Rice Paddy Field Soil Research Articles

Effect of cultivation practice on the heavy metal content of rice paddy field soil in Western Ghats of India

Effect of cultivation practice on the heavy metal content of rice paddy field soil in Western Ghats of India

Bioaugmentation of microbial electrolysis cells with Geobacter sulfurreducens YM18 for enhanced hydrogen production from starch

Double-chamber microbial electrolysis cells (MECs) were operated using starch-based medium as the anolyte and rice paddy-field soil as the anode inoculum, and hydrogen production from the cathode chamber was examined. In order to enhance current generation and hydrogen production, the anode chamber was bioaugmented with Geobacter sulfurreducens strain YM18, and its effects were evaluated based on the performances of non-bioaugmented controls. Results show that the bioaugmented MEC generated threefold greater current during one-month operation and produced sixfold greater amounts of hydrogen than those of the non-bioaugmented control. Quantitative PCR and metabarcoding analyses confirmed successful colonization of anode surfaces with YM18, suggesting the utility of bioaugmentation with YM18 for enhancing the performance of bioelectrochemical systems, including MECs treating biomass wastes.

An iron corrosion-assisted H2-supplying system: a culture method for methanogens and acetogens under low H2 pressures

H2 is an important fermentation intermediate in anaerobic environments. Although H2 occurs at very low partial pressures in the environments, the culture and isolation of H2-utilizing microorganisms is usually carried out under very high H2 pressures, which might have hampered the discovery and understanding of microorganisms adapting to low H2 environments. Here we constructed a culture system designated the “iron corrosion-assisted H2-supplying (iCH) system” by connecting the gas phases of two vials (one for the iron corrosion reaction and the other for culturing microorganisms) to achieve cultures of microorganisms under low H2 pressures. We conducted enrichment cultures for methanogens and acetogens using rice paddy field soil as the microbial source. In the enrichment culture of methanogens under canonical high H2 pressures, only Methanobacterium spp. were enriched. By contrast, Methanocella spp. and Methanoculleus spp., methanogens adapting to low H2 pressures, were specifically enriched in the iCH cultures. We also observed selective enrichment of acetogen species by the iCH system (Acetobacterium spp. and Sporomusa spp.), whereas Clostridium spp. predominated in the high H2 cultures. These results demonstrate that the iCH system facilitates culture of anaerobic microorganisms under low H2 pressures, which will enable the selective culture of microorganisms adapting to low H2 environments.

Denitrification in paddy soil as a cooperative process of different nitrogen oxide reducers, revealed by metatranscriptomic analysis of denitrification-induced soil microcosm

ABSTRACT Denitrification in paddy soils is an environmentally important reaction, which reduces leaching or emission of nitrogen pollutants. This reaction has long been considered to be driven by typical denitrifiers mostly belonging to Alpha-, Beta-, and Gammaproteobacteria. Our recent metatranscriptomic analysis of rice paddy field soil suggested that paddy soil denitrification is a cooperative process of different nitrogen oxide reducers, i.e., NO2 −, NO, and N2O reducers. However, it was not clear whether denitrification actually occurred in the soil samples examined, which was not easy to confirm under field conditions. Therefore, we carried out this study (1) to establish a soil microcosm with the steady activity of denitrification, and (2) to identify microbial communities, which drive each step of denitrification in the soil microcosm by metatranscriptomic analysis. As a result, a chemostat-type soil microcosm with steady denitrification activity was successfully established. Metatranscriptomic analysis of the denitrification-induced soils, together with supportive PCR-based clone library analysis, indicated that the community compositions of microbial drivers at each step of denitrification are different from each other. The results verified our above-mentioned suggestion of denitrification in paddy soil being a cooperative process of different nitrogen oxide reducers. Microbial communities of the cooperative denitrification in paddy soil might be established, and might have advantages to eliminate/detoxify microbiologically and/or chemically generated nitrogen oxides smoothly under changing paddy soil environments.

