泰国水稻土Fe还原细菌对盐分和有机物改良的响应

In paddy soils of Thailand,the addition of organic matter (OM) is used to efficiently limit the effect of salinity on rice culture and production.OM used as an amendment and fertilizer promotes the reduced condition and increases iron solubilization without provoking ferrous toxicity.In this study,the intricate biogeochemical role of iron-reducing bacteria (IRB) involved in the quality of water and soil of paddy fields,particularly when the paddy fields were subject to salinity and organic matter addition,were studied in paddy fields of Thailand.The results demonstrated that the addition of OM increased the proliferation of cultivable IRB and their specific activity.Cultivable IRB communities decreased in the presence of salt.The presence of salt modified the structure of the bacterial populations by favoring the development of alkaline and moderately halophilic bacteria (Virgibacillus spp.,Oceanobacillus spp.,and Paenibacillus spp.).The paddy soils studied contained very diversified (halosensitive,halotolerant,and halophilic) IRB populations that could be adapted to a variety of salinity conditions (0-90 g L 1 NaCl) using different organic substrates (glucose,acetate,and soil organic matter) to maintain significant activities under extreme conditions of salinity.The rhizosphere of rice stimulated IRB community growth without organic matter,whereas organic matter addition limited the rhizosphere effect on IRB cultivable number in saline condition.The interactive action of salinity and organic amendment had a negative impact on the rhizosphere effect.The presence of specific iron-reducing populations (fermentative,iron-respiring,anaerobic,and facultative anaerobic),having different behaviors under salt and redox stresses,appeared to be a key factor that contributed to the control or enhancement of the quality of water and soil in paddy fields.     

不同品种水稻土壤氨氧化细菌和氨氧化古菌群落结构组成

本研究通过提取土壤总DNA,利用特异引物进行PCR扩增和变性梯度凝胶电泳(DGGE),研究了不同品种水稻对稻田土壤氨氧化细菌和氨氧化古菌群落结构组成的影响.结果显示:稻田土壤具有丰富的氨氧化细菌和氨氧化古菌,且氨氧化古菌种类更多;不同品种水稻氨氧化细菌群落结构组成差异较大,其中以"天A/Km71"、"闽优1027"和"Km62/1027"3个品种相似性较高,且明显不同于其余3个品种:而氨氧化古菌群落结构组成在不同土层间表现出较大差异,其中以"天A/Km71"和"Km62/1027"的表土与根际土氨氧化古菌群落组成差异最大.研究表明不同水稻品种及土壤层次对氨氧化微生物群落结构组成具有一定影响,证明氨氧化微生物尤其是氨氧化古菌在稻田土壤生态系统中占有重要地位.     

Effect of organic manure on organic phosphorus fractions in two paddy soils

We investigated the transformation of the organic P fractions from organic manure in two paddy soils (Ultisol, Entisol) and the influence of organic manure or cellulose on organic P under anaerobic conditions. The results obtained from the P fractionation experiment indicated that during the incubation labile and moderately labile organic P fractions increased in the Ultisol and decreased in the Entisol, which might be related to the difference in the organic matter content of both soils. Immediately after the application of organic manure, a large part of labile and moderately labile organic P supplied with the manure was transformed into moderately resistant organic P, possibly Ca- or Mg-inositol P were transformed into Fe-inositol P. During anaerobic incubation, the labile forms of organic P in the soils treated with organic manure were increased along with the incubation period in the first 4 weeks. The change in the moderately labile fraction was dramatic. It increased sharply in the first 2 weeks, then decreased, which was more pronounced in the soils treated with pig faeces. The moderately resistant fraction decreased during the whole incubation period. This indicated that under anaerobic conditions, the moderately resistant fraction can be transformed into labile and moderately labile organic P fractions, perhaps as Fe³⁺-inositol P is reduced to Fe⁺²-inositol P. Cellulose as an organic substrate had an increasing effect on organic P, especially when it was combined with inorganic P. Therefore, it is suggested that the application of inorganic P fertilizer combined with organic manure may be an effective way of protecting inorganic P against intensive sorption in soils.     

Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis

Rice straw including leaf sheaths and blades put in nylon mesh bags was placed in the plow layer of a Japanese paddy field after harvest under upland conditions and after transplanting of rice seedlings under flooded conditions. In addition, rice straw that was decomposed under the upland conditions during the off-crop season in winter was placed again in soil at the time of transplanting. The materials were collected periodically to analyze the community structure of the bacteria and fungi responsible for rice straw decomposition by PCR-RFLP analysis. The PCR products with 27f and 1492r primers designed for bacterial 16S rDNA and with EF3 and EF4 primers designed for fungal 18S rDNA were digested with four restriction endonucleases (Hinf I, Sau3A I, Hae III, EeoR I). Bacterial communities in the decomposing rice straw were different from each other between upland and flooded conditions, between leaf sheaths and blades, and between straw samples with and without decomposition under upland conditions during the off-crop season. Fungal communities in the decomposing rice straw were also different between the leaf sheaths and blades under upland soil conditions. Score plots of bacterial and fungal communities in the principal component analysis were separated from the plot of the straw materials along with the duration of the placement, indicating the succession of bacterial and fungal communities in decomposing rice straw with time.     

Community structure of microaerophilic iron-oxidizing bacteria in Japanese paddy field soils

ABSTRACT

Redox cycle of iron (Fe) is the central process in the biogeochemistry of paddy field soil. Although Fe(II)-oxidizing process is mediated by both abiotic and biotic reactions, microorganisms involved in the process have not been well studied in paddy field soil. The present study investigated the community structure of microaerophilic Fe(II)-oxidizing bacteria (FeOB) in the family Gallionellaceae in the plow layer of paddy fields located in the central (Anjo) and northeastern (Omagari) Japan since the members in the family are the typical FeOB in circumneutral freshwater environments and possibly have the significant role for Fe(II) oxidation in paddy field soils. A primer set targeting 16S rRNA gene of Gallionella-related FeOB was newly designed for the polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative PCR (qPCR) analyses. DGGE analysis showed significant differences in the band patterns between the field sites. Besides, minor differences were observed in the patterns between the soil depths (0–1 cm and below 1 cm) in the Anjo field, while the patterns were relatively stable in the Omagari field during the annual rice cultivation practices. In total 54 bands were sequenced and clustered into 20 operational taxonomic units (OTUs) on the basis of the 97% similarity. Eighteen out of twenty OTUs (50 of 54 bands) were affiliated within the FeOB cluster of Gallionellaceae, some of which were clustered with known microaerophilic FeOB, Ferrigenium kumadai, Ferriphaselus amnicola, ‘Sideroxydans lithotrophicus’ and ‘S. paludicola’. The number of the 16S rRNA gene copies was 10⁵–10⁷ and 10⁶–10⁸ copies g^?1 dried soil in the two paddy fields and negatively correlated to the contents of acetate-extractable Fe(II) in the soils during the rice cultivation period. These results suggested inhabitance of considerable number of diverse Gallionella-related FeOB and their potential involvement in the Fe(II)-oxidizing process of soil, especially during the rice cultivation period in the paddy field soils.     

Lasting influence of biochemically contrasting organic inputs on abundance and community structure of total and proteolytic bacteria in tropical soils

The SOM field experiments in Kenya, which have been initiated in 2002 on two contrasting soils (clayey Humic Nitisol (sand: 17%; silt: 18%; clay: 65%) at Embu, sandy Ferric Alisol (sand: 66%; silt: 11%; clay: 22%) at Machanga), were used for exploring the effect of nine year annual application of biochemically contrasting organic inputs (i.e., Zea mays (ZM; C/N ratio: 59; (lignin + polyphenols)-to-N ratio: 9.8); Tithonia diversifolia (TD; 13; 3.5); Calliandra calothyrsus (CC; 13; 6.7)) on the soil bacterial decomposer community. Soil samples were taken at the onset of the rainy season before application of fresh organic inputs in March 2011. We studied the abundance (quantitative PCR) and community structure (T-RFLP analysis) of the total (i.e., 16S rRNA gene) and specifically proteolytic (i.e., npr gene encoding neutral metalloproteases) bacteria. Alterations of the soil microbial decomposer community were related to differences of quantity (i.e., soil carbon (TC)) and particularly composition of SOC, where mid-infrared spectroscopic (DRIFTS) information, and contents of extractable soil polyphenol (PP) and the newly introduced PP-to-TC ratio served as SOC quality indicators. For total bacteria, effect of organic input quality was minor in comparison to the predominant influence of soil texture. Elevated soil PP content, driven by polypheneol rich organic inputs, was not suppressive for overall bacterial proliferation, unless additional decomposable C substrates were available as indicated by PP-to-TC ratios. In contrast to the total bacterial community, biochemical quality of organic inputs exposed a stronger effect on functionally specialized bacterial decomposers, i.e., proteolytic bacteria. The npr gene abundance was depressed in the TD treated soils as opposed to soils receiving CC, and showed a positive correlation with soil PP. It was suggested that the high presence of lignin and polyphenol relative to the N content in organic inputs was increasing the npr gene abundance to counteract most likely the existence of polyphenol–protein complexes aggravating protein degradation. We concluded from our study that integration of spectroscopic, geochemical (i.e., soil PP) and molecular soil data provides a novel pathway to enhance our understanding of the lasting effect of organic input quality induced SOC quality changes on bacterial decomposers and particularly proteolytic bacteria driving soil organic N cycling.     

