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PubMed2002

Propionate formation by Opitutus terrae in pure culture and in mixed culture with a hydrogenotrophic methanogen and implications for carbon fluxes in anoxic rice paddy soil.

Propionate-forming bacteria seem to be abundant in anoxic rice paddy soil, but biogeochemical investigations show that propionate is not a correspondingly important intermediate in carbon flux in this system. Mixed cultures of Opitutus terrae strain PB90-1, a representative propionate-producing bacterium from rice paddy soil, and the hydrogenotrophic Methanospirillum hungatei strain SK maintained hydrogen partial pressures similar to those in the soil. The associated shift away from propionate formation observed in these cultures helps to reconcile the disparity between microbiological and biogeochemical studies.

Anaerobiosis↗

PubMed1999

Comparative phylogenetic assignment of environmental sequences of genes encoding 16S rRNA and numerically abundant culturable bacteria from an anoxic rice paddy soil.

We used both cultivation and direct recovery of bacterial 16S rRNA gene (rDNA) sequences to investigate the structure of the bacterial community in anoxic rice paddy soil. Isolation and phenotypic characterization of 19 saccharolytic and cellulolytic strains are described in the accompanying paper (K.-J. Chin, D. Hahn, U. Hengstmann, W. Liesack, and P. H. Janssen, Appl. Environ. Microbiol. 65:5042-5049, 1999). Here we describe the phylogenetic positions of these strains in relation to 57 environmental 16S rDNA clone sequences. Close matches between the two data sets were obtained for isolates from the culturable populations determined by the most-probable-number counting method to be large (3 x 10(7) to 2.5 x 10(8) cells per g [dry weight] of soil). This included matches with 16S rDNA similarity values greater than 98% within distinct lineages of the division Verrucomicrobia (strain PB90-1) and the Cytophaga-Flavobacterium-Bacteroides group (strains XB45 and PB90-2), as well as matches with similarity values greater than 95% within distinct lines of descent of clostridial cluster XIVa (strain XB90) and the family Bacillaceae (strain SB45). In addition, close matches with similarity values greater than 95% were obtained for cloned 16S rDNA sequences and bacteria (strains DR1/8 and RPec1) isolated from the same type of rice paddy soil during previous investigations. The correspondence between culture methods and direct recovery of environmental 16S rDNA suggests that the isolates obtained are representative geno- and phenotypes of predominant bacterial groups which account for 5 to 52% of the total cells in the anoxic rice paddy soil. Furthermore, our findings clearly indicate that a dual approach results in a more objective view of the structural and functional composition of a soil bacterial community than either cultivation or direct recovery of 16S rDNA sequences alone.

Anaerobiosis↗

PubMed2003

Changes in soil microbial biomass and Zn extractability over time following zn addition to a paddy soil.

A laboratory incubation study was conducted using a paddy soil spiked with two quantities of Zn as soluble Zn(NO3)2 and unamended controls. Three single extractants (1 M ammonium acetate (pH 7.0), 0.43 M acetic acid and 0.05 M EDTA) were used to assess the bioavailability of Zn. Biological community assessments were made microbial biomass (chloroform fumigation), soil basal respiration and dehydrogenase activity. During the 84-day period of the experiment, addition of Zn at both 500 and 1,000 mg kg(-1) had little detectable effect on soil pH. The concentration of NH4OAc-extractable Zn decreased rapidly within the initial six weeks. The concentration of HOAc-extractable Zn showed no decrease during 84 days incubation. EDTA-extractable Zn was greater than NH4OAc- and HOAc-extractable fractions, and showed a similar trend to NH4OAc-extractable after incubation. Microbial biomass, soil basal respiration and dehydrogenase activity all decreased over time during 84 days incubation. Addition of Zn resulted in a significant increase in specific respiration (qCO2). Microbial biomass and dehydrogenase activity did not appear to be influenced by added Zn, probably due to the strong buffering capacity of the soil. The Zn extracted by EDTA, HOAc and NH4OAc showed close relationships with each other (p < 0.001). Zinc extracted by 0.05 M EDTA and NH4OAc were highly correlated with soil basal respiration and specific respiration rate (p < 0.01). The results suggest that NH4OAc-extractable Zn combined with soil specific respiration could be used as parameters for risk assessment.

