Paddy Field Soil Research Articles

Assessment of Rice Associated Bacterial Ability to Enhance Rice Seed Germination and Rice Growth Promotion

ABSTRACT The application of beneficial bacteria has recently been used for sustainable agriculture. In current research, 71 bacterial isolates were obtained from rice plant and the rhizosphere soil of different paddy fields in Guilan province, Iran. After primitive investigation, 40 bacteria with typical predominant characteristics were selected. By PCR-RFLP of their 16S r-DNA gene, 8 Operational Taxonomic Units (OTUs) totally consisted of 33 isolates were obtained. From all of them, 8 isolates were selected for rice seed germination experiment, then, effective isolates were used for pot experiment to evaluate their ability for promoting rice growth. All of them were able to increase rice growth and yield, but in different potential. These tested isolates were identified as Alcaligenes faecalis (DEp8, O1R4), Pantoea ananatis (AEn1), Bacillus vietnamensis (MR5), Bacillus idriensis (MR2) and Stenotrophomonas maltophilia by partial sequencing of their 16S r-DNA gene. Among them, AEn1 and MR5 produced indole-3- acetic acid (IAA) in larger amounts than the other isolates and the isolates AEn1 and O1R4 were able to solubilize phosphate in higher amounts. According to the results obtained, it can be concluded that AEn1, O1R4 and MR5 can be considered as bacterial inoculants to use as alternatives for chemical fertilizers.

Soil organic carbon and phosphorus availability regulate abundance of culturable phosphate-solubilizing bacteria in paddy fields

Low availability of phosphorus (P) is a major constraint for optimal crop production, as P is mostly present in its insoluble form in soil. Therefore, phosphate-solubilizing bacteria (PSB) from paddy field soils of the Indo-Gangetic Plain, India were isolated, and their abundance was attempted to be correlated with the physicochemical characteristics of the soils. Ninety-four PSB were isolated on Pikovskaya's agar medium, and quantitative phosphate solubilization was evaluated using NBRIP medium. The isolates solubilized P up to a concentration of 1 006 μg mL−1 from tricalcium phosphate with the secretion of organic acids. These isolates were identified by 16S rRNA gene sequence comparison, and they belonged to Gammaproteobacteria (56 isolates), Firmicutes (28 isolates), Actinobacteria (8 isolates), and Alphaproteobacteria (2 isolates). Phylogenetic analysis confirmed the identification by clustering the isolates in the clade of the respective reference organisms. The correlation analysis between PSB abundance and physicochemical characteristics revealed that the PSB population increased with increasing levels of soil organic carbon, insoluble P, K+, and Mg2+. The promising PSB explored in this study can be further evaluated for their biofertilizer potential in the field and for their use as potent bio-inoculants.

Enrichment of anaerobic nitrate-dependent methanotrophic \u2018Candidatus Methanoperedens nitroreducens\u2019 archaea from an Italian paddy field soil

Paddy fields are a significant source of methane and contribute up to 20% of total methane emissions from wetland ecosystems. These inundated, anoxic soils featuring abundant nitrogen compounds and methane are an ideal niche for nitrate-dependent anaerobic methanotrophs. After 2 years of enrichment with a continuous supply of methane and nitrate as the sole electron donor and acceptor, a stable enrichment dominated by ‘Candidatus Methanoperedens nitroreducens’ archaea and ‘Candidatus Methylomirabilis oxyfera’ NC10 phylum bacteria was achieved. In this community, the methanotrophic archaea supplied the NC10 phylum bacteria with the necessary nitrite through nitrate reduction coupled to methane oxidation. The results of qPCR quantification of 16S ribosomal RNA (rRNA) gene copies, analysis of metagenomic 16S rRNA reads, and fluorescence in situ hybridization (FISH) correlated well and showed that after 2 years, ‘Candidatus Methanoperedens nitroreducens’ had the highest abundance of (2.2 ± 0.4 × 108) 16S rRNA copies per milliliter and constituted approximately 22% of the total microbial community. Phylogenetic analysis showed that the 16S rRNA genes of the dominant microorganisms clustered with previously described ‘Candidatus Methanoperedens nitroreducens ANME2D’ (96% identity) and ‘Candidatus Methylomirabilis oxyfera’ (99% identity) strains. The pooled metagenomic sequences resulted in a high-quality draft genome assembly of ‘Candidatus Methanoperedens nitroreducens Vercelli’ that contained all key functional genes for the reverse methanogenesis pathway and nitrate reduction. The diagnostic mcrA gene was 96% similar to ‘Candidatus Methanoperedens nitroreducens ANME2D’ (WP_048089615.1) at the protein level. The ‘Candidatus Methylomirabilis oxyfera’ draft genome contained the marker genes pmoCAB, mdh, and nirS and putative NO dismutase genes. Whole-reactor anaerobic activity measurements with methane and nitrate revealed an average methane oxidation rate of 0.012 mmol/h/L, with cell-specific methane oxidation rates up to 0.57 fmol/cell/day for ‘Candidatus Methanoperedens nitroreducens’. In summary, this study describes the first enrichment and draft genome of methanotrophic archaea from paddy field soil, where these organisms can contribute significantly to the mitigation of methane emissions.

