Bacterial and archaeal communities in saline soils from a Los Negritos geothermal area in Mexico

In recent years, there has been a growing need to understand how salinity affects microbial communities in agricultural soils. Archaeal and bacterial community diversities and structures were investigated by high-throughput sequencing analysis of their 16S rRNA in two arable soils with low electrical conductivity(EC)(2.3 and 2.6 dS m^-1) and a saline soil(EC = 17.6 dS m^-1). The dominant bacterial phyla in the soils were Proteobacteria(relative abundance(RA) = 46.2%), followe...     

基于高通量测序研究草莓根际微生物群落结构和多样性

研究草莓根际土壤微生物群落组成和结构,对健康草莓土壤生态系统的构建和保持具有重要意义。以不同地区草莓根际土壤为研究样本,利用MiSeq平台Illumina第二代高通量测序技术并结合相关生物信息学分析土壤细菌16S rRNA基因V4+V5区域和真菌ITS1+ITS2区域的丰富度和多样性指数以及群落结构。结果表明:从15个草莓根际土壤样本中获得4554个细菌分类操作单元OTU和1298个真菌OTU,草莓根际土壤的优势细菌门为变形菌门、厚壁菌门、放线菌门、酸杆菌门和绿弯菌门,主要的优势细菌属有16种;优势真菌门为子囊菌门、接合菌门和担子菌门,主要的优势真菌属有8种。冗余分析(RDA)显示,全氮和pH对土壤微生物群落结构的影响最大,共解释了61%的群落变化,各因子的贡献率大小依次为土壤全氮pH有效磷全钾全磷有机质速效钾碱解氮;相关性分析也表明,土壤理化指标均与不同优势菌门存在密切的相关关系。本研究结果加深了对草莓根际微生物群落结构和多样性的认识,为深入研究草莓根际微生物多样性及功能与环境因子之间的关系提供了借鉴。     

不同土壤玉米根际挥发性有机物组成和微生物群落特征

【目的】土壤理化性质和微生物群落的差异显著影响玉米根际挥发性有机物 (volatile organic compounds,VOCs) 的产生和释放。对根际VOCs的深入研究有望为充分挖掘根际生物学潜力和根际调控做出积极贡献。【方法】采集山东德州、河北涞水、河北保定、江西南昌、河南孟津、河南商丘等6个地区的旱地耕层土壤进行为期两个月的玉米盆栽试验,利用顶空固相微萃取联合气相色谱–质谱联用检测技术对根际土壤挥发性有机物进行了分析鉴定,利用实时荧光定量PCR技术对根际细菌和真菌进行了定量分析,利用高通量测序技术对根际细菌16S和真菌ITS进行了测序。【结果】从6个旱地土壤中共检测出44种VOCs,主要是烷烃、烯烃、酯类、胺类、有机酸和芳香类化合物,其中多种化合物与植物或微生物的生长代谢密切相关。胺类化合物N-Benzyl-N-ethyl-p-isopropylbenzamide和D-2-Bromolysergic acid diethylamide在6个土壤中均被检出,占总量的54.2%;其次检出最多的是烷烃和烯烃,占总量的31.1%和7.6%。江西南昌土壤释放的VOCs在数量和丰富度上均显著高于其他土壤,且大部分为烷烃和烯烃类化合物;从河北保定土壤中检出了6种特有的有机酸和酯类化合物。供试6种土壤中,河南商丘和河北保定的细菌数量显著高于其他四个地方。南昌土壤真菌数量显著较高,但其细菌数量、丰富度和多样性均显著低于其他土壤。6种土壤中的主要细菌依次为Thaumarchaeota(奇古菌门)、Actinobacteria(放线菌门)、Proteobacteria(变形菌门)、Chloroflexi(绿弯菌门)、Acidobacteria(酸杆菌门)、Firmicutes(厚壁菌门) 和 Unclassified(未分类门),占总细菌群落的92.1%;主要真菌依次为Ascomycota(子囊菌门)、Basidiomycota(担子菌门) 和 Chytridiomycota(壶菌门),占总真菌群落的98.3%。绿弯菌门仅在南昌土壤中占绝对优势,而南昌土壤中奇古菌门和变形菌门的相对丰度显著比其他地区少;子囊菌门在6种土壤中均为绝对优势真菌门。玉米根际释放的VOCs数量和丰富度与pH、硝态氮、细菌多样性和真菌多样性呈显著负相关 (P < 0.05),与铵态氮和真菌数量呈极显著正相关 (P < 0.01);与主要细菌门中的奇古菌门、变形菌门和酸杆菌门呈显著负相关 (P < 0.05),与绿弯菌门呈极显著正相关 (P < 0.01),但是与主要真菌门相关性不显著。【结论】理化性质不同的玉米根际土壤中,微生物群落结构与组成存在显著差异。pH是影响微生物生长的重要因素,酸性土壤中的真菌数量显著高于中性土壤,但是其细菌数量、微生物群落丰富度和多样性均显著小于中性土壤。VOCs的产生和释放受土壤、微生物和植物等众多因素的影响,土壤有机质含量越高、透气性越好、微生物数量越多时,释放的VOCs越丰富。     

