Estimation of the bacterial community diversity of soybean-nodulating bradyrhizobia isolated from Rj-genotype soybeans

Abstract

The diversities of communities of soybean-nodulating indigenous bradyrhizobia in Japan were estimated using mathematical ecology methods based on the results of polymerase chain reaction–restriction fragment length polymorphism analysis of the 16S–23S rDNA internal-transcribed spacer region. Polar ordination analysis indicated a significant correlation between the compositions of bradyrhizobial communities and northern latitudes in Japan. This result suggests that the composition and the geographical distribution of indigenous soybean-nodulating bradyrhizobia might be affected by soil temperature and the associated diversity of the host plants acclimatized to a particular climate. Furthermore, for estimation of the compositional difference in bacterial communities among three different Rj-genotype soybean cultivars, an analysis of the diversity indexes was conducted and this analysis indicated differences in the composition of the communities isolated from the Rj ₂ Rj ₃-genotype compared with those from the non-Rj- and Rj ₄-genotype cultivars. This result suggests that Rj ₂ Rj ₃-genotype soybeans might affect not only compatibility with particular bradyrhizobia, but also preference to bradyrhizobia for nodulation.     

GUS基因标记法对慢生花生根瘤菌竞争结瘤和接种效果的研究

应用GUS基因标记技术,可简便、快速、准确、原位、直观地确定标记花生根瘤菌株形成的根瘤,从而方便地研究标记菌株与土著根瘤菌的竞争结瘤能力。无氮水培试验表明,标记菌株gusA4-5、gusA2-9分别与土著菌混和接种占瘤率为71.4%、77.0%。盆栽试验表明,接种供试菌株Spr4-5、Spr2-9占瘤率分别为57.9%、63.0%,比对照极显著增产52.5%、22.7%;接种Spr4-5比Spr2-9极显著增产24.2%。初步说明两个供试菌株的竞争结瘤力比土著根瘤菌强,菌株Spr2-9强于Spr4-5;Spr4-5比Spr2-9有效性高,是结瘤适量,竞争结瘤能力强的高效菌株。     

Application of the first-order reaction (for) model to modulation by Bradyrhizobium japonicum in the modulation-dilution frequency method and estimation of time of initiation of nodulation

Abstract

Hattori (1985) proposed a model to simulate the relation between the number of bacterial colonies on agar plates and the incubation time, using the following equation:

where N(t) is the number of colonies observed at time t, and N_∞ λ, and t _r are parameters expressing the expected number of colonies observed at an infinite time, the rate of increase in the number of colonies, and the time of initiation of colony formation, respectively. This model is called the first-order reaction (FOR) model because the Eq. 1 is essentially the same as that of the first-order reaction.     

基于MODIS数据和植被特征估算草地生物量

准确估算草地生物量,对全球气候变化背景下的陆地生态系统碳循环研究具有重要意义。过去几十年,草地生物量估算研究大多集中在北方,而南方草地具有类型繁多和分布零散等特征,对其生物量进行评估的报道较少。本文以云南省为例,应用2012—2014年草地生物量野外调查资料和同期MODIS遥感数据,建立草地地上生物量(AGB)遥感估算模型;再引入草地植被群落特征(高度和盖度)信息对统计模型进行优化,并进行生物量空间反演。结果表明:优化后模型的估算精度由原来的35.0%提升为43.7%;反演得到云南省3年年均AGB的总量介于1 026.86万~1 408.54万t,平均为1 221.11万t;从空间分布上看,云南省草地AGB密度总体上呈现西部高东部低、南部高北部低的格局。本研究首次将遥感植被指数数据与实测植被群落特征参数结合,使估算精度比传统的纯粹光学遥感模拟方法显著提升24.9%,但精确估算大面积的草地AGB,需要进一步探索如何将激光雷达数据或遥感立体影像中提取的植被特征信息应用于草地AGB估算研究。     

Effect of thiram (tetramethyl-thiuram-disulphide) application on nodulation in soybean and kidney bean plants: Observation using the root-box-culture technique

Abstract

In agricultural practice, legume seeds are often treated with fungicides to protect them from harmful soil microorganisms. Most fungicides also are toxic to rhizobial growth. Among the synthetic fungicides, thiram (TMTD: tetramethyl-thiuram-disulphide) appeared to be most suitable for leguminous seed protection, because of its low toxicity to some species of rhizobium (NifTAL Project and FAO 1984).     

