不同类型水稻土微生物群落结构特征及其影响因素

选取基于我国土壤地理发生分类的不同类型土壤发育的四种水稻土,利用¹⁵N₂气体示踪法测定生物固氮速率,采用实时荧光定量PCR（Real-time PCR）技术测定细菌丰度,通过16S rRNA基因高通量测序分析微生物群落组成和多样性。结果表明：变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）、绿弯菌门（Chloroflexi）和蓝藻门（Cyanobacteria）是水稻土中优势微生物类群。四种类型土壤发育的水稻土细菌群落结构差异显著（Stress<0.001）,群落结构分异（NMDS1）与土壤pH存在极显著正相关关系（P<0.01）。土壤有机碳和碱解氮含量显著影响水稻土中细菌丰度和群落多样性（P<0.01）。红壤发育的水稻土细菌16S rRNA基因拷贝数显著高于其他三种类型水稻土,但OTU数量、Chao1指数和PD指数均低于其他三种类型水稻土。土壤pH对水稻土生物固氮速率有显著影响（P<0.01）,紫色土发育的水稻土具有最高的生物固氮速率（3.2±0.7 mg×kg^-1×d^-1）,其中优势类群细鞘丝藻属（Leptolyngbya）可能是生物固氮的主要贡献者。研究结果丰富了对水稻土微生物多样性的认识,为通过调控土壤pH和微生物群落组成来提高稻田生物固氮潜力提供了理论依据。     

氮肥水平对稻田细菌群落及N2O排放的影响

作为土壤氮素转化的驱动者,微生物群落结构关系着稻田氮素利用及温室气体N_2O排放等问题。本研究分别基于高通量测序和荧光定量PCR技术,分析了不同氮肥水平[CK(不施氮)、N(施N 180 kg·hm-2)、2/3N(施N 120 kg·hm-2)、1/3N(施N 60 kg·hm-2)]下稻田细菌群落及硝化反硝化关键微生物功能基因丰度的变化。结果显示:氮肥水平提高增加了稻田细菌物种丰富度Chao1指数和群落多样性Shannon指数,改变了细菌群落组成,其中与硝化作用相关的硝化螺菌门Nitrospirae和嗜酸的醋杆菌门Acidobacteria的相对丰度随氮肥水平提高而增加,但甲烷氧化菌Methylosinus的相对丰度随氮肥水平提高而降低。氮肥水平对稻田硝化作用关键微生物氨氧化细菌amo A基因丰度的影响较大,0~5 cm和10~20 cm深度土层中的amo A基因丰度均随氮肥用量增加而提高;反硝化作用关键微生物功能基因nir S、qno B和nos Z的丰度在不施肥处理(CK)中显著低于施肥处理(1/3N、2/3N和N)(P0.05),但1/3N、2/3N和N处理的稻田nir S基因丰度没有明显差异;0~5 cm土层中qno B和nos Z基因丰度存在随氮肥水平提高而增加的趋势,10~20 cm土层中nos Z基因丰度在2/3N和N处理下显著高于1/3N处理(P0.05)。N处理的稻田N_2O排放通量显著高于2/3N及1/3N处理(P0.05),后者又显著高于CK处理(P0.05)。相关分析结果表明稻田N_2O排放通量与0~5 cm土层中硝化螺菌门Nitrospirae相对丰度及10~20 cm土层中amo A基因丰度存在显著相关性(P0.05,n=10)。综上所述,氮肥水平提高增加了稻田细菌群落多样性,促进了稻田N_2O排放,且本研究稻田中硝化作用微生物群落及丰度变化与稻田N_2O排放的关系更为密切。     

Analysis of bacterial communities in soil by PCR-DGGE targeting protease genes

We studied the effects of the application of organic (OM) and inorganic fertilizer (CF) on soil protease activity and proteolytic bacterial communities in rhizosphere and bulk soil on an experimental lettuce field in Hokkaido, Japan. The protease activity always was higher in soils of the OM than with the CF treatment, and also higher in the rhizosphere than in the bulk soil. We analyzed proteolytic bacterial communities by denaturing gradient gel electrophoresis (DGGE) of the alkaline metalloprotease (apr) and neutral metalloprotease (npr) genes. Most apr forms detected were closely related to apr of Pseudomonas fluorescens, and all npr variants closely resembled the gene of Bacillus megaterium. These results were consistent with findings from tests using cultured bacterial communities, indicating a high specificity of our PCR-DGGE for amplifying apr and npr genes. The community compositions of proteolytic bacteria were assessed by principal component analysis of the DGGE profiles. There were significant differences in the effects of CF and OM on the community compositions of apr- and npr-expressing bacteria, and the communities of the two types of bacteria played different roles in rhizosphere and bulk soil. We found significant correlations between the protease activity and the communities of the two types of bacteria. The results indicate that different proteolytic bacteria release different amounts or activities of protease, and that the composition of proteolytic bacterial communities may play a major role in determining overall soil protease activity.     

