辐照对瓜实蝇遗传区性品系成虫肠道微生物的影响

为研究辐照对瓜实蝇肠道微生物群落多样性和结构组成的影响,以100 Gy137Cs辐照来自瓜实蝇遗传区性品系(GSS)的5、8、11和13日龄的雌、雄成虫,并采用Illumina MiSeq测序技术分别对其肠道菌群进行测序分析。结果表明,瓜实蝇雌雄成虫的肠道中存在19个主要的菌属,包括17个属名已知,1个属名未知和1个属不可培养。其中,17个已知属分别属于4个细菌门,即变形菌门(Proteobacteria)(占总量的50%~98%)、厚壁菌门(Firmicutes)(占总量的2%~47%)、拟杆菌门(Bacteroidetes)(占总量的1%~16%)和1个至今微生物界还未确定的稀少菌门(unclassified rare phyla)(总量1%)。此外,辐照降低了瓜实蝇肠道中的微生物多样性以及优势菌的丰富度,且这种影响与瓜实蝇的性别和成虫日龄无关。本研究结果为评估和修复辐照对瓜实蝇的损伤提供了参考。     

不同季节土庄绣线菊根围丛枝菌根真菌群落差异性研究

土庄绣线菊(Spiraea pubescens)是内蒙古大青山干旱生态系统重要的护土灌木,研究季节变化对土庄绣线菊根围丛枝菌根真菌(arbuscular mycorrhizal fungi,AMF)群落的影响,有助于进一步探讨AMF在土庄绣线菊生长发育过程中发挥的作用。采用传统染色检测与Illumina Mi Seq测序相结合的方法,研究季节变化对内蒙古大青山土庄绣线菊AMF侵染率、孢子密度、丰富度、多样性和群落组成的影响。结果显示:在春季、夏季和秋季,AMF侵染率和丛枝丰度不存在显著差异,而孢子密度却存在显著差异。AMF丰富度和多样性在夏季显著低于春季和秋季,但在春季和秋季间差异并不显著;主成分分析(principal coordinate analysis,PCo A)和PERMANOVA分析表明,春季和秋季AMF群落组成与夏季存在显著差异,而在春季和秋季间差异并不显著。     

Effect of super absorbent polymer sodium polyacrylate on the bacterial community and associated chemistry of loessial soil

ABSTRACT

Super absorbent polymers (SAPs) have been applied as soil conditioners to reduce soil water loss, but there are few studies about how SAPs affect structures of soil bacterial community, and these associated chemical residues are uncertain. Treatments under different soil moisture conditions by application of sodium polyacrylate in repacked soil columns were used to investigate their effects on the soil bacterial community structures by Illumina MiSeq sequencing. Alpha diversity analysis showed that adding SAPs had an impact on bacterial diversity. On phylum level, adding SAPs significantly reduced the amount of Actinobacteria (1.9–2.4-fold), Bacteroidetes (1.1–2.1-fold) while increased the amount of Firmicutes (1.9–4.6-fold). At genus level, effects of SAPs on the soil bacterial community structures varied with the soil moisture conditions. Under water deficit, SAPs reduced the soil pH, which promoted the proliferation of Lactobacillus (9.9–29.1-fold), and acid production by these bacteria might further promote the reduction of pH, potentially inhibiting growth of Acidobacteria (1.3–1.8-fold) and Chloroflexi (1.6–2.3-fold). The pyrolysis analysis showed that some substances such as methanesulfonyl chloride, long-chain amides and esters, were only derived from water-saturated soil treated with SAPs, which might subsequently have negative impacts on the environment and associated agriculture.     

青贮发酵对玉米秸秆品质及菌群构成的影响

本研究旨在探讨青贮发酵对玉米秸秆感官指标、发酵品质、营养成分以及门、纲、目、科和属5个水平细菌群落构成及丰度的影响。将去穗后仍青绿的蜡熟期玉米秸秆切短揉搓至1~2 cm,将水分调节至65%~70%后,取青贮前样品(3个重复)和青贮后样品(3个重复)使用聚乙烯袋真空包装,室温贮藏45 d后开启取样,运用实验室检测手段及Mi Seq高通量测序技术分析青贮前后玉米秸秆品质及菌群结构的变化。结果表明:1)青贮发酵45 d后的玉米秸秆青贮饲料呈黄绿色,质地较好,呈酸香味。青贮发酵作用能够使玉米秸秆p H迅速降低(P0.05),乳酸含量显著增加(P0.05),中性洗涤纤维(NDF)及酸性洗涤纤维(ADF)含量有下降趋势(P0.05)。2)玉米秸秆经过青贮发酵后,变形菌门(Proteobacteria)、γ-变形菌纲(Gammaproteobacteria)、肠杆菌目(Enterobacteriales)、肠杆菌科(Enterobacteriaceae)和魏斯氏菌属(Weissella)菌群数量显著降低(P0.05);青贮发酵能够显著增加厚壁菌门(Firmicutes)、芽孢杆菌纲(Bacilli)、乳杆菌目(Lactobacillales)、乳杆菌科(Lactobacillaceae)、片球菌属(Pediococcus)和乳杆菌属(Lactobacillus)菌群数量(P0.05)。综上,青贮发酵改善玉米秸秆感官指标、发酵品质以及营养成分的同时,可以有效降低有害细菌的数量,增加有益菌的数量,从而可以降低致病菌对家畜健康存在的潜在风险。通过实验室检测手段及Miseq高通量测序技术相结合,能够在分析青贮品质的同时,提供青贮前后整个菌落构成及丰度变化的信息,进而为发酵过程的调控提供依据。     