Acetates↗

PubMed2000

Detection of Desulfotomaculum in an Italian rice paddy soil by 16S ribosomal nucleic acid analyses.

Two specific primers were developed for the amplification of 16S rRNA genes of Desulfotomaculum lineage 1 to detect members of the genus Desulfotomaculum in rice field soil. The combination of both primers in PCR allowed the specific amplification and cloning of ten 16S rDNA sequences of this group from rice paddy soil DNA extracts. The phylogenetic analysis showed that these sequences formed a deeply branching cluster within Desulfotomaculum lineage 1, together with two sequences from the database and two sequences from a hydrocarbon-contaminated aquifer. Dissimilarity values to validly described species, including recently isolated strains of Desulfotomaculum from rice paddy microcosms, were higher than 12%. Within the new cluster the cloned sequences formed three separate groups which were each represented by at least two sequences with identities of >/=99% while one sequence represented an additional group. The sequences should represent sulfate-reducing organisms because they clearly fell into the physiologically coherent group of Gram-positive sulfate reducers. The relative abundance of bacteria of the Desulfotomaculum lineage 1 in rice paddy soil and root samples was estimated with rRNA dot blot hybridizations of extracted RNA. The relative RNA content of Desulfotomaculum lineage 1 was 0.55% in the bulk soil and 1% in the rice root samples, respectively, of the total 16S rRNA content (probe Eub338). Hybridization of rRNA with a probe targeting the new cluster represented by the cloned sequences confirmed the high abundance of 16S rRNA sequences from this cluster in the rice paddy field samples. Another hybridization probe detecting Desulfotomaculum acetoxidans and two closely related Desulfotomaculum isolates from rice paddy soil indicated that these bacteria were less abundant.

Journal Article↗

PubMed2000

[Phosphate adsorption characteristics of paddy soils derived from main parent materials in Guangdong Province].

Isothermal adsorption experiment of phosphate on paddy soils drived from five different parent materials in Guangdong Province was carried out. The result showed that the adsorption data of different test soils could be simulated well by Langmuir, Freundlich and Temkin equations, and the Langmuir equation fitted the data best (correlation coefficient r: 0.995-0.999..). As a value of phosphate adsorption characteristics, the product of phosphate adsorption maximum (Xm)and sorption intensity factor(K) calculated by Langmuir equation could be a comprehensive index to characterize the potential phosphate adsorption by paddy soil, and could indicate the order of applying phosphate. The result also indicated that there exists two types of sorption region on the soils tested.

Absorption↗

PubMed1980

Enrichment of Propionibacterium in paddy soil by addition of various organic substances.

Enrichment of Propionibacterium and production of propionic acid in paddy soil after addition of glucose, casamino acids, or Na-lactate, respectively, were investigated. Only in the case of Na-lactate, both enrichment of Propionibacterium (74% of total anaerobes isolated) and production of large amounts of propionic acid were observed. These results suggest that lactate may support the growth of Propionibacterium in paddy soil.

Amino Acids↗

PubMed2004

Anaerobic 2-propanol degradation in anoxic paddy soil and the possible role of methanogens in its degradation.

The anaerobic degradation of 2-propanol in anoxic paddy soil was studied with soil cultures and a 2-propanol-utilizing methanogen. Acetone was the first and the major intermediate involved in the methanogenic degradation of 2-propanol. Analyses with a methanogenesis inhibitor, bacteria antibiotics, and the addition of H2 to the gas phase revealed that 2-propanol oxidation to acetone directly occurred using 2-propanol-utilizing methanogens, but not with H2-producing syntrophic bacteria, for which the removal of acetone is required for complete 2-propanol oxidation. The 2-propanol-utilizing strain IIE1, which is phylogenetically closely related to Methanoculleus palmolei, was isolated from paddy soil, and the potential role of the strain in 2-propanol degradation was investigated. 2-Propanol is one of the representative fermentation intermediates in anaerobic environments. This is the first report on the anaerobic 2-propanol degradation process.

