Bacterial diversity in soils around a lead and zinc mine

Five samples of soil collected from a lead and zinc mine were used to assess the effect of combined contamination of heavy metals on soil bacterial communities using a polyphasic approach including characterization of isolates by culture method, community level catabolic profiling in BIOLOG GN microplates, and genetic community fingerprinting by denaturing gradient gel electrophoresis of 16S rDNA fragments amplified by PCR from community DNA （PCR-DGGE）. The structure of the bacterial community was affected to a certain extent by heavy metals. The PCR-DGGE analysis of 16S rRNA genes showed that there were significant differences in the structure of the microbial community among the soil samples, which were related to the contamination levels. The number of bacteria and the number of denaturing gradient gel electrophoresis （DGGE） bands in the soils increased with increasing distance from the lead and zinc mine tailing, whereas the concentration of lead （Pb） and cadmium （Cd） was decreased. Heavily polluted soils could be characterized by a community that differs from those of lightly polluted soils in richness and structure of dominating bacterial populations. The clustering analysis of the DGGE profiles showed that the bacteria in all the five samples of soil belonged to three clusters. The data from the BIOLOG analysis also showed the same result. This study showed that heavy metal contamination decreased both the biomass and diversity of the bacterial community in soil.     

Carbendazim induces a temporary change in soil bacterial community structure

The effect of carbendazim applications on the diversity and structure of a soil bacterial community was studied under field conditions using temperature gradient gel electrophoresis (TGGE) and partial sequence analysis of PCR-amplified 16S rRNA gene. After four successive introductions of carbendazim at a level of 0.94 kg active ingredient (a.i.)/ha, the genetic diversity (expressed as Shannon index, H0) decreased from 1.43 in the control to 1.29 in treated soil. This harmful e ect seems to increase with the concentration of carbendazim. The value of H0 in the soil treated with carbendazim at 4.70 kg a.i./ha was reduced to 1.05 (P 6 0.05). The structure of soil bacterial community was also a ected after four repeated applications of carbendazim at levels of 0.94, 1.88 and 4.70 kg a.i./ha, as seen in the relative intensities of the individual band. However, the bacterial community in carbendazim-treated soil recovered to that in the control 360 d after the first treatment. The results indicated that repeated applications of carbendazim could reduce soil microbial diversity and alter the bacterial community structure temporarily.     

Soil fungistasis and its relations to soil microbial composition and diversity: a case study of a series of soils with different fungistasis

Fungistasis is one of the important approaches to control soil-borne plant pathogens.Some hypotheses about the mechanisms for soil fungistasis had been established,which mainly focused on the soil bacterial community composition,structure,diversity as well as function.In this study,the bacterial community composition and diversity of a series of soils treated by autoclaving,which coming from the same original soil sample and showing gradient fungistasis to the target soil-borne pathogen fungi Fusarium gr...     

镉胁迫下稻田土壤微生物基因多样性的DGGE分子指纹分析

采用现代分子生物学技术,避开传统的分离培养过程,探讨重金属镉污染条件下稻田土壤微生物种群的基因多样性.经过直接从土壤中抽提总DNA,并对总DNA中16S rDNA及其中 V3可变区序列作PCR扩增、变性梯度凝胶电泳(DGGE)分析等,对镉胁迫下稻田土壤总DNA、微生物种类分布进行了初步的研究,发现不同浓度镉胁迫下稻田土壤间的菌种有明显差异,DGGE技术可以用于污染环境下微生物多样性研究.同时对DGGE分子指纹图谱的生物信息学分析作了初步尝试,为污染环境下土壤微生物多样性研究提供了新的实验方法与依据.     

