The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison

Abstract

Different proxies for changes in structure and/or function of microbiomes have been developed, allowing assessing microbiome dynamics at multiple levels. However, the lack and differences in understanding the microbiome dynamics are due to the differences in the choice of proxies in different studies and the limitations of proxies themselves. Here, using both amplicon and metatranscriptomic sequencings, we compared four different proxies (16/18S rRNA genes, 16/18S rRNA transcripts, mRNA taxonomy and mRNA function) to reveal the impact of a severe summer drought in 2018 on prokaryotic and eukaryotic microbiome structures and functions in two rewetted fen peatlands in northern Germany. We found that both prokaryotic and eukaryotic microbiome compositions were significantly different between dry and wet months. Interestingly, mRNA proxies showed stronger and more significant impacts of drought for prokaryotes, while 18S rRNA transcript and mRNA taxonomy showed stronger drought impacts for eukaryotes. Accordingly, by comparing the accuracy of microbiome changes in predicting dry and wet months under different proxies, we found that mRNA proxies performed better for prokaryotes, while 18S rRNA transcript and mRNA taxonomy performed better for eukaryotes. In both cases, rRNA gene proxies showed much lower to the lowest accuracy, suggesting the drawback of DNA based approaches. To our knowledge, this is the first study comparing all these proxies to reveal the dynamics of both prokaryotic and eukaryotic microbiomes in soils. This study shows that microbiomes are sensitive to (extreme) weather changes in rewetted fens, and the associated microbial changes might contribute to ecological consequences.

Linking Transcriptional Dynamics of Peat Microbiomes to Methane Fluxes during a Summer Drought in Two Rewetted Fens

“…Our data show the environmental changes in water level, redox potential, and soil temperature in times of the summer drought, which are important factors in altering microbial activities. As revealed by our previous study, this drought event strongly impacted the total microbiome composition in both rewetted fens, raising the interest in understanding the related ecological consequences . Here, we focus on methane-cycling populations of the fen microbiomes, which determine the turnover and emissions of CH 4 .…”

“…The detailed process of metatranscriptomic sequencing has been described in Wang et al (2022) . Briefly, the total RNA was extracted using the RNeasy PowerSoil Total RNA Kit (QIAGEN, Hilden, Germany), followed by the DNase treatment and cleaning with the MEGAclear Kit (Thermo Fisher Scientific, Waltham, MA).…”

“…The process of quality check and sorting out of SSU rRNA and putative mRNA fractions from raw sequences has been described in Wang et al SSU rRNA sequences (with a length of 230–250 bp) were subsampled to 200,000 sequences for each sample using USEARCH . Subsampled sequences were then used as queries for BLASTN searches against a modified version of SILVA 128 database .…”

“…Given the drawbacks of DNA proxies in assessing microbial responses to environmental changes, rRNA and mRNA targeting active microorganisms or living biomass are promising proxies. Specifically, mRNA is suggested as the better proxy for revealing the prokaryotic microbiome dynamics . The simultaneous assessment of rRNA and mRNA by metatranscriptomics allows both taxonomically and functionally characterizing microbiomes .…”

“…In the summer of 2018, a severe heatwave and drought occurred in Europe, resulting in significantly higher temperatures and less precipitation compared with former years. − Studies have shown that this extreme weather event had a significant impact on the vegetation spread as well as the microbiome compositions and their dynamics in rewetted peatlands. ,, However, we still lack a comprehensive understanding on how this drought impacted the CH 4 cycling microbiomes and how their dynamics were linked to in situ CH 4 fluxes in rewetted fens. Here, we investigated the dynamics of methanogens and methanotrophs as well as CH 4 fluxes before, during, and after the drought event in two rewetted fen peatlands, using a quantitative metatranscriptomic approach.…”