of Oslo, P.O. 1172 Blindern, 0318 OSLO, Norway
| | - Tor Carlsen
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
| | - Ingrid Bakke
- NTNU/Norwegian University of Science and Technology, Department of Biotechnology, Sem Sælands vei 8, 7491 Trondheim, Norway
| | - Anne-Brit Kolstø
- Laboratory for Microbial Dynamics, School of Pharmacy, University of Oslo, P.O. 1068 Blindern, 0316 Oslo, Norway
| | - Ole Andreas Økstad
- Laboratory for Microbial Dynamics, School of Pharmacy, University of Oslo, P.O. 1068 Blindern, 0316 Oslo, Norway
| | - Håvard Kauserud
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. 1066 Blindern, 0316 Oslo, Norway
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Thomas AC, Jarman SN, Haman KH, Trites AW, Deagle BE. Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias. Mol Ecol 2013; 23:3706-18. [PMID: 24102760 DOI: 10.1111/mec.12523] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 08/30/2013] [Accepted: 09/09/2013] [Indexed: 11/30/2022]
Abstract
Ecologists are increasingly interested in quantifying consumer diets based on food DNA in dietary samples and high-throughput sequencing of marker genes. It is tempting to assume that food DNA sequence proportions recovered from diet samples are representative of consumer's diet proportions, despite the fact that captive feeding studies do not support that assumption. Here, we examine the idea of sequencing control materials of known composition along with dietary samples in order to correct for technical biases introduced during amplicon sequencing and biological biases such as variable gene copy number. Using the Ion Torrent PGM(©) , we sequenced prey DNA amplified from scats of captive harbour seals (Phoca vitulina) fed a constant diet including three fish species in known proportions. Alongside, we sequenced a prey tissue mix matching the seals' diet to generate tissue correction factors (TCFs). TCFs improved the diet estimates (based on sequence proportions) for all species and reduced the average estimate error from 28 ± 15% (uncorrected) to 14 ± 9% (TCF-corrected). The experimental design also allowed us to infer the magnitude of prey-specific digestion biases and calculate digestion correction factors (DCFs). The DCFs were compared with possible proxies for differential digestion (e.g. fish protein%, fish lipid%) revealing a strong relationship between the DCFs and percent lipid of the fish prey, suggesting prey-specific corrections based on lipid content would produce accurate diet estimates in this study system. These findings demonstrate the value of parallel sequencing of food tissue mixtures in diet studies and offer new directions for future research in quantitative DNA diet analysis.
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Affiliation(s)
- Austen C Thomas
- Marine Mammal Research Unit, Fisheries Centre, and Department of Zoology, University of British Columbia, 2202 Main Mall, Vancouver, BC, V6T 1Z4, Canada
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35
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Egge E, Bittner L, Andersen T, Audic S, de Vargas C, Edvardsen B. 454 pyrosequencing to describe microbial eukaryotic community composition, diversity and relative abundance: a test for marine haptophytes. PLoS One 2013; 8:e74371. [PMID: 24069303 PMCID: PMC3771978 DOI: 10.1371/journal.pone.0074371] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 08/05/2013] [Indexed: 11/19/2022] Open
Abstract
Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing.
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Affiliation(s)
- Elianne Egge
- University of Oslo, Department of Biosciences, Marine Biology, Oslo, Norway
- * E-mail: (EE); (BE)
| | - Lucie Bittner
- CNRS UMR7144 & UPMC, Station Biologique de Roscoff, Roscoff, France
- University of Kaiserslautern, Department of Ecology, Kaiserslautern, Germany
| | - Tom Andersen
- University of Oslo, Department of Biosciences, Integrative Biology, Oslo, Norway
| | - Stéphane Audic
- CNRS UMR7144 & UPMC, Station Biologique de Roscoff, Roscoff, France
| | | | - Bente Edvardsen
- University of Oslo, Department of Biosciences, Marine Biology, Oslo, Norway
- * E-mail: (EE); (BE)
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Yao F, Vik U, Brysting AK, Carlsen T, Halvorsen R, Kauserud H. Substantial compositional turnover of fungal communities in an alpine ridge-to-snowbed gradient. Mol Ecol 2013; 22:5040-52. [PMID: 23962113 DOI: 10.1111/mec.12437] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 12/25/2022]
Abstract
The main gradient in vascular plant, bryophyte and lichen species composition in alpine areas, structured by the topographic gradient from wind-exposed ridges to snowbeds, has been extensively studied. Tolerance to environmental stress, resulting from wind abrasion and desiccation towards windswept ridges or reduced growing season due to prolonged snow cover towards snowbeds, is an important ecological mechanism in this gradient. The extent to which belowground fungal communities are structured by the same topographic gradient and the eventual mechanisms involved are less well known. In this study, we analysed variation in fungal diversity and community composition associated with roots of the ectomycorrhizal plant Bistorta vivipara along the ridge-to-snowbed gradient. We collected root samples from fifty B. vivipara plants in ten plots in an alpine area in central Norway. The fungal communities were analysed using 454 pyrosequencing analyses of tag-encoded ITS1 amplicons. A distinct gradient in the fungal community composition was found that coincided with variation from ridge to snowbeds. This gradient was paralleled by change in soil content of carbon, nitrogen and phosphorus. A large proportion (66%) of the detected 801 nonsingleton operational taxonomic units (OTUs) were ascomycetes, while basidiomycetes dominated quantitatively (i.e. with respect to number of reads). Numerous fungal OTUs, many with taxonomic affinity to Sebacinales, Cortinarius and Meliniomyces, showed distinct affinities either to ridge or to snowbed plots, indicating habitat specialization. The compositional turnover of fungal communities along the gradient was not paralleled by a gradient in species richness.
