151
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Vincent JB, Weiblen GD, May G. Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees. Mol Ecol 2016; 25:825-41. [PMID: 26661903 DOI: 10.1111/mec.13510] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/21/2015] [Accepted: 11/30/2015] [Indexed: 01/09/2023]
Abstract
Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.
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Affiliation(s)
- J B Vincent
- Plant Biological Sciences Graduate Program, 250 Biological Sciences Center, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN, 55108, USA
| | - G D Weiblen
- Bell Museum and Department of Plant Biology, 250 Biological Sciences Center, University of Minnesota, 1445 Gortner Avenue, St. Paul, MN, 55108, USA
| | - G May
- Department of Ecology, Evolution and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Circle, Falcon Heights, MN, 55108, USA
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152
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Affiliation(s)
- J. Marion Adeney
- Nicholas School of the Environment Duke University Durham, NC 27708 U.S.A
| | | | - Alberto Vicentini
- Depto. Biodiversidade (CBio) e Coleções Zoológicas Instituto de Pesquisas da Amazônia Manaus AM Brazil
| | - Mario Cohn‐Haft
- Depto. Biodiversidade (CBio) e Coleções Zoológicas Instituto de Pesquisas da Amazônia Manaus AM Brazil
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153
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Fine PVA, Baraloto C. Habitat Endemism in White‐sand Forests: Insights into the Mechanisms of Lineage Diversification and Community Assembly of the Neotropical Flora. Biotropica 2016. [DOI: 10.1111/btp.12301] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Paul V. A. Fine
- Department of Integrative Biology and University and Jepson Herbaria University of California 3040 Valley Life Sciences Building #3140 Berkeley CA 94720 U.S.A
| | - Christopher Baraloto
- INRA UMR Ecologie des Forêts de Guyane 97310 Kourou French Guiana
- Department of Biological Sciences and International Center for Tropical Botany Florida International University Miami FL 33199 U.S.A
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154
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Wang SK, Zuo XA, Zhao XY, Li YQ, Zhou X, Lv P, Luo YQ, Yun JY. Responses of soil fungal community to the sandy grassland restoration in Horqin Sandy Land, northern China. ENVIRONMENTAL MONITORING AND ASSESSMENT 2016; 188:21. [PMID: 26661957 DOI: 10.1007/s10661-015-5031-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
Sandy grassland restoration is a vital process including re-structure of soils, restoration of vegetation, and soil functioning in arid and semi-arid regions. Soil fungal community is a complex and critical component of soil functioning and ecological balance due to its roles in organic matter decomposition and nutrient cycling following sandy grassland restoration. In this study, soil fungal community and its relationship with environmental factors were examined along a habitat gradient of sandy grassland restoration: mobile dunes (MD), semi-fixed dunes (SFD), fixed dunes (FD), and grassland (G). It was found that species abundance, richness, and diversity of fungal community increased along with the sandy grassland restoration. The sequences analysis suggested that most of the fungal species (68.4 %) belonged to the phylum of Ascomycota. The three predominant fungal species were Pleospora herbarum, Wickerhamomyces anomalus, and Deconica Montana, accounting for more than one fourth of all the 38 species. Geranomyces variabilis was the subdominant species in MD, Pseudogymnoascus destructans and Mortierella alpine were the subdominant species in SFD, and P. destructans and Fungi incertae sedis were the dominant species in FD and G. The result from redundancy analysis (RDA) and stepwise regression analysis indicated that the vegetation characteristics and soil properties explain a significant proportion of the variation in the fungal community, and aboveground biomass and C:N ratio are the key factors to determine soil fungal community composition during sandy grassland restoration. It was suggested that the restoration of sandy grassland combined with vegetation and soil properties improved the soil fungal diversity. Also, the dominant species was found to be alternative following the restoration of sandy grassland ecosystems.
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Affiliation(s)
- Shao-Kun Wang
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China.
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China.