设施种植模式对土壤细菌多样性及群落结构的影响

为了研究有机和常规设施种植模式及轮作对土壤细菌多样性和群落结构的影响,本研究采用Illumina平台Hiseq 2500高通量测序技术,于2016年6月(作物处于收获期)对北京市顺义区不同设施种植模式(分别为有机设施种植模式和常规设施种植模式下的叶菜连作、茄果连作和叶茄轮作)下土壤细菌进行16S r RNA测序。测序质控后共获得17 278个操作分类单元(operational taxonomic units,OTUs),共计318 851条有效序列。比较不同种植模式和轮作下土壤细菌多样性、细菌群落结构组成、相对丰度及土壤理化性质与细菌群落多样性关系的差异性。结果表明:土壤微生物群落结构在有机和常规设施种植模式下差异明显,有机设施种植土壤细菌多样性高于常规设施种植;有机设施种植下轮作与连作土壤细菌群落结构表现出明显差异,而常规设施种植下,两者没有明显差异;有机种植模式下,轮作土壤细菌群落多样性高于连作土壤;设施种植土壤细菌群落主要属于鞘氨醇单胞菌属(Sphingomonas,5.05%)和芽孢杆菌属(Bacillus,4.84%),相对丰度大于0.5%的共有14个属。有机设施种植土壤含有较多促进植物生长、有机质分解的细菌,常规设施种植土壤中降解化学杀虫剂、防治土壤病害、促进硝化过程的细菌较多。RDA分析结果显示土壤细菌群落主要受全磷、速效磷、有机质的影响。Tumebacillus、Candidatus Solibacter和Acidothermus都是分解有机质、利用碳源的细菌属,与土壤有机质含量呈正相关关系。由此可见,设施条件下,有机和常规种植土壤微生物群落结构的差异性主要源于肥料使用、有害生物防治措施和管理方式的不同。有机设施种植模式下,轮作更有利于发挥其改良土壤营养循环和防治土壤病虫害的作用。上述结果为在微生物水平上研究设施条件下不同种植模式的土壤生态质量差异提供了参考。     

黄土丘陵沟壑区典型林地土壤微生物、酶活性和养分特征

通过对陕西吴起县黄土沟壑区退耕还林地不同林分(沙棘、刺槐、油松、小叶杨)根际与非根际土壤养分、酶活性和微生物特征进行研究,比较4种典型林分及退耕草地“根际效应”及根际对养分的截留效应,评价根际效应对土壤特性产生不同改良效果,为黄土沟壑区退耕地人工林科学选择造林树种提供理论支持。研究表明:1根际与非根际土壤中有机质含量、有效磷含量、碱解氮含量和速效钾含量表现出显著差异,有机质、有效磷、速效钾含量均呈现明显的根际聚集现象。2根际土壤微生物数量和土壤酶活性总体高于非根际,仅油松样地中过氧化氢酶活性和小叶杨样地中脲酶活性根际低于非根际。3根际土壤中脲酶活性与细菌和真菌数量相关性达到显著水平,过氧化氢酶活性与真菌相关性达到显著水平;有机质含量与细菌、放线菌数量和脲酶活性相关性达到显著水平;碱解氮、有效磷含量均与细菌、真菌数量和脲酶活性相关性达到显著水平。在非根际土壤中,土壤养分含量与土壤微生物、土壤酶活性的相关性明显降低。4从土壤肥力综合水平看,根际土壤肥力水平综合得分总体上大于非根际土壤,其中根际土壤中沙棘小叶杨油松刺槐草地。沙棘能大幅度提高土壤肥力,具有较好的土壤改良效果。     