玉米秸秆分解过程中细菌群落组成演化特征

【目的】土壤中存在着大量的分解秸秆的微生物。研究秸秆分解过程中细菌群落组成的演化规律,对了解和调控农田微生物群体组成以促进秸秆分解具有重要意义。【方法】试验于2014年10月至2015年10月在河南省农业科学院原阳试验基地进行,将成熟期玉米秸秆(茎和叶)烘干,剪成长1~2 cm、宽0.3~1 cm的碎片,称12 g样品(相当于8 t/hm^2)装入15 cm×10 cm的尼龙网包(孔径0.04 mm)内,于10月5日冬小麦出苗后埋置在小麦垄间。分别于埋置后0、1、2、4、7、10和12个月收集秸秆包和土壤样品。测定秸秆样品干物质量和碳氮含量,选择埋置了0、2、4、7和12个月的秸秆及其土壤样品分析细菌丰度及群落组成。【结果】秸秆埋入土壤后的前2个月内分解最快,然后逐步减慢,在1、2、4、7、10和12个月后分别降解了总生物量的19.2%、32.9%、44.2%、52.2%、66.8%和73.8%。秸秆埋入土壤后,秸秆和土壤中细菌丰度均显著增加,分别于第4和7个月达到最高后开始下降。秸秆细菌的丰度指标OTUs、ACE、Chao1和多样性指标Shannon随试验时间的延长逐步增加,而Simpson指数随试验时间延长逐步降低,而土壤中这些指标在试验过程中没有显著变化。与刚埋置秸秆时相比,埋置2个月后的秸秆细菌Bacteroidetes门相对丰度明显增加,主导细菌群为Bacteroidetes和Proteobacteria门。Actinobacteria丰度在埋置2个月后明显降低,然后又随试验时间延长逐步增加。Planctomycetes、Saccharibacteria、Verrucomicrobia、Acidobacteria、Chloroflexi和Gemmatimonadetes丰度在原始秸秆中较低,埋入土壤后随试验时间延长逐步增加。Sphingobacteriia、Gammaproteobacteria、Alphaproteobacteria和Flavobacteriia主导前期细菌纲组成,而Actinobacteria、Anaerolineae和Bacilli纲丰度在后期逐步增加。秸秆分解速率主要受其碳含量影响,秸秆细菌群落组成前期与秸秆碳含量相关,后期与秸秆氮含量相关。随着试验的进展,秸秆细菌群落组成与土壤中的细菌群落组成趋同。【结论】秸秆埋入土壤后前2个月的分解速率最高,随后逐步降低。秸秆分解前期细菌群落由富营养型组分Bacteroidetes和Proteobacteria门和Sphingobacteriia、Gammaproteobacteria、Flavobacteriia和Alphaproteobacteria纲主导,随后被逐步增加的贫营养型组分Actinobacteria、Acidobacteria、Chloroflexi、Saccharibacteria门和Deltaproteobacteria、Actinobacteria纲等代替。秸秆碳氮含量变化是影响秸秆分解及其过程中细菌群落演化的主要原因。     

