Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions

Marina Püpke Marone; Maria Fernanda Zaneli Campanari; Fabio Trigo Raya; Gonçalo Amarante Guimarães Pereira; Marcelo Falsarella Carazzolle

doi:10.7717/peerj.13252

Fungal communities represent the majority of root-specific transcripts in the transcriptomes of Agave plants grown in semiarid regions

PeerJ. 2022 May 2:10:e13252. doi: 10.7717/peerj.13252. eCollection 2022.

Authors

Marina Püpke Marone^#¹, Maria Fernanda Zaneli Campanari^#¹, Fabio Trigo Raya¹, Gonçalo Amarante Guimarães Pereira^{1

2}, Marcelo Falsarella Carazzolle^{1

2}

Affiliations

¹ Department of Genetics, Evolution, Microbiology, and Immunology, University of Campinas, Campinas, São Paulo, Brazil.
² Center for Computing and Engineering Sciences, University of Campinas, Campinas, São Paulo, Brazil.

^# Contributed equally.

Abstract

Agave plants present drought resistance mechanisms, commercial applications, and potential for bioenergy production. Currently, Agave species are used to produce alcoholic beverages and sisal fibers in semi-arid regions, mainly in Mexico and Brazil. Because of their high productivities, low lignin content, and high shoot-to-root ratio, agaves show potential as biomass feedstock to bioenergy production in marginal areas. Plants host many microorganisms and understanding their metabolism can inform biotechnological purposes. Here, we identify and characterize fungal transcripts found in three fiber-producing agave cultivars (Agave fourcroydes, A. sisalana, and hybrid 11648). We used leaf, stem, and root samples collected from the agave germplasm bank located in the state of Paraiba, in the Brazilian semiarid region, which has faced irregular precipitation periods. We used data from a de novo assembled transcriptome assembly (all tissues together). Regardless of the cultivar, around 10% of the transcripts mapped to fungi. Surprisingly, most root-specific transcripts were fungal (58%); of these around 64% were identified as Ascomycota and 28% as Basidiomycota in the three communities. Transcripts that code for heat shock proteins (HSPs) and enzymes involved in transport across the membrane in Ascomycota and Basidiomycota, abounded in libraries generated from the three cultivars. Indeed, among the most expressed transcripts, many were annotated as HSPs, which appear involved in abiotic stress resistance. Most HSPs expressed by Ascomycota are small HSPs, highly related to dealing with temperature stresses. Also, some KEGG pathways suggest interaction with the roots, related to transport to outside the cell, such as exosome (present in the three Ascomycota communities) and membrane trafficking, which were further investigated. We also found chitinases among secreted CAZymes, that can be related to pathogen control. We anticipate that our results can provide a starting point to the study of the potential uses of agaves' fungi as biotechnological tools.

Keywords: Agave; Drought resistance; Fungal communities; Microbiome; Root; Transcriptome.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Agave* / genetics
Ascomycota*
Basidiomycota*
Mexico
Mycobiome* / genetics
Transcriptome / genetics

Grants and funding

This work was supported by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES) n. 88887.373979/2019-00 and 88887.479629/2020-00, Center for Computational Engineering and Sciences - FAPESP/Cepid (2013/08293-7), the São Paulo Research Foundation (FAPESP) grant 2020/02524-0, and CNPq (Nexus Project: Integration Caatinga-Sisal n. 441625/2017-7). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.