Nitric oxide emission response to soil moisture is linked to transcriptional activity of functional microbial groups

Highlights

• AOA lead to a maximum NO-release rate at low soil moistures in a dryland soil.

• Niche separation for distinct microbial groups based on soil moisture occurred.

• Niche separation might explain distinct maxima of NO emissions.

Abstract

Numerous studies have shown that soil moisture controls NO flux from soils. Less is known, however, to what extent microbial N-cycling mediates this control. Does soil moisture control NO release primarily by affecting the physical gas exchange between soil and atmosphere, by modulating microbial activities involved in biotic NO turnover, or by both? Using a novel dynamic chamber system for high-resolution measurement of NO release, we found one or several soil-specific maxima of NO release during dry-out experiments in different soils. A mid-latitude arable soil displayed a single maximum at 0.10 water holding capacity (whc), whereas a dryland farming and a rice paddy soil showed two maxima at 0.65/0.10 and 0.90/0.10 whc, respectively. Transcription of nirS genes in the dryland soil at 0.65 whc was low, but larger than at 0.10 whc, while transcriptional activity of archaeal ammonia oxidizers showed the opposite pattern with higher activity at 0.10 whc, suggesting biogenic NO production at low soil moisture. Our study is a first attempt to link NO emission to soil moisture responses of different microbial groups.

Introduction

Global sources of NO_x (NO + NO₂) are estimated to be in the range of 42–47 Tg (N) a⁻¹ (Denman et al., 2007). Soils act as a significant source of NO and contribute about 9 Tg (N) a⁻¹ which ultimately can be ascribed to microbial N-transformations (Ciais et al., 2013, Homyak et al., 2017). NO_x catalyzes the photochemical production of ozone (O₃) in the troposphere (Haagen-Smit, 1952) and thereby contributes to the greenhouse gas effect. Various laboratory incubation studies have found that the NO release rate, J_NO, follows an optimum curve over a range of soil moistures, which has been tentatively attributed to the soil moisture dependency of NO producing microbial activities (Yu et al., 2008, Ashuri, 2009, Laville et al., 2009).

Previously, the NO relationship to soil moisture was thought to be shaped by the tradeoff between restricted O₂ supply and reduced substrate diffusion in wet and dry soil, respectively (Skopp et al., 1990). Bargsten et al. (2010), studying NO response to soil moisture change under non-limiting diffusion conditions in the laboratory, claimed that the optimum soil moisture for NO emissions will depend on soil-specific gaseous diffusivity and Skiba et al. (1997) identified factors which regulate gaseous diffusivity, such as soil texture, bulk density and water content as central for NO flux in a study with temperate and tropical agricultural soils. Although taking account for denitrification and nitrification as distinct microbial sources for NO, none of the above studies considered the possibility that the soil moisture response of key-microbial groups controls the NO flux.

Nitric oxide (NO) in soils is produced and consumed predominately through the microbially mediated processes of nitrification and denitrification (Conrad, 1996). In unrestricted nitrification, ammonia (NH₃) is oxidized via hydroxylamine (NH₂OH) to nitrite (NO₂⁻) and NO is released as intermediate in the second step (Koslowski et al., 2016). Nitrifiers and heterotrophic denitrifiers are taxonomically unrelated and have distinct physiologies. While aerobic ammonia oxidizers are autotrophs that form phylogenetically coherent groups within the beta- and gamma-proteobacteria (Purkhold et al., 2000) or the Thaumarchaeota (Pester et al., 2011), denitrifiers are phylogenetically diverse heterotrophs with the ability to respire nitrogeneous oxides in the absence of oxygen (Philippot, 2002, Wei et al., 2015).

There is some evidence that taxonomically distinct, but functionally redundant microbial groups such as AOB and AOA have distinct soil moisture optima. For instance, Adair and Schwartz (2008) found a higher abundance of ammonia oxidizing archaea (AOA) than ammonia oxidizing bacteria (AOB) in a semiarid soil which, unlike AOB abundance, was not related to soil temperature or precipitation. They interpreted these findings as indicative for a greater resistance of AOA to desiccation. Soil moisture affects the oxygen availability in soils and thereby the activity of different microbial functional groups (Gleeson et al., 2010). In the present study, we hypothezised that soil NO emissions at different soil moistures are determined by metabolic activities of taxonomically distinct microbial groups and that this should result in distinct maxima of NO flux over a range of soil moistures. Testing this hypothesis is timely as it would violate the assumption of one discrete maximum for NO flux over soil moisture, commonly used for upscaling NO fluxes (Meixner and Yang, 2006, Laville et al., 2009, Yu et al., 2008).

We tested our hypothesis by monitoring NO release of a dryland soil in a dry-out experiment. In addition, different fertilizers ((NH₄)₂SO₄ and KNO₃) were added to stimulate nitrification and denitrification. To link our results to microbial activities, we measured the relative expression of bacterial and archeal amoA (encoding ammonia monooxigenase) as well as nirK and nirS (encoding copper and cytochrome cd₁-containing nitrite reductase, respectively) at soil moistures showing maximum NO release. This approach is based on the assumption that an increase in the numbers of active microorganisms results from increasing ratios of mRNA over DNA copy numbers (Blazewicz et al., 2013, Rocca et al., 2015) and that the transcriptional activation of functional key genes can be used as a proxy for enzyme synthesis.