Universität zu Köln

Starke, Robert, Fiore-Donno, Anna Maria ORCID: 0000-0001-6265-1907, White, Richard Allen, Fernandes, Maysa Lima Parente, Martinovic, Tijana ORCID: 0000-0001-6940-0473, Bastida, Felipe, Delgado-Baquerizo, Manuel and Jehmlich, Nico (2022). Biomarker metaproteomics for relative taxa abundances across soil organisms. Soil Biol. Biochem., 175. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. ISSN 1879-3428

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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 repre-sentation 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Starke, Robert UNSPECIFIED UNSPECIFIED UNSPECIFIED Fiore-Donno, Anna Maria UNSPECIFIED orcid.org/0000-0001-6265-1907 UNSPECIFIED White, Richard Allen UNSPECIFIED UNSPECIFIED UNSPECIFIED Fernandes, Maysa Lima Parente UNSPECIFIED UNSPECIFIED UNSPECIFIED Martinovic, Tijana UNSPECIFIED orcid.org/0000-0001-6940-0473 UNSPECIFIED Bastida, Felipe UNSPECIFIED UNSPECIFIED UNSPECIFIED Delgado-Baquerizo, Manuel UNSPECIFIED UNSPECIFIED UNSPECIFIED Jehmlich, Nico UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-691478
DOI:	10.1016/j.soilbio.2022.108861
Journal or Publication Title:	Soil Biol. Biochem.
Volume:	175
Date:	2022
Publisher:	PERGAMON-ELSEVIER SCIENCE LTD
Place of Publication:	OXFORD
ISSN:	1879-3428
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language Soil Science Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/69147