Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites

Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects that such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial communities we used a combined T-RFLP and pyrosequencing approach to study bacteria, archaea and fungi in spring and autumn at five long term observatories (LTOs) in Europe; each with a particular land use type and contrasting levels of intensification (low and high). Generally, due to large gradients in soil variables, both molecular methods revealed that soil microbial communities were structured according to differences in soil conditions between the LTOs, more so than land use intensity. Moreover, variance partitioning analysis also showed that soil properties better explained the differences in microbial communities than land use intensity effects. Predictable responses in dominant bacterial, archaeal and fungal taxa to edaphic conditions (e.g. soil pH and resource availability) were apparent between the LTOs. Some effects of land use intensification at individual field sites were observed. However, these effects were manifest when land use change affected soil conditions. Uniquely, this study details the responses of different microbial groups to soil type and land use intensification, and their relative importance across a range of European field sites. These findings reinforce our understanding of drivers impacting soil microbial community structure at both field and larger geographic scales.     

不同磷肥用量对水稻土有机碳矿化和细菌群落多样性的影响

以水稻田田间定位试验为研究对象,利用三维荧光光谱技术(3D EEMs)和454测序技术,采集4个施磷水平(0、30、60、90 kg hm-2a-1)土壤,测定其有机碳矿化、溶解有机碳(DOC)组成和结构特征及细菌群落结构和丰度的变化。结果显示:水田施磷增加了土壤速效磷(Olsen-P),从而提高了土壤DOC含量,加速了有机碳的矿化速率和累积矿化量。3D EEMs结果表明,施磷分别显著增加了荧光指数和鲜度指数值1%~10%和3%~21%,而降低了腐殖化指数,且与土壤生化性质(Olsen-P、DOC和β-葡萄糖苷酶)具有显著相关性。说明施磷通过提高Olsen-P,促进了微生物源DOC的生成,同时降低了DOC的芳香化程度、分子量及腐殖化程度,从而提高了DOC生物可降解性。同时,施磷提高了细菌群落的丰度和多样性,特别是磷诱导了多种具有碳降解功能细菌的增加,从而加速了复杂有机碳的降解和甲烷氧化。此外,主成分分析表明稻田磷素施用量在30~60 kg hm-2a-1时对土壤有机碳矿化及细菌群落多样性的提高作用最为明显。因此,适度施磷能显著提高涉碳降解微生物的活性,从而提高DOC的生物可降解性,加速有机碳的矿化速率,促进稻田土壤有机碳循环。     

绿脓杆菌焦磷酸测序检测方法的建立

本试验旨在利用绿脓杆菌的序列信息分析和焦磷酸测序技术,建立一种快速、简单检测绿脓杆菌的方法。从培养的绿脓杆菌中提取DNA,PCR扩增目的基因片段,采用焦磷酸测序技术(pyrosequencing technology,PSQ)针对保守核苷酸区段的测序分析。通过焦磷酸测序后获得的序列信息与已知的目的基因的序列比对,能进一步确证毒株的序列信息为绿脓杆菌。利用焦磷酸测序能快速获取核酸的序列信息,可为毒株及早确证奠定基础。     

甘薯病毒病原相关的microRNA的挖掘及分析

【目的】甘薯的病毒种类比较多,不同的病毒感染会引起相应的症状变化,田间自然发病的甘薯表型不一,这可能与病毒感染类型有关。论文旨在鉴定和研究甘薯中与不同甘薯病毒感染相关的microRNA（miRNA）。【方法】采用Illumina公司高通量测序技术,对来自福建泉州地区同一品种（龙薯9号）、具有不同症状的叶片样本（畸形黄化、疱疹、褪绿矮化和曲叶,样本编号分别为Fj01、Fj02、Fj03和1H）进行高通量测序,利用生物信息学手段挖掘和分析差异表达miRNA,并对差异miRNA和病毒表达进行PCR验证,鉴定基因和病毒在样本中表达情况,分析测序数据的可靠性,利用生物信息学分析进行miRNA靶基因预测和功能分析,探究差异miRNA与病毒种类的相关性。【结果】通过与病毒数据库的比对,发现Fj01、Fj02、Fj03样本（除1H外）均感染了甘薯常见病毒,如甘薯褪绿矮化病毒（Sweet potato chlorotic stunt virus,SPCSV）、甘薯病毒2号（Sweet potato virus 2,SPV2）、甘薯羽状斑驳病毒（Sweet potato feathery mottle virus,SPFMV）、甘薯G病毒（Sweet potato virus G,SPVG）、甘薯C病毒（Sweet potato virus C,SPVC）等,但Fj01、Fj02和Fj03这3个样本的症状并不一致,样本之间只在甘薯不常见的病毒种类中有差异,通过PCR验证了SPFMV和SPVC病毒在样本中的表达情况与测序数据基本一致。在4个样本中共鉴定出679个已知的miRNA和1 004个新的miRNA,通过配对比较分析,其中288个已知的miRNA和433个新的miRNA在4个样本之间有差异性表达,并且这些miRNAs,如miR-156、miR-157、miR-166等家族的成员在4个样本中表达模式各异。同时,采用实时荧光定量PCR验证几个差异miRNAs（如miR-156、novel-miR-40和miR-319m）在各个样本间的表达情况与测序结果基本一致,另外,与脱毒苗样本进行比较,检测到3个miRNA（miR-160a、miR-2096和miR-5387b）在4个症状样本中具有不同程度的上调表达,证明miRNA的表达与植株的表型有关。通过对miRNA靶基因的预测与分析,发现这些差异miRNA的靶基因多数为转录调控因子,编码蛋白多含有ZFP、WD、Myb、SPL等功能区域,这些因子多参与调控植物的基因、代谢通路和抗原识别等来调控植物生长发育、形态建成和抗逆性,表明这些miRNA靶基因的功能多样性。【结论】不同病毒感染确实能够引起miRNA差异表达,并且这些miRNA通过其靶基因参与调控植物的生长发育、抗胁迫性和防御。     

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.     