玉米秸秆分解过程中细菌群落组成演化特征

【目的】土壤中存在着大量的分解秸秆的微生物。研究秸秆分解过程中细菌群落组成的演化规律,对了解和调控农田微生物群体组成以促进秸秆分解具有重要意义。【方法】试验于2014年10月至2015年10月在河南省农业科学院原阳试验基地进行,将成熟期玉米秸秆(茎和叶)烘干,剪成长1~2 cm、宽0.3~1 cm的碎片,称12 g样品(相当于8 t/hm^2)装入15 cm×10 cm的尼龙网包(孔径0.04 mm)内,于10月5日冬小麦出苗后埋置在小麦垄间。分别于埋置后0、1、2、4、7、10和12个月收集秸秆包和土壤样品。测定秸秆样品干物质量和碳氮含量,选择埋置了0、2、4、7和12个月的秸秆及其土壤样品分析细菌丰度及群落组成。【结果】秸秆埋入土壤后的前2个月内分解最快,然后逐步减慢,在1、2、4、7、10和12个月后分别降解了总生物量的19.2%、32.9%、44.2%、52.2%、66.8%和73.8%。秸秆埋入土壤后,秸秆和土壤中细菌丰度均显著增加,分别于第4和7个月达到最高后开始下降。秸秆细菌的丰度指标OTUs、ACE、Chao1和多样性指标Shannon随试验时间的延长逐步增加,而Simpson指数随试验时间延长逐步降低,而土壤中这些指标在试验过程中没有显著变化。与刚埋置秸秆时相比,埋置2个月后的秸秆细菌Bacteroidetes门相对丰度明显增加,主导细菌群为Bacteroidetes和Proteobacteria门。Actinobacteria丰度在埋置2个月后明显降低,然后又随试验时间延长逐步增加。Planctomycetes、Saccharibacteria、Verrucomicrobia、Acidobacteria、Chloroflexi和Gemmatimonadetes丰度在原始秸秆中较低,埋入土壤后随试验时间延长逐步增加。Sphingobacteriia、Gammaproteobacteria、Alphaproteobacteria和Flavobacteriia主导前期细菌纲组成,而Actinobacteria、Anaerolineae和Bacilli纲丰度在后期逐步增加。秸秆分解速率主要受其碳含量影响,秸秆细菌群落组成前期与秸秆碳含量相关,后期与秸秆氮含量相关。随着试验的进展,秸秆细菌群落组成与土壤中的细菌群落组成趋同。【结论】秸秆埋入土壤后前2个月的分解速率最高,随后逐步降低。秸秆分解前期细菌群落由富营养型组分Bacteroidetes和Proteobacteria门和Sphingobacteriia、Gammaproteobacteria、Flavobacteriia和Alphaproteobacteria纲主导,随后被逐步增加的贫营养型组分Actinobacteria、Acidobacteria、Chloroflexi、Saccharibacteria门和Deltaproteobacteria、Actinobacteria纲等代替。秸秆碳氮含量变化是影响秸秆分解及其过程中细菌群落演化的主要原因。     

榆林沙区典型林地不同植被类型对土壤微生物群落结构的影响

  目的  掌握榆林沙区典型林地土壤微生物特征,明确地上植被对土壤微生物群落结构的影响。  方法  采集榆林沙区四种林分类型土壤,分析其土壤微生物群落结构。  结果  测序共产生有效操作分类单元（OTU）15,509个,各林分间OTU及各类多样性指数没有显著性差异。优势菌种及其丰度土层间变化较大,但林分间优势细菌种一致,丰度排名前五的分别是变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、酸杆菌门（Acidobacteria）、厚壁菌门（Firmicutes）和绿弯菌门（Chloroflexi）;樟子松、油松林下土壤中,酸杆菌门所占比例最大、分别达到22.32%和29.02%,而在沙柳和小叶锦鸡儿林下土壤中,变形菌门又成为优势菌,比例占到27.64%和28.51%。变形菌门和放线菌门在灌木林土壤中所占比例要高于乔木。  结论  虽然各优势种丰度在林分间略有差别,但差异不显著（P < 0.05）。说明在一定区域内微生物群落结构复杂程度是受土壤本底的影响,不同季节或者土壤温度、湿度的变化对微生物群落结构的影响在一段时间后消除,群落结构归于稳定。     

