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Veach AM, Stokes CE, Knoepp J, Jumpponen A, Baird R. Fungal Communities and Functional Guilds Shift Along an Elevational Gradient in the Southern Appalachian Mountains. MICROBIAL ECOLOGY 2018; 76:156-168. [PMID: 29204781 DOI: 10.1007/s00248-017-1116-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/20/2017] [Indexed: 05/03/2023]
Abstract
Nitrogen deposition alters forest ecosystems particularly in high elevation, montane habitats where nitrogen deposition is greatest and continues to increase. We collected soils across an elevational (788-1940 m) gradient, encompassing both abiotic (soil chemistry) and biotic (vegetation community) gradients, at eight locations in the southern Appalachian Mountains of southwestern North Carolina and eastern Tennessee. We measured soil chemistry (total N, C, extractable PO4, soil pH, cation exchange capacity [ECEC], percent base saturation [% BS]) and dissected soil fungal communities using ITS2 metabarcode Illumina MiSeq sequencing. Total soil N, C, PO4, % BS, and pH increased with elevation and plateaued at approximately 1400 m, whereas ECEC linearly increased and C/N decreased with elevation. Fungal communities differed among locations and were correlated with all chemical variables, except PO4, whereas OTU richness increased with total N. Several ecological guilds (i.e., ectomycorrhizae, saprotrophs, plant pathogens) differed in abundance among locations; specifically, saprotroph abundance, primarily attributable to genus Mortierella, was positively correlated with elevation. Ectomycorrhizae declined with total N and soil pH and increased with total C and PO4 where plant pathogens increased with total N and decreased with total C. Our results demonstrate significant turnover in taxonomic and functional fungal groups across elevational gradients which facilitate future predictions on forest ecosystem change in the southern Appalachians as nitrogen deposition rates increase and regional temperature and precipitation regimes shift.
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Affiliation(s)
- Allison M Veach
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37831, USA.
| | - C Elizabeth Stokes
- Department of Forest Products, Mississippi State University, Starkville, MS, 39762, USA
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
| | - Jennifer Knoepp
- USDA, Forest Service, Southern Research Station, Center for Forest Watershed Research, Coweeta Hydrologic Laboratory, Otto, NC, 28763, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Richard Baird
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Starkville, MS, 39762, USA
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Taerum SJ, De Martini F, Liebig J, Gile GH. Incomplete Co-cladogenesis Between Zootermopsis Termites and Their Associated Protists. ENVIRONMENTAL ENTOMOLOGY 2018; 47:184-195. [PMID: 29325010 DOI: 10.1093/ee/nvx193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 06/07/2023]
Abstract
Coevolution is a major driver of speciation in many host-associated symbionts. In the termite-protist digestive symbiosis, the protists are vertically inherited by anal feeding among nest mates. Lower termites (all termite families except Termitidae) and their symbionts have broadly co-diversified over ~170 million yr. However, this inference is based mainly on the restricted distribution of certain protist genera to certain termite families. With the exception of one study, which demonstrated congruent phylogenies for the protist Pseudotrichonympha and its Rhinotermitidae hosts, coevolution in this symbiosis has not been investigated with molecular methods. Here we have characterized the hindgut symbiotic protists (Phylum Parabasalia) across the genus Zootermopsis (Archotermopsidae) using single cell isolation, molecular phylogenetics, and high-throughput amplicon sequencing. We report that the deepest divergence in the Zootermopsis phylogeny (Zootermopsis laticeps [Banks; Isoptera: Termopsidae]) corresponds with a divergence in three of the hindgut protist species. However, the crown Zootermopsis taxa (Zootermopsis angusticollis [Hagen; Isoptera: Termopsidae], Z. nevadensis nevadensis [Hagen; Isoptera: Termopsidae], and Z. nevadensis nuttingi [Haverty & Thorne; Isoptera: Termopsidae]) share the same protist species, with no evidence of co-speciation under our methods. We interpret this pattern as incomplete co-cladogenesis, though the possibility of symbiont exchange cannot be entirely ruled out. This is the first molecular evidence that identical communities of termite-associated protist species can inhabit multiple distinct host species.