不同施肥处理稻田系统磷素输移特征研究

磷是水体富营养化限制性元素,近年来由于磷肥的过量施用,农田迁移的磷素已成为水体磷素的主要来源。本研究通过野外测坑定位试验,研究有机肥处理(OT)、混施肥处理(MT)和化肥处理(CT)3种施肥处理下,稻田中磷素的迁移流失特征及这3种处理对水稻产量和磷素利用率的影响,以探求稻田系统的最佳施磷方式。结果表明,CT、MT和OT 3种施肥方式的磷径流流失负荷分别为0.56 kg(P)·hm-2、1.13 kg(P)·hm-2和4.20 kg(P)·hm-2,渗漏流失负荷分别为0.42 kg(P)·hm-2、0.44 kg(P)·hm-2和0.45 kg(P)·hm-2;磷的径流流失占流失总量的56.86%~90.38%,是水稻田磷素流失的主要途径。磷的径流流失主要受施肥和降雨的影响,50%左右磷的流失发生在第1次径流过程;磷素渗漏流失特征不受施磷处理的影响,80%以上的流失发生在施肥后的前30 d。在磷素流失形态上,坑面水、渗漏水和径流水中磷素的主要形态均为可溶性磷;在土壤方面,MT处理和OT处理能保证土壤磷营养,CT处理的土壤有效磷和有机质含量则显著下降。3种施肥处理的水稻产量显著高于空白对照,且MT最高,为6 728.84 kg·hm-2;磷肥利用率CT和MT处理显著高于OT,CT和MT间差异不显著。综合比较,混施肥处理在磷素流失、土壤养分利用和水稻产量等方面更符合我国生态农业发展的要求。     

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。     

氮肥对稻田土壤反硝化细菌群落结构和丰度的影响

以氮肥田间定位试验为研究对象,利用PCR-DGGE(聚合酶链反应变性梯度凝胶电泳)和荧光定量PCR(real-time PCR)技术,通过对反硝化细菌nirS基因的检测,分析了定位试验第2年稻田反硝化细菌群落结构和丰度的变化。DGGE图谱及依据其条带位置和亮度数字化数值进行的主成分分析(PCA)结果均显示:在氮肥定位试验第2年,与不施肥对照(CK)比较,在水稻各个生育期(分蘖期、齐穗期和成熟期)内,施用氮肥[150kg(N)·hm-2]的稻田根层土或表土中的反硝化细菌群落结构均无明显变化;且稻田根层土或表土中的反硝化细菌群落结构在水稻各个生育期间也均无明显差异。荧光定量PCR结果显示,在水稻生长发育过程中,施用氮肥的稻田根层土或表土中的反硝化细菌nirS基因拷贝数始终显著(P<0.05)高于其对应的不施肥对照。此外,无论施用氮肥与否,根层土中的反硝化细菌nirS基因拷贝数在水稻成熟期时都会显著(P<0.05)降低;但表土中的nirS基因拷贝数在水稻各生育期间无明显变化;且水稻成熟期时施用氮肥和不施肥的稻田表土中nirS基因拷贝数都显著(P<0.05)高于根层土。同时,与对照比较施用氮肥可促进水稻增产44%。研究表明,短期定位试验中施用氮肥能够显著提高稻田土壤反硝化细菌的丰度,但对其群落结构没有明显影响。     

Effect of land use on the abundance and diversity of autotrophic bacteria as measured by ribulose-1,5-biphosphate carboxylase/oxygenase (RubisCO) large subunit gene abundance in soils

Elucidating the biodiversity of CO₂-assimilating bacterial communities under different land uses is critical for establishing an integrated view of the carbon sequestration in agricultural systems. We therefore determined the abundance and diversity of CO₂ assimilating bacteria using terminal restriction fragment length polymorphism and quantitative PCR of the cbbL gene (which encodes ribulose-1,5-biphosphate carboxylase/oxygenase). These analyses used agricultural soils collected from a long-term experiment (Pantang Agroecosystem) in subtropical China. Soils under three typical land uses, i.e., rice–rice (RR), upland crop (UC), and paddy rice–upland crop rotation (PU), were selected. The abundance of bacterial cbbL (0.04 to 1.25?×?10⁸ copies g^?1 soil) and 16S rDNA genes (0.05–3.00?×?10¹⁰ copies g^?1 soil) were determined in these soils. They generally followed the trend RR?>?PU?>?UC. The cbbL-containing bacterial communities were dominated by facultative autotrophic bacteria such as Mycobacterium sp., Rhodopseudomonas palustris, Bradyrhizobium japonicum, Ralstonia eutropha, and Alcaligenes eutrophus. Additionally, the cbbL-containing bacterial community composition in RR soil differed from that in upland crop and paddy rice–upland crop rotations soils. Soil organic matter was the most highly statistically significant factor which positively influenced the size of the cbbL-containing population. The RR management produced the greatest abundance and diversity of cbbL-containing bacteria. These results offer new insights into the importance of microbial autotrophic CO₂ fixation in soil C cycling.     