Earthworms increase the ratio of bacteria to fungi in northern hardwood forest soils, primarily by eliminating the organic horizon

The exotic earthworm invasion in hardwood forests of the northern United States is associated with many ecosystem-level changes. However, less is known about the effects of the invasion on the composition of the soil microbial community through which ecosystem-level changes are mediated. Further, earthworm effects on soil microbial community composition have not been well studied in the field. To evaluate changes in bacterial and fungal abundance associated with the earthworm invasion we quantified bacterial and fungal biomass by microscopic counts in paired earthworm-invaded (earthworm) and earthworm-free (reference) plots in five forest stands in central New York (USA). Earthworms significantly increased the ratio of bacteria to fungi on an area basis (per m²), by more than two times in mid-summer and early autumn. While this effect was associated primarily with the lack of the fungal-dominated organic horizon in earthworm plots, a higher ratio of bacteria to fungi in the surface 5 cm mineral soil also contributed as it developed between spring and mid-summer. Earthworm reduction of fungal biomass was confirmed by substantially lower growth of fungal hyphae into mesh sand bags in earthworm compared to reference plots. Burrowing activity by the earthworm Lumbricus terrestris increased the ratio of bacteria to fungi over the short-term within earthworm plots, introducing small-scale spatial heterogeneity associated with burrows. Our study suggests that the exotic earthworm invasion in these northern hardwood forests markedly increased the ratio of bacteria to fungi by eliminating the fungal-rich organic horizon, and was associated localized increases in bacterial vs. fungal abundance in mineral soil, setting the stage for future research into linkages between the earthworm invasion, bacterial and fungal abundance, and ecosystem processes.     

The process of manganese depositton in paddy soils

Abstract

The changes in quality and quantity of phenolic substances in the decaying process of rice straw in a soil were compared under moist and flooded conditions for 200 days. The amounts of phenolic substances divided into fractions of humic acid and fulvic acid, ether- and butanol-extractable and organic solvent-unextractable fractions, then the amounts of individual phenolic acids were determined. The following results were obtained.

1) Alkali-extractable total phenolics as well as individual phenolic acids decreased more rapidly under moist, than under flooded, conditions as rice straw decayed in the soil. The phenolics present were mainly attributable to the straw, not to the soil.

2) The decrease in the level of total phenolics in the early stage of the decaying process was mainly due to the decrease in ether-extractable phenolic compounds in the fulvic acid fraction, and in the later stage, was mainly due to the decrease in butanol-extractable phenolics in the humic acid fraction.

3) The amounts of butanol-extractable phenolics and organic solvent-unextractable phenolics were larger in humic acid than in fulvic acid. On the other hand, a larger amount of organic solvent-extractable phenolics, especially ether-extractable phenolics, was present in fulvic acid.

4) The degradation patterns and pathways of individual phenolic acids in the decaying process of rice straw in soil were found to be the lame as those of decaying straw without soil which were reported previously.

5) The level of phenolic substances in the humic acid was not greatly changed during the decaying process, but the phenolic substances in fulvic acid rapidly increased for 30 days and then rapidly decreased to a constant level.     