2-Propanol↗

PubMed2005

Sorption of pyrene on two paddy soils and their particle-size fractions.

In the present study, the sorption of pyrene on two kinds of bulk paddy soils, Gleyic Stagnic Anthrosols, and Ferric accumulic Stagnic Anthrosols as well as their particle-size fractions was investigated. The sorption isotherms fitted well with Freundlich equation. For both soils, the clay fraction( < 2 microm) and coarse sand fraction(2000-250 microm) had higher sorption capacity than fine sand fraction(250-20 microm) and silt fraction(20-2 microm). The log Koc values obtained of each soil and its particle-size fractions were similar, proving that SOM content was a key factor affecting pyrene sorption. The Kd values showed a significant correlation with contents of dithionite-extractable Fe in both paddy soils and a good relationship with CEC in Gleyic Stagnic Anthrosols, indicating possible effects of surface properties of particle-size fractions on the sorption of pyrene.

Adsorption↗

PubMed2003

[Effects of cropping systems on nitrous oxide emissions from paddy soils during the rice-growing season].

Cropping systems influence nitrous oxide (N2O) emissions from agricultural soils. Effects of 3 rice-based cropping systems on N2O emissions from paddy soils in pot experiment were investigated with closed chambers in triplicate. The results demonstrated that the seasonal N2O emission rate of the rice pot under rice-wheat cropping system was obviously higher than that of the early rice pot under double rice-wheat system, being 4.21 and 2.17 kg.hm-2, respectively. No distinct difference was observed between the seasonal average fluxes, which were 116.9 and 117.6 micrograms.m-2.h-1 respectively. Both of above mentioned seasonal average fluxes were greatly higher than that of the late rice pot under early rice-late rice-wheat cropping system and of rice pot under rice-flooding fallow system, being 67.0 and 42.1 micrograms.m-2.h-1 respectively. More than 91% of the seasonal emission was focused on the first half growing period both in the rice season in rice-wheat system and in the early rice season in double rice-wheat system in which the previous cropping was upland wheat. 91% of the seasonal emission was focused on the water drainage period including the mid-season aeration and final drainage in the late rice season in double rice-wheat system in which the previous cropping was lowland rice. The results implied that cropping system and water status of previous cropping impacted N2O emission from paddy soil.

Crops, Agricultural↗

PubMed2000

A deeply branched novel phylotype found in Japanese paddy soils.

Novel 16S rDNA clones which possibly constitute a sister clade from the two known archaeal lineages, Crenarchaeota and Euryarchaeota, were found in paddy soil environments. Overall signature sequences showed that the clone sequences shared a majority of signature sequence features with the Archaea and Eukarya. However, there were at least nine nucleotides which distinguished the novel clones from the domains Archaea and Eukarya. Phylogenetic trees, drawn by maximum-parsimony, neighbour-joining and maximum-likelihood methods, also supported the unique phylogenetic position of the clones. Both signature sequence and phylogenetic analyses strongly suggest that the novel organisms constitute a new group and their phylogenetic positions are distant from the Crenarchaeota and Euryarchaeota. A specific primer set was designed to detect the presence of the novel group of organisms in terrestrial environments. Specific DNA fragments were amplified from all paddy soil DNAs, suggesting that the novel organisms are widely distributed in rice paddy fields in Japan.

Archaea↗

PubMed2003

[Relationship between CH4 and N2O emissions and related microorganism populations in paddy soils under different water management regimes].

Methanogens, methanotrophs, nitrifiers and denitrifiers are the important microorganisms in the production and consumption of CH4 and N2O in soil. In order to understand the microbial processes related to the two greenhouse gases in paddy soil, the four bacteria groups in phaeozem (Hailun) and burozem (Shenyang) were surveyed during rice growth season by using MPN counting technique. The CH4 and N2O emissions were measured with closed chamber method. Two different water management regimes, i.e., continual irrigation and intermittent irrigation, were used for the two paddy soils. The results of multiple regression analysis showed that there was a significantly positive correlation between CH4 emission and methanogen population in both phaeozem and burozem under two water management regimes. In the soil of Shenyang, there was a significantly positive correlation between CH4 emission and methanotropli population. The N2O emission was significantly correlated to the denitrifier population in both phaeozem and burozem under intermittent irrigation, and in the soil of Shenyang, there was a significantly positive correlation between N2O emission and nitrifier population under two water managements.

