转基因水稻秸秆还田对土壤硝化反硝化微生物群落的影响

转基因作物可能通过根系分泌物和植株残体组成的改变及外源基因的转移释放令土壤微生物群落产生变化,影响土壤微生物的生态功能。氨氧化细菌和反硝化细菌是驱动土壤硝化和反硝化过程的关键微生物,其群落结构的变化直接关系土壤氮素的转化与利用。本研究利用荧光定量PCR和PCR-DGGE技术分析了转cry1Ac/cpti双价抗虫基因水稻‘Kf8’秸秆还田降解过程中,土壤氨氧化细菌和反硝化细菌群落丰度与组成的变化,探讨转基因水稻是否存在影响稻田土壤氮素转化与N2O排放的可能。结果显示:无论是氨氧化细菌amo A基因还是反硝化细菌nirS基因,其丰度在转基因水稻‘Kf8’与非转基因水稻‘Mh86’的秸秆还田土壤中都没有显著差异;转基因水稻‘Kf8’和非转基因水稻‘Mh86’秸秆还田降解过程中0~10 cm土层中的amo A基因丰度均显著高于10~20 cm及20~30 cm土层(P0.05);各深度土层中的nirS基因丰度均存在随秸秆还田时间延长而增加的趋势。水稻秸秆还田降解过程中,转基因水稻‘Kf8’的土壤氨氧化细菌和反硝化细菌的群落多样性指数及组成,均与非转基因水稻‘Mh86’没有显著差异。相关分析结果表明土壤氨氧化细菌和反硝化细菌群落组成均与水稻秸秆还田时间存在显著相关性(P=0.002),反硝化细菌群落组成还与土层深度显著相关(P=0.024)。本研究表明转cry1Ac/cpti抗虫基因水稻秸秆还田对稻田土壤硝化和反硝化关键微生物群落不会产生明显影响。就土壤微生物群落而言,转cry1Ac/cpti抗虫基因水稻秸秆还田不存在影响土壤氮素转化与N2O排放的可能。     

抗真菌转基因水稻根际土壤真菌群落结构的动态变化

以非转基因水稻"七丝软粘"为对照,采用传统平板计数法和变性梯度凝胶电泳技术,研究了抗真菌转基因水稻"转品1"和"转品8"生长周期内对根际土壤中可培养真菌数和真菌群落结构的影响。结果显示,相同生育期转基因水稻根际土壤可培养真菌数量与其非转基因对照水稻相比较无显著性差异,表明转基因水稻的种植没有对根际土壤真菌数量产生明显影响;18S rRNA真菌群落DGGE图谱分析显示,相同生育期转基因水稻与其非转基因对照水稻的根际土壤真菌DGGE条带数量和条带位置均无显著性差异,表明转基因水稻的种植没有对根际土壤真菌群落结构产生明显影响。进一步分析相同生育期转基因水稻与其非转基因对照水稻的根际土壤真菌群落香农多样性指数(Shannon diversity index)和均匀度指数(Evenness index)的动态变化,发现两者均没有显著性差异。以上研究结果表明,外源抗真菌基因的导入对水稻根际土壤中真菌群落数量和群落结构均没有明显影响。此外,将不同位置的真菌DGGE条带切胶回收,克隆、测序后,进行系统进化树分析,结果表明根际土壤真菌群落主要归属为子囊菌门(Ascomycota)、担子菌门(Basidiomycota)、壶菌门(Chytridiomycota)、接合菌门(Zygomycota)和未知真菌(unknown fungi)5个类群。     

