scholarly journals Temporal shifts of nitrite reducing communities in a rice field soil in Ibague (Colombia)

2016 ◽  
Vol 34 (1) ◽  
pp. 82-91 ◽  
Author(s):  
Maribeb Castro-González ◽  
Amanda Lima
Keyword(s):  
Community Composition ◽  
Rice Field ◽  
Agricultural Soils ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Operational Taxonomic Units ◽  
Rice Field Soil ◽  
Uncultivated Soil ◽  
Abundance And Diversity ◽  
Key Steps

Denitrification and nitrification are microbial processes that regulate the cycle of nitrogen and nitrous oxide, which is considered an important greenhouse gas. Rice field soils have been known to have strong denitrifying activities; however, the microorganism structure that is responsible for denitrification and the temporal variation of these communities in the agricultural soils of Ibague (Colombia) is not well known. In this study, the denitrifying community composition was compared between a rice field soil and an uncultivated soil at three different times during the year using a terminal restriction fragment length polymorphism analysis of the nirS functional gene, which codes the enzyme that reduces nitrite, one of the key steps in the denitrification process. The results showed changes in the richness, relative abundance and diversity of the operational taxonomic units between the soils and sampling times. The canonical correspondence analysis indicated that the moisture and the pH were the environmental factors that explained the observed changes in the nirS-type denitrifiers' community composition in the studied soils.

scholarly journals Identification of Acetate-Assimilating Microorganisms under Methanogenic Conditions in Anoxic Rice Field Soil by Comparative Stable Isotope Probing of RNA

2006 ◽  
Vol 73 (1) ◽  
pp. 101-109 ◽  
Author(s):  
Tomoyuki Hori ◽  
Matthias Noll ◽  
Yasuo Igarashi ◽  
Michael W. Friedrich ◽  
Ralf Conrad
Keyword(s):  
Stable Isotope ◽  
Rice Field ◽  
Ferric Iron ◽  
Stable Isotope Probing ◽  
Polymorphism Analysis ◽  
Field Soil ◽  
Bacterial Populations ◽  
Density Fractions ◽  
Reverse Transcription Pcr ◽  
Rice Field Soil

ABSTRACT Acetate is the most abundant intermediate of organic matter degradation in anoxic rice field soil and is converted to CH4 and/or CO2. Aceticlastic methanogens are the primary microorganisms dissimilating acetate in the absence of sulfate and reducible ferric iron. In contrast, very little is known about bacteria capable of assimilating acetate under methanogenic conditions. Here, we identified active acetate-assimilating microorganisms by using a combined approach of frequent label application at a low concentration and comparative RNA-stable isotope probing with 13C-labeled and unlabeled acetate. Rice field soil was incubated anaerobically at 25°C for 12 days, during which 13C-labeled acetate was added at a concentration of 500 μM every 3 days. 13C-labeled CH4 and CO2 were produced from the beginning of the incubation and accounted for about 60% of the supplied acetate 13C. RNA was extracted from the cells in each sample taken and separated by isopycnic centrifugation according to molecular weight. Bacterial and archaeal populations in each density fraction were screened by reverse transcription-PCR-mediated terminal restriction fragment polymorphism analysis. No differences in the bacterial populations were observed throughout the density fractions of the unlabeled treatment. However, in the heavy fractions of the 13C treatment, terminal restriction fragments (T-RFs) of 161 bp and 129 bp in length predominated. These T-RFs were identified by cloning and sequencing of 16S rRNA as from a Geobacter sp. and an Anaeromyxobacter sp., respectively. Apparently these bacteria, which are known as dissimilatory iron reducers, were able to assimilate acetate under methanogenic conditions, i.e., when CO2 was the predominant electron acceptor. We hypothesize that ferric iron minerals with low bioavailability might have served as electron acceptors for Geobacter spp. and Anaeromyxobacter spp. under these conditions.

scholarly journals Effects of Amendment with Ferrihydrite and Gypsum on the Structure and Activity of Methanogenic Populations in Rice Field Soil