内蒙古河套灌区不同盐碱程度的土壤细菌群落多样性

采用变性梯度凝胶电泳(DGGE)技术对内蒙古河套灌区三种不同盐碱程度土壤(盐土,强度盐化土,轻度盐化土)不同深度(0~20cm和20~30cm)土壤细菌16S rDNA V3~V6可变区扩增片段进行分析,并对土壤理化性质进行了测定.结果表明:细菌群落多样性随土壤盐碱化程度的加深而减少(轻度盐化土 > 强度盐化土 > 盐土),随土壤深度的增加而降低(细菌群落多样性0~20cm土层大于20~30cm土层).细菌Shannon-Wiener指数在轻度盐化土中最大为3.36,在强度盐化土和盐土分别为3.05和2.49.不同盐碱程度土壤以细菌相似系数聚类,分为0~20cm层与20~30cm层两大族群,土壤细菌群落Shannon-Wiener指数在0~20cm层中(盐土为3.04,强度盐化土为3.29,轻度盐化土为3.36)均大于在20~30cm层(盐土为2.49,强度盐化土为3.05,轻度盐化土为3.14).相关性分析和典范对应分析表明,土壤w(EC)、pH值、w(SOC)、w(TP)是土壤细菌群落结构多样性的显著影响因素,不同盐碱程度土壤中细菌群落的Shannon-Wiener指数与土壤w(EC)(r=-0.542,P < 0.05)、pH(r=-0.526,P < 0.05)呈显著负相关,与土壤w(SOC)(r=0.700,P < 0.01)和w(TP)(r=0.805,P < 0.01)呈极显著正相关.w(EC)和pH对盐碱土壤细菌群落结构的影响力最大. 回收DGGE图谱中20个优势条带进行测序分析,结果显示,变形菌纲(α-变形菌纲、β-变形菌纲、γ-变形菌纲和δ-变形菌纲)是盐碱土壤的主要类群.     

施用生物炭对麦田土壤细菌群落多样性和冬小麦生长的影响

通过长期田间定位试验研究土壤细菌群落的多样性及作物生长对施用生物炭的响应,为生物炭在农田中的合理应用提供科学依据.以冬小麦为研究对象,设置生物炭施加量为0(B0对照)、 5(B1)、 10(B2)和20 t·hm^-2(B3)这4个处理,结合Illumina MiSeq高通量测序技术探究不同生物炭施用量对冬小麦扬花期和成熟期土壤理化性质、土壤细菌群落多样性和作物生长的影响.结果表明,土壤含水量、 pH值、土壤有机碳、全氮、硝态氮含量、冬小麦生物量、氮吸收和产量随着生物炭施用量的增加均表现出增加趋势.高通量测序结果得出B2处理显著降低了扬花期细菌群落α多样性;土壤细菌群落组成对不同施用量的生物炭和物候期的总体响应在分类上一致,本研究以变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、浮霉菌门(Planctomycetes)、芽单胞菌门(Gemmatimonadetes)和放线菌门(Actinobacteria)为优势菌门(相对丰度>5%),酸杆菌门的相对丰度下降,但随着生物炭的施用,变形菌门和浮霉菌门的相对丰度增加.冗余分析、共现...     

生物炭添加对秸秆还田土壤细菌群落结构和多样性影响

为探讨生物炭对秸秆还田土壤细菌群落结构和多样性的影响,采用变性梯度凝胶电泳(PCR-DGGE)技术结合克隆测序技术,对未添加(SW)和添加(SBW)生物炭秸秆还田土壤细菌群落结构和多样性进行表征.DGGE谱图和多样性分析结果表明,生物炭添加增加了秸秆还田土壤细菌DGGE图谱条带位置和灰度值及均匀度的变化,但两个处理土壤细菌群落Shannon-Wiener指数和丰富度没有显著差异(p0.05).聚类分析结果表明,SBW处理土壤细菌群落聚为5类,SW处理土壤细菌群落可聚为6类.DGGE条带测序和结构分析结果表明,生物炭添加导致秸秆还田土壤中Actinobacteria、Nitrospira消失和Spirochaetes、Gemmatimonadetes、Chloroflexi、WS3出现,并导致Firmicutes、Proteobacteria所占比例升高和Acidobacteria、Bacteroides所占比例降低,说明生物炭添加促进了秸秆还田土壤细菌群落组成结构变化.     

