PH-driven shifts in overall and transcriptionally active denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil.

Kristof Brenzinger,Peter Dörsch,Gesche Braker

doi:10.3389/fmicb.2015.00961

Abstract

Soil pH is a strong regulator for activity as well as for size and composition of denitrifier communities. Low pH not only lowers overall denitrification rates but also influences denitrification kinetics and gaseous product stoichiometry. N2O reductase is particularly sensitive to low pH which seems to impair its activity post-transcriptionally, leading to higher net N2O production. Little is known about how complex soil denitrifier communities respond to pH change and whether their ability to maintain denitrification over a wider pH range relies on phenotypic redundancy. In the present study, we followed the abundance and composition of an overall and transcriptionally active denitrifier community extracted from a farmed organic soil in Sweden (pHH2O = 7.1) when exposed to pH 5.4 and drifting back to pH 6.6. The soil was previously shown to retain much of its functioning (low N2O/N2 ratios) over a wide pH range, suggesting a high functional versatility of the underlying community. We found that denitrifier community composition, abundance and transcription changed throughout incubation concomitant with pH change in the medium, allowing for complete reduction of nitrate to N2 with little accumulation of intermediates. When exposed to pH 5.4, the denitrifier community was able to grow but reduced N2O to N2 only when near-neutral pH was reestablished by the alkalizing metabolic activity of an acid-tolerant part of the community. The genotypes proliferating under these conditions differed from those dominant in the control experiment run at neutral pH. Denitrifiers of the nirS-type appeared to be severely suppressed by low pH and nirK-type and nosZ-containing denitrifiers showed strongly reduced transcriptional activity and growth, even after restoration of neutral pH. Our study suggests that low pH episodes alter transcriptionally active populations which shape denitrifier communities and determine their gas kinetics.

Highlights

Soil N2O emissions from denitrification depend on environmental conditions that control the rates of denitrification and the N2O/N2 product ratio
Ratios of >50 after 96 h indicated a tendency of enhanced growth of nosZ-type denitrifiers compared to nitrite reducers (Figure 4, Table S4) which may explain the efficient conversion of N2O to N2 (Philippot et al, 2011)
We found a pronounced succession of transcriptionally active denitrifier community (TADC) and overall denitrifier community (ODC) in batch incubations even at neutral pH, suggesting a strong selective pressure on the extracted community

Summary

Introduction

Soil N2O emissions from denitrification depend on environmental conditions that control the rates of denitrification and the N2O/N2 product ratio. Important soil and chemical factors are oxygen availability (as affected by soil moisture and respiration), temperature, nitrate availability and pH (Wijler and Delwiche, 1954; Nömmik, 1956; Firestone, 1982) Among these factors, soil pH is one of the most crucial ones, because it does affect overall denitrification rates, but more importantly seems to directly control the N2O/(N2O + N2) ratio of denitrification, and N2O emission rates from soils (Šimek and Cooper, 2002; Liu et al, 2010; Bakken et al, 2012). In a recent study, Jones et al (2014) proposed that soil pH controls the abundance of nitrite reductase genes as well as the abundance of the newly discovered nosZ Type II clade in soils with relevance to the soil’s ability to reduce N2O

Methods

Results

Conclusion