1
|
Sepp SK, Vasar M, Davison J, Oja J, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Garibay Oriel R, Hiiesalu I, Koorem K, Kõljalg U, Moora M, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Vasco Palacios AM, Tedersoo L, Zobel M. Global diversity and distribution of nitrogen-fixing bacteria in the soil. Front Plant Sci 2023; 14:1100235. [PMID: 36743494 PMCID: PMC9895822 DOI: 10.3389/fpls.2023.1100235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.
Collapse
Affiliation(s)
- Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Juan José Cantero
- Universidad Nacional de Córdoba, Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina
- Universidad Nacional de Río Cuarto, Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Roberto Garibay Oriel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Taru, Estonia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| |
Collapse
|
2
|
Vasar M, Davison J, Moora M, Sepp SK, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Oja J, Garibay-Orijel R, Hiiesalu I, Koorem K, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Doležal J, Palacios AMV, Tedersoo L, Zobel M. Metabarcoding of soil environmental DNA to estimate plant diversity globally. Front Plant Sci 2023; 14:1106617. [PMID: 37143888 PMCID: PMC10151745 DOI: 10.3389/fpls.2023.1106617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
Collapse
Affiliation(s)
- Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- *Correspondence: Martti Vasar,
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne, University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, WA, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany, The Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
| |
Collapse
|
3
|
Davison J, Vasar M, Sepp SK, Oja J, Al-Quraishy S, Bueno CG, Cantero JJ, Chimbioputo Fabiano E, Decocq G, Fraser L, Hiiesalu I, Hozzein WN, Koorem K, Moora M, Mucina L, Onipchenko V, Öpik M, Pärtel M, Phosri C, Semchenko M, Vahter T, Tedersoo L, Zobel M. Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities. Ecology 2022; 103:e3761. [PMID: 35582944 DOI: 10.1002/ecy.3761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/08/2022]
Abstract
Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that: (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense 'packing' in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions. Current empirical support, however, is mixed. We tested these expectations using published data on arbuscular mycorrhizal (AM) fungal community composition worldwide. We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance. However, contrary to expectation, dominance was pronounced in communities where more specialists were present; and, conversely, richness was higher in communites with more generalists. Thus, resource competition and niche packing appear of limited importance in AM fungal community assembly; rather patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Juan José Cantero
- Universidad Nacional de Córdoba, Instituto Multidisciplinario de Biología Vegetal, CONICET, Córdoba, Argentina.,Universidad Nacional de Río Cuarto, Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne University of Picardie, Amiens, France
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia.,Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonosov State University, Moscow, Russia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia.,School of Earth and Environmental Sciences, University of Manchester, Manchester, UK
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Estonia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Botany, University of Tartu, Tartu, Estonia
| |
Collapse
|
4
|
Kindermann L, Dobler M, Niedeggen D, Fabiano EC, Linstädter A. Dataset on woody aboveground biomass, disturbance losses, and wood density from an African savanna ecosystem. Data Brief 2022; 42:108155. [PMID: 35515994 PMCID: PMC9062271 DOI: 10.1016/j.dib.2022.108155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 11/26/2022] Open
Abstract
This dataset comprises tree inventories and damage assessments performed in Namibia's semi-arid Zambezi Region. Data were sampled in savannas and savanna woodlands along steep gradients of elephant population densities to capture the effects of those (and other) disturbances on individual-level and stand-level aboveground woody biomass (AGB). The dataset contains raw data on dendrometric measures and processed data on specific wood density (SWD), woody aboveground biomass, and biomass losses through disturbance impacts. Allometric proxies (height, canopy diameters, and in adult trees also stem circumferences) were recorded for n = 6,179 tree and shrub individuals. Wood samples were taken for each encountered species to measure specific wood density. These measurements have been used to estimate woody aboveground biomass via established allometric models, advanced through our improved methodologies and workflows that accounted for tree and shrub architecture shaped by disturbance impacts. To this end, we performed a detailed damage assessment on each woody individual in the field. In addition to estimations of standing biomass, our new method also delivered data on biomass losses to different disturbance agents (elephants, fire, and others) on the level of plant individuals and stands. The data presented here have been used within a study published with Ecological Indicators (Kindermann et al., 2022) to evaluate the benefits of our improved methodology in comparison to a standard reference method of aboveground biomass estimations. Additionally, it has been employed in a study on carbon storage and sequestration in vegetation and soils (Sandhage-Hofmann et al., 2021). The raw data of dendrometric measurements can be subjected to other available allometric models for biomass estimation. The processed data can be used to analyze disturbance impacts on woody aboveground biomass, or for regional carbon storage estimates. The data on species-specific wood density can be used for application to other dendrometric datasets to (re-) estimate biomass through allometric models requiring wood density. It can further be used for plant functional trait analyses.