| | - Xiao-An Zuo
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Xue-Yong Zhao
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Yu-Qiang Li
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
- Laboratory of Stress Ecophysiology and Biotechnology (LSEB), CAREERI, CAS, Lanzhou, 730000, China
| | - Xin Zhou
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Peng Lv
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Yong-Qing Luo
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
| | - Jian-Ying Yun
- Naiman Desertification Research Station, Cold and Arid Regions Environmental and Engineering Research Institute (CAREERI), Chinese Academy of Sciences (CAS), 320# Donggang West Road, Lanzhou, 730000, China
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155
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Zuo X, Wang S, Lv P, Zhou X, Zhao X, Zhang T, Zhang J. Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland. Ecol Evol 2015; 6:318-28. [PMID: 26811795 PMCID: PMC4716495 DOI: 10.1002/ece3.1875] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 11/15/2015] [Accepted: 11/19/2015] [Indexed: 11/06/2022] Open
Abstract
The trait-based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community-weighted mean, CWM) and the dispersion of functional trait values (FD is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P < 0.05). Soil fungal richness was positively associated with plant richness, biomass, CWM plant height, and soil gradient aggregated from the principal component analysis, but SEM results showed that plant richness and CWM plant height determined by soil properties were the main factors exerting direct effects. Soil gradient increased fungal richness through indirect effect on vegetation rather than direct effect. The negative indirect effect of FDis on soil fungal richness was through its effect on plant biomass. Our final SEM model based on plant functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.
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Affiliation(s)
- Xiaoan Zuo
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China; Laboratory of Stress Ecophysiology and Biotechnology (LSEB) CAREERICAS Lanzhou 730000 China
| | - Shaokun Wang
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
| | - Peng Lv
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
| | - Xin Zhou
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
| | - Xueyong Zhao
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
| | - Tonghui Zhang
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
| | - Jing Zhang
- Naiman Desertification Research Station Cold and Arid Regions Environmental and Engineering Research Institute Chinese Academy of Sciences Lanzhou 730000 China
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156
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Fine PV. Ecological and Evolutionary Drivers of Geographic Variation in Species Diversity. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054102] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Paul V.A. Fine
- Department of Integrative Biology and University and Jepson Herbaria, University of California, Berkeley, California 94720;
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157
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Bonal D, Burban B, Stahl C, Wagner F, Hérault B. The response of tropical rainforests to drought-lessons from recent research and future prospects. ANNALS OF FOREST SCIENCE 2015; 73:27-44. [PMID: 27069374 PMCID: PMC4810888 DOI: 10.1007/s13595-015-0522-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 08/24/2015] [Indexed: 05/10/2023]
Abstract
KEY MESSAGE We review the recent findings on the influence of drought on tree mortality, growth or ecosystem functioning in tropical rainforests. Drought plays a major role in shaping tropical rainforests and the response mechanisms are highly diverse and complex. The numerous gaps identified here require the international scientific community to combine efforts in order to conduct comprehensive studies in tropical rainforests on the three continents. These results are essential to simulate the future of these ecosystems under diverse climate scenarios and to predict the future of the global earth carbon balance. CONTEXT Tropical rainforest ecosystems are characterized by high annual rainfall. Nevertheless, rainfall regularly fluctuates during the year and seasonal soil droughts do occur. Over the past decades, a number of extreme droughts have hit tropical rainforests, not only in Amazonia but also in Asia and Africa. The influence of drought events on tree mortality and growth or on ecosystem functioning (carbon and water fluxes) in tropical rainforest ecosystems has been studied intensively, but the response mechanisms are complex. AIMS Herein, we review the recent findings related to the response of tropical forest ecosystems to seasonal and extreme droughts and the current knowledge about the future of these ecosystems. RESULTS This review emphasizes the progress made over recent years and the importance of the studies conducted under extreme drought conditions or in through-fall exclusion experiments in understanding the response of these ecosystems. It also points to the great diversity and complexity of the response of tropical rainforest ecosystems to drought. CONCLUSION The numerous gaps identified here require the international scientific community to combine efforts in order to conduct comprehensive studies in tropical forest regions. These results are essential to simulate the future of these ecosystems under diverse climate scenarios and to predict the future of the global earth carbon balance.