Hyperaccumulator straw improves the cadmium phytoextraction efficiency of emergent plant Nasturtium officinale.

With the development of economy, the heavy metal contamination has become an increasingly serious problem, especially the cadmium (Cd) contamination. The emergent plant Nasturtium officinale R. Br. is a Cd-accumulator with low phytoremediation ability. To improve Cd phytoextraction efficiency of N. officinale, the straw from Cd-hyperaccumulator plants Youngia erythrocarpa, Galinsoga parviflora, Siegesbeckia orientalis, and Bidens pilosa was applied to Cd-contaminated soil and N. officinale was then planted; the study assessed the effect of hyperaccumulator straw on the growth and Cd accumulation of N. officinale. The results showed that application of hyperaccumulator species straws increased the biomass and photosynthetic pigment content and reduced the root/shoot ratio of N. officinale. All straw treatments significantly increased Cd content in roots, but significantly decreased Cd content in shoots of N. officinale. Applying hyperaccumulator straw significantly increased the total Cd accumulation in the roots, shoots, and whole plants of N. officinale. Therefore, application of straw from four hyperaccumulator species promoted the growth of N. officinale and improved the phytoextraction efficiency of N. officinale in Cd-contaminated paddy field soil; the straw of Y. erythrocarpa provided the most improvement.

논에서 분리한 메탄산화세균 Methylomonas sp. SM4의 특성과 메탄올 생합성

논에서 분리한 메탄산화세균 Methylomonas sp. SM4의 특성과 메탄올 생합성

水田土壌中の有機酸代謝と水稲生育阻害性に関する研究(第4報) : 酪酸及び醋酸の土壌による吸収, 分解と生育阻害作用

水田土壌中の有機酸代謝と水稲生育阻害性に関する研究(第4報) : 酪酸及び醋酸の土壌による吸収, 分解と生育阻害作用

泥炭質湿田土壌中における生育阻害性物質に関する研究(第5報) : 作土含有物質の分別と根伸長阻害作用

泥炭質湿田土壌中における生育阻害性物質に関する研究(第5報) : 作土含有物質の分別と根伸長阻害作用

Assessment of Paddy Soil Quality Index Based on Differences in the Productivity of Paddy in Wonogiri Regency

Rice or paddy is a staple food in some countries. The need for food is huge as the population growth increase, in Wonogiri regency majority of the land area is used as paddy field and land intensification is done to improve productivity. Land intensification raises the issues of having no definitive measure about the status of soil improvement after the cultivation practices of Paddy (Oryza sativa) has been done, in addition, the diversity of age utilization of paddy field by farmers resulting the differences in productivity that will affect the quality difference of the paddy field soil. The assessment is aimed to determine the soil quality function whether it’s good or bad after doing such land cultivation practices for a certain period. The assessment of soil quality is using data analysis method from the influential indicators based on the nature of at least the Minimum Data Set (MDS) that is obtained based on calculations of Principal Component Analysis (PCA). Indicators that affect, such as, C-Organic,Bulk Density, K-Available, N-Total, and average soil quality were obtained at all points of the sample with a diverse range of values. With the known SQI values, in the future the efforts to maintain and improve the quality of the soil can be done by considering several important factors.

3-1-7 Response of active community of methanogenic archaea in paddy field soil to a management of paddy-upland rotation

3-1-7 Response of active community of methanogenic archaea in paddy field soil to a management of paddy-upland rotation

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.

Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination

There is an increasing concern about rice (Oryza sativa L.) soil microbiomes under the influence of mixed heavy metal contamination. We used the high-throughput Illumina MiSeq sequencing approach to explore the bacterial diversity and community composition of soils in four paddy fields, exhibiting four degrees of mixed heavy metal (Cd, Pb and Zn) pollution, and examined the effects of these metals on the bacterial communities. Our results showed that up to 2 104 to 4 359 bacterial operational taxonomic units (OTUs) were found in the bulk and rhizosphere soils of the paddy fields, with the dominant bacterial phyla (greater than 1% of the overall community) including Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria, Gemmatimonadetes, Chloroflexi, Bacteroidetes and Nitrospirae. A number of rare and candidate bacterial groups were also detected, and Saprospirales, HOC36, SC-I-84 and Anaerospora were rarely detected in rice paddy soils. Venn diagram analysis showed that 174 bacterial OTUs were shared among the bulk soils with four pollution degrees. Rice rhizosphere soils displayed higher bacterial diversity indices (ACE and Chao 1) and more unique OTUs than bulk soils. Total Cd and Zn in the soils were significantly negatively correlated with ACE and Chao 1, respectively, and the Mantel test suggested that total Pb, total Zn, pH, total nitrogen and total phosphorus significantly affected the community structure. Overall, these results provided baseline data for the bacterial communities in bulk and rhizosphere soils of paddy fields contaminated with mixed heavy metals.