寡糖对土壤微生物多样性及群落结构的调节作用

土壤微生物种群类型,对土壤质量和作物生长具有重要影响,研究寡糖对土壤微生物种群的影响特征,有助于正确、高效及安全使用寡糖。本研究利用人工气候室进行土壤培养,土壤施加50mg·L−1的壳寡糖（CSOS）和纤维寡糖（COS）溶液,以清水（CK）为对照处理,培养6d后取样,利用高通量测序技术,分析土壤微生物群落结构组成及多样性分布特征。结果表明：壳寡糖（CSOS）和纤维寡糖（COS）处理均显著改变细菌、真菌的群落结构,提高细菌的物种观测数。变形菌门（Proteobacteria）、酸杆菌门（Acidobacteria）、放线菌门（Actinobacteria）、绿弯菌门（Chloroflexi）、芽单胞菌门（Gemmatimonadetes）和拟杆菌门（Bacteroidetes）为优势细菌门,子囊菌门（Ascomycota）、担子菌门（Basidiomycota）和被孢霉门（Mortierellomycota）为优势真菌门。通过组间群落组成比较分析可知,壳寡糖（CSOS）和纤维寡糖（COS）处理均不同程度降低酸杆菌门（Acidobacteria）的相对丰度,增加变形菌门（Proteobacteria）、放线菌门（Actinobacteria）、芽单胞菌门（Gemmatimonadetes）、壶菌门（Chytridiomycota）以及有益菌属溶杆菌属（Lysobacter）、硝化螺旋菌属（Nitrospira）、Haliangium、芽球菌属（Blastococcus）和链霉菌属（Streptomyces）的相对丰度,但与纤维寡糖（COS）相比,壳寡糖（CSOS）处理微生物群落组成的变化幅度更大。此外,壳寡糖（CSOS）和纤维寡糖（COS）处理在调节土壤微生物群落结构上存在一定差异。其中,壳寡糖（CSOS）处理有益菌属Talaromyces的相对丰度增加195%,纤维寡糖（COS）处理有益菌属假单胞菌属（Pseudomonas）的相对丰度增加215%。综上,壳寡糖和纤维寡糖处理均能优化土壤微生物群落的结构组成,其调控差异性有助于理解不同寡糖的调控机制,推动寡糖的应用与推广。     

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...     

连作对再植枸杞根际细菌群落多样性和群落结构的影响研究

受枸杞道地产区土地资源等因素限制,连作障碍已成为影响枸杞产业发展的重要原因之一,导致严重的经济损失.研究连作条件下枸杞农田土壤生态系统微生物群落的演替规律对枸杞产业的可持续发展具有重要的理论意义.以宁夏银川市南梁农场连作多年的枸杞地为研究对象,利用Illumina MiSeq测序技术分析了连作对再植枸杞根际/非根际细菌群落的影响.结果表明,连作地显著抑制再植枸杞苗地径的增加,且其土壤pH较对照样地显著降低(p<0.05).测序结果证实,与对照样地相比,连作地再植枸杞根际土壤细菌物种数显著降低(p<0.05),细菌群落α多样性下降(p>0.05).主坐标分析表明,连作和对照样地间枸杞非根际细菌群落结构无明显差异,但连作显著改变再植枸杞根际细菌的群落结构.对细菌群落丰度的统计分析发现,连作地枸杞根际浮霉菌门、非根际假单胞菌门的相对丰度较对照样地显著降低(p<0.05).此外,冗余分析结果表明:枸杞园土壤pH和有效磷含量是影响枸杞非根际土壤细菌群落结构变化的主要因素,分别解释了41.8%和35.4%的群落结构变化(p<0.05),其他土壤因子无统计学意义,但土壤理化因子对再植枸杞根际细菌群落结构变化的影响均未达显著水平.这些结果证实连作能够显著抑制再植枸杞生长、影响再植枸杞根际细菌群落结构和多样性,干扰枸杞与土壤细菌群落间的互作关系.这些研究结果将为解析枸杞连作障碍机制提供理论基础.     

