Novel soil-inhabiting clades fill gaps in the fungal tree of life

Tedersoo, Leho; Bahram, Mohammad; Puusepp, Rasmus; Nilsson, R. Henrik; James, Timothy Y.

doi:10.1186/s40168-017-0259-5

Cited by 150 publications

(155 citation statements)

References 45 publications

(72 reference statements)

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“…3); Tedersoo et al. ) suggest that Rozella is sister to a highly diverse clade comprising LB‐Microsporidia, the microsporidian‐like protists described above, and a large diversity of uncharacterized environmental sequences. In this study we investigate these relationships further, integrating morphological, phylogenetic, and sequence diversity data, to determine the phylogenetic and taxonomic boundaries of microsporidia and their immediate relatives.…”

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Clarifying the Relationships between Microsporidia and Cryptomycota

Bass

Czech

Williams

et al. 2018

J Eukaryotic Microbiology

102

103

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Some protists with microsporidian‐like cell biological characters, including Mitosporidium, Paramicrosporidium, and Nucleophaga, have SSU rRNA gene sequences that are much less divergent than canonical Microsporidia. We analysed the phylogenetic placement and environmental diversity of microsporidian‐like lineages that group near the base of the fungal radiation and show that they group in a clade with metchnikovellids and canonical microsporidians, to the exclusion of the clade including Rozella, in line with what is currently known of their morphology and cell biology. These results show that the phylogenetic scope of Microsporidia has been greatly underestimated. We propose that much of the lineage diversity previously thought to be cryptomycotan/rozellid is actually microsporidian, offering new insights into the evolution of the highly specialized parasitism of canonical Microsporidia. This insight has important implications for our understanding of opisthokont evolution and ecology, and is important for accurate interpretation of environmental diversity. Our analyses also demonstrate that many opisthosporidian (aphelid+rozellid+microsporidian) SSU V4 OTUs from Neotropical forest soils group with the short‐branching Microsporidia, consistent with the abundance of their protist and arthropod hosts in soils. This novel diversity of Microsporidia provides a unique opportunity to investigate the evolutionary origins of a highly specialized clade of major animal parasites.

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Clarifying the Relationships between Microsporidia and Cryptomycota

Bass

Czech

Williams

et al. 2018

J Eukaryotic Microbiology

102

103

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“…), and Antonospora locustae (Tedersoo et al. ). Most members of this lineage derive from soil and freshwater habitats, but also from some marine habitats.…”

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confidence: 99%

“…,b; James and Berbee ; Tedersoo et al. ) or with nonfungal organisms in Holomycota (e.g. Karpov et al.…”

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confidence: 99%

Morphology, Ultrastructure, and Molecular Phylogeny of Rozella multimorpha, a New Species in Cryptomycota

Letcher

Longcore

James

et al. 2017

J Eukaryotic Microbiology

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Increasing numbers of sequences of basal fungi from environmental DNA studies are being deposited in public databases. Many of these sequences remain unclassified below the phylum level because sequence information from identified species is sparse. Lack of basic biological knowledge due to a dearth of identified species is extreme in Cryptomycota, a new phylum widespread in the environment and phylogenetically basal within the fungal lineage. Consequently, we are attempting to fill gaps in the knowledge of Rozella, the best-known genus in this lineage. Rozella is a genus of unwalled, holocarpic, endobiotic parasites of hosts including Chytridiomycota, Blastocladiomycota, Oomycota, Basidiomycota, and a green alga, with most species descriptions based on morphology and host specificity. We found a Rozella parasitizing a Pythium host that was a saprobe on spruce pollen bait placed with an aquatic sample. We characterized the parasite with light microscopy, TEM of its zoospores and sporangia, and its 18S/28S rDNA. Comparison with other Rozella species indicates that the new isolate differs morphologically, ultrastructurally, and genetically from Rozella species for which we have data. Features of the zoospore also differ from those of previously studied species. Herein we describe the Rozella as a new species, R. multimorpha.

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“…Because microscopy-based identification is time consuming and laborious, researchers commonly choose to proceed with the molecular identification, even without collecting morphological data on the species. The molecular identification of microorganisms is performed based on the amplification of the 16S rRNA gene for bacteria, cyanobacteria, and archaea (e.g., [90][91][92]), and on the 18S and/or 28S rRNA gene for fungi (e.g., [93,94]). The sequences of these genes are used in microbial taxonomic studies for several reasons: the 16S rRNA gene is found in almost all bacteria, cyanobacteria, and archaea, often as a multigene family or within operons; its function has not changed over time, suggesting that random changes in sequences are a more accurate measure of time (evolution); and the size of this gene, approximately 1500 bp, is large enough for computing purposes [95].…”

Section: The Primary Methods Of Detection In Use Have Already Become mentioning

confidence: 99%

Microbial Diversity: The Gap between the Estimated and the Known

Vitorino

Bessa

2018

Diversity

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Abstract:The ecological and biotechnological services that microorganisms provide to the planet and human society highlight the need to understand and preserve microbial diversity, which is widely distributed, challenging the severity of certain environments. Cataloging this diversity has also challenged the methods that are currently used to isolate and grow microorganisms, because most of the microbiota that are present in environmental samples have been described as unculturable. Factors such as geographic isolation and host preference also hinder the assessment of microbial diversity. However, prejudiced historical practices, including the prioritization of some species of microorganisms merely because they cause diseases, have long shifted research on fungi and bacteria towards medically relevant microorganisms. Thus, most microorganisms that inhabit the planet are still unknown, as is the potential of these species. Current estimates allow us to predict that the diversity of microorganisms that are present in the various terrestrial ecosystems is enormous. However, understanding this diversity is a challenge for the future of microbial ecology research.

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Novel soil-inhabiting clades fill gaps in the fungal tree of life

Cited by 150 publications

References 45 publications

Clarifying the Relationships between Microsporidia and Cryptomycota

Clarifying the Relationships between Microsporidia and Cryptomycota

Morphology, Ultrastructure, and Molecular Phylogeny of Rozella multimorpha, a New Species in Cryptomycota

Microbial Diversity: The Gap between the Estimated and the Known

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