Electricity Generation in Microbial Fuel Cell (MFC) by Bacterium Isolated from Rice Paddy Field Soil

Microbial fuel cell (MFC) is an alternative approach in generating renewable energy by utilising bacteria that will oxidize organic or inorganic substrates, producing electrons yielded as electrical energy. Different species of exoelectrogenic bacteria capable of generating significant amount of electricity in MFC has been identified, using various organic compounds for fuel. Soil sample taken from rice paddy field is proven to contain exoelectrogenic bacteria, thus electricity generation using mixed culture originally found in the soil, and pure culture isolated from the soil is studied. This research will isolate the exoelectrogenic bacterial species in the rice paddy field soil responsible for energy generation. Growth of bacteria isolated from the MFC is observed by measuring the optical density (OD), cell density weight (CDW) and viable cell count. Mixed bacterial species found in paddy field soil generates maximum power of 77.62 μW and 0.70 mA of current. In addition, the research also shows that the pure bacterium in rice paddy field soil can produce maximum power and current at 51.32 μW and 0.28 mA respectively.

논에서 분리한 메탄산화세균 Methylomonas sp. SM4의 특성과 메탄올 생합성

논에서 분리한 메탄산화세균 Methylomonas sp. SM4의 특성과 메탄올 생합성

Population dynamics of electrogenic microbial communities in microbial fuel cells started with three different inoculum sources

Microbial fuel cells (MFCs) are one of the bioelectrochemical systems that exploit microorganisms as biocatalysts to degrade organic matters and recover energy as electric power. Here, we explored how the established electrogenic microbial communities were influenced by three different inoculum sources; anaerobic sludge of the wastewater plant, rice paddy field soil, and coastal lagoon sediment. We periodically characterized both electricity generation with sucrose consumption and 16S rRNA-basis microbial community composition. The electrochemical features of MFCs were slightly different among three inocula, and the lagoon sediment-inoculated MFC showed the highest performance in terms of the treatment time. Meanwhile, although the inoculated microbial communities were highly diverse and quite different, only twelve genera affiliated with δ-Proteobacteria, γ-Proteobacteria, Bacilli, Clostridia/Negativicutes or Bacteroidetes were abundantly enriched in all MFC anode communities. Within them, several fermentative genera were clearly different due to the inocula, while the inocula-specific phylotypes were identified in an electrogenic genus Geobacter. The relative abundances of phylotypes closely-related to Geobacter metallireducens were increased in later stages of all the sucrose-fed MFCs. These results indicate that key microbial members for the functional electrogenic community widely exist in natural ecosystems, but the community members presenting in inoculum sources affected the MFC performances.

Isolation and Characterization of Two Cyanobacterial Strains Calothrix Sp. and Microchaete Sp. from Rice Fields of Karimganj District, Assam, North East India

Studies on various nitrogen fixing microalgal strains found in the rice paddy field soils are carried out in different parts of the world. In the present study two cyanobacterial strains belonging to the order nostocales, Calothrix sp. and Microchaete sp. were isolated from the rice fields of Karimganj district, South Assam, India and characterized based on their morphological, biochemical and molecular analysis. For the phenotypic characterization - growth, pigments (chlorophyll a, total carotenoid content, phycobiliproteins) and biochemical properties (total carbohydrate and soluble proteins) were studied. The study showed that both strains contain lower phycoerythrin content as compared to the other pigments. The Microchaete strain contain a higher total carotenoid content while chlorophyll a accumulation was higher in the Calothrix strain. Phylogenetic compairision was made using 16S rRNA gene sequences including other sequences of Calothrix, Microchaete and Tolypothrix species from GenBank. The results showed that polyphasic approach provides necessary information for the identification of cyanobacterial species using morphological analysis in combination with molecular techniques.

Production, purification and characterization of an ionic liquid tolerant cellulase from Bacillus sp. isolated from rice paddy field soil