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Affiliation(s)
| | | | - Jürgen Liebig
- School of Life Sciences, Arizona State University, Tempe, AZ
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Tempe, AZ
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Tripp EA, Zhang N, Schneider H, Huang Y, Mueller GM, Hu Z, Häggblom M, Bhattacharya D. Reshaping Darwin's Tree: Impact of the Symbiome. Trends Ecol Evol 2017; 32:552-555. [PMID: 28601483 DOI: 10.1016/j.tree.2017.05.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 02/10/2017] [Accepted: 05/06/2017] [Indexed: 12/30/2022]
Abstract
Much of the undescribed biodiversity on Earth is microbial, often in mutualistic or pathogenic associations. Physically associated and coevolving life forms comprise a symbiome. We propose that systematics research can accelerate progress in science by introducing a new framework for phylogenetic analysis of symbiomes, here termed SYMPHY (symbiome phylogenetics).
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Affiliation(s)
- Erin A Tripp
- Department of Ecology and Evolutionary Biology and Museum of Natural History, University of Colorado, Boulder, Colorado, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Harald Schneider
- Department of Ecology, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China; Department of Life Sciences, Natural History Museum, London, UK
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Zhihong Hu
- State Key Laboratory for Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Max Häggblom
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources and Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA.
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U'Ren JM, Arnold AE. Diversity, taxonomic composition, and functional aspects of fungal communities in living, senesced, and fallen leaves at five sites across North America. PeerJ 2016; 4:e2768. [PMID: 27994976 PMCID: PMC5157190 DOI: 10.7717/peerj.2768] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 11/07/2016] [Indexed: 12/17/2022] Open
Abstract
Background Fungal endophytes inhabit symptomless, living tissues of all major plant lineages to form one of earth’s most prevalent groups of symbionts. Many reproduce from senesced and/or decomposing leaves and can produce extracellular leaf-degrading enzymes, blurring the line between symbiotrophy and saprotrophy. To better understand the endophyte–saprotroph continuum we compared fungal communities and functional traits of focal strains isolated from living leaves to those isolated from leaves after senescence and decomposition, with a focus on foliage of woody plants in five biogeographic provinces ranging from tundra to subtropical scrub forest. Methods We cultured fungi from the interior of surface-sterilized leaves that were living at the time of sampling (i.e., endophytes), leaves that were dead and were retained in plant canopies (dead leaf fungi, DLF), and fallen leaves (leaf litter fungi, LLF) from 3–4 species of woody plants in each of five sites in North America. Our sampling encompassed 18 plant species representing two families of Pinophyta and five families of Angiospermae. Diversity and composition of fungal communities within and among leaf life stages, hosts, and sites were compared using ITS-partial LSU rDNA data. We evaluated substrate use and enzyme activity by a subset of fungi isolated only from living tissues vs. fungi isolated only from non-living leaves. Results Across the diverse biomes and plant taxa surveyed here, culturable fungi from living leaves were isolated less frequently and were less diverse than those isolated from non-living leaves. Fungal communities in living leaves also differed detectably in composition from communities in dead leaves and leaf litter within focal sites and host taxa, regardless of differential weighting of rare and abundant fungi. All focal isolates grew on cellulose, lignin, and pectin as sole carbon sources, but none displayed ligninolytic or pectinolytic activity in vitro. Cellulolytic activity differed among fungal classes. Within Dothideomycetes, activity differed significantly between fungi from living vs. non-living leaves, but such differences were not observed in Sordariomycetes. Discussion Although some fungi with endophytic life stages clearly persist for periods of time in leaves after senescence and incorporation into leaf litter, our sampling across diverse biomes and host lineages detected consistent differences between fungal assemblages in living vs. non-living leaves, reflecting incursion by fungi from the leaf exterior after leaf death and as leaves begin to decompose. However, fungi found only in living leaves do not differ consistently in cellulolytic activity from those fungi detected thus far only in dead leaves. Future analyses should consider Basidiomycota in addition to the Ascomycota fungi evaluated here, and should explore more dimensions of functional traits and persistence to further define the endophytism-to-saprotrophy continuum.
