Metacommunity analysis of amoeboid protists in grassland soils

Fiore-Donno, Anna Maria; Weinert, Jan; Wubet, Tesfaye; Bonkowski, Michael

doi:10.1038/srep19068

Cited by 72 publications

(39 citation statements)

References 79 publications

(95 reference statements)

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“…The low degree of overlap of taxa between the study sites Düsseldorf and Frankfurt might indicate a potential influence of geographic location as recently found for Amoebozoa (Fiore‐Donno et al. ), but the sequencing depth in our study was not sufficient to define any site‐ and plant‐specific patterns in bacterivore protists. Our small‐scale cloning and sequencing approach, however, did provide the first insights on the range of phyllosphere protist diversity within a single, distinct taxonomic group of protists.…”

Section: Discussionmentioning

confidence: 48%

High Diversity Revealed in Leaf‐Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

Ploch

Rose

Bass

et al. 2016

J Eukaryotic Microbiology

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The largest biological surface on earth is formed by plant leaves. These leaf surfaces are colonized by a specialized suite of leaf‐inhabiting microorganisms, recently termed “phyllosphere microbiome”. Microbial prey, however, attract microbial predators. Protists in particular have been shown to structure bacterial communities on plant surfaces, but virtually nothing is known about the community composition of protists on leaves. Using newly designed specific primers targeting the 18S rDNA gene of Cercozoa, we investigated the species richness of this common protist group on leaves of four Brassicaceae species from two different locations in a cloning‐based approach. The generated sequences revealed a broad diversity of leaf‐associated Cercozoa, mostly bacterial feeders, but also including known plant pathogens and a taxon of potential endophytes that were recently described as algal predators in freshwater systems. This initial study shows that protists must be regarded as an integral part of the microbial diversity in the phyllosphere of plants.

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Section: Discussionmentioning

confidence: 48%

High Diversity Revealed in Leaf‐Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

Ploch

Rose

Bass

et al. 2016

J Eukaryotic Microbiology

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“…This general underrepresentation of specific groups is known for broad primers because the ribosomal sequences of e.g. amoebozoans are particularly rich in inserts and thus underperform during PCR and the subsequent sequencing step (Geisen et al 2015, Fiore-Donno et al 2016. Further, the highly variable ITS1 can lead to a length bias for groups with long ITS1 sequences which may not be sequenced by the Illumina technology and thus be underrepresented in the sequencing libraries.…”

Section: Habitat-specific Community Structurementioning

confidence: 99%

Effects of short-term flooding on aquatic and terrestrial microeukaryotic communities: a mesocosm approach

Graupner¹,

Röhl²,

Jensen³

et al. 2017

Aquat. Microb. Ecol.

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Freshwater and soil are not strictly isolated habitats. In particular, floods may facilitate the exchange of organisms and nutrients. Flooding can have both a stimulating and a harmful effect on the organisms of the respective habitats. The effects of short-term flooding on microeukaryotic communities in the aquatic and terrestrial habitat have so far been scarcely studied. Here, we investigated the effect of a 24 h artificial inundation on the microeukaryotic community composition in AquaFlow mesocosm systems. We investigated the shift of community composition based on molecular amplicon diversity both on soil and water during flooding and for a period of 12 d after flooding. Community composition was, as expected, strongly different between soil and water. Flooding had a significant effect on the freshwater community, whereas the soil community was hardly affected. In particular, we observed a transfer of nutrients from the terrestrial habitat into the aquatic habitat and identified ~50 taxa that were transferred by the flooding event. This effect of flooding was, however, overlaid by shifts of the communities with time, presumably reflecting an acclimatization to the conditions in the AquaFlow systems.

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“…So‐called “universal eukaryotic primers” have been designed to target a wide range of eukaryotes (Bates et al., ; Massana et al., ; Stoeck et al., ), but experience has revealed three major drawbacks in this approach. First, universal eukaryotic primers miss a great part of the diversity and are biased towards certain taxa (Geisen, Laros, Vizcaíno, Bonkowski, & De Groot, ; Jeon et al., ; Lentendu et al., ), in particular favouring ciliates and selecting against Amoebozoa (Fiore‐Donno, Weinert, Wubet, & Bonkowski, ; Geisen, Laros, et al., ; Lentendu et al., ). Second, a study comparing the outputs of general and cercozoan‐specific primers has shown that structuring effects of environmental factors (e.g., soil fertilization) on communities could only be seen in the data sets generated with specific primers (Lentendu et al., ).…”

Section: Introductionmentioning

confidence: 99%

New barcoded primers for efficient retrieval of cercozoan sequences in high‐throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

Fiore-Donno

Rixen²,

Rippin

et al. 2017

Molecular Ecology Resources

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We describe the performance of a new metabarcoding approach to investigate the environmental diversity of a prominent group of widespread unicellular organisms, the Cercozoa. Cercozoa is an immensely large group of protists, and although it may dominate in soil and aquatic ecosystems, its environmental diversity remains undersampled. We designed PCR primers targeting the hypervariable region V4 of the small subunit ribosomal RNA (SSU or 18S) gene, which is the recommended barcode marker for Cercozoa. The length of the amplified fragment (c. 350 bp) is suitable for Illumina MiSeq, the most cost-effective platform for molecular environmental surveys. We provide barcoded primers, an economical alternative to multiple libraries for multiplex sequencing of over a hundred samples. In silico, our primers matched 68% of the cercozoan sequences of the reference database and performed better than previously proposed new-generation sequencing primers. In mountain grassland soils and in biological soil crusts from a variety of climatic regions, we were able to detect cercozoan sequences encompassing nearly the whole range of the phylum. We obtained 901 operational taxonomic units (OTUs) at 97% similarity threshold from 26 samples, with c. 50,000 sequences per site, and only 8% of noncercozoan sequences. We could report a further increase in the diversity of Cercozoa, as only 43% of the OTUs were 97%-100% similar to any known sequence. Our study thus provides an advanced tool for cercozoan metabarcoding and to investigate their diversity and distribution in the environment.

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Metacommunity analysis of amoeboid protists in grassland soils

Cited by 72 publications

References 79 publications

High Diversity Revealed in Leaf‐Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

High Diversity Revealed in Leaf‐Associated Protists (Rhizaria: Cercozoa) of Brassicaceae

Effects of short-term flooding on aquatic and terrestrial microeukaryotic communities: a mesocosm approach

New barcoded primers for efficient retrieval of cercozoan sequences in high‐throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts

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