Denaturing gradient gel electrophoresis fingerprinting of soil bacteria in the vicinity of the Chinese Great Wall Station, King George Island, Antarctica

Bacterial diversity was investigated in soil samples collected from 13 sites around the Great Wall Station, Fildes Peninsula, King George Island, Antarctica, using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA genes. The classes α-, β-, and γ-Proteobacteria, as well as the phylum Actinobacteria, were found to be the dominant bacteria in the soils around the Great Wall Station. Although the selected samples were not contaminated by oil, a relationship between soil parameters, microbial biodiversity, and human impact was still seen. Sample sites in human impacted areas showed lower bacterial biodiversity (average H′= 2.65) when compared to nonimpacted sites (average H′= 3.05). There was no statistically significant correlation between soil bacterial diversity and total organic carbon (TOC), total nitrogen, or total phosphorus contents of the soil. Canonical correlation analysis showed that TOC content was the most important factor determining bacterial community profiles among the measured soil parameters. In conclusion, microbial biodiversity and community characteristics within relatively small scales (1.5 km) were determined as a function of local environment parameters and anthropogenic impact.     

水田土壤细菌群落对不同重金属污染水平的响应分析——以A县为例

重金属污染问题长期存在于土壤环境中,并对土壤细菌群落结构造成了较大影响,从而引起了广泛的研究.本文选取水田土壤为测试样本,通过高通量测序技术和土壤性质化验对样本进行处理,采用Spearman相关性分析等统计分析方法对不同重金属污染水平下的水田土壤细菌群落进行结构和多样性分析.结果显示,研究区内土壤样点的重金属污染水平可被划分为4个等级,其中,轻度重金属污染水平(LL)区域土壤细菌群落的多样性指数总体上显著低于其他区域,即轻度污染的环境将降低该区域的细菌群落多样性.Nitrospira和Candidatus_Solibacter等菌属在重度重金属污染水平(SL)区域中显示出较强的重金属耐受性.Proteobacteria、Firmicutes和Gemmatimonadetes等菌门在不同等级重金属污染水平区域中表现出一定的耐受性.此外,土壤含水量(SWC)、酸碱度(pH)、速效磷(AP)、有效钾(AK)、总氮(TN)、有机质(OM)、铜(Cu)、铅(Pb)、砷(As)和锌(Zn)等土壤环境因子与细菌群落结构存在显著相关性(p0.05).因此,应该尽快开发利用这些具有重金属耐性和生物修复功能的微生物,为粮食作物的健康生长提供适宜的土壤环境.     

呼伦贝尔沙区土壤细菌群落结构与功能预测

以呼伦贝尔沙区裸沙地、草地、沙地樟子松（Pinus sylvestris var. mongolica）人工林和沙地樟子松天然林四种生境土壤为研究对象,采用野外调查、16S rRNA基因高通量测序和PICRUSt功能预测相结合的研究方法比较分析不同生境土壤细菌群落结构和潜在功能组成特征.结果显示：呼伦贝尔沙区沙地樟子松天然林土壤细菌多样性最高,人工林土壤细菌多样性最低,Shannon指数分别为（8.623±0.193）和（7.432±0.028）,不同生境土壤细菌alpha和beta多样性存在显著差异.草地、沙地樟子松人工林和天然林土壤中变形菌门（Proteobacteria）相对丰度最高,均值分别为29.83%±1.14%、34.73%±1.99%、31.95%±0.21%,裸沙地土壤放线菌门（Actinobacteria）相对丰度最高,均值为26.13%±0.43%.不同生境土壤细菌主要优势属为慢生根瘤菌属（Bradyrhizobium）、RB41,其相对丰度在四种生境中的均值分别为5.29%±2.24%、4.22%±1.23%.PICRUSt功能预测共得到6个一级功能层,40个二级功能层,土壤细菌功能较为丰富,土壤细菌群落在环境信息处理、代谢、遗传信息处理和有机系统方面功能活跃.沙地樟子松天然林核苷酸代谢、酶家族、氨基酸代谢、碳水化合物代谢功能基因较为丰富,保证了沙地樟子松天然林土壤细菌的存活,使其具有较高的多样性.呼伦贝尔沙区不同生境土壤细菌功能基因丰度波动,反映了四种生境的土壤细菌群落组成及多样性的变化,指示了不同生境功能基因对土壤细菌群落的影响规律,可为预测和理解沙区土壤细菌代谢潜力和功能提供参考借鉴.     