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Affiliation(s)
- Fang Yao
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, P.O. Box 1066, 0316, Oslo, Norway
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Bengtsson-Palme J, Ryberg M, Hartmann M, Branco S, Wang Z, Godhe A, De Wit P, Sánchez-García M, Ebersberger I, de Sousa F, Amend AS, Jumpponen A, Unterseher M, Kristiansson E, Abarenkov K, Bertrand YJK, Sanli K, Eriksson KM, Vik U, Veldre V, Nilsson RH. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12073] [Citation(s) in RCA: 365] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Johan Bengtsson-Palme
- Department of Neuroscience and Physiology; The Sahlgrenska Academy; University of Gothenburg; Box 434; 40530; Göteborg; Sweden
| | - Martin Ryberg
- Department of Organismal Biology; Uppsala University; Norbyvägen 18D; Uppsala; 75236; Sweden
| | | | - Sara Branco
- Department of Plant and Microbial Biology; University of California; Berkeley; CA; 94720-3102; USA
| | - Zheng Wang
- Department of Ecology and Evolutionary Biology; Yale University; New Haven; CT 06520-8106; USA
| | - Anna Godhe
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Pierre De Wit
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Marisol Sánchez-García
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville; TN; 37996-1610; USA
| | - Ingo Ebersberger
- Department for Applied Bioinformatics; Institute for Cell Biology and Neuroscience, Goethe University; Max-von-Laue Str. 13; Frankfurt; D-60438; Germany
| | - Filipe de Sousa
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Anthony S. Amend
- Botany Department; University of Hawai'i at Manoa; 3190 Maile Way; Honolulu; HI; 96822; USA
| | - Ari Jumpponen
- Division of Biology; Kansas State University; Manhattan; KS; 66506; USA
| | - Martin Unterseher
- Institute of Botany and Landscape Ecology; Ernst-Moritz-Arndt University Greifswald; Grimmer Str. 88; Greifswald; D-17487; Germany
| | - Erik Kristiansson
- Department of Mathematical Statistics; Chalmers University of Technology; Göteborg; 41296; Sweden
| | - Kessy Abarenkov
- Natural History Museum; University of Tartu; 46 Vanemuise Str.; Tartu; 51014; Estonia
| | - Yann J. K. Bertrand
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - Kemal Sanli
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
| | - K. Martin Eriksson
- Department of Shipping and Marine Technology; Chalmers University of Technology; Göteborg; 41296; Sweden
| | - Unni Vik
- Department of Biosciences; University of Oslo; PO Box 1066, Blindern; Oslo; N-0316; Norway
| | | | - R. Henrik Nilsson
- Department of Biological and Environmental Sciences; University of Gothenburg; Box 461; Göteborg; 40530; Sweden
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Lindahl BD, Nilsson RH, Tedersoo L, Abarenkov K, Carlsen T, Kjøller R, Kõljalg U, Pennanen T, Rosendahl S, Stenlid J, Kauserud H. Fungal community analysis by high-throughput sequencing of amplified markers--a user's guide. THE NEW PHYTOLOGIST 2013; 199:288-299. [PMID: 23534863 PMCID: PMC3712477 DOI: 10.1111/nph.12243] [Citation(s) in RCA: 515] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 02/18/2013] [Indexed: 05/17/2023]
Abstract
Novel high-throughput sequencing methods outperform earlier approaches in terms of resolution and magnitude. They enable identification and relative quantification of community members and offer new insights into fungal community ecology. These methods are currently taking over as the primary tool to assess fungal communities of plant-associated endophytes, pathogens, and mycorrhizal symbionts, as well as free-living saprotrophs. Taking advantage of the collective experience of six research groups, we here review the different stages involved in fungal community analysis, from field sampling via laboratory procedures to bioinformatics and data interpretation. We discuss potential pitfalls, alternatives, and solutions. Highlighted topics are challenges involved in: obtaining representative DNA/RNA samples and replicates that encompass the targeted variation in community composition, selection of marker regions and primers, options for amplification and multiplexing, handling of sequencing errors, and taxonomic identification. Without awareness of methodological biases, limitations of markers, and bioinformatics challenges, large-scale sequencing projects risk yielding artificial results and misleading conclusions.
