Sediment methane dynamics along the Elbe River

Abstract

Methane (CH₄) is an important atmospheric trace gas mostly released from wet anoxic soils and sediments. While many studies have focused on relatively homogenous environments like rice fields and lake sediments, the changing contribution of heterogeneous sediments e.g. along the longitudinal profile of a rivers has not been covered very frequently. Here we investigated sediment samples from 11 locations of the Elbe River. Sediments were incubated to measure methanogenic/methanotrophic potentials and contribution of individual methanogenic pathways using isotope analysis of δ¹³C. Additionally, we determined the diversity of the methanogenic communities (analysis of T-RFLP targeting the mcr-A gene in the sediment samples), while abundances of archaea, methanogens and methanotrophs were determined by qPCR. The CH₄ production was detected in six samples (out of 11 examined) and ranged from 0.12 to 644.72 nmol gDW⁻¹ d⁻¹. Methanotrophy was found in all examined sediment samples and ranged from 654 to 10,875 nmol gDW⁻¹ d⁻¹. Abundance of methanogens and methanotrophs (Mcr-A and pmo-A gene copy numbers) was not significantly different and quite stable around 10⁶ to 10⁷ copies gDW⁻¹. The group specific qPCR showed high fluctuations, while the highest counts were reported for Methanomicrobiales and Methanosarcinales (10⁵ to 10⁸ copies per gram dry sediment), followed by Methanobacteriales (10³ to 10⁵ copies per gram dry sediment). A significant proportion of unidentified methanogens was found in almost every locality. Isotope analysis of δ¹³C showed that (CH₄) is produced mainly by hydrogenotrophic methanogens. We see no trend in the studied parameters along the Elbe River. The molecular data showed no spatial characteristics, while we found hotspots of the measured CH₄ processes (CH₄ production and oxidation) due to other local driving factors (e.g. carbon content). Thus, out results indicate that the observed variability of the CH₄ production and oxidation rates is only indirectly linked to the presence or quantities of different microbial guilds.

Introduction

Methane (CH₄) is a significant component of the aquatic carbon cycling and is involved in many biogeochemical and physical processes. Since biological methane production is mainly linked to wet anoxic soils and sediments, streams and rivers are one of many sources of atmospheric methane contributing 15–40 % to the total CH₄ efflux of wetlands and lakes (Stanley et al., 2016). Sediments are very important sites of riverine metabolism including their role in methanogenesis (Dahm et al., 1987). Generally, the mineralization of the organic matter under anaerobic conditions is carried out by several microbial organisms and results - in the absence of other electron acceptors like nitrate, iron, manganese etc. - in the release of CH₄ and CO₂ (Zeikus, 1983; Schink, 1997). Two major metabolic pathways of methanogens can be differentiated: acetoclastic (acetate conversion to CH₄ and CO₂) and hydrogenotrophic (H₂ and CO₂ to CH₄ and water). These two pathways can be discriminated using isotopic techniques due to diverse strength of isotopic fractionation during different methanogenic pathways, which lead to different isotopic composition of resulted CH₄ (Conrad, 2005).

The CH₄, which is formed in the sediments is subsequently released via diffusion, ebullition or through plants to the surface water or the atmosphere, where it is transported via advection or dispersion, respectively. Simultaneously, the CH₄ is subject of significant oxidation by CH₄ oxidizing bacteria during its transport in aquatic ecosystems. Moreover, all the processes involved in the aquatic CH₄ cycle are subject to large temporal and particularly spatial heterogeneity (Stanley et al., 2016). Understanding the variability of methane-related processes is key factor leading to more precise estimates of lotic ecosystems relevance in the global methane budget, which is recently based on scarce data (Bastviken et al., 2011).

Previous studies conducted in large rivers show, that rivers are mostly oversaturated in dissolved CH₄ with respect to the atmosphere equilibrium (i.e. rivers are a net source of CH₄ to the atmosphere). Frequently observed inverse relationship between discharge and CH₄ concentration is most probably given either by dilution (Kone et al., 2010; Anthony et al., 2012) or by higher temperature during low water periods. Increased temperature further enhances microbial activity and thus decreases oxygen levels (Borges et al., 2018). Notably, CH₄ emissions from rivers may reflect the properties of the surrounding catchments, such as topography, soil type and texture, land use, hydrological connectivity with wetlands and other anthropogenic activities as input of wastewaters (Jones and Mulholland, 1998; Silvennoinen et al., 2008; Yang et al., 2012; Borges et al., 2015). Generally, the studies considering CH₄ in large rivers were focused mainly on its concentration in surface water and its eventual flux to the atmosphere, but the data concerning the sediment related processes are missing (Teodoru et al., 2015; Barbosa et al., 2016). Hence only few data related to CH₄ processes in sediments of large rivers exists and almost no data comes from complex longitudinal studies, despite of fact that river sediments have great potential as source of CH₄ due to high methanogenic biomass (Buriánková et al., 2012).

Many studies examining CH₄ production in stream and rivers confirm that methanogens are ubiquitous members of the microbial community within river hyporheic sediments (e.g. Sanders et al., 2007; Trimmer et al., 2012; Chaudhary et al., 2017). Currently there are seven orders of methanogenic archaea described in the literature: Methanomicrobiales, Methanosarcinales, Methanocellales, Methanobacteriales, Methanococcales, Methanopyrales and Methanomassiliicoccales (Borrel et al., 2011, 2013; Borrel et al., 2014; Lang et al., 2015). Methanomicrobiales and the Methanosarcinales followed by Methanobacteriales dominate the methanogenic communities in freshwater sediments of lakes and rivers (Chan et al., 2005, Chaudhary et al. 2013). Moreover, Methanocellales are common in rice field soils or peats and have rarely been found in lake sediment (Scavino et al., 2013; Galand et al., 2005; Conrad et al., 2010). Our previous studies conducted in another European river (Sitka, Czech republic) revealed three major methanogenic groups using molecular techniques (denaturing gradient gel electrophoresis, terminal restriction fragment length polymorphism [T-RFLP], quantitative polymerase chain reaction [qPCR] and cloning): Methanosarcinales, Methanomicrobiales and Methanobacteriales (Buriánková et al., 2013; Brablcova et al., 2014; Chaudhary et al., 2014, 2017). Hence we focused our attempts to clarify the role of these groups using T-RFLP and qPCR in the present study.

In principle, one can raise four hypotheses to describe the turnover of organic matter in river sediments along the longitudinal profile of a river: either (1) decrease or (2) increase of the CH₄ related processes along the river flow; further (3) no correlation with environmental factors but hotspots of the microbial activities due to other local factors (e.g. carbon content etc.), and (4) no obvious impact resulting in comparable process rates along the riverbed. To validate which of these hypothesis may be applied for river systems, our aim was to describe the following processes and elucidate how our results could support the above-mentioned hypothesis: (i) methanogenic and methanotrophic potential of the sediments, (ii) an isotopic signal of CH₄ including determination of methanogenic pathways to the total CH₄ production, (iii) the community composition (TRFL-P) and quantification (qPCR) of archaea, methanogens and methanotrophs in the sediment samples. Samples for this study were taken during a large sampling campaign along the Elbe River carried out in October 2013, from Špindlerův Mlýn (km 8) to Geesthacht (km 948) (more detailed in Matoušů et al., 2018).