秸秆还田与施肥方式对稻麦轮作土壤细菌和真菌群落结构与多样性的影响

为探索秸秆还田与施肥方式2种农田措施对水稻-小麦(稻麦)轮作土壤微生物群落的影响,阐释其对土壤细菌和真菌群落结构和多样性的影响机制,本研究通过7年稻麦轮作长期定位监测试验,设置无肥空白(CK)、常规施肥(RT)、秸秆还田+常规施肥(RS)和秸秆还田+缓释肥(SS) 4个处理,采用Illumina Miseq高通量测序技术,分析土壤细菌和真菌群落结构和多样性,探索影响微生物群落的主控环境因子。结果表明, SS作物产量在2016年和2017年分别比RT显著提高11.6%和8.2%(水稻)、4.8%和3.6%(小麦),与RS无显著差异。相比RT,秸秆还田处理显著降低了土壤pH,提升了土壤有机碳和铵态氮含量;与RS相比,SS处理提高了铵态氮含量。秸秆还田处理提升了真菌群落多样性,但对细菌群落多样性无显著影响。SS与RS在细菌真菌群落多样性方面均无显著差异。相关性分析表明,细菌群落多样性与土壤pH呈负相关,与总氮含量呈正相关;真菌群落多样性则与土壤有机碳含量显著正相关。NMDS分析表明,施肥对于细菌群落结构影响较大(55.61%),真菌群落结构则对秸秆还田响应更明显(26.94%)。与RT相比,秸秆还田显著提升了细菌放线菌门、绿弯菌门、厚壁菌门的相对丰度,同时显著提升了真菌中子囊菌门的相对丰度,降低了担子菌门和接合菌门的相对丰度,加强了土壤碳氮循环能力并抑制了病原菌。SS与RS相比,仅提升了真菌中子囊菌门的相对丰度。综上,秸秆还田配施缓释肥有助于维持或者提高土壤养分有效性、作物产量及细菌真菌群落多样性,可以促进土壤碳氮循环。     

不同耕作方式下玉米秸秆还田对土壤真菌群落的影响

研究宁夏引黄灌区秸秆还田与籽粒直收玉米配套模式下不同耕作和秸秆还田方式对土壤真菌群落组成及功能的影响,探究土壤真菌群落对耕作和秸秆还田方式响应差异的生物学机制,为优化耕作与秸秆还田方式和提高农田土壤肥力提供理论依据。以宁夏引黄灌区秸秆还田与籽粒直收玉米连作农田土壤为研究对象,采用Illumina MiSeq高通量测序技术,分析2种耕作方式(免耕与深翻)与3种秸秆还田方式(不还田、秸秆半量还田与秸秆全量还田)定位试验条件下,玉米成熟期土壤真菌群落结构与功能的差异,并结合土壤理化性质,进一步探究农田土壤真菌群落结构及功能变化的环境驱动因子。结果表明,免耕结合秸秆半量覆盖还田处理土壤真菌多样性指数表现最优,免耕条件下秸秆不还田与秸秆半量还田处理土壤真菌OTU数均多于深翻,秸秆全量还田处理则相反。各处理优势真菌种群存在明显差异,子囊菌门、担子菌门、被孢菌门、粪壳菌纲、Symmetrospora属、被孢霉属和子囊菌属在各处理中相对丰度普遍较高;免耕处理对不同真菌物种存在不同的影响,可以促进参与木质素腐解的真菌生长发育,降低致病真菌的相对丰度。耕作方式对真菌群落组成的影响显著,免耕结合秸秆不还田、秸秆半量覆盖还田处理下土壤真菌群落组成稳定性较强,其余处理的土壤真菌群落组成稳定性则较差。各处理对真菌群落组成贡献较大的真菌物种存在差异。土壤理化性质与不同菌属的生长繁殖关系密切,主要优势菌属主要受土壤碱解氮、全磷、有效磷、容重的影响。本研究发现,不同耕作与秸秆还田方式改变了农田土壤真菌群落OTU数量、多样性参数以及群落组成,不同的土壤理化性质也是影响各真菌菌属生长繁殖的主要因素;免耕结合适宜的秸秆覆盖还田量能够促进土壤中易腐解秸秆的菌属生长繁殖,利于形成秸秆还田生态圈的良性循环,促进农田土壤生态系统稳定。     