Temporal and functional pattern of secreted enzyme activities in an ectomycorrhizal community

The ectomycorrhizal community of an oak forest has been monitored monthly throughout fifteen months. Eight enzymatic activities secreted by the ectomycorrhizal root tips and involved in the mobilization of nutrients from soil organic matter have been measured using microplate assays, resulting in potential activity patterns of individual fungal species. Both the species structure of the community and the specific activity level of each individual species changed with the season and soil horizon. This versatility may be an adaptative response of the ectomycorrhizal fungal community to a highly variable environment. The results also suggest that some ectomycorrhizal fungi behave as occasional saprobes and contribute to the decomposition of soil organic matter and nutrient cycling together with true saprotrophic fungi.     

不同作物间作对黄瓜病害及土壤微生物群落多样性的影响

分别采用RAPD和T-RFLP技术,研究了小麦、毛苕子和三叶草分别与黄瓜间作对黄瓜病害、黄瓜根际土壤微生物群落多样性和黄瓜产量的影响。结果表明,小麦、毛苕子与黄瓜间作均能提高黄瓜根际土壤微生物群落多样性,其中,小麦-黄瓜间作对黄瓜根际土壤微生物群落多样性的影响最为突出;3种作物分别与黄瓜间作均显著提高了黄瓜产量(p<0.01),其中小麦-黄瓜间作的产量优势最强;同时,3种作物分别与黄瓜间作均降低了黄瓜角斑病、白粉病、霜霉病和枯萎病的病情指数和尖孢镰刀菌的数量。间作有利于提高土壤微生物群落的多样性、减轻病害、提高黄瓜产量。     

接种溶磷真菌对玉米和大豆根际细菌群落结构多样性的影响

Application of phosphate-solubilizing microorganisms （PSMs） has been reported to increase P uptake and plant growth. However, no information is available regarding the ecological consequences of the inoculation with PSMs. The effect of inoculation with phosphate-solubilizing fungal （PSF） isolates Aspergillus niger P39 and Penicillium oxalicum P66 on the bacterial communities in the rhizospheres of maize （Zea mays L. ‘Haiyu 6＇） and soybean （Glycine max Merr. ‘Heinong 35＇） was examined using culture-dependent methods as well as a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis （PCR-DGGE）. Compared with the control, the number of culturable microbes for soybean was significantly greater with P39, whereas for maize, the same was significantly greater with P66. In addition, a greater number of microbes were found in the rhizosphere of maize compared with soybean. The fingerprint of DGGE for 16S rDNA indicated that inoculation with PSF also increased bacterial communities, with the P66 treatment having higher numbers of DGGE bands and a higher Shannon-Weaver diversity index compared with P39; the composition of the microbial community was also more complex with the P66 treatment. Overall, complex interactions between plant species and exotic PSMs affected the structure of the bacterial community in the rhizosphere, but plant species were more important in determining the bacterial community structure than the introduction of exotic microorganisms.     

Nematode succession during composting and the potential of the nematode community as an indicator of compost maturity

