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Fungal Assemblages Associated with Roots of Halophytic and Non-halophytic Plant Species Vary Differentially Along a Salinity Gradient

  • Environmental Microbiology
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Abstract

Structure of fungal communities is known to be influenced by host plants and environmental conditions. However, in most cases, the dynamics of these variation patterns are poorly understood. In this work, we compared richness, diversity, and composition between assemblages of endophytic and rhizospheric fungi associated to roots of two plants with different lifestyles: the halophyte Inula crithmoides and the non-halophyte I. viscosa (syn. Dittrichia viscosa L.), along a spatially short salinity gradient. Roots and rhizospheric soil from these plants were collected at three points between a salt marsh and a sand dune, and fungi were isolated and characterized by ITS rDNA sequencing. Isolates were classified in a total of 90 operational taxonomic units (OTUs), belonging to 17 fungal orders within Ascomycota and Basidiomycota. Species composition of endophytic and soil communities significantly differed across samples. Endophyte communities of I. crithmoides and I. viscosa were only similar in the intermediate zone between the salt marsh and the dune, and while the latter displayed a single, generalist association of endophytes, I. crithmoides harbored different assemblages along the gradient, adapted to the specific soil conditions. In the lower salt marsh, root assemblages were strongly dominated by a single dark septate sterile fungus, also prevalent in other neighboring salt marshes. Interestingly, although its occurrence was positively correlated to soil salinity, in vitro assays revealed a strong inhibition of its growth by salts. Our results suggest that host lifestyle and soil characteristics have a strong effect on endophytic fungi and that environmental stress may entail tight plant–fungus relationships for adaptation to unfavorable conditions.

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Acknowledgements

This research was funded by the Spanish Ministry of Science and Innovation grants AGL2008–00716/AGR and AGL2011–29297. VF was supported by a grant from the international PhD program “Frotticoltura Mediterranea,” Università di Palermo (Italy). The authors would like to thank Dr. Rusty Rodriguez for his critical reading of the manuscript.

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Author notes

  1. Jose G. Maciá-Vicente

    Present address: U.S. Geological Survey, 6505 65th St NE, Seattle, WA, 98115, USA

Authors and Affiliations

  1. Multidisciplinary Institute for Environmental Studies (MIES) “Ramón Margalef,” Department of Marine Sciences and Applied Biology, University of Alicante, Apto. 99, 03080, Alicante, Spain

    Jose G. Maciá-Vicente & Luis V. Lopez-Llorca

  2. Department DEMETRA, Università degli Studi di Palermo, Viale delle Scienze 2, 90128, Palermo, Italy

    Valeria Ferraro & Santella Burruano

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  1. Jose G. Maciá-Vicente
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  2. Valeria Ferraro
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  3. Santella Burruano
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  4. Luis V. Lopez-Llorca
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Corresponding author

Correspondence to Jose G. Maciá-Vicente.

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Table S1

Physicochemical variables of soils sampled in this work (PDF 123 kb)

Table S2

Accession numbers, BLAST results, and taxonomy assignments for sequences obtained in this study. Only one of the BLAST best results are shown, for both comparisons with a database with fungal ITS sequences in GenBank (fungalITSdatabase), and with a database with only fully identified ITS sequences (fungalITSdatabaseID). Abbreviations: n.a., not assigned (XLSX 31 kb)

Table S3

Abundance data for all OTUs defined in this study as either endophytes or soil fungi (XLSX 24 kb)

Figure S1

Phylogenetic analysis of 90 ITS-5.8S rDNA sequences from endophytic and soil fungal isolates representing all OTUs found in this study (in bold), and 133 sequences selected among BLAST best matches. Sequences were aligned using fsa v1.15.2 (Fast Statistical Alignment; Bradley RK et al (2009) PLoS Comput Biol 5(5). doi:10.1371/journal.pcbi.1000392.g001), and a Maximum Likelihood phylogenetic tree was constructed from the alignment using raxml v7.0.4 (Stamatakis A (2006) Bioinformatics 22(21):2688), with the General Time Reversible (GTR) model of nucleotide substitution, Gamma model of rate heterogeneity, estimation of proportion of invariable sites, and 1,000 bootstrap replicates. Sequences from Chytridium confervae (AY349119), Entomophtora muscae (AY997047) and Glomus intraradices (EF989109) were used as outgroup. The best tree with bootstrap support values was selected and edited with the ape v2.3.2 library for r (Paradis E et al (2004) Bioinformatics 20:289-290). Bootstrap values above 70 % are shown next to each branch. Bars next to OTU sequences indicate their proportion of occurrence as endophytes (E) or soil fungi (S), and brackets delimit either fungal orders or outgroup (PDF 869 kb)

Figure S2

(a) Specificity of primers ME3F and ME3R using DNA from different isolates representative of OTU01 and other OTUs. Each PCR reaction was performed in a final volume of 25 μL containing 10 ng of fungal DNA as template, or no DNA for a negative control (c-). Amplification products were visualized in a 2 % agarose electrophoresis gel stained with SYBR Green I. (b) Alignment of sequences obtained from direct amplification of root or soil DNA with primers ME3F and ME3R (see Fig. 5b), with a representative rDNA sequence of OTU01. mafft v6.0 was used to perform the alignment (PDF 456 kb)

Figure S3

Distribution of fungal orders of either endophytic or rhizospheric soil fungal communities. Plots show averaged isolation percentages for each order (PDF 13 kb)

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Maciá-Vicente, J.G., Ferraro, V., Burruano, S. et al. Fungal Assemblages Associated with Roots of Halophytic and Non-halophytic Plant Species Vary Differentially Along a Salinity Gradient. Microb Ecol 64, 668–679 (2012). https://doi.org/10.1007/s00248-012-0066-2

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