Lignocellulosic biomass is a renewable, abundant, and inexpensive resource for biorefining process to produce biofuel and valuable chemicals. To make the process become feasible, it requires the use of both efficient pretreatment and hydrolysis enzymes to generate fermentable sugars. Ionic liquid (IL) pretreatment has been demonstrated to be a promising method to enhance the saccharification of biomass by cellulase enzyme; however, the remaining IL in the hydrolysis buffer strongly inhibits the function of cellulase. This study aimed to isolate a potential IL-tolerant cellulase producing bacterium to be applied in biorefining process. One Bacillus sp., MSL2 strain, obtained from rice paddy field soil was isolated based on screening of cellulase assay. Its cellulase enzyme was purified and fractionated using a size exclusion chromatography. The molecular weight of purified cellulose was 48 kDa as revealed by SDS-PAGE and zymogram analysis. In the presence of the IL, 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]) concentration of 1 M, the cellulase activity retained 77.7% of non-IL condition. In addition, the optimum temperature and pH of the enzyme is 50°C and pH 6.0, respectively. However, this cellulase retained its activity more than 90% at 55°C, and pH 4.0. Kinetic analysis of purified enzyme showed that the Km and Vmax were 0.8 mg/mL and 1000 μM/min, respectively. The characterization of cellulase produced from MSL2 strain was described here. These properties of cellulase made this bacterial strain become potential to be used in the biorefining process.

Effect of Controlled-release Nitrogen Fertilizer on Methane Emission from Paddy Field Soil

An experimental study was conducted to investigate the effect of Controlled Release Nitrogen Fertilizer on CH4 emission from a rice paddy field soil using pot experimental setup. The experiment is designed with three fertilizer types, i.e., controlled-release nitrogen fertilizer (Neem oil coated urea) and urea (U) and organic fertilizers like Gliricidia sepium, cowpea, Farmyard manure etc. There are two rice cultivars Uma and Jyothy were used for the pot experiment. Each experiment replicate triply. Methane flux was measured at different growth stages for the two rice cultivar by one-time application of CRNF compared with Urea and Organic fertilizer. The methane emission was noted at different rice growth stages. Finally the total CH4 emission from the cultivar is also calculated. CH4 emission was decreased at vegetative stage, gradually increased at reproductive stage and decreased at grain filling to maturity. Methane emission was higher from Heading to flowering, accounting for 35.21% to 41.53% of total cumulative emission. CRNF significantly affect the biometric characters like tiller number, plant height, biomass, and yield in rice by using CRNF. Rice yields increased by 11.43 and 11.11% for Uma and Jyothy rice respectively.

Draft Genome Sequence of Bacteroidales Strain 6E, Isolated from a Rice Paddy Field in Japan.

We generated a high-quality draft genome sequence of Bacteroidales strain 6E, a strict anaerobe newly isolated from Japanese rice paddy field soil. The genome consists of 61 contigs, with a total size of 4,436,542 bp and mean G+C content of 45.4%. Annotation predicted 3,620 protein-coding and 54 RNA genes.

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil.

Anaerobic degradation of lignin-derived aromatics is an important metabolism for carbon and nutrient cycles in soil environments. Although there are some studies on degradation of lignin-derived aromatics by nitrate- and sulfate-reducing bacteria, knowledge on their degradation under methanogenic conditions are quite limited. In this study, methanogenic microbial communities were enriched from rice paddy field soil with lignin-derived methoxylated monoaromatics (vanillate and syringate) and their degradation intermediates (protocatechuate, catechol, and gallate) as the sole carbon and energy sources. Archaeal community analysis disclosed that both aceticlastic (Methanosarcina sp.) and hydrogenotrophic (Methanoculleus sp. and Methanocella sp.) methanogens dominated in all of the enrichments. Bacterial community analysis revealed the dominance of acetogenic bacteria (Sporomusa spp.) only in the enrichments on the methoxylated aromatics, suggesting that Sporomusa spp. initially convert vanillate and syringate into protocatechuate and gallate, respectively, with acetogenesis via O-demethylation. As the putative ring-cleavage microbes, bacteria within the phylum Firmicutes were dominantly detected from all of the enrichments, while the dominant phylotypes were not identical between enrichments on vanillate/protocatechuate/catechol (family Peptococcaceae bacteria) and on syringate/gallate (family Ruminococcaceae bacteria). This study demonstrates the importance of cooperation among acetogens, ring-cleaving fermenters/syntrophs and aceticlastic/hydrogenotrophic methanogens for degradation of lignin-derived aromatics under methanogenic conditions.

Effects of NaCl concentration on anode microbes in microbial fuel cells.

