Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape

Lothamer, Kale M.; Brown, Shawn P.; Mattox, J. D.; Jumpponen, Ari

doi:10.1007/s00572-013-0539-2

Cited by 26 publications

(15 citation statements)

References 74 publications

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“…Soil microbes may directly respond to changes in soil geochemistry (Fierer and Jackson, 2006;Rousk et al, 2010), but may also differ among plant species, particularly in the rhizosphere (Grayston et al, 1998;Lothamer et al, 2014). As a result, dissecting the linkages between management decisions that lead to urban greenspace plant species selection, their effects on the soil and rhizosphere microbiomes, and the resultant ecosystem services would be critical next steps to gain deeper appreciation for the interconnectedness between urban land use, soil biogeochemistry, and soil food webs.…”

Section: Discussionmentioning

confidence: 99%

Vegetation Type and Age Drive Changes in Soil Properties, Nitrogen, and Carbon Sequestration in Urban Parks under Cold Climate

et al. 2016

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Urban green spaces provide ecosystem properties fundamental to the provision of ecosystem services, such as the sequestration of carbon and nutrients and serving as a reservoir for organic matter. Although, urban vegetation influences soil physico-chemical properties, it remains unknown whether ecosystem properties depend on plant species portfolios. We tested the influence of three common functional plant groups (evergreen trees, deciduous trees, grass/lawn) for their ability to modify soils in parks of various ages under cold climatic conditions in Finland. We hypothesized that (i) plant functional groups affect soils differently resulting in divergent ecosystem properties, and (ii) that these ecosystem properties also depend on park age. We included 41 urban parks of varying ages (10, 50, and >100 years) and additional control forests. Park soils were sampled for physico-chemical parameters up to 50 cm depth. Our data indicate that plant functional groups modify soils differently, especially between the evergreen and lawn treatments at 50 and >100 year old parks. Soils under evergreen trees had the lowest pH and generally the highest percentage organic matter, percentage total carbon and percentage total nitrogen. Soil pH remained the same, whereas concentrations of organic matter, total carbon and total nitrogen declined by depth. Soils in the reference forests had lower pH but higher percentages organic matter, total carbon, and total nitrogen than those in parks. We estimate that old parks with evergreen trees can store 35.5 and 2.3 kg N m −2 -considerably more than in urban soils in warmer climates. Our data suggest that plant-soil interactions in urban parks, in spite of being constructed environments, are surprisingly similar to those in natural forests.

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Section: Discussionmentioning

confidence: 99%

Vegetation Type and Age Drive Changes in Soil Properties, Nitrogen, and Carbon Sequestration in Urban Parks under Cold Climate

et al. 2016

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“…As a result of available reference alignments and the Naïve Bayesian Classifier (Wang et al, 2007), the LSU region in particular has begun to gain some traction (Lothamer et al, 2013;Porras-Alfaro et al, 2014;Weber et al, 2013). This is because these tools expedite analyses and provide access to a curated annotation tool for the sequence data, supporting the integration of evolutionary and ecological questions, similarly to bacterial systems.…”

Section: Introductionmentioning

confidence: 99%

Analyses of ITS and LSU gene regions provide congruent results on fungal community responses

2014

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“…Recently, Liu et al (17) created a hand-curated fungal database of the largesubunit rRNA (LSU) gene and demonstrated that the naive Bayesian classifier can be used for accurate classification of fungal sequences using this LSU database. Recent surveys of soil fungal communities have successfully used this database to track fungal composition in different locations and responses to environmental perturbations (6,53).…”

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confidence: 99%

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

Porras-Alfaro

Liu

Kuske

et al. 2014

Appl Environ Microbiol

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We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5= section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets. Fungi are one of the most diverse groups of eukaryotic organisms on Earth, with estimates that range from 1.5 to 5.1 million species (1, 2). The use of next-generation sequencing (NGS) is playing a major role in the discovery of new species and ecological studies of fungi. Large molecular data sets are being generated at an extraordinary rate (3-6), but diversity estimations and taxonomic identification at all taxonomic levels are constrained by the lack of accurate, comprehensive taxonomic databases and information on the accuracy of classification tools for comparison of environmental survey data. The detection of emergent fungal diseases, the determination of biogeographical patterns, and definition of strategies for conservation of fungi are just a few examples of research areas that are challenged by the lack of reliable databases and tools (7,8). The large number of sequences generated from platforms of high-throughput sequencing also demand fast and accurate algorithms for sequence analysis and taxonomic classification of fungi.The entire internal transcribed spacer (ITS) rRNA region (approximately 600 bp in length) is composed of two hypervariable regions (ITS1 and ITS2) with the highly conserved 5.8S rRNA gene between them (Fig. 1). The ITS region has been used for many years for diversity estimations and taxonomic identification of fungal isolates and uncultured taxa (9-11) and was adapted as the barcode region for Fungi by the Consortium for the Barcode ...

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Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape

Cited by 26 publications

References 74 publications

Vegetation Type and Age Drive Changes in Soil Properties, Nitrogen, and Carbon Sequestration in Urban Parks under Cold Climate

Vegetation Type and Age Drive Changes in Soil Properties, Nitrogen, and Carbon Sequestration in Urban Parks under Cold Climate

Analyses of ITS and LSU gene regions provide congruent results on fungal community responses

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

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