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Affiliation(s)
- Björn D Lindahl
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30, Gothenburg, Sweden
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Kessy Abarenkov
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Tor Carlsen
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences/Natural History Museum, University of Tartu, 46 Vanemuise St., 51014, Tartu, Estonia
| | - Taina Pennanen
- The Finnish Forest Research Institute, PL 18, FI-01301, Vantaa, Finland
| | - Søren Rosendahl
- Department of Biology, University of Copenhagen, Øster Farimagsgade 2D, 1353, Copenhagen, Denmark
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, SE-750 07, Uppsala, Sweden
| | - Håvard Kauserud
- Department of Biology, University of Oslo, PO Box 1066, Blindern, N-0316, Oslo, Norway
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Abstract
The site-to-site variability in species composition, known as β-diversity, is crucial to understanding spatiotemporal patterns of species diversity and the mechanisms controlling community composition and structure. However, quantifying β-diversity in microbial ecology using sequencing-based technologies is a great challenge because of a high number of sequencing errors, bias, and poor reproducibility and quantification. Herein, based on general sampling theory, a mathematical framework is first developed for simulating the effects of random sampling processes on quantifying β-diversity when the community size is known or unknown. Also, using an analogous ball example under Poisson sampling with limited sampling efforts, the developed mathematical framework can exactly predict the low reproducibility among technically replicate samples from the same community of a certain species abundance distribution, which provides explicit evidences of random sampling processes as the main factor causing high percentages of technical variations. In addition, the predicted values under Poisson random sampling were highly consistent with the observed low percentages of operational taxonomic unit (OTU) overlap (<30% and <20% for two and three tags, respectively, based on both Jaccard and Bray-Curtis dissimilarity indexes), further supporting the hypothesis that the poor reproducibility among technical replicates is due to the artifacts associated with random sampling processes. Finally, a mathematical framework was developed for predicting sampling efforts to achieve a desired overlap among replicate samples. Our modeling simulations predict that several orders of magnitude more sequencing efforts are needed to achieve desired high technical reproducibility. These results suggest that great caution needs to be taken in quantifying and interpreting β-diversity for microbial community analysis using next-generation sequencing technologies. Due to the vast diversity and uncultivated status of the majority of microorganisms, microbial detection, characterization, and quantitation are of great challenge. Although large-scale metagenome sequencing technology such as PCR-based amplicon sequencing has revolutionized the studies of microbial communities, it suffers from several inherent drawbacks, such as a high number of sequencing errors, biases, poor quantitation, and very high percentages of technical variations, which could greatly overestimate microbial biodiversity. Based on general sampling theory, this study provided the first explicit evidence to demonstrate the importance of random sampling processes in estimating microbial β-diversity, which has not been adequately recognized and addressed in microbial ecology. Since most ecological studies are involved in random sampling, the conclusions learned from this study should also be applicable to other ecological studies in general. In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions.