Rhizosphere microbial communities and organic acids secreted by aluminum-tolerant and aluminum-sensitive soybean in acid soil

This study aimed to investigate the correlation between organic acids secreted by two soybeans genotypes, BX10 [aluminum (Al) tolerant] and BD2 (Al sensitive) and rhizosphere microbial communities in acid soil. The organic acids secreted by BX10 and BD2 were significantly different at each growth stage. Both fungi/bacteria and gram-negative bacteria/gram-positive bacteria ratio values were affected by the two soybean genotypes at different growth periods. Compared with BD2, phospholipid fatty acid of BX10 showed higher Shannon diversity at the seedling and flowering stages, but had lower Shannon diversity at the pod-setting stage. Redundancy analysis and canonical correspondence analysis revealed that the organic acids including tartaric acid, lactic acid, and citric acid significantly affected rhizosphere bacterial communities. Sequence analysis indicated that uncultured Acidobacterium, Chloroflexi, and actinomycete enriched in BD2, whereas some uncultured bacteria enriched in BX10. The two soybean genotypes exhibit distinct rhizosphere microbial communities; root organic acid exudates may affect composition of microbial communities of rhizosphere soil: tartaric acid may negatively affect rhizosphere bacteria at the seedling stage, lactic acid may positively affect rhizosphere actinomycetes at the flowering stage, and succinic acid may stimulate fungi at the pod-setting stage.     

A DGGE analysis shows that crop rotation systems influence the bacterial and fungal communities in soils

A better understanding of the relationships among different cropping systems, their effects on soil microbial ecology, and their effects on crop health and productivity is necessary for the development of more efficient, sustainable crop production systems. We used denaturing gradient gel electrophoresis (DGGE) to determine the impacts of crop rotations and crop types on bacterial and fungal communities in the soil. The communities of bacterial 16S rRNA genes and fungal 18S rRNA genes were analyzed in experimental field plots that were kept under 4 different crop rotation systems from 1999 to 2008 (continuous cabbage (Brassica oleracea var. capitata L.), cabbage–lettuce (Lactuca sativa L.) rotation, cabbage–radish (Raphanus sativus L. var. longipinnatus L.H. Bailey) rotation, and a 3-year crop rotation). A principal component analysis (PCA) and a canonical correspondence analysis (CCA) revealed that both the bacterial and fungal communities in bulk soils were influenced by the crop rotation systems. However, the primary factors influencing each community differed: bacterial communities were most affected by soil properties (especially carbon content), while fungal communities were influenced most strongly by rotation times. To elucidate factors that may cause differences in crop rhizosphere microbial communities, the microbial communities in the harvested cabbage rhizospheres were also analyzed. The results suggest that the fungal communities in bulk soil are related to the rhizosphere fungal communities. Our present study indicates that the microbial communities in bulk and rhizosphere soils could be managed by crop rotation systems.     

水稻根际和周围土壤中微生物功能基因丰度与碳、氮状况及其通量之间的关系

Rapid nitrogen（N） transformations and losses occur in the rice rhizosphere through root uptake and microbial activities. However,the relationships between rice roots and rhizosphere microbes for N utilization are still unclear. We analyzed different N forms（NH＋4,NO-3, and dissolved organic N）, microbial biomass N and C, dissolved organic C, CH4 and N2O emissions, and abundance of microbial functional genes in both rhizosphere and bulk soils after 37-d rice growth in a greenhouse pot experiment. Results showed that the dissolved organic C was significantly higher in the rhizosphere soil than in the non-rhizosphere bulk soil, but microbial biomass C showed no significant difference. The concentrations of NH＋4, dissolved organic N, and microbial biomass N in the rhizosphere soil were significantly lower than those of the bulk soil, whereas NO-3in the rhizosphere soil was comparable to that in the bulk soil. The CH4 and N2O fluxes from the rhizosphere soil were much higher than those from the bulk soil. Real-time polymerase chain reaction analysis showed that the abundance of seven selected genes, bacterial and archaeal 16 S rRNA genes, amoA genes of ammonia-oxidizing archaea and ammonia-oxidizing bacteria, nosZ gene, mcrA gene, and pmoA gene, was lower in the rhizosphere soil than in the bulk soil, which is contrary to the results of previous studies. The lower concentration of N in the rhizosphere soil indicated that the competition for N in the rhizosphere soil was very strong, thus having a negative effect on the numbers of microbes. We concluded that when N was limiting, the growth of rhizosphere microorganisms depended on their competitive abilities with rice roots for N.     