甘蔗宿根矮化病感病与非感病株根际土壤生物学性状及细菌群落结构特征

[目的]比较甘蔗宿根矮化病(ratoon stunting disease,RSD)感病植株与非感病植株根际土壤的生物学性状及细菌群落结构特征,旨在为构建甘蔗健康的根际微环境,筛选高效RSD生防细菌提供参考。[方法]通过田间调查和实验室鉴定,以甘蔗RSD感病植株为试材,非感病植株为对照,采集甘蔗RSD感病植株和非感病植株的根际土壤,并基于传统和现代高通量测序技术,分析了甘蔗RSD感病植株和非感病植株根际土壤的生物学性状和细菌群落结构特征。[结果]与甘蔗RSD非感病植株相比,感病植株根际土壤中指示土壤肥力与健康状况的生物学性状指标β-葡糖苷酶、磷酸酶和氨肽酶活性,以及微生物生物量碳、氮、磷显著降低;同时,指示细菌丰富度的Chao1指数和指示细菌多样性的Shannon指数显著下降。门分类水平与非感病甘蔗植株相比,RSD感病植株根际土壤中Proteobacteria(变形杆菌门)、Actinobacteria(放线菌门)、Gemmatimonadetes(芽单胞菌门)和Nitrospirae(硝化螺旋菌门)等优势门类细菌占比呈倍级降低,但Chloroflexi(绿弯菌门)、Acidobacteria(酸杆菌门)、Firmicutes(厚壁菌门)、Cyanobacteria(蓝细菌门)、Planctomycetes(浮霉菌门)、Bacteroidetes(拟杆菌门)等优势门类细菌占比呈倍级增加;在属分类水平,与非感病甘蔗植株相比,RSD感病植株根际土壤中Xanthobacteraceae(黄色杆菌属)、Acidothermus、Gaiellales、Roseiflexus(玫瑰菌属)、Micromonosporaceae(小单孢菌属)和Nitrospira(硝化螺旋菌属)细菌占比呈倍级降低,但Acidobacteria(嗜酸菌属)细菌及部分未知菌属却呈倍级提高。[结论]甘蔗RSD感病植株根际微环境中指示土壤肥力的生物学指标显著降低,细菌丰富度和多样性显著下降,部分优势细菌门属占比发生剧变可能是导致甘蔗RSD发生的重要原因。     

Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase

The ecological staircase of Mendocino (California, USA) is characterized by a succession of uplifted marine terraces that are derived from the same mineralogical parent material but have different ages, levels of fertility, and types of vegetation, from grassland in the youngest and most fertile terrace to a pygmy forest in the older terraces. Such conditions present a unique opportunity to determine how the structure, abundance, and function of bacterial communities vary with soil fertility along this natural chronosequence. Pyrosequencing analysis of 16S rRNA gene amplicons revealed that Acidobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundantly represented phyla. Bacteroidetes, Firmicutes, Verrucomicrobia were significantly enriched in the grasslands, while the less fertile forested terraces showed higher abundance of Acidobacteria Gp2 and Alphaproteobacteria. The pygmy forest soil harboured significantly more Actinobacteria and OP10 than the non-pygmy forest. Between samples from different terraces, the structure of the bacterial community clearly correlated with soil characteristics. Notably, the number of operational taxonomic units was greater in the fertile terrace, as was the density of culturable bacterial populations. Functional characterization of the soil culturable bacteria from the pygmy and non-pygmy forest terraces revealed that the soil bacteria from the non-pygmy terrace were significantly more effective in solubilizing minerals and more abundant than in the pygmy terrace. Our results provide new information on bacterial community structure as a function of soil age, land cover and fertility, which improve our understanding of soil evolution.     

Plot-scale manipulations of organic matter inputs to soils correlate with shifts in microbial community composition in a lowland tropical rain forest

Little is known about the organisms responsible for decomposition in terrestrial ecosystems, or how variations in their relative abundance may influence soil carbon (C) cycling. Here, we altered organic matter in situ by manipulating both litter and throughfall inputs to tropical rain forest soils, and then used qPCR and error-corrected bar-coded pyrosequencing to investigate how the resulting changes in soil chemical properties affected microbial community structure. The plot-scale manipulations drove significant changes in microbial community composition: Acidobacteria were present in greater relative abundance in litter removal plots than in double-litter plots, while Alphaproteobacteria were found in higher relative abundance in double-litter and throughfall reduction plots than in control or litter removal plots. In addition, the bacterial:archaeal ratio was higher in double-litter than no-litter plots. The relative abundances of Actinobacteria, Alphaproteobacteria and Gammaproteobacteria were positively correlated with microbial biomass C and nitrogen (N), and soil N and C pools, while acidobacterial relative abundance was negatively correlated with these same factors. Bacterial:archaeal ratios were positively correlated with soil moisture, total soil C and N, extractable ammonium pools, and soil C:N ratios. Additionally, bacterial:archaeal ratios were positively related to the relative abundance of Actinobacteria, Gammaproteobacteria, and Actinobacteria, and negatively correlated to the relative abundance of Nitrospira and Acidobacteria. Together, our results support the copiotrophic/oligotrophic model of soil heterotrophic microbes suggested by Fierer et al. (2007).     

