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Title (Primary) Biomarker metaproteomics for relative taxa abundances across soil organisms
Author Starke, R.; Fiore-Donno, A.M.; White III, R.A.; Parente Fernandes, M.L.; Martinović, T.; Bastida, F.; Delgado-Baquerizo, M.; Jehmlich, N.
Journal Soil Biology & Biochemistry
Year 2022
Department MOLSYB
Volume 175
Page From art. 108861
Language englisch
Topic T9 Healthy Planet
Keywords Metaproteomics; Biomarker; Relative taxa abundances
Abstract Soil organisms are often classified using methods targeting individual groups of taxa (e.g., bacteria, fungi and invertebrates), which hampers our ability to directly compare the relative abundance of different groups across environmental gradients. We posit that the use of protein biomarkers could help to provide a more real representation of the cross-kingdom soil microbial populations. Here, we tested if the abundant proteins ATP synthase F(0) complex (ATPS), elongation factors (EF), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), GroEL, pyruvate dehydrogenase (PyrDH), RNA polymerase beta chain (RNAP), and translation initiation factor 2 (TIF) could be used to describe the taxonomic composition of microbial communities. As positive control, we used a mock community with different relative abundances of algae, archaea, bacteria, and viruses. We tested this approach on a previously published soil metaproteomes from which we randomly selected samples from forests, grasslands, and shrublands (each n = 10). Unfortunately, the biomarker approach is not feasible for viruses as these organisms do not share single genes. All biomarkers showed decent accuracy to determine the relative abundances of archaea, bacteria, and eukaryota in the mock community. However, false positive hits dominated on phylum level probably due to sequence homology. Archaeal proteins were only detected in the soil samples when EF was used as biomarker at an abundance of 0.7%. Bacteria dominated the EF-metaproteome and were most abundant in shrublands (64.4%) while eukaryotes were more abundant in forests (25.6%). In compliance with previously published results, the correlation analysis revealed the impact of mean annual temperature and pH on both bacteria and eukaryota. Our approach not only shows the potential to use biomarker metaproteomics to unveil the relative taxa abundances across soil organisms but also the need to create mock communities comprising members of all soil taxa.
Persistent UFZ Identifier https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=26770
Starke, R., Fiore-Donno, A.M., White III, R.A., Parente Fernandes, M.L., Martinović, T., Bastida, F., Delgado-Baquerizo, M., Jehmlich, N. (2022):
Biomarker metaproteomics for relative taxa abundances across soil organisms
Soil Biol. Biochem. 175 , art. 108861