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

Verrucomicrobia are ubiquitous in soil, but members of this bacterial phylum are thought to be present at low frequency in soil, with few studies focusing specifically on verrucomicrobial abundance, diversity, and distribution. Here we used barcoded pyrosequencing to analyze verrucomicrobial communities in surface soils collected across a range of biomes in Antarctica, Europe, and the Americas (112 samples), as well as soils collected from pits dug in a montane coniferous forest (69 samples). Data collected from surface horizons indicate that Verrucomicrobia average 23% of bacterial sequences, making them far more abundant than had been estimated. We show that this underestimation is likely due to primer bias, as many of the commonly used PCR primers appear to exclude verrucomicrobial 16S rRNA genes during amplification. Verrucomicrobia were detected in 180 out of 181 soils examined, with members of the class Spartobacteria dominating verrucomicrobial communities in nearly all biomes and soil depths. The relative abundance of Verrucomicrobia was highest in grasslands and in subsurface soil horizons, where they were often the dominant bacterial phylum. Although their ecology remains poorly understood, Verrucomicrobia appear to be dominant in many soil bacterial communities across the globe, making additional research on their ecology clearly necessary.     

腐殖酸对花生连作地土壤真菌群落结构的影响

土传病害的绿色防控是当前农业、生态和环境领域中为建立资源节约型、环境友好型病虫害可持续治理技术体系的重要组成部分。将来自藓类泥炭和风化煤的腐殖酸添加至两个花生种植年限的土壤中（1年和6年）,进行室内恒温培养。对土壤真菌进行内部转录间隔区（internal transcribed spacer,ITS）测序,运用非参数多因素方差分析（PerMANOVA）、相关性分析等方法阐释腐殖酸对土壤真菌群落的影响。结果表明：腐殖酸的添加显著影响了培养94 d以后的土壤真菌群落结构,而添加量对4个培养时间点的土壤真菌群落结构均可产生显著影响;同时腐殖酸显著改变了部分真菌属的相对丰度。腐殖酸对土壤真菌功能的影响,主要表现为显著改变了土壤中真菌功能营养型的组成。其中,随着腐殖酸添加量的增加,土壤植物病原菌的相对丰度均显著降低;相关性分析表明腐殖酸添加量与致病菌镰刀属（Fusarium spp.） 和丝核菌属（Rhizoctonia spp.）的相对丰度呈显著负相关,而与拮抗菌青霉属（Penicillium spp.）的相对丰度呈显著正相关。本研究表明,特定腐殖酸在适当添加量下可显著改变花生地的土壤真菌群落结构和功能营养型组成,尤其是降低了土壤中植物病原菌的相对丰度,但影响程度因花生种植年限的长短而异。本研究结果为腐殖酸生态功能应用拓展提供了理论依据,为土传病害绿色防控技术的研发提供新的视角。     

砒砂岩分布及岩性特征

内蒙古砒砂岩区是黄土高原乃至世界水土流失最为严重的地区之一,针对目前砒砂岩区生态功能退化、水土流失严重等问题,掌握砒砂岩区平茬后沙棘人工林根际土壤微生物特征,明确平茬对沙棘根际土壤微生物群落结构的影响。

本研究以该区已进入衰退期的沙棘（Hippophae rhamnoides）人工林为研究对象,运用Illumina MiSeq高通量测序法对平茬（齐地平茬0 cm,留茬10 cm,15 cm,20 cm）与未平茬条件下沙棘林下根际土壤微生物细菌群落多样性及群落结构微生物数量等指标进行分析。

①根际土壤理化性质中各个指标表明15 cm平茬处理较其它平茬处理优,各个平茬处理下根际土壤pH变化不明显。②15 cm平茬处理特有扩增子序列变异（ASV）且数目最多。细菌群落的alpha多样性土层0 ~ 10 cm最高,平茬处理组15 cm最高,平茬处理组高于未平茬处理。各个平茬模式0 ~ 10 cm根际土壤深度之间成分相似,20 ~ 30 cm根际土壤深度之间成分相似,10 ~ 20 cm根际土壤深度成分不相似,平茬处理组中15 cm分布相对独立。③4个沙棘平茬模式和对照组未平茬根际土壤样本共检测到细菌37门、116纲、227目、356科、634属和697种。门水平属水平下0 ~ 10 cm土层相对丰度最高,门水平属水平下15 cm平茬处理相对丰度最高。④根际土壤理化性质与细菌优势门丰度相关性分析,根际土壤有效磷与大部分细菌优势门具有极显著相关关系。

沙棘留茬高度为15 cm时最好,平茬有利于沙棘林下根际土壤修复,间接反映出平茬对沙棘更新复壮是有利的。研究结果可为砒砂岩区沙棘人工林更新复壮及生态恢复提供理论依据。