Methane↗

PubMed2001

Selenium geochemistry of paddy soils in Yangtze River Delta.

Selenium (Se) content both in total and bioavailable forms were very low (25-35 and 9.5 micrograms/kg, respectively) in waterlogged paddy soils in the central Yangtze River Delta. This was due to changes in geochemistry and the inherent properties of the parent materials of these lowland paddy soils. The very low Se content (23 micrograms/kg) in the parent material resulted in low total Se content in the soil. The main chemical changes under long-term waterlogged conditions are depletion of molecular oxygen, decrease of redox potential, and reduction of Fe (III) to Fe (II) and SeO3(2-) to Se0. This led to low availability of Se in soils, and subsequently low Se content (29 micrograms/kg) in brown rice grain produced in this region. It has been suspected that low Se content in staple food might be one of the major reasons for a high infection rate of the intestine and stomach cancers and the higher death rate caused by these diseases in the region. Foliage spray of Na2SeO3 at early heading stage of rice plant growth improved the Se content of brown rice grain, hull, and straw, and would improve human and animal health.

Biological Availability↗

PubMed2003

[Effect of long-term fertilization practices on mobility of phosphorus in a Huangnitu paddy soil receiving low P input in the Taihu Lake region, Jiangsu Province].

Analysis of mobile forms of phosphorus of a Huangnitu, a typical paddy soil in the Taihu Lake region, Jiangsu was conducted. The soil has been put into a scheme of longterm fertilization treatments for 13 years. Total P content varied in arrange of 0.3-0.5 g.kg-1 under a range of total P fertilizer input of 0-53 kg/(hm2.a). As estimated from the total P pool values by mass balance principle, the soil had been subjected to water loss of P 2-8 kg/(hm2.a), with that under chemical fertilizers only being the biggest. The ratio of soluble P to the total was in a range of 0.2%-0.4%, without significant influence by the different fertilization schemes. While chemical fertilizer plus pig slurry manure applications had remarkably enhanced the resin-P pool by 20-40 mg.kg-1, P mobilization was not observed due to combined application of chemical fertilizers and straw amendments despite of the increase of the SOM. Therefore, P water loss in paddy soils might have active under continuous chemical fertilization alone in agriculture of this region and could not be accounted for by dissolution in water and subsequent runoff migration. For reducing the present prominent non point source pollution of N and P in the region, it is suggested that chemical fertilizers are applied in combination with an appropriate amount of manure or straw return for reducing soil P loss and, in turn, the non-point source pollution loading.

Crops, Agricultural↗

PubMed2006

Remediation of cadmium contamination in paddy soils by washing with chemicals: selection of washing chemicals.

The efficiencies of neutral salts, strong acids, and chelates were tested for extracting cadmium (Cd) from three paddy soils. The higher the selectivity of the cations of the added neutral salts toward soil adsorption sites, the lower the pH in the extracts and the more soil Cd could be extracted. In addition, soil carbon and nitrogen contents and mineral composition were closely associated with the amount of Cd extracted. Calcium chloride and iron(III) chloride were selected as wash chemicals to restore Cd-contaminated paddy soils in situ. Washing with calcium chloride led to the formation of Cd chloride complexes, enhancing Cd extraction from the soils. The washing also substantially decreased soil levels of exchangeable and acid-soluble Cd, which are the major forms of bioavailable Cd for rice (Oryza sativa L.). The optimum conditions for in situ soil washing were also determined for calcium chloride.

Acids↗

PubMed2006

Reducing phosphorus release from paddy soils by a fly ash-gypsum mixture.

