Quantifying Soil Microbiome Abundance by Metatranscriptomics and Complementary Molecular Techniques—Cross‐Validation and Perspectives

作者：Mathilde Borg Dahl, Stella Brachmann, Andrea Söllinger, Marina Schnell, Laureen S Ahlers, Magdalena Wutkowska, Katharina J. Hoff, Neetika Nath, Verena Groß, Haitao Wang, Micha Weil, Marc Piecha, Marc Schaffer, Corinna Jensen, Andreas W. Kuß, Christoph Gall, Erika Wimmer, Thomas Pribasnig, Alexander Tøsdal Tveit, Bjarni D. Sigurðsson, Christa Schleper, Andreas Richter, Tim Urich · 发表于：Molecular Ecology Resources · 年份：2025 · DOI：10.1111/1755-0998.14130 · 被引用次数：5 · 研究领域：Genomics and Phylogenetic Studies、Environmental DNA in Biodiversity Studies、Microbial Community Ecology and Physiology

ABSTRACT Linking meta‐omics and biogeochemistry approaches in soils has remained challenging. This study evaluates the use of an internal RNA extraction standard and its potential for making quantitative estimates of a given microbial community size (biomass) in soil metatranscriptomics. We evaluate commonly used laboratory protocols for RNA processing, metatranscriptomic sequencing and quantitative reverse transcription polymerase chain reaction (qRT‐PCR). Metatranscriptomic profiles from soil samples were generated using two library preparation protocols and prepared in triplicates. RNA extracted from pure cultures of Saccharolobus solfataricus was added to the samples as an internal nucleic acid extraction standard (NAE std ). RNA reads originating from NAE std were identified with a 99.9% accuracy. A remarkable replication consistency between triplicates was seen (average Bray–Curtis dissimilarity 0.03 ± 0.02), in addition to a clear library preparation bias. Nevertheless, the between‐sample pattern was not affected by library type. Estimates of 16S rRNA transcript abundance derived from qRT‐PCR experiments, NAE std and a previously published quantification method of metatranscriptomics (hereafter qMeTra) were compared with microbial biomass carbon (MBC) and nitrogen (MBN) extracts. The derived biomass estimates differed by orders of magnitude. While most estimates were significantly correlated with each other, no correlation was observed between NAE std and MBC extracts....