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Affiliation(s)
- Damien Bonal
- />INRA, UMR « Ecologie et Ecophysiologie Forestières », Université de Lorraine-INRA, F-54280 Champenoux, France
| | - Benoit Burban
- />INRA, UMR «Ecologie des Forêts de Guyane», AgroParisTech-CIRAD-INRA-CNRS-Université de Guyane-Université des Antilles, Campus Agronomique, 97387 Kourou, Guyane Française France
| | - Clément Stahl
- />CIRAD, UMR « Ecologie des Forêts de Guyane », AgroParisTech- CIRAD-INRA-CNRS-Université de Guyane-Université des Antilles, Campus Agronomique, 97387 Kourou, Guyane Française France
- />University of Antwerpen, Campus Agronomique, 97387 Kourou, Guyane Française France
| | - Fabien Wagner
- />National Institute for Space Research (INPE), São José dos Campos, SP 12227-010 Brazil
| | - Bruno Hérault
- />CIRAD, UMR « Ecologie des Forêts de Guyane », AgroParisTech- CIRAD-INRA-CNRS-Université de Guyane-Université des Antilles, Campus Agronomique, 97387 Kourou, Guyane Française France
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158
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Miyamoto Y, Sakai A, Hattori M, Nara K. Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains. THE ISME JOURNAL 2015; 9:1870-9. [PMID: 25647348 PMCID: PMC4511943 DOI: 10.1038/ismej.2015.8] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/13/2014] [Accepted: 12/19/2014] [Indexed: 01/12/2023]
Abstract
Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the regional scale. Soil cores were collected from various forest types along an elevation gradient in southwestern Japan. Fungal species were identified by the internal transcribed spacer regions of the rDNA using direct sequencing. The occurrence of fungal species in this study was compared with a previous study conducted on a mountain separated by ∼550 km. In total, we recorded 454 EM fungi from 330 of 350 soil cores. Forty-seven fungal species (∼20% of the total excluding singletons) were shared between two mountains, mostly between similar forest types on both mountains. Variation partitioning in redundancy analysis revealed that climate explained the largest variance in EM fungal composition. The similarity of forest tree composition, which is usually determined by climatic conditions, was positively correlated with the similarity of the EM fungal composition. However, the lack of large host effects implied that communities of forest trees and EM fungi may be determined independently by climate. Our data provide important insights that host plants and mutualistic fungi may respond to climate change idiosyncratically, potentially altering carbon and nutrient cycles in relation to the plant-fungus associations.
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Affiliation(s)
- Yumiko Miyamoto
- Department of Natural Environmental Studies, The University of Tokyo, Tokyo, Japan
| | - Atsushi Sakai
- Forestry and Forest Products Research Institute, Kochi, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, The University of Tokyo, Tokyo, Japan
| | - Kazuhide Nara
- Department of Natural Environmental Studies, The University of Tokyo, Tokyo, Japan
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159
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Jena SK, Tayung K, Rath CC, Parida D. Occurrence of culturable soil fungi in a tropical moist deciduous forest Similipal Biosphere Reserve, Odisha, India. Braz J Microbiol 2015. [PMID: 26221092 PMCID: PMC4512052 DOI: 10.1590/s1517-838246120131367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Similipal Biosphere Reserve (SBR) is a tropical moist deciduous forest dominated by the species Shorea robusta
. To the best of our knowledge their rich biodiversity has not been explored in term of its microbial wealth. In the present investigation, soil samples were collected from ten selected sites inside SBR and studied for their physicochemical parameters and culturable soil fungal diversity. The soil samples were found to be acidic in nature with a pH ranging from of 5.1–6.0. Highest percentage of organic carbon and moisture content were observed in the samples collected from the sites, Chahala-1 and Chahala-2. The plate count revealed that fungal population ranged from 3.6 × 10
4
–2.1 × 10
5
and 5.1 × 10
4
–4.7 × 10
5
cfu/gm of soil in summer and winter seasons respectively. The soil fungus, Aspergillus niger
was found to be the most dominant species and Species Important Values Index (SIVI) was 43.4 and 28.6 in summer and winter seasons respectively. Among the sites studied, highest fungal diversity indices were observed during summer in the sites, Natto-2 and Natto-1. The Shannon-Wiener and Simpson indices in these two sites were found to be 3.12 and 3.022 and 0.9425 and 0.9373 respectively. However, the highest Fisher’s alpha was observed during winter in the sites Joranda, Natto-2, Chahala-1 and Natto-1 and the values were 3.780, 3.683, 3.575 and 3.418 respectively. Our investigation revealed that, fungal population was dependent on moisture and organic carbon (%) of the soil but its diversity was found to be regulated by sporulating species like Aspergillus
and Penicillium
.