Understanding of how operational parameters affect the composition of exoelectrogenic microbes is an important step in the development of efficient microbial fuel cells (MFCs). In the present study, single-chamber MFCs were inoculated with rice paddy-field soil and continuously supplied with an acetate medium containing different concentrations of NaCl (0–1.8 M). Polarization analyses showed that power output increased as the NaCl concentration increased to 0.1 M, while it was markedly diminished over 0.3 M. The increase in power output was associated with an increased abundance of anode microbes as assessed by protein assays. Notably, the power increase was also accompanied by an increase in the abundance ratio of Geobacter bacteria to total anode bacteria as assessed by pyrosequencing of 16S rRNA gene amplicons and specific quantitative PCR. Although most Geobacter species are known to exhibit high growth rates in freshwater media without NaCl, the present study shows that 0.1 M NaCl facilitates the growth of Geobacter in MFC anode biofilms. This result suggests that the optimum salt concentration in MFC is determined by the balance of two factors, namely, the solution conductivity and salt tolerance of exoelectrogens.

Taxonomic composition of denitrifying bacterial isolates is different among three rice paddy field soils in Japan

Denitrification is one of the important nitrogen transformation processes in rice (Oryza sativa L.) paddy soil. We have performed both culture-dependent and -independent studies to investigate the key players in denitrification in rice paddy soil. Our previous works suggested the possibility that community composition of denitrifying populations is different among soils. To confirm this possibility, in the present study, denitrifying bacteria were isolated from rice paddy field soils (Kumamoto and Tokyo) in Japan by the functional single-cell isolation method, and examined for their taxonomic position. Combined with our previously isolated strains from Niigata paddy field soil, our results clearly indicated that the taxonomic composition of the denitrifying bacterial community is different at the genus level among three soils. A significant difference in mean potential denitrification activity of the isolates at the genus level was also found. Soil and/or other environmental factors could shape the community structure of denitrifiers in rice paddy soil.

Use of cassette-electrode microbial fuel cell for wastewater treatment

Cassette-electrode microbial fuel cells (CE-MFCs) have been developed for the conversion of biomass wastes into electric energy. The present study modified CE-MFC for its application to wastewater treatment and examined its utility in a long-term (240 days) experiment to treat a synthetic wastewater, containing starch, yeast extract, peptone, plant oil, and a detergent (approximately 500mg of total chemical oxygen demand [COD] per liter). A test MFC reactor (1l in capacity) was equipped with 10 cassette electrodes with total anode and cathode projection areas of 1440cm(2), and the operation was initiated by inoculating with rice paddy-field soil. It was demonstrated that CE-MFC achieved COD removal rates of 80% at hydraulic-retention times of 6h or greater, and electricity was generated at a maximum power density of 150mWm(-2) and Coulombic efficiency of 20%. Microbial communities established on anodes of CEs were analyzed by pyrosequencing of PCR-amplified 16S rRNA gene fragments, showing that Geobacter, Clostridium, and Geothrix were abundantly detected in anode biofilms. These results demonstrate the utility of CE-MFC for wastewater treatment, in which Geobacter and Geothrix would be involved in the electricity generation.

Dysgonomonas oryzarvi sp. nov., isolated from a microbial fuel cell

A Gram-stain-negative, non-motile and coccoid- to short-rod-shaped bacterium, designated strain Dy73(T), was isolated from a microbial fuel cell that had been inoculated with rice paddy field soil and fed starch, peptone and fish extract as fuels. On the basis of 16S rRNA gene sequence phylogeny, strain Dy73(T) was affiliated with the genus Dysgonomonas in the phylum Bacteroidetes, and most closely related to Dysgonomonas mossii CCUG 43457(T) with a 16S rRNA gene sequence similarity value of 99.7 %. However, the DNA-DNA relatedness value between strain Dy73(T) and Dysgonomonas mossii CCUG 43457(T) was 34.8%. In addition, strain Dy73(T) was found to be different from other recognized species of the genus Dysgonomonas in taxonomically important traits, including habitat, DNA G+C content, bile resistance and fatty-acid composition. Based on these characteristics, strain Dy73(T) represents a novel species of the genus Dysgonomonas for which the name Dysgonomonas oryzarvi sp. nov. is proposed. The type strain is Dy73(T) ( = JCM 16859(T) = KCTC 5936(T)).

