Long‐term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA

Abstract

Assessing the extent to which changes in lacustrine biodiversity are affected by anthropogenic or climatic forces requires extensive palaeolimnological data. We used high-throughput sequencing to generate time-series data encompassing over 2200 years of microbial eukaryotes (protists and Fungi) diversity changes from the sedimentary DNA record of two lakes (Lake Bourget in French Alps and Lake Igaliku in Greenland). From 176 samples, we sequenced a large diversity of microbial eukaryotes, with a total 16 386 operational taxonomic units distributed within 50 phylogenetic groups. Thus, microbial groups, such as Chlorophyta, Dinophyceae, Haptophyceae and Ciliophora, that were not previously considered in lacustrine sediment record analyses appeared to be potential biological markers of trophic status changes. Our data suggest that shifts in relative abundance of extant species, including shifts between rare and abundant taxa, drive ecosystem responses to local and global environmental changes. Community structure shift events were concomitant with major climate variations (more particularly in Lake Igaliku). However, this study shows that the impacts of climatic fluctuations may be overpassed by the high-magnitude eutrophication impacts, as observed in the eutrophicated Lake Bourget. Overall, our data show that DNA preserved in sediment constitutes a precious archive of information on past biodiversity changes.

Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming

“…A relatively high richness in the MECs from Lake Bourget was revealed over the last 100 years (6,515 OTUs) in comparison with the richness detected for the last 2,100 years in the same lake applying the same methodology (11,344 OTUs; Capo et al ., ). Studies investigating lacustrine MEC diversity generally differ in their experimental procedures (choice of barcodes, depth of sequencing and the stringency of bioinformatics treatments).…”

“…The low proportion and richness found here for Amoebozoa, Exacavata are classical in lakes MECs (e.g., Nolte et al ., , Mangot et al ., , Simon et al ., ; Capo et al ., ; Filker et al ., ). However, our stringent methodological procedure has certainly accentuated this pattern, in particular due to the choice we made to remove of all OTUs which were not detected in the two replicates done for each sample; for instance, Parabasalia (Excavata) and Euglenozoa (Excavata) were recorded in the molecular inventories before this filtering.…”

“…This moderate richness is partly explained by the lower sequencing depth obtained in this study (around 1,300–3,300 DNA sequences per sample; Coolen et al ., ). Comparing the taxonomic composition (proportion of the main phylogenetic groups within MECs) is less problematic than comparing only the taxa number, and when considering the assemblage composition from paleo‐reconstructions (few references are available Coolen et al ., ; Capo et al ., ) and limnological survey (Lepère et al ., ; Debroas et al ., ; Filker et al ., ), a general pattern is observed. Two groups generally dominate lacustrine microbial eukaryotes: Alveolata, which are mainly represented by Dinophyceae and Ciliophora and Fungi, which are mainly represented by Dikarya, Chytridiomycota and Cryptomycota.…”

Late Quaternary climate change explains soil fungal community composition rather than fungal richness in forest ecosystems

“…Similarly, fungal community composition in the sediment of two European lakes was related to the past two millennia of paleoclimatic variations (Capo et al, 2016). The relationship between late Quaternary climate change and soil fungal community composition may be caused by altering the relative abundance of fungi (Capo et al, 2016), as reported in previous studies that regions where the late Quaternary climate oscillations were similar tend to promote assemblages with similar certain community compositions (Svenning et al, 2015).…”

“…While there is a paucity of studies to compare this to, it has been shown that fungal richness in the sediment of two European lakes was not related to the past two millennia of paleoclimatic variations (Capo et al, 2016). While there is a paucity of studies to compare this to, it has been shown that fungal richness in the sediment of two European lakes was not related to the past two millennia of paleoclimatic variations (Capo et al, 2016).…”