Variations in the microalgal structure in paddy soil in Osaka, Japan: comparison between surface and subsurface soils

Fujita, Yūkō; Nakahara, Hiroyuki

doi:10.1007/s10201-006-0167-z

Cited by 15 publications

(6 citation statements)

References 20 publications

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“…For example, one prominent DGGE fragment exclusively observed in rRNA-gene-based analysis (band 10J in Fig. 2 ) demonstrated a close relationship with planktonic green alga Desmodesumus (formerly Scenedesmus ), which is commonly observed in rice fields ( 14 ). This suggested that rice field soil stores not only the seeds of soil microeukaryotes but also that of aquatic microeukaryotes that proliferate when the soil is flooded for rice cultivation.…”

Section: Discussionmentioning

confidence: 99%

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

et al. 2014

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Irrigated rice field soil is subjected to frequent changes in oxygen status due to the water regime by agricultural management. In this study, the community response of microeukaryotes in rice field soil to the oxygen status was explored in a microcosm experiment under defined conditions. Water-saturated soil was incubated under a two-level factorial design of oxygen and organic enrichment with plant residue. The eukaryotic microbial community composition, which was either present or potentially active in the soils, was analyzed using denaturing gradient gel electrophoresis (DGGE) targeting the 18S rRNA gene or reverse-transcribed 18S rRNA. Oxygen availability was a primary factor shaping the microeukaryotic community in both DNA- and RNA-based analyses, revealing a shift within a week of incubation. Plant residue also affected the microeukaryotic community, which was more notable in the active community showing rRNA expression with time. Sequences of amplicons in DGGE bands indicated that protozoa (ciliates, flagellates, and amoebae) were the most prominent microeukaryotes in water-saturated rice field soil both in DNA- and RNA-based analyses. The use of a modified primer for soil protozoa suggested the functional importance of Heterolobosea amoeba in rice field soil, particularly in anoxic soil with organic enrichment.

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Section: Discussionmentioning

confidence: 99%

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

et al. 2014

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“…Thus surface soil at a depth of 0–5 cm is presumably suitable for the investigation of phototrophs. In fact, the investigations of the diversities of algae ( Fujita and Nakahara, 2006 ) and cyanobacteria ( Song et al ., 2005 ) are also conducted at such depth in paddy surface soil. AAnPB are found to be widespread in almost all extant ecosystems ( Yurkov, 2006 ).…”

Section: Discussionmentioning

confidence: 99%

Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO₂

Feng

Lin

Mao

et al. 2010

Microbial Biotechnology

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SummaryAerobic anoxygenic phototrophic bacteria (AAnPB) are recognized as an important group driving the global carbon cycling. However, the diversity of AAnPB in terrestrial environment remains largely unknown as well as their responses to the elevated atmospheric CO2. By using culture‐independent techniques, the diversity of AAnPB in paddy soil and the changes in response to the rising atmospheric CO2 were investigated within China FACE (Free‐air CO2 enrichment) platform. There was a phylogenetically diverse AAnPB community with large population size residing in paddy soil. The community structure of AAnPB in bulk and rhizospheric soils stayed almost identical, while the population size was higher in rhizospheric [2.0–2.5 × 108 copy number of pufM genes g−1 dry weight soil (d.w.s.)] than that in bulk (0.7–0.8 × 108 g−1 d.w.s.) soils. Elevated atmospheric CO2 appeared to significantly stimulate AAnPB abundance (up to 1.4–1.5 × 108 g−1 d.w.s.) and result in a higher AAnPB percentage in total bacterial community (from 0.5% up to 1.5%) in bulk soil, whereas no significant effect was observed in rhizospheric soil. Our results would extend the functional ecotypes of AAnPB and indicate that environmental changes associated with the rising atmospheric CO2 might affect AAnPB community in paddy soil.

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“…The 13 CO 2 product by anaerobic formate oxidation could stimulate the growth of photoautotrophic organisms under illumination. Cyanobacteria Oscillatoria and algae Scenedesmus were found to be the dominant photoautotrophic microbes in paddy soil (Fujita and Nakahara 2006;Asari et al 2008). 4a) and algae Scenedesmus (bands 12, 13, and 14 in Fig.…”

Section: Discussionmentioning

confidence: 92%

A phototrophy-driven microbial food web in a rice soil

et al. 2010

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Purpose Light is a major driver of primary productivity in most ecosystems on Earth. Phototrophic microorganisms harvest light to synthesize organic biomass for sustaining the global energy and carbon flow. However, the bottom-up model of phototrophic microorganisms as primary production and food source for higher trophic levels remains unclear in the terrestrial environment. Materials and methods Rice soil microcosms treated with different carbon sources ( 13 C-formate, 12 C-formate, or a control without formate) were incubated for 21 days under illumination. For each microcosm, genomic DNA were extracted and fractionated by isopycnic ultracentrifugation. Subsequently, the analyses were conducted on these samples with real-time quantitative PCR, PCR-denaturant gradient gel electrophoresis fingerprinting, and sequencing analysis of bacterial 16S rRNA, eukaryotic 18S rRNA, and photosynthetic functional genes. Results and discussion Our analysis indicated that formate carbon was assimilated by a subset of bacteria and eukaryotes. Based on molecular fingerprinting and sequencing analysis, the primary producers were determined to be the microorganisms affiliated with purple phototrophic bacteria, cyanobacteria, and algae. The detection of protozoa and fungi-like 18S rRNA gene sequences in the 13 C-enriched DNA fractions suggested that these organisms acted as consumers. They fed on nutrients derived from labeled phototrophic microorganisms. Conclusions Molecular evidence suggests that in the lightdriven microbial food web, the carbon flow from formate is initiated by phototrophic primary and secondary producers. Their biomasses subsequently sustain the growth of consumers in the rice soil.

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Variations in the microalgal structure in paddy soil in Osaka, Japan: comparison between surface and subsurface soils

Cited by 15 publications

References 20 publications

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO₂

A phototrophy-driven microbial food web in a rice soil

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Variations in the microalgal structure in paddy soil in Osaka, Japan: comparison between surface and subsurface soils

Cited by 15 publications

References 20 publications

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

Microeukaryotic Community and Oxygen Response in Rice Field Soil Revealed Using a Combined rRNA-Gene and rRNA-Based Approach

Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO2

A phototrophy-driven microbial food web in a rice soil

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Diversity of aerobic anoxygenic phototrophic bacteria in paddy soil and their response to elevated atmospheric CO₂