◦ number of fungal taxa • Dominance: ◦ relative proportion • Habitat / Season: ◦ distribution among habitat / season Source:http://www.mycolog.com/chapter11b.htm
passively introduced via wind, rainwater, inflowing streams • Littoral zone: ◦ hotspot for all kinds of fungi • Pelagic zone: ◦ only specialized species Source: (1) Christian M. Wurzbacher et al. (2010) Fungi in lake ecosystems (2) Sébastien Monchy et al. (2011) Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing
min score of 15 • BLAST: 500 reads per month per habitat • MEGAN with SILVA taxonomy ◦ LCA: min support 5 and min score 50 • UPARSE: 97% sequence similarity • SINA: ◦ 70% sequence similarity and 10 reads support
benthic • but overall wide variations • more specific classification at blast ◦ less reads mapped to fungal taxa ◦ max 40 reads per sample Discussion: Biodiversity
detected with Blast (SILVA) ◦ Same with SINA (online) ◦ Sub sampling may be problematic ◦ too specific classification • Bacteria found although eucaryotic primer • Pipeline (without MEGAN) at https://bitbucket.org/flekschas/biodivex2
Pipeline ◦ Similarity threshold ◦ NCBI database instead of SILVA • Blast - Pipeline ◦ SILVA LSU taxonomy good but could be better ◦ SILVA to NCBI mapping kind of old (2 years)
flekschas
joisino
masatoto
0325
yuukit
hiroyaonoe
tomzimmermann
eumesy
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elith
matsumoto_r
tammyeverts
lynnandtonic
chrislema
brettharned
chriscoyier
danielanewman
mclloyd
marcduiker
shpigford
eileencodes
maltzj
mza