秸秆还田对植烟土壤养分及真菌群落多样性的影响

通过2009~2012年的秸秆还田定位试验,研究不同用量小麦及玉米秸秆还田对植烟土壤养分及真菌群落多样性的影响。研究结果表明:有机质及速效养分指标均随秸秆还田量的增加而增加,且等量玉米秸秆还田效果优于小麦秸秆。PCR-DGGE的检测结果显示秸秆还田能一定程度提高土壤真菌群落的多样性,其中真菌丰度和香浓多样性指数随着玉米秸秆还田量的增加而增加,而小麦秸秆在中量还田时(4500 kg hm~(-2))多样性最高,且等量玉米秸秆还田在提高真菌多样性的效果优于小麦秸秆。此外,秸秆还田各处理土壤的真菌群落结构相似性较高,真菌多样性相似系数均大于0.73。特异条带的测序显示,与对照相比,小麦秸秆1500 kg hm~(-2)还田处理中,隐囊菌属真菌(Apanoascus)及毛壳属真菌(Chaetomium)出现,玉米秸秆还田7500 kg hm~(-2)处理,两种特异性的真菌类群(Uncultured Eukaryote和Fungal sp.CRS567818T-1)出现。且土壤真菌多样性与土壤有机质、全钾及碱解氮呈显著正相关。可见,秸秆还田能够增加土壤养分含量,提高烟田土壤真菌群落多样性,这有助于烟草土传病害控制、烟田生态系统的健康维护及其可持续发展。     

秸秆还田模式下种植密度对玉米根际土壤真菌群落的影响及其驱动因素分析

秸秆还田和适宜的种植密度有利于改良土壤理化性质,优化微生物群落结构。本研究采用Illumina MiSeq高通量测序技术,在宁夏引黄灌区玉米农田开展连续5a设置裂区试验,探讨不同秸秆还田模式(H1：秸秆粉碎深翻还田、H0：秸秆不还田)和种植密度(D1:67500株·hm^-2、D2:82500株·hm^-2、D3:97500株·hm^-2)下玉米成熟期根际土壤真菌多样性、群落结构的变化及其驱动因素。结果表明：(1)秸秆还田模式和种植密度两因素交互效应极显著提高了土壤真菌群落Chao1指数、ACE指数及香农指数(P<0.01),以H1D2处理下最高。(2)农田玉米根际土壤真菌群落主要由子囊菌门(63.50%～81.82%)、担子菌门(4.83%～18.03%)和被孢霉门(3.18%～9.61%)等14个门及509个属的真菌组成,真菌群落组成分析表明,秸秆还田模式各密度处理间群落结构不同,优势菌门和优势菌属相对丰度差异较大。(3)秸秆还田模式和种植密度两因素交互效应极显著降低土壤pH值,提高了有机质、碱解氮及速效磷含量(P&...     

麦秸秆和沼液配施对水稻苗期生长和土壤微生物的调控

研究了等量氮素肥料处理下小麦秸秆全量还田结合化肥(S-CF)、小麦秸秆全量还田结合沼液(S-BS)和全量化肥(CF)处理对水稻幼苗生长、氮磷积累及土壤微生物群落的影响。结果表明,不同施肥处理的水稻幼苗生长明显被促进,其中CF处理的促进效果最好,其次是S-BS处理。S-BS处理的水稻叶片可溶性糖含量明显高于其他施肥处理,其叶片含氮量也明显高于CF处理。CF处理的土壤细菌总量明显高于S-BS处理,而S-BS处理的土壤细菌总量均显著高于对照(CK,不施肥)和S-CF处理;其中CF处理变形菌门细菌相对丰度显著高于其他处理。而CK和S-CF处理的真菌总量明显高于S-BS和CF处理,S-BS处理的真菌总量最低,其中,CK土壤优势真菌子囊菌门、担子菌门的相对丰度显著高于其他处理,S-CF处理土壤的壶菌门真菌相对丰度也显著高于其他处理。S-CF和S-BS处理的细菌Chao1丰富度指数和香农(Shannon)多样性指数要明显高于CF处理和CK,而S-CF处理的土壤真菌的Chao1指数和香农指数要明显高于CK,CF处理的土壤真菌Chao1指数和香农指数最低。秸秆、沼液短期替代化肥的处理下水稻植株生长低于全化肥处理的,但秸秆、沼液、化肥结合施用对水稻幼苗的促生作用依然很明显,尤其是秸秆还田结合沼液灌溉的全量替代化肥处理。全量替代化肥处理下,即秸秆和沼液处理的土壤质量和细菌丰富度及多样性即使在短期施用条件下也被明显促进。     