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Affiliation(s)
- Santanu K Jena
- Department of Botany, North Orissa University, Odisha, India
| | - Kumanand Tayung
- Department of Botany, North Orissa University, Odisha, India
| | - Chandi C Rath
- Department of Botany, North Orissa University, Odisha, India
| | - Debraj Parida
- Department of Botany, North Orissa University, Odisha, India
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160
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Li H, Wang X, Liang C, Hao Z, Zhou L, Ma S, Li X, Yang S, Yao F, Jiang Y. Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests. Sci Rep 2015; 5:12234. [PMID: 26184121 PMCID: PMC4505317 DOI: 10.1038/srep12234] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/22/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding ecological linkages between above- and below-ground biota is critical for deepening our knowledge on the maintenance and stability of ecosystem processes. Nevertheless, direct comparisons of plant-microbe diversity at the community level remain scarce due to the knowledge gap between microbial ecology and plant ecology. We compared the α- and β- diversities of plant and soil bacterial communities in two temperate forests that represented early and late successional stages. We documented different patterns of aboveground-belowground diversity relationships in these forests. We observed no linkage between plant and bacterial α-diversity in the early successional forest, and even a negative correlation in the late successional forest, indicating that high bacterial α-diversity is not always linked to high plant α-diversity. Beta-diversity coupling was only found at the late successional stage, while in the early successional forest, the bacterial β-diversity was closely correlated with soil property distances. Additionally, we showed that the dominant competitive tree species in the late successional forest may play key roles in driving forest succession by shaping the soil bacterial community in the early successional stage. This study sheds new light on the potential aboveground-belowground linkage in natural ecosystems, which may help us understand the mechanisms that drive ecosystem succession.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Xugao Wang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Chao Liang
- 1] State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China [2] Great Lakes Bioenergy Research Center, University of Wisconsin, Madison 53706, USA
| | - Zhanqing Hao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Lisha Zhou
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Sam Ma
- State Key Laboratory of Genetic Resources and Evolution, Computational Biology and Medical Ecology Lab, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiaobin Li
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Shan Yang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Fei Yao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
| | - Yong Jiang
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110164, China
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161
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LeBlanc N, Kinkel LL, Kistler HC. Soil fungal communities respond to grassland plant community richness and soil edaphics. MICROBIAL ECOLOGY 2015; 70:188-95. [PMID: 25399511 DOI: 10.1007/s00248-014-0531-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 11/03/2014] [Indexed: 05/21/2023]
Abstract
Fungal communities in soil have significant influences on terrestrial ecosystem dynamics, yet our understanding of the drivers of fungal diversity and community structure in soil is limited. Fungal communities associated with the rhizosphere of four native perennial grassland plant species, two legumes and two grasses, grown in monoculture and polyculture in a long-term field experiment were characterized. Reference databases were developed for, and amplicon libraries sequenced from, multiple-copy rRNA and single-copy protein-coding loci. Clustering and alignment-based pipelines were utilized to evaluate differences in fungal community structure and diversity in response to plant host, plant community richness, and soil edaphics. Fungal diversity increased in the rhizosphere of plants growing in polyculture plant communities as compared to monoculture plant communities. Fungal community structure was differentiated between legumes and grasses growing in monoculture but not in polyculture. To specifically monitor fungi in the genus Fusarium in the soil, the protein-coding locus was used to increase phylogenetic resolution and enrich for this taxon. These data show that fungal community richness and structure are strongly linked with plant community dynamics and associated soil edaphic characteristics in these grassland soils.
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Affiliation(s)
- Nicholas LeBlanc
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
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162
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Peay KG, Russo SE, McGuire KL, Lim Z, Chan JP, Tan S, Davies SJ. Lack of host specificity leads to independent assortment of dipterocarps and ectomycorrhizal fungi across a soil fertility gradient. Ecol Lett 2015; 18:807-816. [PMID: 26032408 DOI: 10.1111/ele.12459] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/13/2015] [Accepted: 05/06/2015] [Indexed: 11/29/2022]
Abstract
Plants interact with a diversity of microorganisms, and there is often concordance in their community structures. Because most community-level studies are observational, it is unclear if such concordance arises because of host specificity, in which microorganisms or plants limit each other's occurrence. Using a reciprocal transplant experiment, we tested the hypothesis that host specificity between trees and ectomycorrhizal fungi determines patterns of tree and fungal soil specialisation. Seedlings of 13 dipterocarp species with contrasting soil specialisations were seeded into plots crossing soil type and canopy openness. Ectomycorrhizal colonists were identified by DNA sequencing. After 2.5 years, we found no evidence of host specificity. Rather, soil environment was the primary determinant of ectomycorrhizal diversity and composition on seedlings. Despite their close symbiosis, our results show that ectomycorrhizal fungi and tree communities in this Bornean rain forest assemble independently of host-specific interactions, raising questions about how mutualism shapes the realised niche.
