Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

Rosling, Anna; Cox, Filipa; Cruz-Martínez, Karelyn; Ihrmark, Katarina; Grelet, Gwen; Lindahl, Björn D.; Menkis, Audrius; James, Timothy Y.

doi:10.1126/science.1206958

Cited by 271 publications

(188 citation statements)

References 61 publications

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“…This lack of vertical stratification in soils may reduce nutrient capture and lead to "leakier" nutrient cycles, as is often the case in other highly managed systems [73,74]. The high relative abundance of the Archaeorhizomycetales in the oil palm fungal communities is also noteworthy given that this group of fungi is newly described [75]. Prior to its description in 2011, it was one of the most abundant groups of unidentified fungi in environmental DNA sequence libraries, but due to the paucity of molecular studies in tropical forests, there has been little documentation of its occurrence outside of boreal and temperate forests.…”

Section: Discussionmentioning

confidence: 99%

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.

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Section: Discussionmentioning

confidence: 99%

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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“…If, on the other hand, there are no -or significantly fewer -mismatches in the region corresponding to the 5.8S in the BLAST alignment, this would suggest that the sequence is authentic, if very deviant from everything else. Indeed, several large groups of previously unknown fungi have been described in recent years (e.g., Jones et al 2011;Rosling et al 2011). …”

Section: Guideline 4 Sequences Can Be Broken In Other Puzzling Waysmentioning

confidence: 99%

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson¹,

Tedersoo²,

Abarenkov³

et al. 2012

169

125

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Larsson K-H, Larsson E, Kõljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-63. doi: 10.3897/mycokeys.4.3606 Abstract Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contribut- Nilsson et al. / MycoKeys 4: 37-63 (2012) 38 ing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.

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“…Amplicon-based studies of environmental DNA reveal unknown fungal lineages and thousands of novel species, apparently comprising the majority of fungi in most ecosystems (Schadt et al 2003;Monchy et al 2011;Rosling et al 2011;Amend et al 2012;Tedersoo et al 2014). While these surveys provide great insight into habitats, distributions, and diversity of the vast and largely undescribed richness of fungal species, they provide little information on biological properties of the detected lineages and rarely can be linked to additional DNA sequences other than from the nuc ribosomal RNA operon.…”

mentioning

confidence: 99%

Phytophthora×serendipitasp. nov. andP.×pelgrandis, two destructive pathogens generated by natural hybridization

Veld¹,

Rosendahl

Hong

2012

Mycologia

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Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

Cited by 271 publications

References 61 publications

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Phytophthora×serendipitasp. nov. andP.×pelgrandis, two destructive pathogens generated by natural hybridization

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