Collapse
Affiliation(s)
- Liana Kindermann
- Biodiversity Research / Systematic Botany, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Maulbeerallee 1, Potsdam 14469, Germany.,Grassland Ecology and Grassland Management, Institute of Crop Science and Resource Conservation (INRES), Agricultural Faculty, University of Bonn, Bonn 53115, Germany
| | - Magnus Dobler
- Biodiversity Research / Systematic Botany, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Maulbeerallee 1, Potsdam 14469, Germany
| | - Daniela Niedeggen
- Terrestrial Ecology Group, Institute of Zoology, Department of Biology, Faculty of Science and Mathematics, University of Cologne, 50674 Cologne, Germany
| | - Ezequiel Chimbioputo Fabiano
- Department of Wildlife Management and Tourism Studies, University of Namibia Katima-Mulilo Campus, Ngweze, Katima-Mulilo 1096, Namibia
| | - Anja Linstädter
- Biodiversity Research / Systematic Botany, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Maulbeerallee 1, Potsdam 14469, Germany.,Grassland Ecology and Grassland Management, Institute of Crop Science and Resource Conservation (INRES), Agricultural Faculty, University of Bonn, Bonn 53115, Germany
| |
Collapse
|
5
|
Vasar M, Davison J, Sepp SK, Oja J, Al-Quraishy S, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Fraser L, Hiiesalu I, Hozzein WN, Koorem K, Moora M, Mucina L, Onipchenko V, Öpik M, Pärtel M, Phosri C, Vahter T, Tedersoo L, Zobel M. Global taxonomic and phylogenetic assembly of AM fungi. Mycorrhiza 2022; 32:135-144. [PMID: 35138435 DOI: 10.1007/s00572-022-01072-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.
Collapse
Affiliation(s)
- Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia.
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Jane Oja
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - C Guillermo Bueno
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Juan José Cantero
- CONICET, Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía Y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, France
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Inga Hiiesalu
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Kadri Koorem
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, Australia
- Department of Geography and Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonosov State University, Moscow, Russia
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Meelis Pärtel
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 2 Liivi St, 50409, Tartu, Estonia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Microbiology Center, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
| |
Collapse
|
6
|
Davison J, Moora M, Semchenko M, Adenan SB, Ahmed T, Akhmetzhanova AA, Alatalo JM, Al-Quraishy S, Andriyanova E, Anslan S, Bahram M, Batbaatar A, Brown C, Bueno CG, Cahill J, Cantero JJ, Casper BB, Cherosov M, Chideh S, Coelho AP, Coghill M, Decocq G, Dudov S, Fabiano EC, Fedosov VE, Fraser L, Glassman SI, Helm A, Henry HAL, Hérault B, Hiiesalu I, Hiiesalu I, Hozzein WN, Kohout P, Kõljalg U, Koorem K, Laanisto L, Mander Ü, Mucina L, Munyampundu JP, Neuenkamp L, Niinemets Ü, Nyamukondiwa C, Oja J, Onipchenko V, Pärtel M, Phosri C, Põlme S, Püssa K, Ronk A, Saitta A, Semboli O, Sepp SK, Seregin A, Sudheer S, Peña-Venegas CP, Paz C, Vahter T, Vasar M, Veraart AJ, Tedersoo L, Zobel M, Öpik M. Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi. New Phytol 2021; 231:763-776. [PMID: 33507570 DOI: 10.1111/nph.17240] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.
