A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth

Nan Yang; Wenbin Zhang; Dan Wang; Dingding Cao; Yanyu Cao; Weihong He; Ziting Lin; Xiaofeng Chen; Guiping Ye; Zhiming Chen; Jianjun Chen; Xiangying Wei

doi:10.3389/fmicb.2023.1287582

A novel endophytic fungus strain of Cladosporium: its identification, genomic analysis, and effects on plant growth

Front Microbiol. 2023 Nov 23:14:1287582. doi: 10.3389/fmicb.2023.1287582. eCollection 2023.

Authors

Nan Yang^#¹, Wenbin Zhang^#¹, Dan Wang¹, Dingding Cao¹, Yanyu Cao¹, Weihong He¹, Ziting Lin¹, Xiaofeng Chen¹, Guiping Ye¹, Zhiming Chen², Jianjun Chen³, Xiangying Wei¹

Affiliations

¹ Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, Fujian Province, China.
² Institute of Cytology and Genetics, Hengyang Medical School, University of South China, Hengyang, Hunan, China.
³ Mid-Florida Research and Education Center, Department of Environmental Horticulture, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL, United States.

^# Contributed equally.

Abstract

Introduction: Endophytic microorganisms are bacteria or fungi that inhabit plant internal tissues contributing to various biological processes of plants. Some endophytic microbes can promote plant growth, which are known as plant growth-promoting endophytes (PGPEs). There has been an increasing interest in isolation and identification of PGPEs for sustainable production of crops. This study was undertaken to isolate PGPEs from roots of a halophytic species Sesuvium portulacastrum L. and elucidate potential mechanisms underlying the plant growth promoting effect.

Methods: Surface-disinfected seeds of S. portulacastrum were germinated on an in vitro culture medium, and roots of some germinated seedlings were contaminated by bacteria and fungi. From the contamination, an endophytic fungus called BF-F (a fungal strain isolated from bacterial and fungal contamination) was isolated and identified. The genome of BF-F strain was sequenced, its genome structure and function were analyzed using various bioinformatics software. Additionally, the effect of BF-F on plant growth promotion were investigated by gene cluster analyses.

Results: Based on the sequence homology (99%) and phylogenetic analysis, BF-F is likely a new Cladosporium angulosum strain or possibly a new Cladosporium species that is most homologous to C. angulosum. The BF-F significantly promoted the growth of dicot S. portulacastrum and Arabidopsis as well as monocot rice. Whole genome analysis revealed that the BF-F genome has 29,444,740 bp in size with 6,426 annotated genes, including gene clusters associated with the tryptophan synthesis and metabolism pathway, sterol synthesis pathway, and nitrogen metabolism pathway. BF-F produced indole-3-acetic acid (IAA) and also induced the expression of plant N uptake related genes.

Discussion: Our results suggest that BF-F is a novel strain of Cladosporium and has potential to be a microbial fertilizer for sustainable production of crop plants. The resulting genomic information will facilitate further investigation of its genetic evolution and its function, particularly mechanisms underlying plant growth promotion.

Keywords: BF-F; Cladosporium; IAA; PGP gene clusters; genome sequencing; plant growth-promoting fungi (PGPF).

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This research was financially supported by the Natural Science Foundation of Fujian province (2020H0046 and 2022 J011139) and Fuzhou Institute of Oceanography 2022 Research Project 2022F04.