Effect of UV-irradiation on plate counts of bacteria from paddy field soil

Effect of UV-irradiation on plate counts of bacteria from paddy field soil

水田土壌の機能と微生物群集構造(生物多様性の中の機能ネットワークを探る,シンポジウム)

水田土壌の機能と微生物群集構造(生物多様性の中の機能ネットワークを探る,シンポジウム)

メタン生成古細菌の特徴と水田土壌における生態(環境と土壌微生物,シンポジウム)

メタン生成古細菌の特徴と水田土壌における生態(環境と土壌微生物,シンポジウム)

Effects of different fertilizer application methods on the community of nitrifiers and denitrifiers in a paddy soil

Nitrifiers and denitrifiers are the key drivers of N cycling in paddy soil. Little is known about the effects of different fertilization methods, especially side bar fertilization, on the community of nitrifiers and denitrifiers in paddy soils. Here we assess the relationships between soil physicochemical properties, denitrification and nitrification activities, and the underlying microbial communities in a surface layer of paddy field soil treated with different fertilization methods. Soil was unfertilized (control), treated with conventional chemical fertilizer (CF), CF plus pig manure (MC), or slow-release fertilizer (SR), or by slow-release side bar fertilization (SB). Soil was sampled after one season of early and late rice growth. We determined soil physicochemical properties, potential nitrification rates (PNR), and denitrification enzyme activities (DEA). Ammonia-oxidizing archaeal (AOA) and bacterial (AOB) communities were assessed via their ammonia monooxygenase (amoA) genes, and denitrifiers via nitrite reductases (nirK and nirS) and nitrous oxide reductase (nosZ). Quantitative PCR was used to assess gene abundance, terminal restriction fragment polymorphism (T-RFLP) to investigate fertilization effects on microbial communities, and clone library sequencing and phylogenetic analysis to explore the taxonomic diversity of the nitrifiers and denitrifiers. Fertilization significantly increased the amount of NH4 +-N in the soil of SB and MC treatments, whereas MC lowered the NO3 −-N level. DEA was higher for MC and CF than the other treatments. The PNR in MC-treated soil was significantly lower than that in CF-treated soil. There were no significant differences in AOA and nirS copy numbers; however, nirK and nosZ copy numbers were higher for MC compared with CF. The number of AOA terminal restriction fragments (TRFs) increased significantly with N addition and reached the highest level for SB, whereas the number of AOB TRFs did not change significantly between treatments. Similarly, the number of nirK TRFs increased under fertilization, with the highest number obtained for SR; however, no significant change was observed for nirS and nosZ TRFs across different treatments, except for their relative abundance. All AOA amoA genotypes were in archaeal group 1.1b, whereas 95% AOB were in Nitrosospira cluster 3a. More than 40% of nirS OTUs were affiliated with Herbaspirillum, a key N-cycle player in this paddy soil. The SB and MC treatments had significant effects on soil N, DEA, and PNR levels, and affected the community of N-functional microbes. SB in combination with pig manure would contribute to the improvement of paddy soil fertility.

Biogeochemistry of methanogenesis with a specific emphasis on the mineral-facilitating effects

The Earth surface contains various oxic and anoxic environments. The later include natural wetlands, river and lake sediments, paddy field soils and landfills. In the last few decades, the biogeochemical cycle of carbon in anoxic environments, which leads to the production and emission of methane, a potent greenhouse gas in the atmosphere, has drawn great attentions from both scientific and public sectors. New organisms and mechanisms involved in methanogenesis and carbon cycling have been uncovered. Interspecies electron transfer is considered as a crucial step in methanogenesis in anoxic environments. Electron-carrying mediators, like H2 and formate, are known to play the key role in electron transfer. Recently, it has been found that in addition to the conventional electron transfer via chemical mediators, direct interspecies electron transfer (DIET) can occur. In this Review, we describe the ecology and biogeochemistry of methanogenesis and highlight the effect of microbe-mineral interaction on microbial syntrophy. Recent advances in the study of DIET may pave the way towards a mechanistic understanding of methanogenesis and the influence of microbe-mineral interaction on this process.