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

Repeated fertilizer applications to cultivated soils may alter the composition and activities of microbial communities in terrestrial agro-ecosystems. In this study, we investigated the effects of different long term fertilization practices (control (CK), three levels of mineral fertilizer (N₁P₁K₁, N₂P₂K₂, and N₃P₃K₃), and organic manure (OM)) on soil environmental variables and microbial communities by using phospholipid fatty acid (PLFA) biomarkers analysis in subtropical China. Study showed that OM treatment led to increases in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents, while the mineral fertilizer treatment led to increases in dissolved organic carbon (DOC) content. Changes in soil microbial communities (eg. bacteria, actinomycetes) were more noticeable in soils subjected to organic manure applications than in the control soils or those treated with mineral fertilizer applications. Fungal PLFA biomarkers responded differently from the other PLFA groups, the numerical values of fungal PLFA biomarkers were similar for all the OM and mineral fertilizer treatments. PCA analysis showed that the relative abundance of most PLFA biomarkers increased in response to OM treatment, and that increased application rates of the mineral fertilizer changed the composition of one small fungal PLFA biomarker group (namely 18:3ω6c and 16:1ω5c). Further, from the range of soil environmental factors that we examined, SOC, TN and TP were the key determinants affecting soil microbial community. Our results suggest that organic manure should be recommended to improve soil microbial activity in subtropical agricultural ecosystems, while increasing mineral fertilizer applications alone will not increase microbial growth in paddy soils.     

Effects of long-term fertilization with different substitution ratios of organic fertilizer on paddy soil

In recent years, the abuse of chemical fertilizers has caused numerous environmental problems, such as soil acidification and compaction. Replacing chemical fertilizers with organic fertilizers can effectively alleviate these problems. However, the effects of alternative organic fertilizers remain unclear. To explore the effects of organic fertilizer substitution on rice yield and paddy soil physicochemical properties and bacterial community structure, we conducted a 5-year experiment using different proportions of organic fertilizer substitution in a double-cropping rice field in Jiangxi, China. Our results showed that replacing chemical fertilizers with organic fertilizers can reduce soil acidification, increase soil organic matter content, nutrient contents, and enzyme activities, improve soil physicochemical properties and microbial community, and enhance soil metabolism. Appropriate organic substitution also had positive effects on rice production. These findings enhance our understanding of the effects of different alternative organic fertilization methods and have important theoretical significance for the promotion of the use of organic fertilizers in the future.     

Methanotrophy-driven accumulation of organic carbon in four paddy soils of Bangladesh

Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere.However,soil organic carbon accumulation associated with microbial methane oxidation is poorly understood.Therefore,to investigate methane-derived carbon incorporation into soil organic matter,paddy soils originated from different parent materials(Inceptisol,Entisol,and Alfisol) were collected after rice harvesting from four major rice-producing regions in Bangladesh.Following microcosm incubation with 5%(volume/volume)¹³ CH₄,soil¹³ C-atom abundances significantly increased from background level of 1.08% to 1.88%–2.78%,leading to a net methane-derived accumulation of soil organic carbon ranging from 120 to 307 mg kg^-1.Approximately 23.6%–60.0% of the methane consumed was converted to soil organic carbon during microbial methane oxidation.The phylogeny of¹³ C-labeled pmoA(enconding the alpha subunit of the particulate methane monooxygenase) and 16 S rRNA genes further revealed that canonical α(type II) and γ(type I) Proteobacteria were active methane oxidizers.Members within the Methylobacter-and Methylosarcina-affiliated type Ia lineages dominated active methane-oxidizing communities that were responsible for the majority of methane-derived carbon accumulation in all three paddy soils,while Methylocystis-affiliated type IIa lineage was the key contributor in one paddy soil of Inceptisol origin.These results suggest that methanotroph-mediated synthesis of biomass plays an important role in soil organic matter accumulation.This study thus supports the concept that methanotrophs not only consume the greenhouse gas methane but also serve as a key biotic factor in maintaining soil fertility.     

稻田厌氧氨氧化菌群落结构对氮肥的响应

为探明稻田厌氧氨氧化菌多样性及其对氮肥用量的响应状况,利用厌氧氨氧化菌16S rRNA基因特异引物对定位试验稻田土壤DNA进行PCR-DGGE(聚合酶链反应变性梯度凝胶电泳)并结合DNA克隆测序,研究了氮肥供应量对厌氧氨氧化菌群落结构的影响。DGGE图谱及依据其条带位置和亮度数值计算的多样性指数均显示:高氮处理[N3:225 kg(N).hm 2]的厌氧氨氧化菌群落结构多样性在表层或根层土壤中均显著(P<0.05)高于中、低氮[N2:150 kg(N).hm 2;N1:75 kg(N).hm 2]处理和不施肥对照(CK);同时,高氮处理下表层土壤厌氧氨氧化菌群落多样性指数显著高于根层土壤(P<0.05)。冗余分析(RDA)结果表明,表层土壤中厌氧氨氧化菌群落结构组成与不同氮肥水平处理存在显著相关性(P=0.006)。此外,本试验获得厌氧氨氧化菌DGGE条带DNA序列18条,登录GenBank并获得登录号。研究表明稻田厌氧氨氧化菌群落结构对高氮水平具有较强的响应,尤其是在表层土壤中。     