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Affiliation(s)
- Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Sabrina E Russo
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0118, USA
| | - Krista L McGuire
- Department of Biology, Barnard College of Columbia University, New York, NY, 10027, USA.,Department of Ecology, Evolution & Environmental Biology, Columbia University, Washington, New York, NY, 10027, USA
| | - Zhenyu Lim
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Ju Ping Chan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, 68588-0118, USA
| | - Sylvester Tan
- Center for Tropical Forest Science, Smithsonian Institution, Washington, D.C., 20013-7012, USA
| | - Stuart J Davies
- Center for Tropical Forest Science, Smithsonian Institution, Washington, D.C., 20013-7012, USA
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163
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Pautasso M, Schlegel M, Holdenrieder O. Forest health in a changing world. MICROBIAL ECOLOGY 2015; 69:826-842. [PMID: 25502075 DOI: 10.1007/s00248-014-0545-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 11/27/2014] [Indexed: 06/04/2023]
Abstract
Forest pathology, the science of forest health and tree diseases, is operating in a rapidly developing environment. Most importantly, global trade and climate change are increasing the threat to forest ecosystems posed by new diseases. Various studies relevant to forest pathology in a changing world are accumulating, thus making it necessary to provide an update of recent literature. In this contribution, we summarize research at the interface between forest pathology and landscape ecology, biogeography, global change science and research on tree endophytes. Regional outbreaks of tree diseases are requiring interdisciplinary collaboration, e.g. between forest pathologists and landscape ecologists. When tree pathogens are widely distributed, the factors determining their broad-scale distribution can be studied using a biogeographic approach. Global change, the combination of climate and land use change, increased pollution, trade and urbanization, as well as invasive species, will influence the effects of forest disturbances such as wildfires, droughts, storms, diseases and insect outbreaks, thus affecting the health and resilience of forest ecosystems worldwide. Tree endophytes can contribute to biological control of infectious diseases, enhance tolerance to environmental stress or behave as opportunistic weak pathogens potentially competing with more harmful ones. New molecular techniques are available for studying the complete tree endobiome under the influence of global change stressors from the landscape to the intercontinental level. Given that exotic tree diseases have both ecologic and economic consequences, we call for increased interdisciplinary collaboration in the coming decades between forest pathologists and researchers studying endophytes with tree geneticists, evolutionary and landscape ecologists, biogeographers, conservation biologists and global change scientists and outline interdisciplinary research gaps.
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Affiliation(s)
- Marco Pautasso
- Forest Pathology & Dendrology, Institute of Integrative Biology (IBZ), ETH Zurich, 8092, Zurich, Switzerland,
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164
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165
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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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166
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Huang XF, Zhou D, Guo J, Manter D, Reardon K, Vivanco J. Bacillus
spp. from rainforest soil promote plant growth under limited nitrogen conditions. J Appl Microbiol 2015; 118:672-84. [DOI: 10.1111/jam.12720] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/04/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
Affiliation(s)
- X.-F. Huang
- Center for Rhizosphere Biology; Colorado State University; Fort Collins CO USA
- Department of Chemical and Biological Engineering; Colorado State University; Fort Collins CO USA
| | - D. Zhou
- Center for Rhizosphere Biology; Colorado State University; Fort Collins CO USA
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing China
| | - J. Guo
- Department of Plant Pathology; College of Plant Protection; Nanjing Agricultural University; Nanjing China
| | - D.K. Manter
- USDA-ARS Soil-Plant-Nutrient Research Unit; Fort Collins CO USA
| | - K.F. Reardon
- Department of Chemical and Biological Engineering; Colorado State University; Fort Collins CO USA
- Cell and Molecular Biology Graduate Program; Colorado State University; Fort Collins CO USA
| | - J.M. Vivanco
- Center for Rhizosphere Biology; Colorado State University; Fort Collins CO USA
- Cell and Molecular Biology Graduate Program; Colorado State University; Fort Collins CO USA
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167
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Nam YJ, Kim H, Lee JH, Yoon H, Kim JG. Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands. J GEN APPL MICROBIOL 2015; 61:67-74. [DOI: 10.2323/jgam.61.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Yoon-Jong Nam
- Department of Life Sciences and Biotechnology, Kyungpook National University
| | - Hyun Kim
- Department of Life Sciences and Biotechnology, Kyungpook National University
| | - Jin-Hyung Lee
- Department of Life Sciences and Biotechnology, Kyungpook National University
| | - Hyeokjun Yoon
- Department of Life Sciences and Biotechnology, Kyungpook National University
| | - Jong-Guk Kim
- Department of Life Sciences and Biotechnology, Kyungpook National University
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168
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Kennedy P, Nguyen N, Cohen H, Peay K. Missing checkerboards? An absence of competitive signal in Alnus-associated ectomycorrhizal fungal communities. PeerJ 2014; 2:e686. [PMID: 25548729 PMCID: PMC4273934 DOI: 10.7717/peerj.686] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 11/15/2014] [Indexed: 11/20/2022] Open
Abstract
A number of recent studies suggest that interspecific competition plays a key role in determining the structure of ectomycorrhizal (ECM) fungal communities. Despite this growing consensus, there has been limited study of ECM fungal community dynamics in abiotically stressful environments, which are often dominated by positive rather than antagonistic interactions. In this study, we examined the ECM fungal communities associated with the host genus Alnus, which live in soils high in both nitrate and acidity. The nature of ECM fungal species interactions (i.e., antagonistic, neutral, or positive) was assessed using taxon co-occurrence and DNA sequence abundance correlational analyses. ECM fungal communities were sampled from root tips or mesh in-growth bags in three monodominant A. rubra plots at a site in Oregon, USA and identified using Illumina-based amplification of the ITS1 gene region. We found a total of 175 ECM fungal taxa; 16 of which were closely related to known Alnus-associated ECM fungi. Contrary to previous studies of ECM fungal communities, taxon co-occurrence analyses on both the total and Alnus-associated ECM datasets indicated that the ECM fungal communities in this system were not structured by interspecific competition. Instead, the co-occurrence patterns were consistent with either random assembly or significant positive interactions. Pair-wise correlational analyses were also more consistent with neutral or positive interactions. Taken together, our results suggest that interspecific competition does not appear to determine the structure of all ECM fungal communities and that abiotic conditions may be important in determining the specific type of interaction occurring among ECM fungi.