稻秸对土壤细菌群落分子多态性的影响

模拟稻秸原位还田条件,分别在水稻土和红壤中添加水稻秸秆培养70d ,第0、5、2 5、4 5、70天采集土样。采用非机械破壁法直接提取水稻土和红壤细菌总DNA ,水稻土细菌总DNA经过二次纯化;红壤细菌总DNA经过一次纯化后,PCR扩增其16SrDNAV3可变区,均可获得清晰的目的条带,对扩增产物进行DGGE分析,结果显示:水稻土和红壤样品的DGGE条带增加,说明稻秸能够增加土壤细菌群落分子多态性的丰富度,随着培养期的延长,施有稻秸的处理中土壤细菌群落多态性的变化远远复杂于空白对照土壤中的细菌群落变化;同时发现在稻秸刺激下不同土壤细菌群落多态性高峰期出现时间不同     

稻田土壤真菌群落多样性和组成对麦秸还田的响应

在室内模拟试验下,采用常规分析和高通量测序技术,研究了淹水培养30 d后,不同量小麦秸秆(0、10、20和50 g/kg)施用下两种类型的稻田土壤(高砂土和黄泥土)真菌群落多样性和组成的演替规律及其驱动因子。结果表明:秸秆还田显著降低了高砂土真菌群落多样性并改变了高砂土真菌群落组成,但不同量秸秆还田下,高砂土真菌群落组成并无显著性差异;而秸秆还田对黄泥土真菌群落多样性并无显著影响,与未施用秸秆相比,低秸秆施用量(10和20 g/kg)并未显著改变黄泥土中真菌群落组成,而当秸秆施用量为50 g/kg时,黄泥土真菌群落组成明显迁移。进一步的典范相关分析(CCA)发现,pH、EC和有机质(SOM)是影响秸秆还田后高砂土真菌群落迁移的重要因子,而pH、EC、SOM和碳氮比(C/N)是影响秸秆还田后黄泥土真菌群落迁移的主要调控因子。综合分析认为,秸秆还田主要通过改变土壤性质来调控真菌群落结构,而不同类型土壤的真菌群落多样性和组成对秸秆还田的响应不同。     

铜梁县秸秆还田施用腐熟剂试验研究

研究了秸秆还田和施用不同腐熟剂品种处理对秸秆腐烂速度、土壤理化性质,以及中稻经济性状和产量的影响。结果表明:(1)秸秆还田对增加土壤有机质,改善土壤理化性状,提供有机肥源,提高水稻产量等方面具有较明显的效果。(2)秸秆还田施用不同品种腐熟剂间的水稻产量基本没有差异;但秸秆还田处理的水稻产量极显著优于不秸秆还田处理;秸秆还田施用腐熟剂处理极显著优于不施腐熟剂处理和单一秸秆还田处理。     

Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem, estimated by denaturing gradient gel electrophoresis

Diversity of methanogenic archaeal communities in Japanese paddy field ecosystem was evaluated by the denaturing gradient gel electrophoresis (DGGE) after PCR amplification of the 16S rRNA genes (16S rDNAs), sequencing analysis and data evaluation by principal component analysis. Data were obtained from samples collected from the plowed soil layer, rice roots, rice straws incorporated in soil, plant residues (mixture of weeds, rice litters, rice roots, and rice stubbles) in soil, and composing rice straw. The number of bands of DGGE profiles ranged from 12 to 26 with the highest numbers in rice roots and rice straws incorporated in soil. However, the diversity indices based on both the numbers and intensity of bands indicated that the community of the plowed soil layer was the most diverse, even, and stable. Sequencing of the main DGGE bands showed the presence of Methanomicrobiales, Methanosarcinales, Methanobacteriaceae, and Methanocellales. The plowed soil layer included all phylogenetic groups of the methanogenic archaea of the other studied habitats, with prevalence of the members of Methanomicrobiales and Methanocellales. The phylogenetic diversity was compared with that of paddy soils collected in Italy, China, and the Philippines and that of 12 anaerobic environments (fen, waste, coast, permafrost, natural gas field, bovine rumen, riparian soil, termite, ciliate endosymboints, lake sediment, landfill, and seep rumen). The phylogenetic diversity was more similar among paddy soils than with the other anaerobic environments. Probably, the methanogenic archaeal communities of the paddy field soils were characterized by indigenous members and some of the members of the community of the plowed soil layer colonized rice roots, rice straws, and plant residues.     