2002 ◽  
Vol 68 (5) ◽  
pp. 2484-2494 ◽  
Author(s):  
Tillmann Lueders ◽  
Michael W. Friedrich
Keyword(s):  
Rice Field ◽  
Small Subunit ◽  
Strong Increase ◽  
Polymorphism Analysis ◽  
Ssu Rrna ◽  
The Novel ◽  
Field Soil ◽  
Sulfate Reducing ◽  
Rice Field Soil ◽  
Reducing Bacteria

ABSTRACT Methane emission from paddy fields may be reduced by the addition of electron acceptors to stimulate microbial populations competitive to methanogens. We have studied the effects of ferrihydrite and gypsum (CaSO4 · 2H2O) amendment on methanogenesis and population dynamics of methanogens after flooding of Italian rice field soil slurries. Changes in methanogen community structure were followed by archaeal small subunit (SSU) ribosomal DNA (rDNA)- and rRNA-based terminal restriction fragment length polymorphism analysis and by quantitative SSU rRNA hybridization probing. Under ferrihydrite amendment, acetate was consumed efficiently (<60 μM) and a rapid but incomplete inhibition of methanogenesis occurred after 3 days. In contrast to unamended controls, the dynamics of Methanosarcina populations were largely suppressed as indicated by rDNA and rRNA analysis. However, the low acetate availability was still sufficient for activation of Methanosaeta spp., as indicated by a strong increase of SSU rRNA but not of relative rDNA frequencies. Unexpectedly, rRNA amounts of the novel rice cluster I (RC-I) methanogens increased significantly, while methanogenesis was low, which may be indicative of transient energy conservation coupled to Fe(III) reduction by these methanogens. Under gypsum addition, hydrogen was rapidly consumed to low levels (∼0.4 Pa), indicating the presence of a competitive population of hydrogenotrophic sulfate-reducing bacteria (SRB). This was paralleled by a suppressed activity of the hydrogenotrophic RC-I methanogens as indicated by the lowest SSU rRNA quantities detected in all experiments. Full inhibition of methanogenesis only became apparent when acetate was depleted to nonpermissive thresholds (<5 μM) after 10 days. Apparently, a competitive, acetotrophic population of SRB was not present initially, and hence, acetotrophic methanosarcinal populations were less suppressed than under ferrihydrite amendment. In conclusion, although methane production was inhibited effectively under both mitigation regimens, different methanogenic populations were either suppressed or stimulated, which demonstrates that functionally similar disturbances of an ecosystem may result in distinct responses of the populations involved.

scholarly journals Response of the protistan community of a rice field soil to different oxygen tensions

2017 ◽  
Vol 93 (5) ◽  
Author(s):  
Yuriko Takenouchi ◽  
Kazufumi Iwasaki ◽  
Jun Murase
Keyword(s):  
Rice Field ◽  
Field Soil ◽  
Rice Field Soil ◽  
Oxygen Tensions

scholarly journals Streptacidiphilus oryzae sp. nov., an actinomycete isolated from rice-field soil in Thailand

2006 ◽  
Vol 56 (6) ◽  
pp. 1257-1261 ◽  
Author(s):  
Liming Wang ◽  
Ying Huang ◽  
Zhiheng Liu ◽  
Michael Goodfellow ◽  
Carlos Rodríguez
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Rice Field ◽  
Gene Tree ◽  
Morphological Properties ◽  
Rrna Gene ◽  
New Taxon ◽  
Field Soil ◽  
Rice Field Soil

The taxonomic position of ten acidophilic actinomycetes isolated from an acidic rice-field soil was established using a polyphasic approach. 16S rRNA gene sequences determined for the isolates were aligned with corresponding sequences of representatives of the genera Kitasatospora, Streptacidiphilus and Streptomyces and phylogenetic trees were inferred using four tree-making algorithms. The isolates had identical sequences and formed a distinct branch at the periphery of the Streptacidiphilus 16S rRNA gene tree. The chemotaxonomic and morphological properties of representative isolates were consistent with their assignment to the genus Streptacidiphilus. The isolates shared nearly identical phenotypic profiles that readily distinguished them from representatives of the established species of Streptacidiphilus. It is evident from the genotypic and phenotypic data that the isolates form a homogeneous group that corresponds to a novel species in the genus Streptacidiphilus. The name proposed for this new taxon is Streptacidiphilus oryzae sp. nov.; the type strain is strain TH49T (=CGMCC 4.2012T=JCM 13271T).

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