Seasonal dynamics of bacterial and archaeal methanogenic communities in flooded rice fields and effect of drainage.

Bjã¶Rn Breidenbach,Ralf Conrad

doi:10.3389/fmicb.2014.00752

Bjã¶Rn Breidenbach, Ralf Conrad

Open Access

https://doi.org/10.3389/fmicb.2014.00752

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Abstract

We studied the resident (16S rDNA) and the active (16S rRNA) members of soil archaeal and bacterial communities during rice plant development by sampling three growth stages (vegetative, reproductive and maturity) under field conditions. Additionally, the microbial community was investigated in two non-flooded fields (unplanted, cultivated with upland maize) in order to monitor the reaction of the microbial communities to non-flooded, dry conditions. The abundance of Bacteria and Archaea was monitored by quantitative PCR showing an increase in 16S rDNA during reproductive stage and stable 16S rRNA copies throughout the growth season. Community profiling by T-RFLP indicated a relatively stable composition during rice plant growth whereas pyrosequencing revealed minor changes in relative abundance of a few bacterial groups. Comparison of the two non-flooded fields with flooded rice fields showed that the community composition of the Bacteria was slightly different, while that of the Archaea was almost the same. Only the relative abundance of Methanosarcinaceae and Soil Crenarchaeotic Group increased in non-flooded vs. flooded soil. The abundance of bacterial and archaeal 16S rDNA copies was highest in flooded rice fields, followed by non-flooded maize and unplanted fields. However, the abundance of ribosomal RNA (active microbes) was similar indicating maintenance of a high level of ribosomal RNA under the non-flooded conditions, which were unfavorable for anaerobic bacteria and methanogenic archaea. This maintenance possibly serves as preparedness for activity when conditions improve. In summary, the analyses showed that the bacterial and archaeal communities inhabiting Philippine rice field soil were relatively stable over the season but reacted upon change in field management.

Highlights

Methane (CH4) is the second most important greenhouse gas after carbon dioxide (CO2) and has a 25 times larger global warming potential than CO2 (Forster et al, 2007)
Copy numbers of bacterial and archaeal 16S rDNA and rRNA were quantified at three different growth stages and in differently cropped fields (Figure 1)
Both bacterial and archaeal 16S rDNA copy numbers were highest during rice growth at reproductive stage, whereas the 16S rRNA copy numbers were constant during the whole season (Figures 1A,B)

Summary

Introduction

Methane (CH4) is the second most important greenhouse gas after carbon dioxide (CO2) and has a 25 times larger global warming potential than CO2 (Forster et al, 2007). The global budget of atmospheric CH4 is on the order of 500–600 Tg per year (Forster et al, 2007) and rice fields contribute in the range of 25–300 Tg CH4 per year (Chen and Prinn, 2005; Bridgham et al, 2013). In rice fields CH4 is produced as end product of the anaerobic degradation of organic matter by a complex microbial community consisting of hydrolytic and fermentative bacteria, and methanogenic archaea (Zinder, 1993; Conrad, 2007). Flooded rice fields have been used as a model system for studying the functioning of anoxic methanogenic microbial communities (Conrad, 2007, 2009). In rice fields methane is produced by two major physiological guilds, the acetotrophic and the hydrogenotrophic methanogens. In a recent study of a Korean rice field, numbers of archaea and methanogens changed by less than a factor of two throughout a cropping season (Lee et al, 2014)

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