One of the key issues in compost research is to assess when the compost has reached a mature stage. The maturity status of the compost determines the quality of the final soil amendment product. The nematode community occurring in a Controlled Microbial Composting (CMC) process was analyzed with the objective of assessing whether the species composition could be used as a bio-indicator of the compost maturity status. The results obtained here describe the major shifts in species composition that occur during the composting process. Compared to terrestrial ecosystems, nematode succession in compost differs mainly in the absence of K-strategists and numerical importance of diplogastrids. At the beginning of the composting process (thermophilic phase), immediately after the heat peak, the nematode population is primarily built by bacterial feeding enrichment opportunists (cp-1) (Rhabditidae, Panagrolaimidae, Diplogastridae) followed by the bacterial-feeding general opportunists (cp-2) (Cephalobidae) and the fungal-feeding general opportunists (Aphelenchoididae). Thereafter, during the cooling and maturation stage, the bacterial-feeding-predator opportunistic nematodes (Mononchoides sp.) became dominant. Finally, at the most mature stage, the fungal-feeding Anguinidae (mainly Ditylenchus filimus) were most present. Both, the Maturity Index (MI) and the fungivorous/bacterivorous ratio (f/b ratio), increase as the compost becomes more mature (ranging, respectively, from 1 to 1.86 and from 0 to 11.90). Based on these results, both indices are suggested as potential suitable tools to assess compost maturity.     

黑土长期定位试验原状土搬迁对土壤真菌群落多样性的影响

采用PCR-DGGE及其特异性条带克隆测序的方法,研究黑土长期定位试验原状土整体搬迁对土壤真菌群落结构多样性的影响。对同为小麦茬的搬迁前(2010年)和搬迁后(2013年)土壤真菌群落结构的研究表明:DGGE图谱中搬迁前后2个土层不同处理的样品间条带的数量和亮度存在部分变化;对DGGE图谱进行聚类分析可得,真菌群落结构在2个土层各处理中搬迁前后有部分变化,其中MNPK处理的变化较为显著;对DGGE图谱主成分分析结果可得,在0~20 cm土层中各处理虽然搬迁前和搬迁后产生分异,但搬迁前后的3年中处理间的分布规律相似,在20~40 cm土层中搬迁前和搬迁后MNPK和CK处理的分布规律发生了变化。搬迁前和搬迁后土壤真菌群落结构受到搬迁扰动的影响远小于耕作方式、植被类型、土壤肥力等的影响。     

Analysis of genetic diversity of soybean germplasm from five different origins using RAPD markers

The pattern of genetic diversity among 92 genotypes of soybean from 5 different origins/sources (Pakistan, the USA, Asian Vegetable Research Development Centre (AVRDC), Japan and North Korea) was analyzed using randomly amplified polymorphic DNA markers. Out of 20 random primers 6 tested, 10 were polymorphic among genotypes and they yielded 107 markers, with an average of 10.7 markers per primer. The proportion of polymorphic bands within genotypes ranged from 0.47 to 0.71 with an average of 0.59. Pakistani and US genotypes exhibited the highest number of polymorphic bands (95%), while North Korean genotypes revealed the lowest (60%). The mean band frequency of the primers among genotypes was 0.57 with a range of 0.08–0.99. The Shannon’s index and Nei’s genetic diversity index revealed that primer OPF-06 showed maximum genetic diversity among the genotypes. Dendrogram constructed using Unweighted Pair Group Mean Average (UPGMA) method divided the genotypes into 5 main groups consisting of 13 clusters. The results of cluster analysis indicated that the genetic diversity between Pakistani and US or AVRDC genotypes is much larger than that between Pakistani and North Korean or Japanese genotypes. The Pakistani genotypes had distinct bands from plant introductions. Therefore, the Pakistani genotypes may be useful to soybean breeders.     

闽北檫树群落乔木层物种多样性特征研究

采用对数级数模型对檫树群落物种多度分布格局进行预测与检验结果表明 ,该檫树群落物种多度分布遵从对数级数分布 ,即群落的均匀度相对较小 ,群落稳定且具有较高的生物多样性。     

陕北黄土丘陵区退耕地植物群落演替特征

为了解黄土丘陵区侵蚀地貌退耕地植物群落演替模式及其基本特征,以陕北安塞纸坊沟流域的20块不同年限退耕地和荒坡为研究对象,采用空间代替时间序列的方法进行植物群落的调查和演替特征的分析。结果表明:退耕地植物群落大致经历了茵陈蒿群落—杂类草—狗尾草群落—长芒草群落—铁杆蒿群落—茭蒿群落的演替过程。植物群落的Shannon-Wiener指数、Simpson多样性指数、Margalef丰富度指数和Pielou均匀度指数均表现出随演替进行而上升的变化规律,但上升的速率各异;演替前期和中期的群落基本上属于对数级数分布,说明该阶段的物种组成主要是生态位预占模式起作用,演替后期的群落属于对数正态分布,可能是生态位预占、周围繁殖体的侵入压力、种间竞争和其他因素共同作用的结果;群落盖度变化与演替时间符合二次函数变化规律。     