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Affiliation(s)
- Peter Kennedy
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
- Department of Biology, Lewis & Clark College, Portland, OR, USA
| | - Nhu Nguyen
- Department of Plant Biology, University of Minnesota, St. Paul, MN, USA
| | - Hannah Cohen
- Department of Biology, Lewis & Clark College, Portland, OR, USA
| | - Kabir Peay
- Department of Biology, Stanford University, Palo Alto, CA, USA
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169
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170
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Shen C, Liang W, Shi Y, Lin X, Zhang H, Wu X, Xie G, Chain P, Grogan P, Chu H. Contrasting elevational diversity patterns between eukaryotic soil microbes and plants. Ecology 2014. [DOI: 10.1890/14-0310.1] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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171
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Bonito G, Reynolds H, Robeson MS, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol 2014; 23:3356-70. [PMID: 24894495 DOI: 10.1111/mec.12821] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/09/2014] [Accepted: 05/20/2014] [Indexed: 11/30/2022]
Abstract
Microbial communities in plant roots provide critical links between above- and belowground processes in terrestrial ecosystems. Variation in root communities has been attributed to plant host effects and microbial host preferences, as well as to factors pertaining to soil conditions, microbial biogeography and the presence of viable microbial propagules. To address hypotheses regarding the influence of plant host and soil biogeography on root fungal and bacterial communities, we designed a trap-plant bioassay experiment. Replicate Populus, Quercus and Pinus plants were grown in three soils originating from alternate field sites. Fungal and bacterial community profiles in the root of each replicate were assessed through multiplex 454 amplicon sequencing of four loci (i.e., 16S, SSU, ITS, LSU rDNA). Soil origin had a larger effect on fungal community composition than did host species, but the opposite was true for bacterial communities. Populus hosted the highest diversity of rhizospheric fungi and bacteria. Root communities on Quercus and Pinus were more similar to each other than to Populus. Overall, fungal root symbionts appear to be more constrained by dispersal and biogeography than by host availability.
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Affiliation(s)
- Gregory Bonito
- Royal Botanic Gardens, Melbourne, VIC., 3141, Australia; Department of Biology, Duke University, Durham, NC, 27708, USA
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172
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de Menezes AB, Prendergast-Miller MT, Richardson AE, Toscas P, Farrell M, Macdonald LM, Baker G, Wark T, Thrall PH. Network analysis reveals that bacteria and fungi form modules that correlate independently with soil parameters. Environ Microbiol 2014; 17:2677-89. [DOI: 10.1111/1462-2920.12559] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/02/2014] [Accepted: 07/02/2014] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Peter Toscas
- CSIRO Digital Productivity and Services Flagship; Clayton South VIC Australia
| | - Mark Farrell
- Waite Campus; CSIRO Agriculture Flagship; Glen Osmond SA Australia
| | | | - Geoff Baker
- Black Mountain; CSIRO Agriculture Flagship; Canberra ACT 2601 Australia
| | - Tim Wark
- CSIRO Digital Productivity and Services Flagship, QCAT; Pullenvale QLD Australia
| | - Peter H. Thrall
- Black Mountain; CSIRO Agriculture Flagship; Canberra ACT 2601 Australia
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173
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Abu-Ghosh S, Droby S, Korine C. Seasonal and plant-dependent variations in diversity, abundance and stress tolerance of epiphytic yeasts in desert habitats. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:373-382. [PMID: 24992536 DOI: 10.1111/1758-2229.12161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 03/01/2014] [Indexed: 06/03/2023]
Abstract
We studied the epiphytic yeast species of the plants of the Negev Desert and the Dead Sea region, Israel, which are considered one of the most extreme hyper-arid lands in the world. For this purpose, we developed isolation protocols; we performed morphological, cultural and molecular identification tests and compared yeast diversity between the locations and the plants. The composition of the yeast populations present in the study's plants underwent seasonal fluctuations, whereas differences in community compositions were significant within sites. The maximum number of species of yeast occurred in autumn and Cryptococcus spp. were predominant year round. The isolated yeast strains showed an unusual tolerance to extreme growth conditions, such as high temperatures (up to 72% viability at 50°C), lethal hydrogen peroxide and NaCl concentrations. These results suggest that epiphytic yeasts inhabit the plants of the Dead Sea region and the Negev Desert have a community structure that is unique to the plant species and have a high tolerance to the harsh conditions that enables them to adapt to an arid ecosystem.