有机物料循环对红壤稻田系统有机质积累的贡献研究

中长期定位试验研究有机物料循环再利用对红壤稻田系统土壤有机质积累的贡献结果表明,红壤稻田系统有机物料自然归还量可达6 16 2kg/hm2 ,人为归还量可达13480kg/hm2 ;仅依靠系统内有机物料的自然归还,其土壤有机质亏缺为5 0 %左右,呈下降趋势;系统内可循环再利用的有机物料全部还田,土壤有机质盈余率可达80 %以上;预测结果显示有机物料循环再利用5 0年内可提高土壤有机质19.4～32 .6 g/kg ,增长率达83.6 %～14 0 .5 %     

两个水稻品种根际土壤细菌和氨氧化细菌的群落结构差异

通过根盒试验比较了籼稻汕优63和粳稻武运粳7号苗期不同采样期根际土和土体土壤的硝化强度以及氨氧化细菌数量的差异,并且采用16S rDNA PCR-DGGE(Denaturing gradient gel electrophoresis)指纹图谱技术比较分析了上述两种水稻苗期不同采样期根际和土体土壤中细菌及其氨氧化细菌的群落结构变化。结果表明,两个水稻品种根际土壤中硝化强度和氨氧化细菌的数量随着生育期的延长均表现出一定的正相关性,汕优63籼稻根部土壤中的细菌和氨氧化细菌的丰富度和群落变化特征随着水稻生育时期的延长较武运7号粳稻的变化更为多样,说明籼稻品种根系和根际硝化作用更强,在其根系附近会产生更多的硝态氮。这种差异性严重影响水稻植株对氮素的利用效率。     

土地管理方式对盐化水稻土生物地球化学机能的影响

Most lowlands in Northeast Thailand （Isaan region） are cultivated with rice and large areas are affected by salinity, which drastically limits rice production. A field experiment was conducted during the 2003 rainy season to explore the interactions between salinity and land management in two fields representative of two farming practices： an intensively managed plot with organic inputs and efficient water management, and one without organic matter addition. Field measurements, including pH, Eh, electrical conductivity （EC）, and soil solution chemistry, were performed at three depths, with a particular focus on Fe dynamics, inside and outside saline patches.
High reducing conditions appeared after flooding particularly in plots receiving organic matter and reduction processes leading to oxide reduction and to the release of Fe and, to a lesser extend, Mn to the soil solution. Oxide reduction led to the consumption of H^＋ and the more the Fe reduction was, the higher the pH was, up to 6.5. Formation of hydroxy-green rust were likely to be at the origin of the pH stabilization. In the absence of organic amendments, high salinity prevented the establishment of the reduction processes and pH value remained around 4. Even under high reduction conditions, the Fe concentrations in the soil solution were below commonly observed toxic values and the amended plot had better rice production yield.     

Nitrogen-fixing microorganisms in paddy soils (Part 3) distribution of non-sulphur purple bacteria in paddy soils

The possible significance of blue-green algae in the nitrogen economy of paddy soil has been pointed out by many investigators.     

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 16 S 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 Mg~(2+). 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.     

Nitrogen fixation in paddy soils

Several important features of the N. fixation in paddy fields which were reported previously were confirmed and some new additional results regarding the evaluation of the N₂ fixation in the rhizosphere were obtained by reinvestigation in the fields. In addition, rice plants were cultivated in the submerged soil in pots and various parts of the soil were analyzed for the N₂-fixing activity as well as several other properties. The results of the pot experiments were found to be fairly similar to those observed in the field investigations, indicating the validity of the submerged soil in a pot as a rather simulated model for the actual paddy field. By using this model system, the following facts were ascertained: (1) Water-percolation had almost no effect on the N₂-fixing activities of both the rhizosphere and the non-rhizosphere soils. (2) Suppressing effect of washing the root of rice plant on the N₂-fixing activity was slight in the seedling stage and marked in the tillering and flowering stages. (3) The N₂-fixing activity of a single rice root varied from tip to base.