The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest

Priyanka Roy Chowdhury; Stefan M Golas; Lauren V Alteio; Joshua T E Stevens; Andrew F Billings; Jeffrey L Blanchard; Jerry M Melillo; Kristen M DeAngelis

doi:10.3389/fmicb.2021.666558

The Transcriptional Response of Soil Bacteria to Long-Term Warming and Short-Term Seasonal Fluctuations in a Terrestrial Forest

Front Microbiol. 2021 Aug 27:12:666558. doi: 10.3389/fmicb.2021.666558. eCollection 2021.

Authors

Priyanka Roy Chowdhury¹, Stefan M Golas², Lauren V Alteio³, Joshua T E Stevens⁴, Andrew F Billings², Jeffrey L Blanchard³, Jerry M Melillo⁵, Kristen M DeAngelis^{2

3}

Affiliations

¹ Department of Biology, Keene State College, Keene, NH, United States.
² Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.
³ Organismic and Evolutionary Biology, University of Massachusetts Amherst, Amherst, MA, United States.
⁴ Department of Biological Sciences, University of South Carolina, Columbia, SC, United States.
⁵ The Ecosystems Center, Marine Biological Laboratories, Woods Hole, MA, United States.

Abstract

Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.

Keywords: carbon cycle; global warming; meta-transcriptomes; microbial; terrestrial.