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Affiliation(s)
- Said Abu-Ghosh
- Department of Postharvest Science, The Volcani Center, Agricultural Research Organization (ARO), Bet Dagan, 50250, Israel
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174
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Pellissier L, Niculita-Hirzel H, Dubuis A, Pagni M, Guex N, Ndiribe C, Salamin N, Xenarios I, Goudet J, Sanders IR, Guisan A. Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps. Mol Ecol 2014; 23:4274-90. [PMID: 25041483 DOI: 10.1111/mec.12854] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 06/18/2014] [Accepted: 07/05/2014] [Indexed: 01/20/2023]
Abstract
Studying patterns of species distributions along elevation gradients is frequently used to identify the primary factors that determine the distribution, diversity and assembly of species. However, despite their crucial role in ecosystem functioning, our understanding of the distribution of below-ground fungi is still limited, calling for more comprehensive studies of fungal biogeography along environmental gradients at various scales (from regional to global). Here, we investigated the richness of taxa of soil fungi and their phylogenetic diversity across a wide range of grassland types along a 2800 m elevation gradient at a large number of sites (213), stratified across a region of the Western Swiss Alps (700 km(2)). We used 454 pyrosequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs). The OTU diversity-area relationship revealed uneven distribution of fungal taxa across the study area (i.e. not all taxa are everywhere) and fine-scale spatial clustering. Fungal richness and phylogenetic diversity were found to be higher in lower temperatures and higher moisture conditions. Climatic and soil characteristics as well as plant community composition were related to OTU alpha, beta and phylogenetic diversity, with distinct fungal lineages suggesting distinct ecological tolerances. Soil fungi, thus, show lineage-specific biogeographic patterns, even at a regional scale, and follow environmental determinism, mediated by interactions with plants.
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Affiliation(s)
- L Pellissier
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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175
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Moyersoen B, Weiß M. New neotropical sebacinales species from a Pakaraimaea dipterocarpacea forest in the Guayana Region, Southern Venezuela: structural diversity and phylogeography. PLoS One 2014; 9:e103076. [PMID: 25072467 PMCID: PMC4114518 DOI: 10.1371/journal.pone.0103076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/19/2014] [Indexed: 11/19/2022] Open
Abstract
Pakaraimaea dipterocarpacea, a member of the Dipterocarpaceae endemic in the Guayana region, is associated with a diverse community of ectomycorrhizal (ECM) fungi. Amongst the 41 ECM fungal species detected in a 400 m2 P. dipterocarpacea ssp. nitida plot in Southern Venezuela, three species belonged to the Sebacinales. We tested whether ECM anatomotype characterization can be used as a feasible element in an integrative taxonomy in this diverse fungal group, where the relevance of fruitbody morphology for species delimitation seems limited. Using a combination of ECM morpho-anatomical characterizations and phylogenetic analyses based on nuclear ITS and LSU sequences, we report three new species. The main distinguishing features of Sebacina guayanensis are the yellowish cell walls together with conspicuous undifferentiated, uniform compact (type B) rhizomorphs. Staghorn-like hyphae are characteristic of S. tomentosa. The combination of clusters of thick-walled emanating hyphae, including hyphae similar to awl-shaped cystidia with basal dichotomous or trichotomous ramifications, and the presence of type B rhizomorphs were characteristic of a third, yet unnamed species. The three species belong to three different, possibly specifically tropical clades in Sebacinales Group A. The geographic distribution of phylogenetically related strains was wide, including a Dicymbe forest in Guyana and an Ecuadorian rainforest with Coccoloba species. We show that ECM morpho-anatomy can be used, in combination with other analyses, to delineate species within Sebacinales Group A. In addition to phylogenetic information, type B rhizomorphs observed in different Sebacinales clades have important ecological implications for this fungal group. The phylogeography of Sebacinales suggests that dispersion and host jump are important radiation mechanisms that shaped P. dipterocarpacea ECM fungal community. This study emphasizes the need for more sequence data to evaluate the hypothesis that phylogeographic relationships between neo- and paleotropical ECM fungal species could be attributed to the vicariance of cross-continental hosts such as the Dipterocarpacae.
