Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide

Lindahl, Björn D.; Nilsson, R. Henrik; Tedersoo, Leho; Abarenkov, Kessy; Carlsen, Tor; Kjøller, Rasmus; Kõljalg, Urmas; Pennanen, Taina; Rosendahl, Søren; Stenlid, Jan; Kauserud, Håvard

doi:10.1111/nph.12243

Cited by 763 publications

(653 citation statements)

References 119 publications

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“…The term microbial has often been (and is still sometimes) used for studies only describing bacteria [60,132]. Additionally, besides exhibiting very diverse life forms, fungi spread across three ecological categories: saprophytes, mycorrhizae and pathogens/parasites, which have been targeted individually by researchers [133,134]. However, recent research clearly demonstrates that all three categories matter for soil functioning [133].…”

Section: Methodsological Issues In the Study Of Fungal Biominerals Fromentioning

confidence: 99%

Role of Fungi in the Biomineralization of Calcite

2016

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Abstract:In the field of microbial biomineralization, much of the scientific attention is focused on processes carried out by prokaryotes, in particular bacteria, even though fungi are also known to be involved in biogeochemical cycles in numerous ways. They are traditionally recognized as key players in organic matter recycling, as nutrient suppliers via mineral weathering, as well as large producers of organic acids such as oxalic acid for instance, an activity leading to the genesis of various metal complexes such as metal-oxalate. Their implications in the transformation of various mineral and metallic compounds has been widely acknowledged during the last decade, however, currently, their contribution to the genesis of a common biomineral, calcite, needs to be more thoroughly documented. Calcite is observed in many ecosystems and plays an essential role in the biogeochemical cycles of both carbon (C) and calcium (Ca). It may be physicochemical or biogenic in origin and numerous organisms have been recognized to control or induce its biomineralization. While fungi have often been suspected of being involved in this process in terrestrial environments, only scarce information supports this hypothesis in natural settings. As a result, calcite biomineralization by microbes is still largely attributed to bacteria at present. However, in some terrestrial environments there are particular calcitic habits that have been described as being fungal in origin. In addition to this, several studies dealing with axenic cultures of fungi have demonstrated the ability of fungi to produce calcite. Examples of fungal biomineralization range from induced to organomineralization processes. More examples of calcite biomineralization related to direct fungal activity, or at least to their presence, have been described within the last decade. However, the peculiar mechanisms leading to calcite biomineralization by fungi remain incompletely understood and more research is necessary, posing new exciting questions linked to microbial biomineralization processes.

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Section: Methodsological Issues In the Study Of Fungal Biominerals Fromentioning

confidence: 99%

Role of Fungi in the Biomineralization of Calcite

2016

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“…It is worth mentioning that, although the ITS region has been broadly accepted as a universal barcode marker for fungi (Schoch et al, 2011), the selection of primer sets targeting either ITS1 or ITS2 goes with differential amplification biases against specific fungal lineages, in particular against those of Glomeromycota (Větrovský et al, 2015) and Chytridiomycota (Lindahl et al, 2013). In particular, within the phylum Glomeromycota there is the effect of homoplasy (that is, correspondence between parts arising from evolutionary convergence), where the same individual can carry divergent copies of ITS sequences.…”

Section: Dna Sequence Analysismentioning

confidence: 99%

“…Collectively, these are key methodological constrains that must be acknowledged and further considered in ecological data interpretation. For a detailed user guide to fungal community assessment using highthroughput sequencing analysis, see Lindahl et al (2013).…”

Section: Dna Sequence Analysismentioning

confidence: 99%

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities

et al. 2016

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Marine-to-terrestrial transition represents one of the most fundamental shifts in microbial life. Understanding the distribution and drivers of soil microbial communities across coastal ecosystems is critical given the roles of microbes in soil biogeochemistry and their multifaceted influence on landscape succession. Here, we studied the fungal community dynamics in a well-established salt marsh chronosequence that spans over a century of ecosystem development. We focussed on providing high-resolution assessments of community composition, diversity and ecophysiological shifts that yielded patterns of ecological succession through soil formation. Notably, despite containing 10-to 100-fold lower fungal internal transcribed spacer abundances, early-successional sites revealed fungal richnesses comparable to those of more mature soils. These newly formed sites also exhibited significant temporal variations in β-diversity that may be attributed to the highly dynamic nature of the system imposed by the tidal regime. The fungal community compositions and ecophysiological assignments changed substantially along the successional gradient, revealing a clear signature of ecological replacement and gradually transforming the environment from a marine into a terrestrial system. Moreover, distance-based linear modelling revealed soil physical structure and organic matter to be the best predictors of the shifts in fungal β-diversity along the chronosequence. Taken together, our study lays the basis for a better understanding of the spatiotemporally determined fungal community dynamics in salt marshes and highlights their ecophysiological traits and adaptation in an evolving ecosystem.

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“…Tang et al 2012;Lindahl et al 2013). Despite the fact that ITS provides high taxonomic resolution power (e.g.…”

Section: Selection Of Versatile Primers Based On High Resolution Markersmentioning

confidence: 99%

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

Zhan

MacIsaac

2014

Conserv Genet

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Identification of rare species and mapping their distributions is crucial for understanding natural species distributions and causes and consequences of accelerating species declines. However, detection of rare species in both terrestrial and especially aquatic communities typically dominated by numerous microscopic species (i.e. rare biosphere) represents a formidable technical challenge. Rapid advances in high-throughput sequencing (HTS) technologies have revolutionized biodiversity studies in the rare biosphere, and also stimulated associated debates. Here we summarize research progress, discuss debates and problems, and propose possible solutions and future studies to address these issues. In addition, we provide take-home messages for experimental design and data interpretation when utilizing HTS techniques for rare biosphere exploration in ecology and conservation biology.

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Fungal community analysis by high‐throughput sequencing of amplified markers – a user's guide

Cited by 763 publications

References 119 publications

Role of Fungi in the Biomineralization of Calcite

Role of Fungi in the Biomineralization of Calcite

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities

Rare biosphere exploration using high-throughput sequencing: research progress and perspectives

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