Flooded Soils

Conrad, Ralf; Frenzel, Peter

doi:10.1002/047126363x.agr344

Cited by 18 publications

(21 citation statements)

References 279 publications

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“…Wetland rice field soil has distinct biogeochemical cycles and microbial communities from upland soils (Conrad and Frenzel 2002;Kirk 2004), and rice roots growing in a submerged soil give the specific habitat for microorganisms through supply of oxygen and organic matter to the rhizosphere depending on the growth stage (Gotō & Tai, 1956;Andal et al 1956). The rice roots in the early growth-stage release oxygen to the surrounding soil making the rhizosphere oxic (Gotō and Tai 1956;Joshi et al 1973).…”

Section: Introductionmentioning

confidence: 99%

“…The rice roots in the early growth-stage release oxygen to the surrounding soil making the rhizosphere oxic (Gotō and Tai 1956;Joshi et al 1973). The rice rhizosphere becomes anoxic when roots grow older due to the enhanced microbial activities on the released organic substrates and sloughed-off cells over the oxygen supply (Conrad and Frenzel 2002). Kimura et al (1979) showed that the rice roots have specific rhizosphere effect on both aerobic and anaerobic microorganisms.…”

Section: Introductionmentioning

confidence: 99%

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Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Asiloglu

Honjo²,

Saka³

et al. 2015

Soil Science and Plant Nutrition

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Rice roots provide a specific habitat for microorganisms in the rhizosphere of a submerged field through supply of oxygen and organic matter. Many studies have focused on the microbial community in the rice rhizosphere, but less is still known about the microeukaryotic community structure of rice rhizosphere. This study explored the microeukaryotic community structure of a rice rhizosphere through denaturing gradient gel electrophoresis (DGGE) targeting 18S rRNA gene. The rice roots and the rhizosphere soil samples, which were collected from a field under rice-wheat rotation system, were separately analyzed. To characterize the rice rhizosphere-specific community, the bulk soil of rice field and the wheat rhizosphere samples were also examined. DGGE fingerprints showed that the microeukaryotic community of rice roots were distinct from the community of the bulk soil and showed a temporal shift with the growth stage. The rhizosphere soil community was distinct from the root and bulk soil communities, but this could be explained by that the root and bulk soil communities were shared in the rhizosphere. The rice rhizosphere community was also distinct from those in the wheat rhizosphere. Microeukaryotes that characterized the rice rhizosphere (roots and the rhizosphere soil) community could be affiliated to Polymyxa, flagellates, and oomycetes, which suggested that microeukaryotes with various ecological roles, e.g., parasites, bacterial grazers, and decomposers, inhabit the rice rhizosphere. The results showed that the rice root and its growth stages are key factors shaping the microeukaryotic community structure in the rhizosphere.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Asiloglu

Honjo²,

Saka³

et al. 2015

Soil Science and Plant Nutrition

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“…Most of the electrons from substrate oxidation flow into methanogenesis as predominant terminal reduction processes in rice paddies; however, iron oxide reduction is the second most important electron sink (Yao et al, 1999). Conceptually, iron oxide reduction occurs directly after flooding of rice field soil, and at interfaces such as water-soil and the rhizosphere, in which oxygen diffusion fuels the re-oxidation of iron(II) in steep chemical gradients (Conrad and Frenzel, 2002;Conrad, 2007). After flooding, oxidants (oxygen4nitrate4sulfate and iron(III) oxides) are reduced sequentially according to the thermodynamic theory (Ponnamperuma, 1972;Patrick and Reddy, 1978).…”

Section: Introductionmentioning

confidence: 99%

Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing

et al. 2009

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In anoxic rice field soil, ferric iron reduction is one of the most important terminal electron accepting processes, yet little is known about the identity of iron-reducing microorganisms. Here, we identified acetate-metabolizing bacteria by RNA-based stable isotope probing in the presence of iron(III) oxides as electron acceptors. After reduction of endogenous iron(III) for 21 days, isotope probing with 13 C-labeled acetate (2 mM) and added ferric iron oxides (ferrihydrite or goethite) was performed in rice field soil slurries for 48 and 72 h. Ferrihydrite reduction coincided with a strong suppression of methanogenesis (77%). Extracted RNA from each treatment was density resolved by isopycnic centrifugation, and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of 16S rRNA of bacterial and archaeal populations. In heavy, isotopically labeled RNAs of the ferrihydrite treatment, predominant 13 C-assimilating populations were identified as Geobacter spp. (B85% of all clones). In the goethite treatment, iron(II) formation was not detectable. However, Geobacter spp. (B30%), the d-proteobacterial Anaeromyxobacter spp. (B30%), and novel b-Proteobacteria were predominant in heavy rRNA fractions indicating that 13 C-acetate had been assimilated in the presence of goethite, whereas none were detected in the control heavy RNA. For the first time, active acetate-oxidizing iron(III)-reducing bacteria, including novel hitherto unrecognized populations, were identified as a functional guild in anoxic paddy soil.

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“…Methanogenic archaea are characteristic members of the microbial communities of anoxic wetland soils, e.g. flooded rice fields, where they are found in high abundance and diversity (Conrad and Frenzel, 2002). However, low numbers of culturable methanogenic archaea have also been found in oxic upland soils (Peters and Conrad, 1995; Küsel et al ., 1999).…”

Section: Introductionmentioning

confidence: 99%

Community analysis of methanogenic archaea within a riparian flooding gradient

Kemnitz¹,

Chin²,

Bodelier³

et al. 2004

Environmental Microbiology

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101

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Anoxic soils in river floodplains (or riparian soils) are a source of methane emission. However, little is known about the ecology and community structure of archaeal methanogenic microbes, which are a crucial component of methane flux in those habitats. We studied the archaeal community in the vertical profile of four different sites along the River Waal in the Netherlands. These sites differ in their annual flooding regime ranging from never or seldom to permanently flooded. The archaeal community structure has been characterized by terminal restriction fragment length polymorphism (T-RFLP) and comparative sequence analysis of the archaeal SSU rRNA gene and the mcrA gene. The latter gene codes for the alpha-subunit of methyl-coenzyme M reductase. Additionally, the potential methanogenic activity was determined by incubation of soil slurries under anoxic conditions. The community composition differed only slightly with the depth of the soil (0-20 cm). However, the diversity of archaeal SSU rRNA genes increased with the frequency of flooding. Terminal restriction fragment length polymorphism analysis of mcrA gene amplicons confirmed the results concerning methanogenic archaea. In the never and rarely flooded soils, crenarchaeotal sequences were the dominant group. In the frequently and permanently flooded soils, Methanomicrobiaceae, Methanobacteriaceae, Methanosarcinaceae and the uncultured Rice Clusters IV and VI (Crenarchaeota) were detectable independently from duration of anoxic conditions. Methanosaetaceae, on the other hand, were only found in the permanently and frequently flooded soils under conditions where concentrations of acetate were < 30 microM. The results indicate that methanogens as well as other archaea occupy characteristic niches according to the flooding conditions in the field. Methanosaetaceae, in particular, seem to be adapted (or proliferate at) to low acetate concentrations.

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Flooded Soils

Cited by 18 publications

References 279 publications

Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Community structure of microeukaryotes in a rice rhizosphere revealed by DNA-based PCR-DGGE

Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing

Community analysis of methanogenic archaea within a riparian flooding gradient

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