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Affiliation(s)
- Bernard Moyersoen
- School of Biological Sciences, Cruickshank Building, University of Aberdeen, Aberdeen, United Kingdom
| | - Michael Weiß
- Department of Biology, University of Tübingen, Tübingen, Germany
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176
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Endemism and functional convergence across the North American soil mycobiome. Proc Natl Acad Sci U S A 2014; 111:6341-6. [PMID: 24733885 DOI: 10.1073/pnas.1402584111] [Citation(s) in RCA: 291] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure-function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.
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177
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Sequence depth, not PCR replication, improves ecological inference from next generation DNA sequencing. PLoS One 2014; 9:e90234. [PMID: 24587293 PMCID: PMC3938664 DOI: 10.1371/journal.pone.0090234] [Citation(s) in RCA: 280] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/27/2014] [Indexed: 12/23/2022] Open
Abstract
Recent advances in molecular approaches and DNA sequencing have greatly progressed the field of ecology and allowed for the study of complex communities in unprecedented detail. Next generation sequencing (NGS) can reveal powerful insights into the diversity, composition, and dynamics of cryptic organisms, but results may be sensitive to a number of technical factors, including molecular practices used to generate amplicons, sequencing technology, and data processing. Despite the popularity of some techniques over others, explicit tests of the relative benefits they convey in molecular ecology studies remain scarce. Here we tested the effects of PCR replication, sequencing depth, and sequencing platform on ecological inference drawn from environmental samples of soil fungi. We sequenced replicates of three soil samples taken from pine biomes in North America represented by pools of either one, two, four, eight, or sixteen PCR replicates with both 454 pyrosequencing and Illumina MiSeq. Increasing the number of pooled PCR replicates had no detectable effect on measures of α- and β-diversity. Pseudo-β-diversity - which we define as dissimilarity between re-sequenced replicates of the same sample - decreased markedly with increasing sampling depth. The total richness recovered with Illumina was significantly higher than with 454, but measures of α- and β-diversity between a larger set of fungal samples sequenced on both platforms were highly correlated. Our results suggest that molecular ecology studies will benefit more from investing in robust sequencing technologies than from replicating PCRs. This study also demonstrates the potential for continuous integration of older datasets with newer technology.
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178
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Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest. ISME JOURNAL 2014; 8:1548-50. [PMID: 24451208 DOI: 10.1038/ismej.2013.253] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/13/2013] [Accepted: 12/11/2013] [Indexed: 11/09/2022]
Abstract
Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.
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179
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Meiser A, Bálint M, Schmitt I. Meta-analysis of deep-sequenced fungal communities indicates limited taxon sharing between studies and the presence of biogeographic patterns. THE NEW PHYTOLOGIST 2014; 201:623-635. [PMID: 24111803 DOI: 10.1111/nph.12532] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 08/27/2013] [Indexed: 06/02/2023]
Abstract
High-throughput amplicon sequencing gives new insights into fungal community ecology. Massively generated molecular data lead to the discovery of vast fungal diversity. However, it is unclear to what extent operational taxonomic units (OTUs) overlap among independent studies, because no comparative studies exist. We compared fungal diversity based on the internal transcribed spacer (ITS1) region among 10 published studies. Starting from the raw 454 pyrosequencing data, we used a uniform pipeline to prune the reads. We investigated fungal richness and taxonomic composition among phyllosphere and soil fungal communities, as well as biogeographic signals in the data. We did not find globally distributed OTUs, even when comparing fungal communities from similar habitats (phyllosphere or soil). This suggests that high local fungal diversity scales up to high global diversity. The most OTU-rich classes in the phyllosphere were Dothideomycetes (21%) and Sordariomycetes (14%), and in the soil were Sordariomycetes (13%) and Agaricomycetes (12%). The richness estimates suggest the presence of undiscovered fungal diversity even in deeply sequenced study systems. The small number of OTUs shared among studies indicates that globally distributed taxa and habitat generalists may be rare. Latitudinal diversity decline and distance decay relationships suggest the presence of biogeographic patterns similar to those in plants and animals.
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Affiliation(s)
- Anjuli Meiser
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Imke Schmitt
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
- Biodiversity and Climate Research Centre BiK-F, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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180
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