长期施用有机肥潮土细菌的多样性及功能预测

  【目的】  细菌作为土壤中最多的微生物物种,其多样性是土壤质量和土壤健康的标志。施肥不仅为土壤细菌提供了矿质养分,也为细菌提供了不同的碳源。探究长期不同施肥下潮土细菌的多样性及其功能,对于深入理解土壤养分转化的微生物驱动过程及优化施肥管理措施具有重要意义。  【方法】  选取潮土上连续37年不施肥(CK)、单施化学氮肥(N)、单施有机肥(M)、有机肥和化学氮肥配施(MN) 的4个处理,采用高通量测序方法分析土壤细菌丰度(16S rRNA基因拷贝数)、α多样性和β多样性,采用FAPROTAX功能预测的方法分析主要功能种群的丰度在处理间的差异,采用Mantel 检验分析细菌多样性等与产量、土壤养分含量间的相关关系。  【结果】  长期施用有机肥显著提高了土壤细菌丰度,MN和M处理下土壤中的16S rRNA基因拷贝数分别是CK和N处理平均值的11.8和10.7倍(P< 0.05)。土壤细菌多样性指数(Shannon index)和丰富度指数(Chao1 index)均在M处理下最高。潮土中变形菌门、酸杆菌门和放线菌门为优势菌门。与CK相比,施肥处理均提高了潮土拟杆菌门、厚壁菌门和疣微菌门的相对丰度。与N处理相比,MN处理显著提高了潮土变形菌门、厚壁菌门和拟杆菌门的丰度,降低了酸杆菌门的丰度。潮土细菌生态功能以化能异养、有氧化能异养、发酵作用、硝化作用和硝酸盐还原为主,相应种群丰度均在1%以上。MN处理下化能异养功能细菌的丰度较其他处理显著提高2.2%～4.2%。MN和M处理中起发酵作用的种群相对丰度是其他处理的3倍以上。与CK 相比,3个施肥处理均显著增加了光异作用和光异养作用功能种群的相对丰度。土壤细菌β多样性和功能结构均与土壤有机质(SOM)、全氮(TN)、硝态氮(NO₃?-N)含量及作物产量呈显著(P < 0.05)或极显著(P < 0.01)相关。  【结论】  长期施用有机肥提高了潮土中细菌的数量和多样性,提高了土壤中变形菌门、厚壁菌门和拟杆菌门的丰度,降低了酸杆菌门的丰度。有机肥和化肥配施处理中化能异养型细菌丰度较高,可能是施用有机肥后优化土壤养分循环和响应作物产量提高的主要菌群,今后可进一步深入研究其菌群组成和功能调控。     

Long-term effect of plastic film mulching and fertilization on bacterial communities in a brown soil revealed by high through-put sequencing

The objective of this study was to access the effect of long-term fertilization and film mulching application on soil properties and bacterial community structure. We used 16S rRNA gene to investigate soil bacterial community composition by high through-put sequencing. The results demonstrated that predominant groups in the bacterial community were: Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Firmicutes, Planctomycetes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi and Cyanobacteria. Long-term fertilization of combined manure and nitrogen application caused significant decrease in soil bacterial diversity and richness compared to non-fertilization control, though manure fertilization alone played a significant role in restoring bacterial diversity. Film mulching and manure fertilization significantly increased the relative abundances of soil bacterial groups mentioned above. Furthermore, film mulching played significant role in shaping the bacterial community structure regardless of fertilization. Redundancy analysis (RDA) showed that soil moisture content, pH, total N and soil organic C had significant (P < 0.05) influence on dominant bacterial groups. Altogether, plastic film mulching and manure application prevented loss of soil bacterial diversity and abundance during long-term fertilization. These findings showed the detrimental use of combined manure and nitrogen fertilization to soil microbes and the useful application of manure fertilization coupled with film mulching to soil biodiversity in long-term fertilization experiments.     

