<i>Rhizoglomus</i>, a new genus of the <i>Glomeraceae</i>

Sieverding, Ewald; Silva, Gladstone Alves da; Berndt, Reinhard; Oehl, Fritz

doi:10.5248/129.373

Cited by 123 publications

(71 citation statements)

References 22 publications

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“…To determine how nucleotide diversity (), rarefied OTU richness, and OTU diversity may vary across different taxonomic groups, we tested the magnitude and statistical significance of variance components corresponding to AM fungal genera, species, and isolates using mixed models with the MIXED procedure in SAS (v.9.4; SAS Institute, Inc., Cary, NC). We followed the consensus AM fungal genus names proposed previously (52), except for Rhizoglomus instead of Rhizophagus (20) and Claroideoglomus and Entrophospora, which we considered the same genus for statistical tests (see Results and Discussion). Total variance was calculated as the sum of the variances explained by differences among isolates, species, and genera and was considered to be significantly different from zero if at least one of those variance components was significantly different from zero.…”

Section: Methodsmentioning

confidence: 99%

“…However, in contrast to most other microbes, in AM fungi, this sequence variation can occur within a single multinucleate cell (18,19). While recent genome sequencing of isolates of the genus Rhizoglomus (20) has expanded our understanding of genetic variation in AM fungi beyond the rRNA genes (21)(22)(23), it remains largely unknown how either genome-wide or rRNA gene sequence variation may itself differ across evolutionary lineages. Previous studies that sampled a limited amount of rRNA gene sequence variation found that sequences from morphologically defined species generally formed clades on the gene tree (24)(25)(26), which is an essential prerequisite for clustering sequences into species-level OTUs.…”

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confidence: 99%

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Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

House

Ekanayake

Ruan

et al. 2016

Appl Environ Microbiol

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Arbuscular mycorrhizal (AM) fungi form mutualisms with plant roots that increase plant growth and shape plant communities. Each AM fungal cell contains a large amount of genetic diversity, but it is unclear if this diversity varies across evolutionary lineages. We found that sequence variation in the nuclear large-subunit (LSU) rRNA gene from 29 isolates representing 21 AM fungal species generally assorted into genus-and species-level clades, with the exception of species of the genera Claroideoglomus and Entrophospora. However, there were significant differences in the levels of sequence variation across the phylogeny and between genera, indicating that it is an evolutionarily constrained trait in AM fungi. These consistent patterns of sequence variation across both phylogenetic and taxonomic groups pose challenges to interpreting operational taxonomic units (OTUs) as approximations of species-level groups of AM fungi. We demonstrate that the OTUs produced by five sequence clustering methods using 97% or equivalent sequence similarity thresholds failed to match the expected species of AM fungi, although OTUs from AbundantOTU, CD-HIT-OTU, and CROP corresponded better to species than did OTUs from mothur or UPARSE. This lack of OTU-to-species correspondence resulted both from sequences of one species being split into multiple OTUs and from sequences of multiple species being lumped into the same OTU. The OTU richness therefore will not reliably correspond to the AM fungal species richness in environmental samples. Conservatively, this error can overestimate species richness by 4-fold or underestimate richness by one-half, and the direction of this error will depend on the genera represented in the sample. IMPORTANCEArbuscular mycorrhizal (AM) fungi form important mutualisms with the roots of most plant species. Individual AM fungi are genetically diverse, but it is unclear whether the level of this diversity differs among evolutionary lineages. We found that the amount of sequence variation in an rRNA gene that is commonly used to identify AM fungal species varied significantly between evolutionary groups that correspond to different genera, with the exception of two genera that are genetically indistinguishable from each other. When we clustered groups of similar sequences into operational taxonomic units (OTUs) using five different clustering methods, these patterns of sequence variation caused the number of OTUs to either over-or underestimate the actual number of AM fungal species, depending on the genus. Our results indicate that OTU-based inferences about AM fungal species composition from environmental sequences can be improved if they take these taxonomically structured patterns of sequence variation into account. Sequences of rRNA genes have revolutionized our understanding of microbial diversity (1, 2) and the factors structuring microbial communities (3). When used in combination with high-throughput sequencing, rRNA gene sequences have provided critical insights into the composition and dynami...

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Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

House

Ekanayake

Ruan

et al. 2016

Appl Environ Microbiol

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“…In this work we adopted the classification proposed by Oehl et al (2011), including recently described new taxa (i.e. Goto et al 2012 andSieverding et al 2014). After AMF species identification, provide directly from field, we calculated the following ecological index: diversity index (H) proposed by Shannon & Weaver (1949), and dominance index (C) proposed by Simpson (1949) for each studied AMF community.…”

Section: Site Description and Sampling Methodsmentioning

confidence: 99%

Could biological invasion by Cryptostegia madagascariensis alter the composition of the arbuscular mycorrhizal fungal community in semi-arid Brazil?

et al. 2016

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“…Species identification was based on the descriptions provided by Schenck and Perez (1987), publications with descriptions of new families and genera (i.e., Oehl et al 2008), and by consulting the international culture collection of arbuscular mycorrhizal fungi database-INVAM (http://invam.caf.wvu.edu). In this work, we followed the classification proposed by Oehl et al (2011), including recently new described taxa (i.e., Goto et al 2012;Redecker et al 2013;Sieverding et al 2014). In addition to species identification, we also assessed spore abundance by counting the total number of spores, spore abundance of each AMF species by recording the number of spores of each AMF species recorded in the samples, and the species occurrence frequency (FOi) of each AMF species.…”

Section: Arbuscular Mycorrhizal Fungi Community Characterizationmentioning

confidence: 99%

Arbuscular mycorrhizal fungal community assembly in the Brazilian tropical seasonal dry forest

Souza

Freitas

2017

Ecol Process

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Introduction: Here, we compare the arbuscular mycorrhizal fungal (AMF) community composition in soils from the root zone of the exotic invasive species Prosopis juliflora (EXO soils) and soils from the root zone of the native species Mimosa tenuiflora (NAT soils) from five locations in the Brazilian tropical seasonal dry forest, Paraíba, Brazil, using morphological analyses. Results: AMF community composition in EXO and NAT soils were dissimilar. Available phosphorus, diversity index, spore abundance, and species richness were the main factors differing between the EXO and NAT soils. In general, the most dominant order present in the soils were Glomerales (44.8%) and Gigasporales (41.4%). The most abundant AMF genus in all studied soils was Funneliformis. Conclusions: Differences in AMF community composition were associated with (1) differences in the dominant plant species (P. juliflora vs. M. tenuiflora) and (2) changes in soil chemical factors (soil, pH, total organic carbon, total nitrogen, and available P) in EXO soils. These results contribute to a deeper view of the AMF communities in exotic soils and open new perspectives for ecological processes involving AMF species and exotic plant species in the Brazilian tropical seasonal dry forest.

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Rhizoglomus, a new genus of the Glomeraceae

Cited by 123 publications

References 22 publications

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering

Could biological invasion by Cryptostegia madagascariensis alter the composition of the arbuscular mycorrhizal fungal community in semi-arid Brazil?

Arbuscular mycorrhizal fungal community assembly in the Brazilian tropical seasonal dry forest

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