A better understanding of functional roles of fungi in the decomposition process: using precursor rRNA containing ITS regions as a marker for the active fungal community

Purahong, Witoon; Krüger, Dirk

doi:10.1007/s13595-012-0210-7

Cited by 12 publications

(7 citation statements)

References 22 publications

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“…no preculturing), which reported low bacterial diversity in mine substrates and early rehabilitation soils, compare to undisturbed sites [ 15 , 46 ]. It should be noted that use of eDNA to determine taxonomic richness includes both living and dead organisms [ 47 , 48 ], which results in more species being detected. Furthermore, the selectivity of the culturing methods, used in our study, most probably resulted in lower taxonomic richness being recorded in forest soil, thus resulting in similar taxonomic richness of living bacteria between forest soil and mine substrates.…”

Section: Discussionmentioning

confidence: 99%

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

et al. 2021

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Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.

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Section: Discussionmentioning

confidence: 99%

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

et al. 2021

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“…Notice should be taken to the fact that the culture method did not out-compete the eDNA in terms of diversity detection, and both methods only revealed different side of the community. Whilst eDNA detected both viable and dead microbes [8,50], enrichment culture only detected the viable ones, some of which were missed by eDNA. Thus, using enrichment cultures along with the eDNA method could present more comprehensive information than using eDNA alone.…”

Section: Revealed Hidden Viable Bacterial Taxa In Tropical Forest Soils Using Amplicon Sequencing Of Enrichment Culturesmentioning

confidence: 99%

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Sansupa

Wahdan

Disayathanoowat

et al. 2021

Biology

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This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

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“…The RNA study is interesting as it demonstrates that the detected fungal OTUs are not only spores but they also include the viable and/or active fungi (Nawaz et al 2018). Life span of the precursor RNA containing ITS regions is very short, thus it can be considered to represent the active community during the last few minutes before sampling (Kos and Tollervey 2010;Purahong and Krüger 2012). Specifically, only metabolically active fungi are continuously transcribing rRNA precursor molecules and their ITS regions can be detected in the precursor rRNA pool (Anderson and Parkin 2007; Rajala et al 2011).…”

Section: Diversity Of Fungi In Groundwatermentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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A better understanding of functional roles of fungi in the decomposition process: using precursor rRNA containing ITS regions as a marker for the active fungal community

Abstract: International audienc

Cited by 12 publications

References 22 publications

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures

Can we use environmental DNA as holotypes?

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