Responses of an Agricultural Soil Microbiome to Flooding with Seawater after Managed Coastal Realignment.

Kamilla Sjøgaard,Alexander Treusch,Thomas Valdemarsen

doi:10.3390/microorganisms6010012

Kamilla Sjøgaard, Alexander Treusch + Show 1 more

Open Access

https://doi.org/10.3390/microorganisms6010012

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Journal: Microorganisms	Publication Date: Jan 26, 2018
Citations: 17	License type: CC BY 4.0

Affiliation: University of Southern Denmark

Abstract

Coastal areas have become more prone to flooding with seawater due to climate-change-induced sea-level rise and intensified storm surges. One way to cope with this issue is by “managed coastal realignment”, where low-lying coastal areas are no longer protected and instead flooded with seawater. How flooding with seawater impacts soil microbiomes and the biogeochemical cycling of elements is poorly understood. To address this, we conducted a microcosm experiment using soil cores collected at the nature restoration project site Gyldensteen Strand (Denmark), which were flooded with seawater and monitored over six months. Throughout the experiment, biogeochemical analyses, microbial community fingerprinting and the quantification of marker genes documented clear shifts in microbiome composition and activity. The flooding with seawater initially resulted in accelerated heterotrophic activity that entailed high ammonium production and net removal of nitrogen from the system, also demonstrated by a concurrent increase in the abundances of marker genes for ammonium oxidation and denitrification. Due to the depletion of labile soil organic matter, microbial activity decreased after approximately four months. The event of flooding caused the largest shifts in microbiome composition with the availability of labile organic matter subsequently being the most important driver for the succession in microbiome composition in soils flooded with seawater.

Highlights

Sea-level rise driven by climate change is expected to impact ~70% of the global coastlines during the 21st century [1]
The capability for denitrification is not confined to a specific group of Bacteria or Archaea [19], making predictions about this anaerobic respiration pathway based on taxonomic assignments using the 16S rRNA gene uncertain at best
The flooding with seawater and its intrusion into the soil cores initiated some rapid changes in the soils, both physical and biogeochemical

Summary

Introduction

Sea-level rise driven by climate change is expected to impact ~70% of the global coastlines during the 21st century [1]. An increasingly popular strategy is “managed coastal realignment”, where low-lying coastal areas are permanently flooded with seawater by the intentional breaching of existing dikes and building of new dikes further inland [6,7] This generates buffer zones for storm surges, protecting the more valuable agricultural areas and settlements inland [8,9]. Flooding with seawater will cause a shift towards anoxic conditions below a depth of few millimeters This will limit soil organic matter (SOM) degradation to mainly anaerobic processes such as fermentation [14] and stimulate respiration with alternative electron acceptors, for instance sulfate (SO42−) reduction [15,16] or denitrification [17,18]. Functional genes encoding enzymes in the denitrification pathway are used instead, with the genes for both the cytochrome cd1- (nirS) and the copper (nirK) nitrite (NO2−) reductase being molecular markers for the key step in denitrification, the reduction of NO2− to nitric oxide [19]

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