不同时期的柑橘果实中真菌种类分析

柑橘采后真菌病害发生普遍,对柑橘产业造成了极大的威胁。柑橘体内存在丰富的真菌类群,为了了解柑橘成熟和衰老过程中果实内生真菌的多样性和变化动态,本论文通过MiSeq技术解读真菌ITS区域序列,分别对生长期、成熟期和贮藏期的晚蜜一号果实的果皮和果肉的内生真菌种类进行了分析。发现相比于果肉,果皮中真菌在目和属水平的多样性更为丰富,而成熟期果肉中真菌种类多于果皮。不同生长阶段的两种组织中优势的真菌属也不同,果皮在生长期以Medicopsis和刺盘孢属(Colletotrichum)占绝对优势,成熟期为刺盘孢属,贮藏期以葡萄孢属(Botrytis)、Erythrobasidium和Strelitziana较为常见;而果肉中生长期主要为青霉属(Penicillium)和枝孢菌属(Cladosporium),约占1/4,成熟期半数以上为葡萄孢属,及至贮藏期约90%为链格孢属(Alternaria)和青霉属,其中链格孢属约占2/3。常见植物病原真菌如枝孢菌属(Cladosporium)、巨座壳属(Magnaporthe)、核盘菌属(Sclerotinia)、葡萄孢属(Botrytis)、白粉菌属(Erysiphe)、青霉属(Penicillium)、链格孢属(Alternaria)和镰孢霉属(Fusarium)等在果肉中的数量高于果皮。果肉中存在较大数量的常见植物病原真菌,不同属真菌在不同样品中呈不同的变化动态,暗示采后病变是多种真菌交互作用的结果,采后病害的防治可以提前至开花期。     

A comprehensive analysis of the response of the fungal community structure to long-term continuous cropping in three typical upland crops

Certain agricultural management practices are known to affect the soil microbial community structure; however, knowledge of the response of the fungal community structure to the long-term continuous cropping and rotation of soybean, maize and wheat in the same agroecosystem is limited. We assessed the fungal abundance, composition and diversity among soybean rotation, maize rotation and wheat rotation systems and among long-term continuous cropping systems of soybean, maize and wheat as the effect of crop types on fungal community structure. We compared these fungal parameters of same crop between long-term crop rotation and continuous cropping systems as the effect of cropping systems on fungal community structure. The fungal abundance and composition were measured by quantitative real-time PCR and Illumina MiSeq sequencing. The results revealed that long-term continuous soybean cropping increased the soil fungal abundance compared with soybean rotation, and the fungal abundance was decreased in long-term continuous maize cropping compared with maize rotation. The long-term continuous soybean cropping also exhibited increased soil fungal diversity. The variation in the fungal community structure among the three crops was greater than that between long-term continuous cropping and rotation cropping. Mortierella, Guehomyces and Alternaria were the most important contributors to the dissimilarity of the fungal communities between the continuous cropping and rotation cropping of soybean, maize and wheat. There were 11 potential pathogen and 11 potential biocontrol fungi identified, and the relative abundance of most of the potential pathogenic fungi increased during the long-term continuous cropping of all three crops. The relative abundance of most biocontrol fungi increased in long-term continuous soybean cropping but decreased in long-term continuous maize and wheat cropping. Our results indicate that the response of the soil fungal community structure to long-term continuous cropping varies based upon crop types.     

池塘和工厂化养殖牙鲆肠道菌群结构的比较分析

为研究池塘和工厂化养殖条件下牙鲆肠道菌群结构差异及其与饵料、水环境、底质等的关系,采用MiSeq高通量测序技术和生物信息学分析手段,构建了牙鲆(Paralichthys olivaceus)肠道、养殖水体、饵料和池塘底泥等7个样品的16s rRNA基因测序文库,分析了不同样品中菌群组成和生物多样性。结果表明：池塘养殖牙鲆肠道（B1）中以厚壁菌门（30.49%）、变形菌门（19.16%）和梭杆菌门（11.11%）为主,其中芽孢杆菌属（27.66%）占绝对优势,弧菌属（0.16%）丰度最小;工厂化养殖牙鲆肠道（B5）中以变形菌门（44.31%）、厚壁菌门（11.57%）和放线菌门（4.79%）为主,其中不动杆菌属（10.37%）丰度最大,弧菌属（4.05%）相对B1中丰度较高。牙鲆肠道优势菌群主要与营养代谢调节相关,同时有益微生物和有害微生物也是肠道菌群的重要组成部分。差异性和系统进化分析表明两种养殖条件下牙鲆肠道菌群结构与饵料中菌群关系密切,此外受养殖水环境中菌群影响较大。研究结果将为今后牙鲆养殖专用高效微生态制剂的研制和养殖环境微生态调控技术构建提供理论依据。     

