Seasonal and ecohydrological regulation of active microbial populations involved in DOC, CO2, and CH4 fluxes in temperate rainforest soil

David V D’Amore,Colleen T E Kellogg,William W Mohn,Thierry J Heger,David J Levy-Booth,Patrick J Keeling,Steven J Hallam,Ian J W Giesbrecht

doi:10.1038/s41396-018-0334-3

Abstract

The Pacific coastal temperate rainforest (PCTR) is a global hot-spot for carbon cycling and export. Yet the influence of microorganisms on carbon cycling processes in PCTR soil is poorly characterized. We developed and tested a conceptual model of seasonal microbial carbon cycling in PCTR soil through integration of geochemistry, micro-meteorology, and eukaryotic and prokaryotic ribosomal amplicon (rRNA) sequencing from 216 soil DNA and RNA libraries. Soil moisture and pH increased during the wet season, with significant correlation to net CO2 flux in peat bog and net CH4 flux in bog forest soil. Fungal succession in these sites was characterized by the apparent turnover of Archaeorhizomycetes phylotypes accounting for 41% of ITS libraries. Anaerobic prokaryotes, including Syntrophobacteraceae and Methanomicrobia increased in rRNA libraries during the wet season. Putatively active populations of these phylotypes and their biogeochemical marker genes for sulfate and CH4 cycling, respectively, were positively correlated following rRNA and metatranscriptomic network analysis. The latter phylotype was positively correlated to CH4 fluxes (r = 0.46, p < 0.0001). Phylotype functional assignments were supported by metatranscriptomic analysis. We propose that active microbial populations respond primarily to changes in hydrology, pH, and nutrient availability. The increased microbial carbon export observed over winter may have ramifications for climate–soil feedbacks in the PCTR.

Highlights

Supplementary information The online version of this article contains supplementary material, which is available to authorized users.Fraser University, Burnaby, BC, Canada 4 The University of Applied Sciences Western Switzerland, CHANGINS, Delémont, Switzerland 5 U.S Department of Agriculture, Forest Service, Pacific NorthwestResearch Station, Juneau, Alaska, USA 6 Department of Botany, University of British Columbia, Vancouver, British Columbia, CanadaSoils of the Pacific coastal temperate rainforest (PCTR) of North America sequester globally important amounts of carbon (~198–900 Mg C ha−1) [1] and contribute some of the highest rates of dissolved organic carbon (DOC) export to coastal margins in the world (10.5–29.9 g C m−2 y−1) [2]
We hypothesized that soil conditions in distinct ecohydrological classes would structure total microbial communities (H1); that putatively active microbial populations would respond to micro-climactic variables in distinct seasons (H2); and that winter periods would increase anaerobic metabolic processes leading to increased net CH4 flux (H3)
Gaseous carbon fluxes correlated with increasing soil moisture, pH, and nutrient availability during wet periods

Summary

Introduction

We hypothesized that soil conditions in distinct ecohydrological classes (peat bog and bog forest) would structure total microbial communities (H1); that putatively active microbial populations would respond to micro-climactic variables in distinct seasons (H2); and that winter periods would increase anaerobic metabolic processes leading to increased net CH4 flux (H3). We demonstrated seasonal differences in the structure of putatively active microbial community members, including a response to previously uncharacterized increased pH and inorganic nitrogen concentrations in winter, resulting in enhanced net flux of both CO2 and CH4 Together, these data allowed us to develop and assess a conceptual model of seasonal changes in microbial carbon cycling in major PCTR ecohydrological classes (Fig. 1a)

Material and Methods

E Soil Gas Flux

Results and discussion

B A B DD

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