应用PCR-DGGE技术研究处理含氨废气的生物滤塔中微生物多样性

变性梯度凝胶电泳技术(DGGE)在微生物生态学领域有着广泛的应用.本文应用DGGE技术对处理含氨废气的生物滤塔中微生物多样性随时间的变化进行了研究.在生物滤塔运行的不同时间采集滤塔中的填料样品,进行了生物滤塔对氨处理效果的分析和DGGE分析.结果显示,污泥和混合填料生物滤塔氨的出气浓度在经过一段时间后,逐渐升高,而堆肥生物滤塔的运行情况较好,对氨的去除效率始终在98%以上.PCR-DGGE图谱显示,不同时间的相同填料中微生物DGGE图谱有着明显的差异性.Shannon指数分析表明,填料中微生物的多样性都随着反应器运行时间的延长而有所减少.运行一个月后,混合填料的微生物多样性指数最低为0.389;其次为污泥填料,其多样性指数为0.473;堆肥填料的微生物多样性程度最高为0.569.生物滤塔对氨的去除效果与填料中微生物多样性Shannon指数之间有一定的相关关系.主成分分析(PCA)显示对于堆肥和污泥来说,填料样品之间微生物群落结构相似性较高,而混合填料样品间的微生物群落结构相似性较低.     

重金属复合污染农田土壤的微生物群落遗传多样性研究

采集了浙江省富阳市环山乡某冶炼厂小高炉附近受铜、锌、铅、镉不同程度复合污染的4个农田土壤样品，首先扩增土壤总DNA中的16S rDNA，然后进行变性梯度凝胶电泳(Denaturing Gradient Gel Electrophoresis)，分析了长期受重金属复合污染的农田土壤的微生物群落遗传多样性变化．结果表明，不同程度的重金属复合污染明显改变了农田土壤的微生物群落遗传多样性，但与多样性的改变不是简单的负相关关系，最大的多样性指数出现在中等污染程度的土壤中．     

微生物有机肥对樱桃园土壤细菌群落的影响

采用田间试验,探究微生物有机肥对樱桃园土壤细菌群落的影响.利用高通量测序和实时定量PCR技术,研究不施肥（CK）、常规施肥（CN）和施微生物有机肥（CB）处理土壤细菌数量、多样性和群落结构的变化.结果表明,施微生物有机肥显著提高了土壤有机质、全氮、碱解氮和速效磷含量.结合16S rRNA基因拷贝数和α^-多样性指数结果,发现施微生物有机肥能提高细菌数量,且提高细菌多样性和丰富度.不同施肥处理显著改变了细菌群落结构.门水平上,变形菌门、酸杆菌门、厚壁菌门、芽单胞菌门、放线菌门为优势类群,共占细菌总量的74.3%~85.1%.目水平上,CB处理中Acidobacteria_Gp4和Gp6相对丰度显著低于CK处理,而Acidobacteria_Gp7较CK处理增加了75.4%.冗余分析结果表明,环境因子解释了细菌群落变化的92.3%,土壤有机质、全氮含量和pH值是造成樱桃园土壤细菌群落结构差异的主要原因.因此,施用微生物有机肥能显著提高土壤养分含量、土壤细菌数量及群落多样性,对于培肥地力极为重要.     