基于高通量测序的两种植被恢复类型根际土壤细菌多样性研究

为研究库布齐沙地生态恢复过程中不同植被恢复类型土壤微生物细菌群落结构、多样性的变化特征,以流动沙地为对照,运用高通量测序技术,对自然恢复的油蒿群落、人工种植的中间锦鸡儿群落根际和非根际土壤细菌多样性进行了研究,并分析了土壤理化性质对其分布的影响。结果表明:(1)与流沙对照相比,两种植被恢复类型对细菌多样性产生了正效应,细菌群落丰度、多样性和均匀度明显增加。其中,自然恢复的油蒿群落土壤细菌丰度高于人工种植的中间锦鸡儿群落;(2)变形菌门、酸杆菌门和放线菌门为研究区土壤中的优势细菌类群,其中变形菌门在各样地丰度比例最高,变形菌的4个亚群变化趋势一致,α-变形菌相对含量在油蒿和中间锦鸡儿群落根际土壤中明显增加,尤其是自然恢复的油蒿群落根际土壤中α-变形菌得到了很好的恢复;(3)土壤有机质、全氮、速效氮、速效钾含量和土壤含水量是影响土壤细菌群落丰度和多样性的主要土壤因子,典型相关分析表明土壤有机质、全氮、全钾、速效钾、速效氮含量对于研究区土壤细菌群落遗传多样性的变化起着重要作用。     

Paddy management on different soil types does not promote lignin accumulation

Paddy soil management is generally thought to promote the accumulation of soil organic matter (SOM) and specifically lignin. Lignin is considered particularly susceptible to accumulation under these circumstances because of the recalcitrance of its aromatic structure to biodegradation under anaerobic conditions (i.e ., during inundation of paddy fields). The present study investigates the effect of paddy soil management on SOM composition in comparison to nearby agricultural soils that are not used for rice production (non‐paddy soils). Soil types typically used for rice cultivation were selected, including Alisol, Andosol and Vertisol sites in Indonesia (humid tropical climate of Java) and an Alisol site in China (humid subtropical climate, Jiangxi province). These soil types represent a range of soil properties to be expected in Asian paddy fields. All upper‐most A horizons were analysed for their SOM composition by solid‐state ¹³C nuclear magnetic resonance (NMR) spectroscopy and for lignin‐derived phenols by the CuO oxidation method. The SOM composition was similar for all of the above named parent soil types (non‐paddy soils) and was also not affected by paddy soil management. A substantial proportion (up to 23%) of the total aryl‐carbon in some paddy and non‐paddy soils was found to originate from condensed aromatic‐carbon (e.g ., charcoal). This may be attributed to the burning of crop residues. On average, the proportion of lignin was low and made up 20% of the total SOM, and showed no differences between straw, particulate organic matter (POM), and the bulk soil material. The results from CuO oxidation are consistent with the data obtained from solid‐state ¹³C NMR spectroscopy. The extraction of lignin‐derived phenols revealed low VSC (vanillyl, syringyl, cinnamyl) values for all investigated soils in a range (4 to 12 g kg⁻¹ OC) that was typical for agricultural soils. In comparison to adjacent non‐paddy soils, the data do not provide evidence for a substantial accumulation of phenolic lignin‐derived structures in the paddy soils, even for those characterized by higher organic carbon (OC) contents (e.g ., Andosol‐ and Alisol (China)‐derived paddy soils). We conclude that the properties of the parent soil types are more important for the lignin content of the soils than the effect of paddy management itself.     