不同类型粪肥还田对土壤酶活性及微生物群落的影响

畜禽粪便作为有机肥还田可以维持和提高土壤有机质、改良土壤,有利于农业可持续发展。不同类型粪肥还田后对土壤生物学性状的影响不同,为探究这一问题,在内蒙古乌兰察布市设置田间试验,包括化肥(F)、羊粪(GM)、猪粪(PM)、牛粪(CM)4个处理,研究其对土壤养分、酶活性及微生物群落的影响。结果表明,施用粪肥较化肥具有增加土壤有机质、全氮、有效磷、铵态氮等养分含量的趋势。不同粪肥较化肥处理的土壤脲酶、蔗糖酶、碱性磷酸酶和过氧化氢酶活性最高增幅分别为32.4%、150.4%、26.8%和30.1%。牛粪处理的土壤微生物生物量碳氮显著提高,分别较化肥增加33.2%和33.4%。不同处理在细菌门水平上的优势种群较一致,放线菌门(Actinobacteria)、变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、绿弯菌门(Chloroflexi)、厚壁菌门(Firmicutes)是优势种群。本试验条件下,牛粪处理更能提高土壤微生物生物量碳氮,短期内施用不同粪肥对于提高土壤微生物群落多样性差异不显著,土壤pH、有效磷、铵态氮是影响土壤微生物群落结构的主要环境因子。     

Influence of grass species and soil type on rhizosphere microbial community structure in grassland soils

A number of studies have reported species specific selection of microbial communities in the rhizosphere by plants. It is hypothesised that plants influence microbial community structure in the rhizosphere through rhizodeposition. We examined to what extent the structure of bacterial and fungal communities in the rhizosphere of grasses is determined by the plant species and different soil types. Three grass species were planted in soil from one site, to identify plant-specific influences on rhizosphere microbial communities. To quantify the soil-specific effects on rhizosphere microbial community structure, we planted one grass species (Lolium perenne L.) into soils from three contrasting sites. Rhizosphere, non-rhizosphere (bulk) and control (non-planted) soil samples were collected at regular intervals, to examine the temporal changes in soil microbial communities. Rhizosphere soil samples were collected from both root bases and root tips, to investigate root associated spatial influences. Both fungal and bacterial communities were analysed by terminal restriction fragment length polymorphism (TRFLP). Both bacterial and fungal communities were influenced by the plant growth but there was no evidence for plant species selection of the soil microbial communities in the rhizosphere of the different grass species. For both fungal and bacterial communities, the major determinant of community structure in rhizospheres was soil type. This observation was confirmed by cloning and sequencing analysis of bacterial communities. In control soils, bacterial composition was dominated by Firmicutes and Actinobacteria but in the rhizosphere samples, the majority of bacteria belonged to Proteobacteria and Acidobacteria. Bacterial community compositions of rhizosphere soils from different plants were similar, indicating only a weak influence of plant species on rhizosphere microbial community structure.     

黄河三角洲刺槐根际与非根际细菌结构及多样性

为精确分析黄河三角洲刺槐根际与非根际土壤细菌群落定殖情况,本研究采用高通量测序方法对刺槐根际与非根际土壤细菌结构及多样性进行了研究。研究表明,根际土壤细菌共有36门214属,非根际土壤细菌共有33门153属。变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)细菌丰度超过15%,是根际与非根际土壤中的优势菌落。根际与非根际土壤中酸杆菌门、硝化螺旋菌门(Nitrospirae)丰度差异显著。根际土壤中红游动菌属(Rhodoplanes)、溶杆菌属(Lysobacter)、热单胞菌属(Thermomonas)、链霉菌属(Streptomyces)及非根际土壤中红游动菌属、溶杆菌属、链霉菌属、Kaistobacter细菌丰度超过4%。根际土壤中固氮菌丰度显著高于非根际土壤,解磷、解钾细菌丰度差异不显著。根际与非根际土壤细菌Chao丰富度分别为2 054、2 376,差异显著。根际与非根际土壤细菌之间的权重(Weighted Unifrac)距离在0.12~0.25之间。综上所述,黄河三角洲刺槐根际与非根际土壤细菌结构具有一定差异,多样性差异显著。     