Microbial response to CaCO3 application in an acid soil in southern China

Calcium carbonate (CaCO₃) application is widely used to ameliorate soil acidification. To counteract soil and bacterial community response to CaCO₃ application in an acidic paddy soil in southern China, a field experiment was conducted with four different dosages of CaCO₃ addition, 0, 2.25, 4.5 and 7.5?tons/ha, respectively. After one seasonal growth of rice, soil physicochemical properties, soil respiration and bacterial communities were investigated. Results showed that soil pH increased accordingly with increasing dose of CaCO₃ addition, and 7.5?tons/ha addition increased soil pH to neutral condition. Moderate dose of CaCO₃ application (4.5?tons/ha) significantly increased soil dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) content, enhanced soil respiration, while the excessive CaCO₃ application (7.5?tons/ha) decreased these soil properties. High-throughput sequencing results illustrated that moderate dose of CaCO₃ application increased the richness and alpha diversity of soil bacterial community. Compared with control, the relative abundance of Anaerolineaceae family belonging to Chloroflexi phylum increased by 38.7%, 35.4% and 24.5% under 2.25, 4.5 and 7.5?tons/ha treatments, respectively. Redundancy analysis (RDA) showed that soil pH was the most important factor shaping soil bacterial community. The results of this study suggest that proper dose of CaCO₃ additions to acid paddy soil in southern China could have positive effects on soil properties and bacterial community.     

中药废水污泥群落结构解析中PCR-DGGE引物的选择与评价

在中药废水生物活性污泥群落DGGE解析过程中,为了探讨16S rDNA通用引物的扩增效率和对污泥细菌群落的表征能力,选用包括简并性引物在内的11对通用引物扩增16S rDNA序列的4个可变区,并应用DGGE图谱评价不同引物的扩增效率和微生物种群多样性.结果表明,采用不同引物对进行DGGE分析时,微生物种群多样性存在着显...     

DNA和cDNA水平对比研究施肥对稻田土壤细菌多样性的影响

依托长沙农业环境观测研究站不同施肥方式长期定位试验,直接从土壤中抽提总DNA和RNA,应用T-RFLP和RTPCR技术在DNA和c DNA水平对比研究施肥对亚热带稻田土壤细菌丰度和群落结构的影响.结果表明,施肥和秸秆还田显著改变了土壤细菌群落组成(DNA水平)和转录组成(c DNA水平)结构,且不同处理中DNA水平的T-RFLP图谱与cDNA水平相差很大.施肥和秸秆还田降低了土壤中存在的细菌多样性,对土壤中转录的细菌多样性没有影响.土壤16S rRNA基因丰度(DNA水平)平均是其转录丰度(c DNA水平)的337倍,与不施氮肥处理(N0)相比,平衡施肥(NPK)没有改变土壤细菌的数量,在平衡施肥的基础上进行秸秆还田增加了土壤细菌的数量,但高量与低量秸秆还田没有显著差异.RDA分析表明,稻田土壤中铵态氮含量是调控各处理土壤中存在及转录的细菌群落的关键因子.总体而言,不管在DNA还是c DNA水平,研究施肥对土壤细菌丰度的影响均是可行并可信的;但只有在c DNA水平开展研究,才能有效发现细菌群落对环境的适应性.     

松花江下游沿江湿地土地利用变化对土壤细菌群落多样性的影响

本研究旨在明确生境质量变化对土壤细菌群落的影响,为松花江退化湿地选择科学的修复方法提供参考依据.于2018年使用Illumina MiSeq PE300第二代高通量测序平台对松花江下游的5种土地利用类型湿地（天然湿地、稻田地、玉米田、采砂迹地及恢复湿地）土壤细菌16S rDNA进行测序,分析不同土地利用类型土壤细菌群落多样性和功能的差异.结果表明：沿江湿地开垦为玉米田造成土壤细菌的Ace、Chao1和Shannon指数显著降低（P<0.05）,采砂迹地的仿湿地修复使土壤细菌的Ace、Chao1和Shannon指数显著提高（P<0.05）.天然湿地、稻田、玉米田和采砂迹地的土壤细菌群落结构差异显著（P<0.05）,采砂迹地与恢复湿地的土壤细菌群落结构相似.沿江湿地土壤细菌划分为40门、105纲、258目、421科、802属和1673种,变形菌门、放线菌门、酸杆菌门、绿弯菌门、拟杆菌门、疣微菌门、厚壁菌门和芽单胞菌门为各样地共有的优势菌门（相对丰度>1%）.相比之下,拟杆菌门偏好稻田土壤环境,变形菌门和芽单胞菌门偏好玉米田土壤环境,放线菌门偏好采砂迹地土壤环境.湿地土壤细菌具有新陈代谢、环境信息处理、遗传信息处理、细胞过程、人类疾病和有机系统这6类一级代谢通路、46类二级代谢通路和19类主要二级代谢通路（相对丰度>1%）.土壤pH、含水量、碱解氮和碳氮比是沿江湿地土壤细菌群落多样性的主要影响因子.由此可见,改变沿江湿地土地用途降低了土壤生态系统稳定性,增加了湿地退化的潜在生态风险.     