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Below-ground fine-scale distribution and soil versus fine root detection of fungal and soil oomycete communities in a French beech forest. FUNGAL ECOL 2013. [DOI: 10.1016/j.funeco.2013.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rungrassamee W, Klanchui A, Chaiyapechara S, Maibunkaew S, Tangphatsornruang S, Jiravanichpaisal P, Karoonuthaisiri N. Bacterial population in intestines of the black tiger shrimp (Penaeus monodon) under different growth stages. PLoS One 2013; 8:e60802. [PMID: 23577162 PMCID: PMC3618293 DOI: 10.1371/journal.pone.0060802] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 03/03/2013] [Indexed: 12/30/2022] Open
Abstract
Intestinal bacterial communities in aquaculture have been drawn to attention due to potential benefit to their hosts. To identify core intestinal bacteria in the black tiger shrimp (Penaeus monodon), bacterial populations of disease-free shrimp were characterized from intestines of four developmental stages (15-day-old post larvae (PL15), 1- (J1), 2- (J2), and 3-month-old (J3) juveniles) using pyrosequencing, real-time PCR and denaturing gradient gel electrophoresis (DGGE) approaches. A total of 25,121 pyrosequencing reads (reading length = 442±24 bases) were obtained, which were categorized by barcode for PL15 (7,045 sequences), J1 (3,055 sequences), J2 (13,130 sequences) and J3 (1,890 sequences). Bacteria in the phyla Bacteroides, Firmicutes and Proteobacteria were found in intestines at all four growth stages. There were 88, 14, 27, and 20 bacterial genera associated with the intestinal tract of PL15, J1, J2 and J3, respectively. Pyrosequencing analysis revealed that Proteobacteria (class Gammaproteobacteria) was a dominant bacteria group with a relative abundance of 89% for PL15 and 99% for J1, J2 and J3. Real-time PCR assay also confirmed that Gammaproteobacteria had the highest relative abundance in intestines from all growth stages. Intestinal bacterial communities from the three juvenile stages were more similar to each other than that of the PL shrimp based on PCA analyses of pyrosequencing results and their DGGE profiles. This study provides descriptive bacterial communities associated to the black tiger shrimp intestines during these growth development stages in rearing facilities.
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Affiliation(s)
- Wanilada Rungrassamee
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Amornpan Klanchui
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Sage Chaiyapechara
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Sawarot Maibunkaew
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- Genomic Research Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Pikul Jiravanichpaisal
- Aquatic Molecular Genetics and Biotechnology Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Laboratory, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
- * E-mail:
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Zhan A, Hulák M, Sylvester F, Huang X, Adebayo AA, Abbott CL, Adamowicz SJ, Heath DD, Cristescu ME, MacIsaac HJ. High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities. Methods Ecol Evol 2013. [DOI: 10.1111/2041-210x.12037] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Aibin Zhan
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
- Research Center for Eco-Environmental Sciences; Chinese Academy of Sciences; 18 Shuangqing Road Haidian District Beijing 100085 China
| | - Martin Hulák
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Francisco Sylvester
- Facultad de Ciencias Exactas y Naturales; Departamento de Ecología; Genética y Evolución and Consejo Nacional de Investigaciones Científicas y Técnicas; Universidad de Buenos Aires; Buenos Aires Argentina
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (MGB); Ministry of Education, College of Marine Life Sciences; Ocean University of China; 5 Yushan Road Qingdao 266003 China
| | - Abisola A. Adebayo
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Cathryn L. Abbott
- Pacific Biological Station; Fisheries and Oceans Canada; 3190 Hammond Bay Road Nanaimo British Columbia V9T 6N7 Canada
| | - Sarah J. Adamowicz
- Biodiversity Institute of Ontario and Department of Integrative Biology; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
| | - Melania E. Cristescu
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
- Department of Biology; McGill University; 1205 Docteur Penfield Montreal Quebec H3A 1B1 Canada
| | - Hugh J. MacIsaac
- Great Lakes Institute for Environmental Research; University of Windsor; 401 Sunset Avenue Windsor Ontario N9B 3P4 Canada
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Miller CS, Handley KM, Wrighton KC, Frischkorn KR, Thomas BC, Banfield JF. Short-read assembly of full-length 16S amplicons reveals bacterial diversity in subsurface sediments. PLoS One 2013; 8:e56018. [PMID: 23405248 PMCID: PMC3566076 DOI: 10.1371/journal.pone.0056018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/09/2013] [Indexed: 01/10/2023] Open
Abstract
In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the “long tail” of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.
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Affiliation(s)
- Christopher S Miller
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America.