Methanogenesis facilitated by electric syntrophy via (semi)conductive iron‐oxide minerals

Methanogenesis is an essential part of the global carbon cycle and a key bioprocess for sustainable energy. Methanogenesis from organic matter is accomplished by syntrophic interactions among different species of microbes, in which interspecies electron transfer (IET) via diffusive carriers (e.g. hydrogen and formate) is known to be the bottleneck step. We report herein that the supplementation of soil microbes with (semi)conductive iron-oxide minerals creates unique interspecies interactions and facilitates methanogenesis. Methanogenic microbes were enriched from rice paddy field soil with either acetate or ethanol as a substrate in the absence or presence of (semi)conductive iron oxides (haematite or magnetite). We found that the supplementation with either of these iron oxides resulted in the acceleration of methanogenesis in terms of lag time and production rate, while the supplementation with an insulative iron oxide (ferrihydrite) did not. Clone-library analyses of 16S rRNA gene fragments PCR-amplified from the enrichment cultures revealed that the iron-oxide supplementation stimulated the growth of Geobacter spp. Furthermore, the addition of a specific inhibitor for methanogenesis suppressed the growth of Geobacter spp. These results suggest that Geobacter grew under syntrophic association with methanogens, and IET could occur via electric currents through (semi)conductive iron-oxide minerals (termed 'electric syntrophy'). Given the ubiquity of conductive minerals in nature, such energetic interactions may occur widely in soil and sediments and can be used to develop efficient bioenergy processes.

Influence of Temperature and Oil Content on the Soil/Air Partition Coefficient for Hexachlorobenzene in Oil-Contaminated Rice Paddy Field Soil

The soil/air partition coefficients (K SA ) for hexachlorobenzene (HCB) in oil-contaminated (crude oil and diesel) rice paddy field soils were measured in a solid fugacity meter at different oil concentrations over the temperature range of 5 to 30°C at 100% relative humidity. The results showed that values of K SA increased with a decrease of temperature. As for oil content, there is a critical separate phase concentration (CSPC) above which K SA increased with increasing of oil content. When oil content is above CSPC, oil plays a role as a separate phase that enhances the sorption capacity of the soil. At a given temperature (20°C) values of CSPC depended on the natural organic matter (NOM) contents of the soil, while for a given oil concentration they depended on the temperature. The normalized oil/air partition coefficients ) for HCB deduced from K SA for oils and experimentally determined with crude oil/quartz sand system were similar and 0.7–7 times higher than the normalized organic/air partition coefficient ), which implied that oil was a super sorbent. The enthalpies (ΔHSA) for crude oil and diesel were 64.9 and 55.7 kJ mol−1, respectively.

논토양에서 파종시기와 재배기간이 사일리지용 옥수수의 생육특성, 건물수량 및 사료적 가치에 미치는 영향

Sang Moo Lee* and Jae Hun LeeDepartment of Animal Science, Kyungpook National UniversityABSTRACTThis study was carried out to investigate the effects of the seeding dates and growth periods on the growth characteristics, dry matter yield and feed value of corn for silage in paddy field. The experimental design was arranged in a randomized block design with three replications. Treatments consisted of five seeding dates, 1 May(T1), 8 May(T2), 15 May(T3), 22 May(T4) and 29 May(T5). And harvesting time homologized by August 24. Therefore, growing periods were 115 days(T1), 108 days(T2), 101 days(T3), 94 days(T4) and 87 days(T5), respectively. In maturities at harvest time, T1, T2, T3, T4 and T5 were full dent, early dent, late dough, dough and early dough stage, respectively. Plant height and numbers of root system were highest in T5(p T2>T3>T4>T5(p T3>T1>T2>T5, and total NEAA(nonessential amino acids) were higher in order of T1>T4>T2>T3>T5, and total amino acids were higher in order of T4>T1>T3>T2>T5. But no significant differences were found among the treatments. TUFA(total unsaturated fatty acid) and TSFA(total saturated fatty acid) were in order of T1>T2>T3>T5>T4 (p<0.01). Minerals were the highest in T4(4,721.25mg/kg), and T2(2,970.80mg/kg) was the lowest as compared to other treatments(p<0.05). Based on the above results, seeding dates could be recommended as early May, and harvest times is yellow ripe stage for qualitative and quantitative production of corn for silage in rice paddy field soil.(Key words :Silage corn, Dry matter, Feed value, Seeding dates, Growth period, Paddy field)

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes ( nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/ nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.