施肥及秸秆还田对砂姜黑土细菌群落的影响

利用Illumina平台Miseq高通量测序技术对小麦分蘖期砂姜黑土耕层土壤细菌进行高通量测序,结合相关生物信息学分析,探讨了不施化肥秸秆不还田(CK)、施化肥秸秆不还田(F)以及不施化肥秸秆还田(W)3种处理土壤细菌群落组成、多样性和结构的变化。结果显示,测序共获得14 873个OTUs,计173 323条读数,平均读长439 bp。砂姜黑土细菌优势门(相对丰度10%)为变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和拟杆菌门(Bacteroidetes);优势纲(相对丰度10%)为α-变形菌纲(Alphaproteobacteria)、β-变形菌纲(Betaproteobacteria)、酸杆菌纲(Acidobacteria)、鞘脂杆菌纲(Sphingobacteriia)和γ-变形菌纲(Gammaproteobacteria);优势属(相对丰度1%)共47个,3个处理中均有分布的优势属21个,F处理的细菌优势属的种类最多,为39个。相对丰度最大的门、纲和属分别是变形菌门(38.7%~43.1%)、α-变形菌纲(14.5%~18.1%)和鞘氨醇单胞菌属(Sphingomonas)(4.6%~7.7%)。F处理细菌丰富度指数(Chao1指数和ACE指数)显著低于CK及W处理,W处理和CK处理土壤细菌丰富度指数无显著差异,与CK处理相比,F处理ACE指数降低22.8%。W处理土壤细菌Shannon多样性指数显著大于CK及F处理,W处理Shannon指数较CK处理提高4.1%,而F处理土壤细菌Shannon指数与CK处理无显著差异。F处理Simpson指数显著高于CK及W处理;F处理Simpson指数较CK处理提高38.1%,而W处理细菌Simpson指数最小,显著低于CK处理,较CK降低23.8%。分层聚类图显示在属的水平上,W处理和CK处理土壤细菌群落结构相似性较高,F处理与CK处理及W处理细菌群落结构差异较大。施化肥对土壤细菌优势类群组成、相对丰度及群落结构的影响大于秸秆还田,施化肥显著降低了土壤细菌丰富度,秸秆还田显著提高了土壤细菌的多样性。     

Pineapple–banana rotation reduced the amount of Fusarium oxysporum more than maize–banana rotation mainly through modulating fungal communities

Continuous cropping with banana results in an enrichment of Fusarium oxysporum f. sp. cubense race 4 (FOC) in soil, causing the soil-borne disease Fusarium wilt. Crop rotation has been an effective method of controlling various soil-borne diseases. However, no information is currently available concerning variations in soil microbial community structure in banana crop rotations. Thus, the influence of two-year crop rotation systems of pineapple–banana and maize–banana on the population density of FOC and soil microbial community structure was investigated to identify which rotation system is more effective in FOC suppression and differences in microbial community composition among different rotations. Bacterial and fungal communities were interrogated by pyrosequencing of the 16 S RNA gene and the internal transcribed spacer (ITS) region. The pineapple–banana rotation was more effective than maize–banana in reducing FOC abundances and suppressing Fusarium wilt disease incidence. Allelopathic effects of pineapple root exudates on FOC were not observed. Greater fungal community variations than bacterial were identified between the two rotation systems, suggesting that fungal communities may play a more important role in regulating FOC abundances. Furthermore, in the pineapple–banana rotation, Acidobacteria, Planctomycetes, Chloroflexi phyla, Gp1, Gp2 and Burkholderia bacterial genera increased while the fungal phyla Basidiomycota, (esp. Gymnopilus) increased and Sordariomycetes decreased. Such changes may be important microbial factors in the decrease in FOC.     

土地利用方式对万木林土壤氨氧化微生物丰度的影响

以我国亚热带地区典型花岗岩发育酸性红壤为研究对象,选取福建建瓯万木林自然保护区封禁保护下5种自然植被和1种人工种植植被土壤,采用荧光实时定量PCR(Real-time PCR)技术测定了土壤氨氧化细菌(AOB)和氨氧化古菌(AOA)的群落丰度,采用15N稳定同位素成对标记和数值模型相结合的方法测定了土壤初级硝化速率。结果显示,长期封禁保护下的自然植被土壤pH低,土壤AOB数量偏低。人为种植和管理显著提高了土壤pH,促进了AOB的生长,其丰度比自然条件下提高了2个数量级,土壤初级硝化速率也显著提高,并与AOB数量存在显著的相关性,表明AOB是硝化作用的主要贡献者。5种自然植被条件下AOA的amoA基因拷贝数占泉古菌16S rRNA基因的比例都小于1%(0.01%～0.64%),在农业利用方式下上升到5.32%,表明并非所有泉古菌都具备氨氧化功能基因amoA,氮肥施用可能促进了氨氧化古菌的生长。