Protistan and fungal diversity in soils and freshwater lakes are substantially different

Abstract

Freshwater and soil habitats hold rich microbial communities. Here we address commonalities and differences between both habitat types. While freshwater and soil habitats differ considerably in habitat characteristics organismic exchange may be high and microbial communities may even be inoculated by organisms from the respective other habitat. We analyze diversity pattern and the overlap of taxa of eukaryotic microbial communities in freshwater and soil based on Illumina HiSeq high-throughput sequencing of the amplicon V9 diversity. We analyzed corresponding freshwater and soil samples from 30 locations, i.e. samples from different lakes across Germany and soil samples from the respective catchment areas. Aside from principle differences in the community composition of soils and freshwater, in particular with respect to the relative contribution of fungi and algae, soil habitats have a higher richness. Nevertheless, community similarity between different soil sites is considerably lower as compared to the similarity between different freshwater sites. We show that the overlap of organisms co-occurring in freshwater and soil habitats is surprisingly low. Even though closely related taxa occur in both habitats distinct OTUs were mostly habitat–specific and most OTUs occur exclusively in either soil or freshwater. The distribution pattern of the few co-occurring lineages indicates that even most of these are presumably rather habitat-specific. Their presence in both habitat types seems to be based on a stochastic drift of particularly abundant but habitat-specific taxa rather than on established populations in both types of habitats.

Global patterns and rates of habitat transitions across the eukaryotic tree of life

“…Identical sequences in multiple habitats can also be the result of contamination (for example, refs. 36 , 112 ). Therefore, to be conservative in what was considered to be present in an environment, we retained only those OTUs that were composed of at least 100 reads or were present in at least two distinct samples.…”

CARD‐FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes

“…However, eukaryotic 18S rRNA encoding gene sequences of natural protistan communities provide valuable information on the distribution patterns of various protistan groups in a broad variety of aquatic habitats (e.g. Logares et al ., 2012 ; de Vargas et al ., 2015 ; Bock et al ., 2020 ; Sieber et al ., 2020 ) and for designing novel probes for catalyzed reporter deposition fluorescence in situ hybridization (CARD‐FISH), targeting the major protistan groups in aquatic environments (Piwosz et al ., 2021 ). The CARD‐FISH became an indispensable tool for studying eukaryotic communities in the plankton, focusing on their ecological role and trophic interactions (Not et al ., 2005 , 2008 ; Mangot et al, 2009 ; Lepère et al, 2010 ; Unrein et al ., 2014 ; Mukherjee et al ., 2015 ; Piwosz et al ., 2016 ).…”

“…Furthermore, we expect that these shallow lakes, rich in organic particles with associated bacteria, such as algal and colonial cyanobacterial blooms, host large populations of bacterivorous Kinetoplastea, considered as grazers on particle‐associated bacteria (Caron, 1987 ; Zubkov and Sleigh, 2000 ; Mukherjee et al ., 2015 ). Members of another ubiquitous group of freshwaters flagellates, Katablepharidacea (Arndt et al ., 2000 ; Bock et al ., 2020 ; Sieber et al ., 2020 ), are considered mostly as algivorous or omnivorous HNF. However, we hypothesize that they are important bacterivores in prokaryote‐rich hypertrophic lakes.…”

Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion

“…S9 ) and fungal diversity is not affected by zinc, suggesting that a direct impact is unlikely 142 . This is not surprising as the fungal fraction is low in pelagic freshwaters 143 , 144 and the nature of compositional data may obscure shifts especially in rare taxa. In summary, it is evident that zinc is strongly unsettling the balance between heterotrophs and phototrophs.…”