Collapse
Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- School of Earth and Environmental Sciences, University of Manchester, Manchester,, M13 9PL, UK
| | | | - Talaat Ahmed
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Asem A Akhmetzhanova
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Juha M Alatalo
- Environmental Science Centre, Qatar University, Doha, 2713, Qatar
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Elena Andriyanova
- Institute of Biological Problems of the North Far East Branch of Russian Academy of Sciences, Magadan, 685000, Russia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 756 51, Sweden
| | - Amgaa Batbaatar
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Charlotte Brown
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - C Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - James Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, X5000HUA, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, X5804BYA, Argentina
| | - Brenda B Casper
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Mikhail Cherosov
- Institute of Biological Problems of the Cryolithozone, Siberian Branch of the Russian Academy of Sciences, Yakutsk, 677000, Russia
| | - Saida Chideh
- Département de Recherche en Sciences de l'Environnement, Université de Djibouti, Private bag 1904, Djibouti, Djibouti
| | - Ana P Coelho
- Department of Biology and CESAM, University of Aveiro, Aveiro, 3810-193, Portugal
| | - Matthew Coghill
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés, Jules Verne University of Picardie, Amiens, F-80037, France
| | - Sergey Dudov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Ezequiel Chimbioputo Fabiano
- Department of Wildlife Management and Ecotourism, University of Namibia, Private bag 1096, Katima Mulilo, Namibia
| | - Vladimir E Fedosov
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
- Botanical Garden-Institute FEB RAS, Vladivostok, 690024, Russia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Sydney I Glassman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Aveliina Helm
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Hugh A L Henry
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bruno Hérault
- CIRAD, UPR Forêts et Sociétés, Yamoussoukro, Côte d'Ivoire
- Forêts et Sociétés, Université de Montpellier, CIRAD, Montpellier, 34000, France
- Institut National Polytechnique Félix Houphouët-Boigny, INP-HB, Yamoussoukro, Côte d'Ivoire
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Wael N Hozzein
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Bani Suwayf, 62511, Egypt
| | - Petr Kohout
- Institute of Microbiology, Czech Academy of Science, Prague, 14220, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, 12843, Czechia
| | - Urmas Kõljalg
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Ülo Mander
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Murdoch, Perth, WA, 6150, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, 7602, South Africa
| | - Jean-Pierre Munyampundu
- School of Science, College of Science and Technology, University of Rwanda, Kigali, 3900, Rwanda
| | - Lena Neuenkamp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Institute of Plant Sciences, University of Bern, Bern, 3013, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu, 51006, Estonia
| | - Casper Nyamukondiwa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private bag 16, Palapye, Botswana
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Vladimir Onipchenko
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, 48000, Thailand
| | - Sergei Põlme
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
- Natural History Museum, University of Tartu, Tartu, 51014, Estonia
| | - Kersti Püssa
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Argo Ronk
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-4544, USA
| | - Alessandro Saitta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, 90128, Italy
| | - Olivia Semboli
- Center of Studies and Research on Pharmacopoeia and Traditional African Medicine, University of Bangui, Bangui, Central African Republic
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Alexey Seregin
- Department of Ecology and Plant Geography, Faculty of Biology, Moscow Lomonsov State University, Moscow, 119991, Russia
| | - Surya Sudheer
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Clara P Peña-Venegas
- Instituto Amazónico de Investigaciones Científicas Sinchi, Leticia, Amazonas, 910001, Colombia
| | - Claudia Paz
- Departamento de Biodiversidade, Universidade Estadual Paulista, Rio Claro, São Paulo, 13506-900, Brazil
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Annelies J Veraart
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, Nijmegen, 6525AJ, the Netherlands
| | - Leho Tedersoo
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, 51005, Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 51005, Estonia
| |
Collapse
|
7
|
Affiliation(s)
| | - Chris Sutherland
- Department of Environmental Conservation University of Massachusetts‐Amherst Amherst Massachusetts
| | - Angela K. Fuller
- U.S. Geological Survey, New York Cooperative Fish and Wildlife Research Unit, Department of Natural Resources Cornell University Ithaca New York
| | | | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul Porto Alegre Brazil
- Instituto Pró‐Carnívoros Atibaia Brazil
| | - Laurie Marker
- Ecology Division Cheetah Conservation Fund Otjiwarongo Namibia
| |
Collapse
|
8
|
Ahlswede S, Fabiano EC, Keeping D, Birkhofer K. Using the Formozov–Malyshev–Pereleshin formula to convert mammal spoor counts into density estimates for long‐term community‐level monitoring. Afr J Ecol 2019. [DOI: 10.1111/aje.12587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Ahlswede
- Department of Ecology Brandenburg University of Technology Cottbus Germany
| | | | - Derek Keeping
- Department of Renewable Resources University of Alberta Edmonton Alberta Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Cottbus Germany
| |
Collapse
|