Comparison of Culturing and Metabarcoding Methods to Describe the Fungal Endophytic Assemblage of Brachypodium rupestre Growing in a Range of Anthropized Disturbance Regimes

Abstract

Fungal endophytes develop inside plants without visible external signs, and they may confer adaptive advantages to their hosts. Culturing methods have been traditionally used to recognize the fungal endophytic assemblage, but novel metabarcoding techniques are being increasingly applied. This study aims to characterize the fungal endophytic assemblage in shoots, rhizomes and roots of the tall grass Brachypodium rupestre growing in a large area of natural grasslands with a continuum of anthropized disturbance regimes. Seven out of 88 taxa identified via metabarcoding accounted for 81.2% of the reads (Helotiaceae, Lachnum sp. A, Albotricha sp. A, Helotiales A, Agaricales A, Mycena sp. and Mollisiaceae C), revealing a small group of abundant endophytes and a large group of rare species. Although both methods detected the same trends in richness and fungal diversity among the tissues (root > rhizome > shoot) and grasslands (low-diversity > high-diversity grasslands), the metabarcoding tool identified 5.8 times more taxa than the traditional culturing method (15 taxa) but, surprisingly, failed to sequence the most isolated endophyte on plates, Omnidemptus graminis. Since both methods are still subject to important constraints, both are required to obtain a complete characterization of the fungal endophytic assemblage of the plant species.

Two novel endophytic Tolypocladium species identified from native pines in south Florida

“…For instance, HTS analysis of tall grass Brachypodium rupestre (shoots, rhizomes, and roots) identified abundant and rare species of endophytes which were 5.8 times more enriched in number of taxa when compared to the traditional culture-based method. However, metabarcoding approaches were unable to detect the most abundant endophyte, Omnidemptus graminis, recovered through culturing ( Durán et al 2021 ). In addition, the number of OTUs recovered through HTS approaches may vary depending on the primer employed in the assays.…”

Plant Microbiome: Origin, Composition, and Functions

“…Данные о количестве грибных копий генов в эндосфере корней растений практически отсутствуют в научной литературе [12,21,22]. Среди бактерий доминируют Protebacteria (до 50%), однако представлены и Actinobacteria, Bacteroidetes, Firmicutes, Acidobacteria, определены и другие типы бактерий -Chloroflexi, Cyanobacteria, Armatimonadetes, Verrucomicrobia, Planctomycetes и Nitrospirae, которые представляют меньшую часть сообщества [11,[23][24][25]. У микромицетов распределение таксонов сходно с таковым в ризосфере, за исключением того, что суммарно на долю Ascomycota и Basidiomycota приходится более 98% организмов.…”

Discovering the Diversity of Cultivable Endophytic Fungi in a Decumbent Subshrub Endemic of the Brazilian Tropical Savanna

“…Both types of methodology offer advantages and disadvantages. Culture-independent approaches, such as metabarcoding, allow closer knowledge of the real diversity of these microbial communities (Chi et al, 2019;Durán et al, 2021;Wang et al, 2022). Culture-dependent approaches, in turn, are less e cient to infer ecological analysis (Chi et al, 2019;Durán et al, 2021;Wang et al, 2022).…”

“…The community of endophytic fungi associated with plant species from various ecosystems has been examined by culture-independent (Chi et al, 2019;Durán et al, 2021;Wang et al, 2022) and culture-dependent methods (Li et al, 2016;Yao et al, 2017;Du et al, 2020;Wang et al, 2022). Both types of methodology offer advantages and disadvantages.…”

“…Culture-independent approaches, such as metabarcoding, allow closer knowledge of the real diversity of these microbial communities (Chi et al, 2019;Durán et al, 2021;Wang et al, 2022). Culture-dependent approaches, in turn, are less e cient to infer ecological analysis (Chi et al, 2019;Durán et al, 2021;Wang et al, 2022). However, they are cheaper, more accessible and provide data on easily cultivated fungi, which represent a potential genetic and biotechnological resource (Li et al, 2016;Yao et al, 2017;Du et al, 2020;Wang et al, 2022).…”