Single particle analysis reveals that bacterial community structures are semi-specific to the type of soil particle

Abstract

With the aim of understanding how diverse bacteria are distributed within a heterogeneous soil, we compared local bacterial communities on individual soil particles. We picked up 11 coarse sand-sized particles (quartz, whitish feldspar, yellow feldspar or unidentified brown particles) from a sandy soil, extracted DNA from each particle, and carried out partial 16S rDNA polymerase chain reaction denaturing gradient gel electrophoresis analysis. Bacterial communities located on soil particles of the same type were more similar in composition than communities located on particles of the other types. Thus, the local structure of a bacterial community is related to the type of soil particle, which suggests that a high diversity of soil bacteria emerges through a combination of local bacterial communities on different types of soil particles.     

光照强度对菌藻共生生物膜细菌群落结构的影响

为了探索3种不同光照强度对菌藻共生生物膜细菌群落结构的影响,该研究设计在淡水养殖池塘水质条件下,开展3种不同光照强度水平（CK组0,T1组4 750 lx,T2组7 580 lx）对菌藻共生生物膜内细菌的群落结构的研究。结果显示：菌藻生物膜细菌群落结构发育对不同的微生态环境有不同的响应,T1处理和T2处理的Alpha多样性指数,包括获得的OTUs数量（Number of Operational Taxonomic Units）（498.5±7.16、517.2±10.36）、Chao1指数（Chao1 index）（648.7±35.64、672.8±30.69）和Shannon指数（Shannon index）（4.68±0.01、4.85±0.03）显著高于CK处理（406.6±8.18,521.5±18.62,3.53±0.02）,CK组菌藻生物膜的细菌群落在总体数量上处于弱势,显著低于T1和T2处理;随着光照强度的增加,菌藻生物膜的优势细菌类群所占百分比的次序发生了改变;变形菌门（Proteobacteria）,拟杆菌门（Bacteroidetes）、绿弯菌门（Chloroflexi）和放线菌门（Actinobacteria）在3个处理中均为优势菌种,但丰度有显著差异。硝化螺菌属（Nitrospira）在CK组和T1处理的属水平相对丰度为2.72%±0.93%和2.57%±0.46%,显著高于T2组;红杆菌属（Rhodobacter）相对丰度随着光照强度的增大而逐渐升高,T1组假单胞菌属（Pseudomonas）的相对丰度平均值显著高于CK组及T2组,菌藻生物膜细菌群落结构发育对不同的光照强度有不同的响应,随着光照强度的变化,菌藻生物膜的优势细菌类群所占百分比的次序发生改变;T1组拥有较高的硝化和反硝化能力,CK组在降解多种有机物的能力方面较强。     

Estimation of rainfall erosivity using 5- to 60-minute fixed-interval rainfall data from China

The 30-min rainfall erosivity index (EI₃₀) is commonly used in the Universal Soil Loss Equation for predicting soil loss from agricultural hillslopes. EI₃₀ is calculated from the total kinetic energy and the maximum 30-min rainfall intensity of a storm. Normally, EI₃₀ values are calculated from breakpoint rainfall information taken from continuous recording rain gauge charts, however, in many places in China and other parts of the world the detailed chart-recorded rain gauge data relative to storm intensities are not readily available, while hourly rainfall is readily available. The objective of this study was to assess the accuracy of EI₃₀ estimations based on 5-, 10-, 15-, 30-, and 60-min time-resolution rainfall data as compared to EI₃₀ estimations from breakpoint rainfall information. 456 storm events from five soil conservation stations in eastern China were used. The values of EI₃₀ based on the fixed-time-interval data were less than those calculated from breakpoint data. The average conversion factors (ratio of values calculated from the breakpoint data to those from the fixed-interval data) for the five stations decreased from 1.105 to 1.009 for the estimation of E values, from 1.668 to 1.007 for I₃₀ values, and from 1.730 to 1.014 for EI₃₀ values as the time resolution increased from 60 to 5 min. The maximum 30-min rainfall intensity was the major source of error in estimating EI₃₀ for 60-min fixed-interval data, while storm kinetic energy played a proportionately more significant role as the fixed-interval data decreased from 60 to 5 min.     