Molecular characterization of methane-oxidizing bacteria associated with rice straw decomposition in a rice field

Abstract

Methane-oxidizing bacteria (MOB) are crucial to the reduction of CH₄ emitted to the atmosphere. However, it is unclear how MOB in rice straw are affected by straw decomposition processes. In a Japanese rice field, a year-round experiment was set up to study the effects of agricultural practice (rice cultivation/winter fallow), straw parts (leaf sheath/blade) and the site of straw placement (plow layer/soil surface) on MOB communities in rice straw using denaturing gradient gel electrophoresis (DGGE) and DNA sequencing analyses of key MOB functional genes (pmoA and amoA). Thirty-eight different DGGE bands were observed over the entire investigation period. Principal component analysis of DGGE pattern suggested that agricultural practice is the key factor regulating the MOB communities. Sequencing of dominant DGGE bands showed that: (1) during the rice cultivation period, methanotrophs (particularly type I methanotrophs) dominated the MOB community, (2) during the winter fallow season both type I and type II methanotrophs were dominant in sheath segments placed both on the soil surface and in the plow layer, whereas ammonia oxidizers seemed to dominate blade segments placed in the plow layer. Alignment of diagnostic amino acid sequences of MOB suggested the presence of novel ammonia oxidizers in rice straw in rice fields.     

Soil microbial community responses to Bt transgenic rice residue decomposition in a paddy field

Purpose

Genetic modifications (GM) of commercial crops offer many benefits. However, microbial-mediated decomposition might be affected by GM crop residues in agricultural ecosystems. The objective of this study was to assess the possible impacts of cry1Ab gene transformation of rice on soil microbial community composition associated with residue decomposition in the paddy field under intensive rice cultivation.

Materials and methods

A 276-day field trial was set up as a completely randomized design for two types of rice residues, KMD (Bt) and Xiushui 11 (non-Bt parental variety) in triplicate by conventional intensive rice cropping system. The litterbag method was used in the rice residue decomposition and a total of 120 straw and root litterbags were either placed on the soil surface or buried at 10 cm depth in the field on Dec. 24, 2005. The litterbags were sampled periodically and their soil bacterial and fungal communities were determined by terminal restriction fragment length polymorphism (T-RFLP). The additive main effects with multiplicative interaction (AMMI) model were performed for the analysis of T-RFLP on binary variables of peak presence (presence/absence). The analysis of variance and linear regressions were performed for analysis of AMMI data.

Results and discussion

Total AMMI model analysis revealed that microbial community composition in the litterbags was affected by temporal and spatial factors. Compared with the non-Bt rice residue treatment, Bt rice straw had no significant effects on the soil bacterial and fungal community composition during the study period, regardless of the litterbags being placed on the surface or buried in the soil. There were no significant differences in the bacterial community composition profiles in root decomposition between Bt transgenic and non-Bt varieties. However, significant differences in soil fungal community composition between the buried Bt and non-Bt rice roots were observed in soils sampled on days 31, 68, and 137, indicating that Bt roots incorporated into paddy soil may affect soil fungal community during the initial stage of their decomposition.

Conclusions

There were some significant differences in fungal community composition between Bt rice root and non-Bt root treatments at the early stage of root decomposition in the paddy field. It is important that, before Bt rice is released for commercial production, more research should be conducted to evaluate the ecological effects of the Bt rice residues returned to paddy field upon grain harvesting.     

Cyanobacterial communities of rice straw left on the soil surface of a paddy field

To estimate diversity, seasonal variation, and phylogeny of the cyanobacterial communities in rice straw placed in nylon mesh bags and left on the soil surface of a paddy field, total DNA was extracted from straw, amplified by polymerase chain reaction targeting 16S rRNA genes of cyanobacteria, and the amplicons were separated by denaturing gradient gel electrophoresis (DGGE). These DGGE bands were sequenced. The paddy field was under flooded condition after transplanting of rice (Experiment 1) and under drained conditions after harvest (Experiment 2). The residual samples on the soil surface under upland conditions were collected just before spring plowing and were placed again on the soil surface after transplanting under flooded conditions. DGGE band patterns of cyanobacterial communities of rice straw were different under drained conditions, under flooded conditions when fresh rice straw samples were placed (Experiment 1), and under flooded conditions when residual rice straw samples were replaced (Experiment 2), indicating that the communities were influenced by both water regime of the paddy field and the degree of the rice straw decomposition. Sequence analysis of DGGE bands indicated that most of the cyanobacteria in rice straw on the soil surface in the paddy field were filamentous members belonging to Subsections III and IV. Filamentous cyanobacterial cells were observed in rice straw under flooded conditions by epifluorescence microscopy.     

