Endophytic fungal community of Dysphania ambrosioides from two heavy metal‐contaminated sites: evaluated by culture‐dependent and culture‐independent approaches

Abstract

SummaryEndophytic fungal communities of Dysphania ambrosioides, a hyperaccumulator growing at two Pb‐Zn‐contaminated sites, were investigated through culture‐dependent and culture‐independent approaches. A total of 237 culturable endophytic fungi (EF) were isolated from 368 tissue (shoot and roots) segments, and the colonization rate (CR) ranged from 9.64% to 65.98%. The isolates were identified to 43 taxa based on morphological characteristics and rDNA ITS sequence analysis. Among them, 13 taxa (30.23%) were common in plant tissues from both sites; however, dominant EF were dissimilar. In culture‐dependent study, 1989 OTUs were obtained through Illumina Miseq sequencing, and dominant EF were almost same in plant tissues from both sites. However, some culturable EF were not observed in total endophytic communities. We suggest that combination of both culture‐dependent and culture‐independent methods will provide more chances for the precise estimation of endophytic fungal community than using either of them. The tissue had more influence on the culturable fungal community structure, whereas the location had more influence on the total fungal community structure (including culturable and unculturable). Both culture‐dependent and culture‐independent studies illustrated that endophytic fungal communities of D. ambrosioides varied across the sites, which suggested that HM concentration of the soil may have some influence on endophytic fungal diversity.

Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential againstNeonectria ditissima

“…Geographic region had no effect and season had only a small effect on endophyte communities. In contrast, region was a determinant factor influencing endophytic fungi in various tissues of different plant species, such as leaves of Ageratina altissima (Christian et al ), and roots and shoots of Dysphania ambrosioides (Parmar et al ). A possible reason could be differences in key endophyte communities between domesticated plants and wild plants.…”

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

“…For example, endophyte identification studies in Pinus taeda , Vitis vinifera and Dysphania ambrosioides via HTS have resulted in greater species richness when compared to culture-dependent methods, and have revealed distinct clades. However, the same studies have further revealed the absence of certain easily culturable taxa in the endophytic community structure derived via culture-independent techniques (e.g., HTS) [ 168 , 169 , 170 ]. Fungal endophyte communities elucidated by HTS likely depend more on the DNA extraction method, primers, and the platform used for sequencing and analysis.…”

Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

“…Currently we have no reliable information on the ratio of cultivable to uncultivable fungal endophytes, but environmental DNA surveys suggest that the diversity of species is far greater than the diversity of cultivated isolates (Wu B. et al, 2019 ). A study on the endophytic fungal community of Dysphania ambrosioides , found that almost 10 times more species can be identified by amplicon sequencing than can be isolated by cultivation (Parmar et al, 2018 ). In order to increase the number of cultivable species and study their biosynthetic potential, it is of utmost importance to improve cultivation and isolation procedures.…”