利用无人机多光谱估算小麦叶面积指数和叶绿素含量

利用无人机遥感的方式进行农作物长势监测是目前精准农业、智慧农业发展的重要方向,为了探究无人机多光谱反演小麦叶面积指数（Leaf Area Index,LAI）和叶绿素含量的模型估算潜力,该研究在3个飞行高度（30、60、120 m）采集多光谱影像,通过使用全波段差值光谱指数（Difference Spectral Index,DSI）、比值光谱指数（Ratio Spectral Index,RSI）、归一化光谱指数（Normalized Spectral Index,NDSI）和经验植被指数与地面实测数据进行相关性分析,获得不同高度下的光谱指数与LAI和叶绿素含量的关系模型及其决定系数,以决定系数为依据分别构建多元逐步回归、偏最小二乘回归和人工神经网络等模型,分析不同飞行高度无人机多光谱反演小麦冠层LAI和叶绿素含量SPAD（Soil and Plant Analyzer Development）值的精度。结果表明：1）30 m高度下,绿-红比值光谱指数与小麦LAI的相关性最高,相关系数为0.84;60 m高度下,红-蓝比值光谱指数与小麦叶绿素含量的相关性最高,相关系数为0.68;2）在60 m高度下,经验植被指数与小麦LAI和叶绿素含量的相关性较好, 最大相关系数分别为0.77和0.5。3）利用偏最小二乘回归反演小麦LAI的精度最高,决定系数为0.732,均方根误差为0.055;利用人工神经网络模型反演小麦叶绿素含量的精度最高,决定系数为0.804,均方根误差0.135。该研究成果为基于无人机平台的高通量作物监测提供理论依据,并为筛选无人机多光谱波段实现作物长势参数快速估测提供应用参考。     

Leaf litter is the main driver for changes in bacterial community structures in the rhizosphere of ash and beech

The rhizosphere and the surrounding soil harbor an enormous microbial diversity and a specific community structure, generated by the interaction between plant roots and soil bacteria. The aim of this study was to address the influences of tree species, tree species diversity and leaf litter on soil bacterial diversity and community composition. Therefore, mesocosm experiments using beech, ash, lime, maple and hornbeam were established in 2006, and sampled in October 2008 and June 2009. Mesocosms were planted with one, three or five different tree species and treated with or without litter overlay.Cluster analysis of DGGE-derived patterns revealed a clustering of 2008 sampled litter treatments in two separated clusters. The corresponding treatments sampled in 2009 showed separation in one cluster. PCA analysis based on the relative abundance of active proteobacterial classes and other phyla in beech and ash single-tree species mesocosm indicated an effect of sampling time and leaf litter on active bacterial community composition. The abundance of next-generation sequencing-derived sequences assigned to the Betaproteobacteria was higher in the litter treatments, indicating a higher activity, under these conditions. The Deltaproteobacteria, Nitrospira and Gemmatimonadetes showed an opposite trend and were more active in the mesocosms without litter. The abundance of alphaproteobacterial sequences was higher in mesocosms sampled in 2009 (P = 0.014), whereas the Acidobacteria were more active in 2008 (P = 0.014). At the family level, we found significant differences of the litter vs. non-litter treated group. Additionally, an impact of beech and ash as tree species on soil bacterial diversity was confirmed by the Shannon and Simpson indices. Our results suggest that leaf litter decomposition in pH-stable soils affect the soil bacterial composition, while tree species influence the soil bacterial diversity.