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Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing

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Abstract

Microbial decomposers, especially a fungal group called aquatic hyphomycetes, play a critical role in processing plant litter in freshwaters by increasing its palatability to invertebrate shredders. Traditionally, communities of aquatic hyphomycetes have been assessed through the identification of spores, which misses non-sporulating taxa. Among new technologies, 454 pyrosequencing stands out as most promising for large-scale species identification. However, very few attempts have been made to validate its effectiveness for assessing the diversity of stream-dwelling fungal communities. We attempted to gain greater insight into the diversity of aquatic fungal communities in streams exposed to various degrees of eutrophication by using the 454 pyrosequencing technology. A total of 173,889 ITS2 pyrosequencing reads with hits for fungi were obtained from the 5 investigated streams. The majority of operational taxonomic units (OTUs) belonged to Ascomycota and the identification to the genus level was achieved for 169 OTUs. Of the total, 135,257 reads (ca. 78 %) showed close affinities to aquatic hyphomycete species. Pyrosequencing showed declining fungal diversity in the most eutrophic streams, which was congruent with a reduced diversity found through spore identification. Dominance patterns revealed by connecting representative OTUs to ITS sequences from aquatic hyphomycetes were similar to those determined by traditional spore identification techniques. However, 454 pyrosequencing provided a more comprehensive view of fungal diversity; it captured almost twice as many taxa as spore counts. This study validates the effectiveness of 454 pyrosequencing for surveying the diversity of stream-dwelling fungal decomposer communities. Its application may accelerate the use of these communities for monitoring the integrity of freshwaters.

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Acknowledgments

The European Regional Development Fund – Operational Competitiveness Programme (FEDER-POFC-COMPETE) (FCOMP-01-0124-FEDER-013954) and the Portuguese Foundation for Science and Technology supported this study (PEst-OE/BIA/UI4050/2014 and PTDC/AACAMB/113746/2009) and S. Duarte (SFRH/BPD/47574/2008). The authors want also to thank to Conceição Egas from Biocant for the help during interpretation of data from pyrosequencing.

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  1. Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal

    S. Duarte, J. Trabulo, F. Cássio & C. Pascoal

  2. Department of Biology, Mount Allison University, Sackville, NB, E4L 1G7, Canada

    F. Bärlocher

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  1. S. Duarte
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Correspondence to S. Duarte.

Appendix to Duarte et al. - Supplementary information

Appendix to Duarte et al. - Supplementary information

Table 3 Total number of reads (a) and OTUs (b) with good quality; total number of reads (c) and OTUs (d) with a hit in NCBI, and coverage (%) of total diversity (e); total n° of reads (f) and OTUs (g) with a hit in NCBI for fungi and coverage (%) of fungal diversity (h); and total n° of reads (i) and OTUs (j) with a hit in NCBI for aquatic hyphomycete species (AQH), based on 454-pyrosequencing analyses from environmental DNA extracted from oak leaves decomposing at the 5 streams (1, Agra; 2, Oliveira; 3, Andorinhas; 4, Selho; and 5, Couros). T1, T2 and T3 represent 9, 23 and 43 days of stream immersion
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Table 4 Relative abundance (%) of each fungal class/subphylum based on 454-pyrosequencing analyses from environmental DNA extracted from oak leaves decomposing in the 5 streams (1, Agra; 2, Oliveira; 3, Andorinhas; 4, Selho and 5, Couros). T1, T2 and T3 represent 9, 23 and 43 days of stream immersion
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Table 5 List of the orders found based on 454-pyrosequencing analyses from environmental DNA extracted from oak leaves decomposing in the 5 streams
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Table 6 List of the families found based on 454-pyrosequencing analyses from environmental DNA extracted from oak leaves decomposing in the 5 streams
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Table 7 List of the genera and species found based on 454-pyrosequencing analyses from environmental DNA extracted from oak leaves decomposing in the 5 streams
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Duarte, S., Bärlocher, F., Trabulo, J. et al. Stream-dwelling fungal decomposer communities along a gradient of eutrophication unraveled by 454 pyrosequencing. Fungal Diversity 70, 127–148 (2015). https://doi.org/10.1007/s13225-014-0300-y

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