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.     

Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

By using cultivation-independent techniques, community changes of methane-oxidizing bacteria (MOB) in rice bulk soils were investigated under field conditions in a Japanese rice field. The representative soil samples were collected during the typical rice growing season and nonrice growing period all year round. Statistical characterization of denaturing gradient gel electrophoresis (DGGE) community patterns of MOB pmoA/amoA functional gene fragments showed that MOB community structures in the rice bulk soils remained largely unchanged throughout the investigated period. The total intensity of six common DGGE bands that appeared consistently throughout the investigated period accounted for 64% of the total intensity of all 18 different DGGE bands detected. The low squared distance of the Ward cluster analysis of the DGGE pattern and the high Sorensen similarity coefficient (81%) also implied the high similarity of the MOB community structures. The stable MOB community structure did not couple well with the wide variation of soil water contents all year round. Sequencing analysis of the nine characteristic bands including six common bands revealed the presence of Type I, Type II methanotrophs, and β-proteobacterial ammonia oxidizers in rice bulk soils. In comparison with MOB type species, three DGGE bands showed a wide variation of the highly conserved amino acid residues, implying the presence of novel MOB bacteria inhabiting the rice bulk soil. The high diversity of MOB composition suggested that rice bulk soils might serve as an ideal reservoir for the dynamic changes of MOB in a rice field ecosystem in response to environment changes.     

Two-year field study shows little evidence that PPO-transgenic rice affects the structure of soil microbial communities

There is global concern about the environmental consequences associated with transgenic crops. Their effects on the soil ecosystem are of special interest when assessing ecological safety and integrity. Although many efforts have been made to develop crops genetically modified to have resistance to protoporphyrin oxidase (PPO)-inhibiting herbicides, little is known about their influence on soil microbial communities. We conducted a 2-year field study and an analysis via terminal restriction fragment length polymorphism (T-RFLP) to assess the impacts of PPO-transgenic rice on bacterial and fungal communities. In the first year we sampled the rhizosphere and surrounding bulk soil, while in the second year we sampled rhizosphere soil only. No differences were observed in the diversity indices and community composition of microbial communities between transgenic rice and its parental non-transgenic counterpart (cultivar Dongjin). Instead, community variation was strongly dependent on growth stage and year. Therefore, we observed no adverse effects by these crops of modified rice on the microbial community composition in paddy soils.     

Succession and phylogenetic profile of eukaryotic communities in rice straw incorporated into a rice field: Estimation by PCR-DGGE and sequence analyses

Abstract

Succession and the phylogenetic profile of eukaryotic communities associated with rice straw decomposition in a rice field were studied using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by 18S rDNA sequencing. Nylon mesh bags containing leaf sheaths or blades were buried in the plow layer of a rice field under flooded conditions after transplanting (Experiment 1) and under drained conditions during the off-crop season (Experiment 2). In addition, rice straw samples in Experiment 2 were taken out before plowing in spring and re-placed in the rice field under flooded conditions at transplanting. Statistical analyses based on DGGE patterns showed that eukaryotic communities were divided into two groups, namely group A before the placement in soil, after the mid-season drainage in Experiment 1 and under the drained conditions in Experiment 2 and group B before the mid-season drainage in Experiment 1 and under the flooded conditions in Experiment 2. Based on the sequence analysis of DGGE bands, which characterized the eukaryotic communities, succession of the communities was revealed, that is, most of the bands in group A were closely related to fungi, whereas the bands in group B were closely related to protozoa. These results indicated that eukaryotic communities associated with rice straw decomposition in the rice field are mainly affected by soil conditions, such as oxic or reduced conditions, irrespective of rice straw parts (leaf sheaths and blades).