Current Insight into Culture-Dependent and Culture-Independent Methods in Discovering Ascomycetous Taxa

Abstract

Culture techniques are vital in both traditional and modern fungal taxonomy. Establishing sexual–asexual links and synanamorphs, extracting DNA and secondary metabolites are mainly based on cultures. However, it is widely accepted that a large number of species are not sporulating in nature while others cannot be cultured. Recent ecological studies based on culture-independent methods revealed these unculturable taxa, i.e., dark taxa. Recent fungal diversity estimation studies suggested that environmental sequencing plays a vital role in discovering missing species. However, Sanger sequencing is still the main approach in determining DNA sequences in culturable species. In this paper, we summarize culture-based and culture-independent methods in the study of ascomycetous taxa. High-throughput sequencing of leaf endophytes, leaf litter fungi and fungi in aquatic environments is important to determine dark taxa. Nevertheless, currently, naming dark taxa is not recognized by the ICN, thus provisional naming of them is essential as suggested by several studies.

Fungal diversity in the soil Mycobiome: Implications for ONE health

“…Fungal diversity tends to be higher in healthy soil than in disturbed or contaminated soil. Edaphic conditions, plant-microbe interactions, and biotic factors influence fungal population composition [ 83 ]. Agricultural practices have also been found to influence the composition of the soil mycobiome and affect plant health, suggesting the potential for managing and manipulating soil fungi to improve crop productivity [ 17 ].…”

The Endophytic Fungi Diversity, Community Structure, and Ecological Function Prediction of Sophora alopecuroides in Ningxia, China

“…Owing to the limitations of medium composition and culture conditions, the with-culture method preferentially selects some species in the sample and the species that grow rapidly in culture overwhelm the species that grow slowly, so fewer taxa are obtained [55]. However, the HTS method was able to make up for the selection limitations of traditional culture selection, realize the in situ analysis of microbial population structure in a natural state, and present the microbial community structure information that is closest to the real state in plants [56]. In most cases, the taxon obtained by HTS is higher than the culturable method and has more accuracy and reliability.…”

Life on top: cryptoendolithic ascomycetes and microalgae isolated from over 6000 m altitude

“…The culture-dependent approach is flawed by the fact that only a fraction of the microorganisms can grow in culture, leaving the rest of the diversity undetected. This certainly leads to an underestimation of the entire biodiversity of the rock communities (Wijayawardene et al 2021). Moreover, cultures may be affected by contaminant microorganisms which can be erroneously included in the original community.…”