Nanofauna (flagellates, amoebae) diversity in relation to land use and ecosystem functioning NANOFAUNA DIVERSITY (NANOFAUN)
Final Report Abstract
The project with 2 Co-PIs (H. Arndt and M. Bonkowski) was designed to reflect the taxonomic expertise of our respective groups. While the Arndt group focused on flagellate taxonomy, our expertise was on amoeboid protists. Our major aim in the first funding phase was the establishment of a high-throughput sequencing technique to quantify the amoeboid protists, especially in the phylum Amoebozoa. Major challenges had to be overcome: i) it was impossible to generate a reliable reference database from public databases, and we had to assemble our own reference data base by isolating, cultivating and sequencing hundreds of amoeboid taxa – and doing proper taxonomy on them as well. 2) I underestimated the challenges of primer design for Amoebozoa due to their extreme variability in the conserved regions of their SSU sequence. 3) The bioinformatics pipelines for data analysis also needed to be established. For example, we developed a method based on the coamplification of a well-characterized ‘mock’ community to clearly define the cut-off values for OTU assignment. 4) With the change from Roche 454 to Illumina sequencing, again new primers had to be designed and new bioinformatic pipelines had to be established. At the end of the first funding phase, all the prerequisites for our first HTS survey were in place: We had a reference data base, we had specific primers for Acanthamoeba, and we had established a close collaboration with Tesfaye Wubet in the Buscot group to solve the bioinformatic challenges. We are now one of the few groups worldwide that have the tools ready to describe the large uncultivated protist diversity in soils and to gain data on protist diversity on a scale suitable to sequence all 150 plots in the grasslands and forest ecosystems at the same time. Currently we have primers to cover Myxomycets and Acanthamoeba in the Amoebozoa, and the large group of Cercozoa. Primers for Oomycetes will follow. Now our data can complement the data on fungi (Buscot/Wubet) and bacteria, and it is agreed in the MicroSYTeM subproject that we will calculate microbial co-occurrence networks with the aim to uncover for the first time multitrophic connections between bacteria, protists and fungi in grassland soils.The MicroSYTeM subproject is also where we hope to get statistical support for the spatial modelling of protist distribution and protist-bacteria-fungi co-occurrence and SEM in the SCALEMIC project.
Publications
- (2012) Environmental factors affect acidobacterial communities below the subgroup level in grassland and forest soils. Applied and Environmental Microbiology78:7398-7406
Naether A, Foesel BU, Nägele V, Wüst PK, Weinert J, Bonkowski M, Alt F, Oelmann Y, Polle A, Lohaus G, Fischer M, Schöning I, Nieschulze J, Pfeiffer S, Prati D, Renner S, Wells K, Kalko EKV, Linsenmair KE, Schulze ED, Weisser WW, Overmann J, Friedrich MW
(See online at https://doi.org/10.1128/AEM.01325-12) - (2012) General Relationships between Abiotic Soil Properties and Soil Biota across Spatial Scales and Different Land-Use Types. PLoS ONE, 7, e43292
Birkhofer K., Schöning I., Alt F., Herold N., Klarner B., Maraun M., Marhan S., Oelmann Y., Wubet T., Yurkov A., Begerow D., Berner D., Buscot F.o., Daniel R., Diekötter T., Ehnes R.B., Erdmann G., Fischer C., Foesel B., Groh J., Gutknecht J., Kandeler E., Lang C., Lohaus G., Meyer A., Nacke H., Näther A., Overmann J., Polle A., Pollierer M.M., Scheu S., Schloter M., Schulze E.-D., Schulze W., Weinert J., Weisser W.W., Wolters V., Schrumpf M.
(See online at https://doi.org/10.1371/journal.pone.0043292) - (2013) Community structure of cultivable Protists in different grassland and forest soils of Thuringia. Pedobiologia 56:1-7
Domonell A, Brabender M, Nitsche F, Bonkowski M, Arndt H
(See online at https://doi.org/10.1016/j.pedobi.2012.07.001) - (2013) Determinants of Acidobacteria activity inferred from the relative abundances of 16D rRNA transcripts in German grassland and forest soils. Applied and Environmental Microbiology 16.3: 658-675
Foesel BU, Nägele V, Naether A, Wüst PK, Weinert J, Bonkowski M, Lohaus G, Polle A, Alt F, Oelmann Y,Fischer M, Friedrich MW, Overmann J
(See online at https://doi.org/10.1111/1462-2920.12162) - (2014) Two new species of the genus Stenamoeba (Discosea, Longamoebia): cytoplasmic MTOC is present in one more amoebae lineage.European Journal of Protistology 50: 153-165
Geisen S, Weinert J, Kudryavtsev A, Glotova A, Bonkowski M, Smirnov A
(See online at https://doi.org/10.1016/j.ejop.2014.01.007) - 2015. First insight into dead wood protistan diversity: a molecular sampling of bright-spored Myxomycetes (Amoebozoa, slime-moulds) in decaying beech logs. FEMS Microbiology Ecology 91, fiv050
Clissmann, F., Fiore-Donno, A.M., Hoppe, B., Krüger, D., Kahl, T., Unterseher, M., Schnittler, M.
(See online at https://doi.org/10.1093/femsec/fiv050) - (2016) Metacommunity analysis of amoeboid protists in grassland soils. Scientific Reports 6: 19068
Fiore-Donno AM, Weinert J, Wubet T, Bonkowski M
(See online at https://doi.org/10.1038/srep19068) - (2016) Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecological Indicators 69: 213-223
Griffiths BS, Römbke J, Schmelz R, Scheffczyk A, Faber J, Bloem J, Pérès G, Cluzeau D, Chabbi A, Suhadolc M, Sousa P, Martins da SIlva P, Carvalho F, Mendes S, Morais P, Francisco R, Pereira C, Bonkowski M, Geisen S, Bardgett R, de Vries F, Bolger T, Dirilgen T, Schmidt O, Winding A, Hendriksen N, Johansen A, Philippot L, Plassart P, Bru D, Thompson B, Griffiths R, Keith A, Rutgers M, Mulder C, Hannula E, Creamer R, Stone D
(See online at https://doi.org/10.1016/j.ecolind.2016.04.023)