A mixture of fly ash and phospho-gypsum (50:50, wtwt(-1)) was selected to study its potential to supply Ca and Si to rice while reducing B toxicity. We expected that the high Ca content in this mixture might convert water-soluble P to less soluble forms and thereby reduce the loss of soil P to surface runoff. The mixture was applied at rates of 0, 20, 40, and 60 Mgha(-1) in two paddy soils of contrasting textures (silt loam in Yehari and loamy sand in Daegok). The mixture significantly reduced water-soluble phosphate (W-P) in the surface soils by shifting from W-P and iron bound-P (Fe-P) to calcium bound-P (Ca-P) and aluminum bound-P (Al-P) during rice cultivation in both soils. Lancaster and Mehlich 3 extractable P increased significantly with application rate due to high contents of P and Si in the mixture. Mixtures of fly ash and phospho-gypsum should reduce P loss from rice paddy soils and increase soil fertility.

Calcium↗

PubMed2001

Effects of butachlor on microbial populations and enzyme activities in paddy soil.

This paper reports the influences of the herbicide butachlor (n-butoxymethlchloro -2', 6'-diethylacetnilide) on microbial populations, respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that the number of actinomycetes declined significantly after the application of butachlor at different concentrations ranging from 5.5 microg g(-1) to 22.0 microg g(-1) dried soil, while that of bacteria and fungi increased. Fungi were easily affected by butachlor compared to the bacteria. The growth of fungi was retarded by butachlor at higher concentrations. Butachlor however, stimulated the growth of anaerobic hydrolytic fermentative bacteria, sulfate-reducing bacteria (SRB) and denitrifying bacteria. The increased concentration of butachlor applied resulted in the higher number of SRB. Butachlor inhibited the growth of hydrogen-producing acetogenic bacteria. The effect of butachlor varied on methane-producing bacteria (MPB) at different concentrations. Butachlor at the concentration of 1.0 microg g(-1) dried soil or less than this concentration accelerated the growth of MPB, while at 22.0 microg g(-1) dried soil showed an inhibition. Butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 microg g(-1) dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed during the period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

Acetanilides↗

PubMed2002

Effects of butachlor on microbial enzyme activities in paddy soil.

This paper reports the influences of the herbicide butachlor (n-butoxymethl-chloro-2', 6'-diethylacetnilide) on microbial respiration, nitrogen fixation and nitrification, and on the activities of dehydrogenase and hydrogen peroxidase in paddy soil. The results showed that after application of butachlor with concentrations of 5.5 micrograms/g dried soil, 11.0 micrograms/g dried soil and 22.0 micrograms/g dried soil, the application of butachlor enhanced the activity of dehydrogenase at increasing concentrations. The soil dehydrogenase showed the highest activity on the 16th day after application of 22.0 micrograms/g dried soil of butachlor. The hydrogen peroxidase could be stimulated by butachlor. The soil respiration was depressed within a period from several days to more than 20 days, depending on concentrations of butachlor applied. Both the nitrogen fixation and nitrification were stimulated in the beginning but reduced greatly afterwards in paddy soil.

Acetanilides↗

PubMed1997

Concentration of global fallout 99Tc in rice paddy soils collected in Japan.

Analysis of global fallout 99Tc in environmental samples should provide useful information for predicting the nuclide behaviour under natural conditions which is important from the viewpoint of radioecology. Concentrations of 99Tc in rice paddy soils collected in Japan have been studied. After chemical separation, 99Tc in the final solution was measured by ICP-MS. The activity ratio of 99Tc/137Cs was used to understand the 99Tc behaviour in the environment because the fission yields of 99Tc and 137Cs from 235U or 239Pu are almost the same. The theoretical activity ratio from fission which is calculated now is about 3.0 x 10(-4). Our results showed that the range of activity ratios of 99Tc/137Cs in the soil samples was (2.0-5.2) x 10(-3); these ratios were one order of magnitude higher than the theoretical one. 99Tc has been accumulating in rice paddy soil like 137Cs has, although their mechanisms might differ. One of the reasons for the high ratio in the surface soil might be the ratios in the atmospheric samples, which have increased from the order of 10(-3) to 10(-2) (García-León et al., 1993).

Journal Article↗