不同油菜品种对盐碱土壤理化性质与微生物多样性的影响

【目的】研究不同油菜品种对土壤细菌群落和结构的影响并分析对土壤理化性质的影响为新疆地区盐碱地种植油菜提供理论依据。【方法】以不同油菜品种1、16-P22外、华5号和金油158为研究对象,应用Illumina MiSeq测序技术。,筛选出更适宜盐碱地种植的油菜品种。【结果】种植油菜品种16-P22外对降低盐碱地土壤pH值、提高碱解氮、速效磷、有机质含量效果最显著(P<0.05);土壤样品微生物群落丰富度间无显著性差异,微生物群落多样性指数最大为1。不同油菜品种土壤中优势菌门为Proteobacteria、Actinobacteria、Acidobacteria和Chloroflexi,Pontibacter 耐盐菌属相对丰度大小顺序为16-P22外>1 >金油158>华5号; PCA主成分分析显示细菌群落中相似性最高在16-P22外与华5号之间;土壤碱解氮和速效磷与土壤细菌群落分布显著相关。【结论】油菜品种16-P22外更适宜盐碱地上进行种植,促进盐碱土壤优势菌群的形成。     

Porcine reproductive and respiratory syndrome virus whole-genome sequencing efficacy with field clinical samples using a poly(A)-tail viral genome purification method

The genomic surveillance of porcine reproductive and respiratory syndrome virus (PRRSV) is based on sequencing of the ORF5 gene of the virus, which covers only 4% of the entire viral genome. It is expected that PRRSV whole-genome sequencing (WGS) will improve PRRSV genomic data and allow better understanding of clinical discrepancies observed in the field when using ORF5 sequencing. Our main objective was to implement an efficient method for WGS of PRRSV from clinical samples. The viral genome was purified using a poly(A)-tail viral genome purification method and sequenced using Illumina technology. We tested 149 PRRSV-positive samples: 80 sera, 33 lungs, 33 pools of tissues, 2 oral fluids, and 1 processing fluid (i.e., castration liquid). Overall, WGS of 67.1% of PRRSV-positive cases was successful. The viral load, in particular for tissues, had a major impact on the PRRSV WGS success rate. Serum was the most efficient type of sample to conduct PRRSV WGS poly(A)-tail assays, with a success rate of 76.3%, and this result can be explained by improved sequencing reads dispersion matching throughout the entire viral genome. WGS was unsuccessful for all pools of tissue and lung samples with Cq values > 26.5, whereas it could still be successful with sera at Cq ≤ 34.1. Evaluation of results of highly qualified personnel confirmed that laboratory skills could affect PRRSV WGS efficiency. Oral fluid samples seem very promising and merit further investigation because, with only 2 samples of low viral load (Cq = 28.8, 32.8), PRRSV WGS was successful.     

Biocontrol of soil diseases and soil profile associated with rhizosphere of rice (Oryza sativa Subsp. Japonica) growing paddy fields in Kansai region,Japan

ABSTRACT

This research focused on in vitro and in vivo biocontrol of two major rice diseases, Bacterial Leaf Blight caused by Xanthomonus oryzae pv oryzae (Xoo) and Sheath Blight caused by Rhizoctonia solani. Furthermore, the soil of paddy fields in Kansai region, Japan was analysed for the presence of these pathogens, and their microbial communities were evaluated according to the location and management systems. For biocontrol, the rhizospheric bacteria were isolated and molecularly identified. The results indicated that DAR17225040 and DAR17225017 were 99% similar to Bacillus aryabhattai and Bacillus megaterium. The isolated bacteria were able to suppress Bacterial Leaf Blight and Sheath Blight disease 78% and 86% respectively, under greenhouse conditions. The 16S amplicon sequencing (Illumina MiSeq 250bp) was used to analyse the bacterial community in paddy fields of soil taken from five locations under conventional and organic systems. Xoo and R. solani were detected in sampled soil, however, no clear difference was noted, regarding systems. From amplicon sequencing data, Chloroflexi, Acidobacteria, Proteobacteria, Actinobacteria, Planctomycetes were the dominant phyla of rice soil in Kansai region. The phylum Kazan-3B-28 was found more in organic system than conventional. The bacterial community was more affected by location and soil type than by management systems.