Martin Rulik, Adam Bednarik, Vaclav Mach, Lenka Brablcova, Iva Buriankova, Pavlina Badurova and Kristyna Gratzova

Additional information is available at the end of the chapter http://dx. doi. org/10.5772/52718

1. Introduction

Methane (CH4) is an atmospheric trace gas present at concentration of about 1.8 ppmv, that represents about 15% of the anthropogenic greenhouse effect (Forster et al. 2007). The atmospheric CH4 concentration has increased steadily since the beginning of the industrial revolution (~ 0.7 ppmv) and is stabilized at ~1.8 ppmv from 1999 to 2005 (Forster et al. 2007). An unexpected increase in the atmospheric growth of CH4 during the year 2007 has been recently reported (Rigby et al. 2008), indicating that the sources and sinks of atmospheric CH4 are dynamics, evolving, and not well understood. Freshwater sediments, including wetlands, rice paddies and lakes, are thought to contribute 40 to 50 % of the annual atmospheric methane flux (Cicerone & Oremland 1988; Conrad 2009).

The river hyporheic zone, volume of saturated sediment beneath and beside streams containing some proportion of water from surface channel, plays a very important role in the processes of self-purification because the river bed sediments are metabolically active and are responsible for retention, storage and mineralization of organic matter transported by the surface water (Hendricks 1993; Jones & Holmes 1996, Baker et al. 1999, Storey et al.

1999, Fischer et al. 2005). The seemingly well-oxygenated hyporheic zone contains anoxic and hypoxic pockets („anaerobic microzones") associated with irregularities in sediment surfaces, small pore spaces or local deposits of organic matter, creating a ‘mosaic’ structure of various environments, where different microbial populations can live and different microbially mediated processes can occur simultaneously (Baker et al. 1999, Morrice et al.

2000, Fischer et al. 2005). Moreover, hyporheic-surface exchange and subsurface hydrologic flow patterns result in solute gradients that are important in microbial metabolism. Oxidation processes may occur more readily where oxygen is replenished by surface water infiltration, while reduction processes may prevail where surface-water exchange of oxygen

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is less, and the reducing potential of the environment is greater (Hendricks 1993). As water moves through the hyporheic zone, decomposition of the organic matter consumes oxygen, creating oxygen gradients along the flow path. Thus, compared to marine or lake surface sediments, where numerous studies on O2 profiles have showed that O2 concentrations become zero within less than 3 mm from the surface, the hyporheic sediment might be well — oxygenated habitats even up to the depth of 80 cm (e. g. Bretschko 1981, Holmes et al. 1994) . The extent of the oxygen gradient is determined by the interplay between flow path lengh, water velocity, the ratio of surface to ground water, and the amount and quality of organic matter. Organic matter decomposition in sediments is an important process in global and local carbon budgets as it ultimately recycles complex organic compounds from terrestrial and aquatic environments to carbon dioxide and methane. Methane is a major component in the carbon cycle of anaerobic aquatic systems, particularly those with low sulphate concentrations. Since a relatively high production of methane has been measured in river sediments (e. g. Schindler & Krabbenhoft 1998, Hlavacova et al. 2005, Sanders et al. 2007, Wilcock & Sorrell 2008, Sanz et al. 2011), we proposed that river sediments may act as a considerable source of this greenhouse gas which is important in global warming (Hlavacova et al. 2006).

Breakdown of organic matter and gas production are both results of well functioned river self-purification. This degrading capacity, however, requires intensive contact of the water with biologically active surfaces. Flow over various morphological features ranging in size from ripples and dunes to meanders and pool-riffle sequences controls such surface — subsurface fluxes. Highly permeable streambeds create opportunities for subsurface retention and long-term storage, and exchange with the surface water is frequent. Thus, study of the methane production within hyporheic zone and its subsequent emission to the atmosphere can be considered as a measure of mineralization of organic matter in the freshwater ecosystem and might be used in evaluation of both the health and environmental quality of the rivers studied.

Methane (CH4) is mostly produced by methanogenic archaea (Garcia et al. 2000, Chaban et al. 2006) as a final product of anaerobic respiration and fermentation, but there is also aerobic methane formation (e. g. Karl et al. 2008). Methanogenic archaea are ubiquitous in anoxic environments and require an extremely low redox potential to grow. They can be found both in moderate habitats such as rice paddies (Grosskopf et al. 1998a, b), lakes (Jurgens et al. 2000, Keough et al. 2003) and lake sediments (Chan et al. 2005), as well as in the gastrointestinal tract of animals (Lin et al. 1997) and in extreme habitats such as hydrothermal vents (Jeanthon et al. 1999), hypersaline habitats (Mathrani & Boone 1995) and permafrost soils (Kobabe et al. 2004, Ganzert et al. 2006). Rates of methane production and consumption in sediments are controlled by the relative availability of substrates for methanogenesis (especially acetate or hydrogen and carbon dioxide). The most important immediate precursors of methanogenesis are acetate and H2/CO2. The acetotrophic methanogens convert acetic acid to CH4 and CO2 while the hydrogenotrophic methanogens convert CO2 with H2 to CH4 (Conrad 2007).

Methane oxidation can occur in both aerobic and anaerobic environments; however, these are completely different processes involving different groups of prokaryotes. Aerobic methane oxidation is carried out by aerobic methane oxidizing bacteria (methanotrophs, MOB), while anaerobic methane oxidizers, discovered recently, thrive under anaerobic conditions and use sulphate or nitrate as electron donors for methane oxidation (e. g. Strous & Jetten 2004). MOB are a physiologically specialized group of methylotrophic bacteria capable of utilizing methane as a sole source of carbon and energy, and they have been recognized as major players in local and global elemental cycling in aerobic environments (Hanson & Hanson 1996, Murrell et al. 1998, Costelo & Lidstrom 1999, Costelo et al. 2002, McDonald et al. 2008). Aerobic MOB have been detected in a variety of environments, and in some they represent significant fractions of total microbial communities (e. g. Henckel et al. 1999; Carini et al, 2005, Trotsenko & Khmelenina 2005, Kalyuzhnaya et al. 2006). However, the data on the diversity and activity of methanotrophic communities from the river ecosystems are yet fragmentary. Methanotrophs play an important role in the oxidation of methane in the natural environment, oxidizing methane biologically produced in anaerobic environments by the methanogenic archaea and thereby reducing the amount of methane released into the atmosphere.

The present investigation is a part of a long-term study focused on organic carbon and methane dynamics and microbial communities in hyporheic zone of a Sitka, small lowland stream in Czech Republic. The overall purpose of this research was to characterize spatial distribution of both methanogens and methanotrophs within hyporheic sediments and elucidate the differences in methane pathways and methane production/consumption as well as methane fluxes and atmospheric emissions at different sites along a longitudinal profile of the stream.