Low temperature carbonization of chicken manure to char and its effect on growth of Oryza sativa L. Koshihikari and Brassica rapa komatsuna

Considering the demand for transforming poultry waste into eco-friendly manure, we carbonized chicken manure at 402, 449 and 528 °C and determined the physicochemical properties. We evaluated the effectiveness of the ensuing carbonized chicken manure (CCM) as a fertilizer using Brassica rapa, var. komatsuna and Oryza sativa L., var. japonica, cv. Koshihikari, in the upland and the paddy field soil, respectively. Herein, we carried out duplicate treatment of CCM (carbonized at 528 °C) either alone or in combination with nitrogen and measured the growth from three or more plants. The plots with the recommended chemical fertilizers containing nitrogen (N), phosphorus (P) and potassium (K) and with no fertilizers were used as controls for growth measurement. The vessel tests indicated that when applied alone, the CCM plot could not support the normal growth of both the plants. However, the CCM plot restored the plant growth with simultaneous application of nitrogen, and the growth in the CCM + N plot was comparable to that observed in the NPK plot. By estimating the growth in the NPK plots as 100%, the growth percentages of fresh weights of komatsuna were 12% in the CCM plot, 79% in the N plot and 99% in the CCM + N plot. Likewise, the plant heights of Koshihikari were 43% in the CCM plot, 77% in the N plot and 99% in the CCM + N plot. Our data suggest CCM supplementation to N fertilizers as a potential replacement of inorganic fertilizers like P and K for effective environmental management.

Weed communities and their negative impact on rice yield in no-input paddy fields in the northern part of Japan

Although weeds cause serious yield losses in agriculture, relatively few studies have been conducted on the relationship between weeds and yield loss in no-input rice production systems, where no herbicides are used. This study investigated weed communities in rice paddy fields and their influence on rice yield, by comparing 16 no-input paddy fields in northern Japan. The weed seed community in the paddy field soils, before transplanting, were analyzed using a spontaneous germination test, and the established weed communities in the fields were examined at the full heading growth stage of the rice. The weed community structures showed a marked difference between the seeds in the soil and the established weed communities. Although eight weed species germinated from the soil, only four weed species were observed in the fields at the full heading stage of the rice. The two dominant weed species, Monochoria vaginalis and Cyperaceae, accounted for 84% of the total weed biomass in the field. The multiple linear regression analysis revealed that during the period of no-input cultivation, soil NO3 concentrations, air temperature, and sunlight hours had significant effects on the biomass of M. vaginalis, but not on Cyperaceae. Furthermore, the two dominant weed species had different impact on rice yield; Cyperaceae had a large negative effect on rice yield, whereas M. vaginalis did not. These results indicated that weed management in no-input paddies should be directed towards the control of specific weed species such as Cyperaceae sp., rather than the entire weed community.

Kinetic and molecular analyses reveal isoprene degradation potential of Methylobacterium sp.

Efforts were made to isolate and characterize bacteria capable of growing on methane and organic compounds, and to achieve the simultaneous degradation of more than one pollutant. Among the methanotrophs, species of Methylobacterium was able to catabolize a variety of hydrocarbons, including the branched-chain alkenes. Therefore, laboratory incubations experiments were carried out in batch mode to assess the potential of Methylobacterium sp. PV1 for degrading isoprene, the low-molecular-weight alkene, the most abundant non-methane volatile hydrocarbon present in the environment. Methylobacterium sp. PV1, isolated from paddy field soil, was characterized by pmoA and 16S rRNA gene sequencing and FAME analysis, and used for isoprene degradation. The kinetics of biodegradation is studied using the Michaelis-Menten model. The optimum degradation (80%) with maximum average relative degradation rate was observed at 150ppm isoprene. The degradation products were also analyzed using FTIR.

Thermally activated persulfate oxidation of NAPL chlorinated organic compounds: effect of soil composition on oxidant demand in different soil-persulfate systems.

This study investigates the interaction of persulfate with soil components and chlorinated volatile organic compounds (CVOCs), using thermally activated persulfate oxidation in three soil types: high sand content; high clay content; and paddy field soil. The effect of soil composition on the available oxidant demand and CVOC removal rate was evaluated. Results suggest that the treatment efficiency of CVOCs in soil can be ranked as follows: cis-1,2-dichloroethene > trichloroethylene > 1,2-dichloroethane > 1,1,1-trichloroethane. The reactions of soil components with persulfate, shown by the reduction in soil phase natural organics and mineral content, occurred in parallel with persulfate oxidation of CVOCs. Natural oxidant demand from the reaction of soil components with persulfate exerted a large relative contribution to the total oxidant demand. The main influencing factor in oxidant demand in paddy-soil-persulfate systems was natural organics, rather than mineral content as seen with sand and clay soil types exposed to the persulfate system. The competition between CVOCs and soil components for oxidation by persulfate indicates that soil composition exhibits a considerable influence on the available oxidant demand and CVOC removal efficiency. Therefore, soil composition of natural organics and mineral content is a critical factor in estimating the oxidation efficiency of in-situ remediation systems.