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Blaalid R, Kumar S, Nilsson RH, Abarenkov K, Kirk PM, Kauserud H. ITS1 versus ITS2 as DNA metabarcodes for fungi. Mol Ecol Resour 2013; 13:218-24. [PMID: 23350562 DOI: 10.1111/1755-0998.12065] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 11/15/2012] [Accepted: 11/20/2012] [Indexed: 11/28/2022]
Abstract
The nuclear ribosomal Internal Transcribed Spacer ITS region is widely used as a DNA metabarcoding marker to characterize the diversity and composition of fungal communities. In amplicon pyrosequencing studies of fungal diversity, one of the spacers ITS1 or ITS2 of the ITS region is normally used. In this methodological study we evaluate the usability of ITS1 vs. ITS2 as a DNA metabarcoding marker for fungi. We analyse three data sets: two comprising ITS1 and ITS2 sequences of known taxonomic affiliations and a third comprising ITS1 and ITS2 environmental amplicon pyrosequencing data. Clustering analyses of sequences with known taxonomy using the bioinformatics pipeline ClustEx revealed that a 97% similarity cut-off represent a reasonable threshold for estimating the number of known species in the data sets for both ITS1 and ITS2. However, no single threshold value worked well for all fungi at the same time within the curated UNITE database, and we found that the Operational Taxonomic Unit (OTU) concept is not easily translated into the level of species because many species are distributed over several clusters. Clustering analyses of the 134 692 ITS1 and ITS2 pyrosequences using a 97% similarity cut-off revealed a high similarity between the two data sets when it comes to taxonomic coverage. Although some groups are under- or unrepresented in the two data sets due to, e.g. primer mismatches, our results indicate that ITS1 and ITS2 to a large extent yield similar results when used as DNA metabarcodes for fungi.
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Affiliation(s)
- R Blaalid
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, PO Box 1066 Blindern, Oslo, NO-0316, Norway
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Carlsen T, Aas AB, Lindner D, Vrålstad T, Schumacher T, Kauserud H. Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies? FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2012.06.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Davey ML, Heegaard E, Halvorsen R, Kauserud H, Ohlson M. Amplicon-pyrosequencing-based detection of compositional shifts in bryophyte-associated fungal communities along an elevation gradient. Mol Ecol 2012. [DOI: 10.1111/mec.12122] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marie L. Davey
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
- Microbial Evolution Research Group (MERG); Department of Biology; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Einar Heegaard
- Norwegian Forest and Landscape Institute; Fanaflaten 4 NO-5244 Fana Norway
| | - Rune Halvorsen
- Department of Botany, Natural History Museum; University of Oslo; PO Box 1172 Blindern NO-0318 Oslo Norway
| | - Håvard Kauserud
- Microbial Evolution Research Group (MERG); Department of Biology; University of Oslo; PO Box 1066 Blindern NO-0316 Oslo Norway
| | - Mikael Ohlson
- Department of Ecology and Natural Resource Management; Norwegian University of Life Sciences; PO Box 5003 NO-1432 Ås Norway
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Davey ML, Heegaard E, Halvorsen R, Ohlson M, Kauserud H. Seasonal trends in the biomass and structure of bryophyte-associated fungal communities explored by 454 pyrosequencing. THE NEW PHYTOLOGIST 2012; 195:844-856. [PMID: 22758207 DOI: 10.1111/j.1469-8137.2012.04215.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bryophytes are a dominant vegetation component of the boreal forest, but little is known about their associated fungal communities, including seasonal variation within them. Seasonal variation in the fungal biomass and composition of fungal communities associated with three widespread boreal bryophytes was investigated using HPLC assays of ergosterol and amplicon pyrosequencing of the internal transcribed spacer 2 (ITS2) region of rDNA. The bryophyte phyllosphere community was dominated by Ascomycota. Fungal biomass did not decline appreciably in winter (P=0.272). Significant host-specific patterns in seasonal variation of biomass were detected (P=0.003). Although seasonal effects were not the primary factors structuring community composition, collection date significantly explained (P=0.001) variation not attributed to locality, host, and tissue. Community homogenization and a reduction in turnover occurred with the onset of frost events and subzero air and soil temperatures. Fluctuations in the relative abundance of particular fungal groups seem to reflect the nature of their association with mosses, although conclusions are drawn with caution because of potential methodological bias. The moss-associated fungal community is dynamic, exhibiting seasonal turnover in composition and relative abundance of different fungal groups, and significant fungal biomass is present year-round, suggesting a winter-active fungal community.
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Affiliation(s)
- Marie L Davey
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Einar Heegaard
- Norwegian Forest and Landscape Institute, Fanaflaten 4, NO-5244 Fana, Norway
| | - Rune Halvorsen
- Department of Botany, Natural History Museum, University of Oslo, PO Box 1172 Blindern, NO-0318 Oslo, Norway
| | - Mikael Ohlson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway
| | - Håvard Kauserud
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, PO Box 1066 Blindern, NO-0316 Oslo, Norway
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Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability. Appl Environ Microbiol 2012; 78:6438-49. [PMID: 22773636 DOI: 10.1128/aem.01162-12] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.
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