Characterization of nitrifying bacteria communities of soils from different ecological regions of China by molecular and conventional methods

Soil nitrification rate is very different among soil types, as a result of differences in physical and chemical properties. Little is known about the composition of the nitrifying bacteria community. In this investigation, three soils (fluvo-aquic soil, permeable paddy soil and red earth) from different geo-ecological regions in China were characterized for their nitrification activities and their nitrifying bacteria communities determined either by molecular approaches or by conventional culture methods. A 28-day long-term soil incubation showed that the maximum nitrification potential was found in the fluvo-aquic soil with almost 100% of inorganic N present as NO₃^–-N, while the minimum nitrification potential was in red earth with only a 4.9% conversion rate from ammonium into nitrate. There was no relationship between nitrification potential and numbers of nitrifiers in the soil. The conventional most probable number (MPN) method could enumerate ammonia oxidizers, but failed in enumerating nitrite oxidizers. Therefore, we used an MPN-PCR procedure which gave a convincing nitrite oxidizer count result, instead of MPN-diphylamine. Soils were characterized by denaturing gradient gel electrophoresis (DGGE) of DNA extracted from soils and amplified using a primer specific for the 16S rRNA gene and/or for the amoA gene. The DGGE columns of the three soils differed from each other. There were two similar bands present in DGGE columns of the fluvo-aquic and permeable paddy soils, but no similar band was found in DGGE columns of the red earth. The sequence of amoA indicated that all ammonia oxidizers in these soils were grouped into Nitrosospira clusters 1 and 3, and each soil had a common band similar to the other soils and a special band which differed from the other soils.     

Distributions and environmental drivers of archaea and bacteria in paddy soils

Purpose

The aim of this study is to investigate the abundance, diversity, and distribution of archaea and bacteria as affected by environment parameters in paddy soils, with focus on putative functional microbial groups related to redox processes. Because there is generally a high iron content in the soil, we also want to test a hypothesis that soil iron concentration significantly affects microbial diversity and distribution.

Materials and methods

Quantitative PCR and barcoded pyrosequencing of 16S ribosomal RNA genes were employed to investigate the abundance and community composition of archaeal and bacterial communities in 27 surface paddy soil samples. Pearson’s correlation, analysis of variance, partial least squares regression, principal coordinates analysis, and structural equation models were performed for the analyses of gene copy numbers, α-diversity, β-diversity, and relative abundances of archaea and bacteria and their relationships with environmental factors.

Results and discussion

Archaeal abundance was correlated greatest with temperature, but bacterial abundance was affected mainly by soil organic matter and total nitrogen content. Soil pH and concentrations of different ions were associated with archaeal and bacterial β-diversity. The relative abundances of Euryarchaeota and Thaumarchaeota were 61.3 and 13.1% of archaea and correlated with soil pH, which may affect the availability of substrates to methanogens and ammonia oxidizers. Dominant bacterial phyla were Proteobacteria (32.4%), Acidobacteria (17.8%), Bacteroidetes (9.3%), and Verrucomicrobia (6.0%). The relative abundances of putative bacterial reducers of nitrate, Fe(III), sulfate, and sulfur, and oxidizers of ammonia, nitrite, reduced sulfur, and C1 compounds had positive, negative, or non-significant correlations with the concentrations of their substrates. Soil iron concentration was correlated only with the distributions of some putative iron-reducing bacteria.

Conclusions

In paddy soils characterized by dynamic redox processes, archaea and bacteria differ in relationships of abundance, diversity, and distribution with environmental factors. Especially, the concentrations of electron donors or acceptors can explain the distributions of some but not all the putative functional microbial groups related to redox processes. Depending on pH range, soil pH has a strong impact on microbial ecology in paddy soils.

     

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

Abstract

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity.     

Long-term submergence of non-methanogenic oxic upland field soils helps to develop the methanogenic archaeal community as revealed by pot and field experiments

