Succession of Bacterial Populations during Plant Residue Decomposition in Rice Field Soil

Abstract

The incorporation of rice residues into paddy fields strongly enhances methane production and emissions. Although the decomposition processes of plant residues in rice field soil has been documented, the structure and dynamics of the microbial communities involved are poorly understood. The purpose of the present study was to determine the dynamics of short-chain fatty acids and the structure of bacterial communities during residue decomposition in a rice field soil. The soil was anaerobically incubated with the incorporation of rice root or straw residues for 90 days at three temperatures (15, 30, and 45°C). The dynamics of fatty acid intermediates showed an initial cumulative phase followed by a rapid consumption phase and a low-concentration quasi-steady state. Correspondingly, the bacterial populations displayed distinct successions during residue decomposition. Temperature showed a strong effect on the dynamics of bacterial populations. Members of Clostridium (clusters I and III) were most dominant in the incubations, particularly in the early successions. Bacteroidetes and Chlorobi were abundant in the later successions at 15 and 30°C, while Acidobacteria were selected at 45°C. We suggest that the early successional groups are responsible for the decomposition of the easily degradable fraction of residues, while the late successional groups become more important in decomposing the less-degradable or resistant fraction of plant residues. The bacterial succession probably is related to resource availability during residue decomposition. The fast-growing organisms are favored at the beginning, while the slow-growing bacteria are better adapted in the later stages, when substrate availability is limiting.

Novel Clostridium populations involved in the anaerobic degradation of Microcystis blooms

“…The occurrence of these processes in the fermentation systems was confirmed by the presence of methanogenic Archaea (our unpublished data), which anaerobically utilize low molecular weight intermediates (for example, acetate or H 2 /CO 2 ) to produce CH 4 (Supplementary Figure S6). Furthermore, in this work, two dominant clusters succeeded each other more than four times during the incubation (at 25 1C and 35 1C), which is uncommon for bacterial communities in closed systems (Rui et al, 2009). The diverse Clostridium clusters could also have some degree of competition, especially at higher temperatures.…”

“…This anaerobic decomposition of organic material generally includes hydrolytic, homoacetogenic and methanogenic processes (for example, Rui et al, 2009). Many obligate or facultative anaerobic microbes may be involved in the anaerobic fermentation.…”

Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil

“…This cluster has been found being responsible for acetate production from CO 2 in rice root preparations incubated at 25 1C (Lu et al, personal communication). In addition, members of Clostridium cluster I have been found being responsible for the decomposition of easily degradable residue components and for the fast accumulation of fatty acids in a Chinese rice field soil during the early phase of incubation at 15 and 30 1C (Rui et al, 2009). Noll et al (2010) reported that Clostridium cluster I and III developed in parallel to the thermal (45 1C) turnover of acetate and propionate.…”

“…Nevertheless, it is noteworthy that Italian rice field soil in which the temperatures range typically from 15 1C to 30 1C (Schü tz et al, 1990) contains a methanogenic microbial community with acetogens and acetate oxidizers functioning under thermal conditions. Rice field soils from other geographical regions apparently also contain a thermophilic methanogenic community (Wu et al, 2006;Rui et al, 2009). Moreover, we were interested whether these bacteria could also become active as acetogens, when the temperature was decreased to 15 1C, which is at the low end of the temperature range in Italian rice fields in situ.…”

Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

“…The 50 ml reaction mixture contained 1 ml of DNA template (in 1:10 dilution of original extracts), 5 ml of 10Â buffer, 3.6 ml of 25 mM MgCl 2 , 1 ml of a 10 mM concentration of the dNTP, 2 ml of 10 mg L À1 bovine serum albumin, 1.6 ml of each primer (10 mM) and 2.5 U of Taq DNA polymerase (Takara). The thermal profile for amplification was as described previously (Rui et al, 2009). The 6-carboxyfluorescein-labeled PCR products were purified using an agarose gel DNA extraction kit (Takara) and digested at 37 C overnight by HaeIII (Fermentas, Canada), and the DNA fragments were size separated using a 3130xl Genetic Analyzer (Applied Biosystems) (Peng et al, 2008).…”