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Affiliation(s)
- Jana M U'Ren
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States of America; Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, AZ, United States of America
| | - A Elizabeth Arnold
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States of America; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States of America
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Field KJ, Leake JR, Tille S, Allinson KE, Rimington WR, Bidartondo MI, Beerling DJ, Cameron DD. From mycoheterotrophy to mutualism: mycorrhizal specificity and functioning in Ophioglossum vulgatum sporophytes. THE NEW PHYTOLOGIST 2015; 205:1492-1502. [PMID: 25615559 DOI: 10.1111/nph.13263] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/08/2014] [Indexed: 06/04/2023]
Abstract
Mycorrhizal functioning in the fern Ophioglossum is complex and poorly understood. It is unknown whether mature O. vulgatum sporophytes form mutualistic associations with fungi of the Glomeromycota and with what specificity. Are green sporophytes able to 'repay' fungal carbon (C) invested in them by mycorrhizal partners during the initially heterotrophic gametophyte and early sporophyte stages of the lifecycle? We identified fungal partners of O. vulgatum sporophytes using molecular techniques and supplied them with (33) P-orthophosphate and O. vulgatum sporophytes with (14) CO2 . We traced the movement of fungal-acquired nutrients and plant-fixed C between symbionts and analysed natural abundance (13) C and (15) N isotope signatures to assess nutritional interactions. We found fungal specificity of O. vulgatum sporophytes towards a mycorrhizal fungus closely related to Glomus macrocarpum. Our radioisotope tracers revealed reciprocal C-for-phosphorus exchange between fern sporophytes and fungal partners, despite competition from surrounding vegetation. Monocultures of O. vulgatum were enriched in (13) C and (15) N, providing inconclusive evidence of mycoheterotrophy when experiencing competition from the surrounding plant community. We show mutualistic and specific symbiosis between a eusporangiate fern and fungi of the Glomeromycota. Our findings suggest a 'take now, pay later' strategy of mycorrhizal functioning through the lifecycle O. vulgatum, from mycoheterotrophic gametophyte to mutualistic aboveground sporophyte.
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Affiliation(s)
- Katie J Field
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Jonathan R Leake
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Stefanie Tille
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Kate E Allinson
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - William R Rimington
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, UK
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin I Bidartondo
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, UK
| | - David J Beerling
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Duncan D Cameron
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
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Unterseher M. Diversity of Fungal Endophytes in Temperate Forest Trees. ENDOPHYTES OF FOREST TREES 2011. [DOI: 10.1007/978-94-007-1599-8_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Abarenkov K, Tedersoo L, Nilsson RH, Vellak K, Saar I, Veldre V, Parmasto E, Prous M, Aan A, Ots M, Kurina O, Ostonen I, Jõgeva J, Halapuu S, Põldmaa K, Toots M, Truu J, Larsson KH, Kõljalg U. PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences. Evol Bioinform Online 2010. [PMCID: PMC3023303 DOI: 10.4137/ebo.s6271] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.
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Affiliation(s)
- Kessy Abarenkov
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Leho Tedersoo
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - R. Henrik Nilsson
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
- Department of Plant and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden
| | - Kai Vellak
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Irja Saar
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Vilmar Veldre
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Erast Parmasto
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
- Institute of Agriculture and Environment, Estonian University of Life Sciences, 181 Riia St., 51014 Tartu, Estonia
| | - Marko Prous
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Anne Aan
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Margus Ots
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Olavi Kurina
- Institute of Agriculture and Environment, Estonian University of Life Sciences, 181 Riia St., 51014 Tartu, Estonia
| | - Ivika Ostonen
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Janno Jõgeva
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Siim Halapuu
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Kadri Põldmaa
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
| | - Märt Toots
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
- Institute of Statistics, University of Tartu, 2 Liivi St., 50409 Tartu, Estonia
| | - Jaak Truu
- Institute of Molecular and Cell Biology, University of Tartu, 23 Riia St., 51010 Tartu, Estonia
| | - Karl-Henrik Larsson
- Natural History Museum of Oslo University, Box 1172, Blindern, N-0318 Oslo, Norway
| | - Urmas Kõljalg
- Natural History Museum of Tartu University, 46 Vanemuise St., 51014 Tartu, Estonia
- Institute of Ecology and Earth Sciences, University of Tartu, 46 Vanemuise St., 51014 Tartu, Estonia
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Parrent JL, Peay K, Arnold AE, Comas LH, Avis P, Tuininga A. Moving from pattern to process in fungal symbioses: linking functional traits, community ecology and phylogenetics. THE NEW PHYTOLOGIST 2010; 185:882-886. [PMID: 20356343 DOI: 10.1111/j.1469-8137.2010.03190.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Comas LH, Tuininga AR, Callahan HS. Advancing our current understanding of plant-fungal symbioses: bridging scales from local to global. THE NEW PHYTOLOGIST 2010; 185:871-873. [PMID: 20356340 DOI: 10.1111/j.1469-8137.2010.03188.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Louise H Comas
- Intercollege Graduate Program in Ecology, Department of Horticulture, The Pennsylvania State University, University Park, PA 16902, USA.
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