The community structure of methanogenic archaea is relatively stable,i.e.,it is sustained at a high abundance with minimal changes in composition,in paddy field soils irrespective of submergence and drainage.In contrast,the abundance in non-methanogenic oxic soils is much lower than that in paddy field soils.This study aimed to describe methanogenic archaeal community development following the long-term submergence of non-methanogenic oxic upland field soils in pot and field experiments.In the pot experiment,a soil sample obtained from an upland field was incubated under submerged conditions for 275 d.Soil samples periodically collected were subjected to culture-dependent most probable number(MPN)enumeration,polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE)analysis of archaeal 16 S r RNA gene,and quantitative PCR analysis of the methyl-coenzyme M reductase alpha subunit gene(mcr A)of methanogenic archaea.The abundance of methanogenic archaea increased from 102 to 103 cells g-1 dry soil and 104 to 107 copies of mcr A gene g-1 dry soil after submergence.Although no methanogenic archaeon was detected prior to incubation by the DGGE analysis,members from Methanocellales,Methanosarcinaceae,and Methanosaetaceae proliferated in the soils,and the community structure was relatively stable once established.In the field experiment,the number of viable methanogenic archaea in a rice paddy field converted from meadow(reclaimed paddy field)was monitored by MPN enumeration over five annual cycles of field operations.Viability was also determined simultaneously in a paddy field where the plow layer soil from a farmer’s paddy field was dressed onto the meadow(dressed paddy field)and an upland crop field converted from the meadow(reclaimed upland field).The number of viable methanogenic archaea in the reclaimed paddy field was below the detection limit before the first cultivation of rice and in the reclaimed upland field.Then,the number gradually increased over five years and finally reached 103–104 cells g-1 dry soil,which was comparable to that in the dressed paddy field.These findings showed that the low abundance of autochthonous methanogenic archaea in the non-methanogenic oxic upland field soils steadily proliferated,and the community structure was developed following repeated and long-term submergence.These results suggest that habitats suitable for methanogenic archaea were established in soil following repeated and long-term submergence.     

Soil purple phototrophic bacterial diversity under double cropping (rice‐wheat) with free‐air CO2 enrichment (FACE)

Soil purple phototrophic bacterial (PPB) communities and their responses to elevated atmospheric carbon dioxide (CO₂) concentration and nitrogen (N) fertilizer were investigated under a rotation of paddy rice (Oryza sativa L.) and winter wheat (Triticum aestivum L. cv. Yangmai 14) cultivation in a FACE (free‐air CO₂ enrichment) system. Community structures and abundances of PPB were determined by denaturing gradient gel electrophoresis (DGGE) and real‐time quantitative PCR respectively, targeting the pufM gene, which encodes a protein in the light reaction centre of PPB. Soil PPB communities were more diverse and larger under rice than under wheat cultivation, which may be attributed to the flooding of the paddy field and soil moisture changes. Elevated atmospheric CO₂ concentration significantly increased the abundance and biodiversity of PPB in soils under rice cultivation, while N fertilizer application rate had less effect on the abundance and diversity. Phylogenetic analysis showed that two common dominant DGGE bands belonged to Bradyrhizobium‐ and Rhodopseudomonas palustris‐like PPB in both rice and wheat soils. The results demonstrated a significant shift in soil PPB communities during the rice‐wheat rotation, and a strong positive response of PPB communities to an elevated atmospheric CO₂ concentration. Our results also indicated that a diverse and abundant soil PPB community could occur in upland crop fields as well as in aquatic environments and paddy‐rice fields. These findings extend our understanding of the ecological significance of PPB in terrestrial soil environments and their responses to future climate change.     

Rhizosphere microbiota assemblage associated with wild and cultivated soybeans grown in three types of soil suspensions

Soil microbial community composition is determined by the soil type and the plant species. By sequencing the V3-V4 region of the bacterial 16S rRNA gene amplicons, the current study assessed the bacterial community assemblage in rhizosphere and bulks soils of wild (Glycine soja) and cultivated (Glycine max) soybeans grown in the suspensions of three important soil types in China, including black, red and soda-saline-alkali soils. The alpha-diversity of the bacterial community in the rhizosphere was significantly higher than that of the bulk soils suggesting that bulk soil lacks plant nurturing effect under the current study conditions. Black and red soils were enriched with nitrifying and nitrogen-fixing bacteria but the soda-saline-alkali soil suspension had more denitrifying bacteria, which may reflect agronomic unsuitability of the latter. We also observed a high abundance of Bradyrhizobium and Pseudomonas, enriched cellulolytic bacteria, as well as a highly connected molecular ecological network in the G. soja rhizosphere soil. Taken all, the current study suggest that wild soybeans may have evolved to recruit beneficial microbes in its rhizosphere that can promote nutrients requisition, biostasis and disease-resistance, therefore ecologically more resilient than cultivated soybeans.