不同秸秆还田方式对旱地红壤细菌群落、有机碳矿化及玉米产量的影响

为探讨长期不同秸秆还田方式对旱地红壤细菌群落、有机碳矿化及玉米产量的影响,基于中国科学院鹰潭红壤生态实验站设置的不同秸秆还田方式长期定位试验(9 a),选取不施肥(CK)、单施化肥(N)、化肥+秸秆(NS)、化肥+秸秆猪粪配施(NSM)和化肥+生物质炭(NB)这5个处理,通过高通量测序技术研究旱地红壤细菌多样性和群落结构差异,揭示了细菌群落对土壤有机碳矿化和玉米产量的影响机制.结果表明:①不同秸秆还田处理下,红壤化学性质发生显著变化,其中NSM处理对旱地红壤肥力的综合提升效果最好,并显著提高了玉米产量.②相比于CK和N处理,秸秆还田处理均提高了细菌多样性.主成分分析发现,秸秆还田处理改变了土壤细菌群落结构.③秸秆还田处理提高了土壤有机碳矿化能力,NSM处理的土壤有机碳矿化速率和累积矿化量最高.④相关性分析表明土壤AN/AP比值显著改变了细菌群落结构,结构方程模型结果表明,土壤AN/AP比可能通过影响土壤细菌多样性和群落结构,间接提高了土壤有机碳矿化能力和玉米产量.本研究结果为协同提升旱地红壤生物多样性和耕地地力水平,保障健康红壤生态系统和粮食安全提供了科学依据.     

Effects of vegetation type on soil microbial community structure and catabolic diversity assessed by polyphasic methods in North China

Soil microbes play a major role in ecological processes and are closely associated with the aboveground plant community.In order to understand the effects of vegetation type on the characteristics of soil microbial communities,the soil microbial communities were assessed by plate counts,phospholipid fatty acid (PLFA) and Biolog microplate techniques in five plant communities,i.e.,soybean field (SF),artificial turf (AT),artificial shrub (AS),natural shrub (NS),and maize field (MF) in Jinan,Shandong Province,North China.The results showed that plant diversity had little discernible effect on microbial biomass but a positive impact on the evenness of utilized substrates in Biolog microplate.Legumes could significantly enhance the number of cultural microorganisms,microbial biomass,and community catabolic diversity.Except for SF dominated by legumes,the biomass of fungi and the catabolic diversity of microbial community were higher in less disturbed soil beneath NS than in frequently disturbed soils beneath the other vegetation types.These results confirmed that high number of plant species,legumes,and natural vegetation types tend to support soil microbial communities with higher function.The present study also found a significant correlation between the number of cultured bacteria and catabolic diversity of the bacterial community.Different research methods led to varied results in this study.The combination of several approaches is recommended for accurately describing the characteristics of microbial communities in many respects.     

矿区不同植被复垦模式对土壤细菌群落结构的影响

以安太堡露天煤矿复垦区为研究对象,用PCR-DGGE技术分析不同复垦植被(榆树、落叶松、杏树、云杉和刺槐)及复垦年限(15年和20年)对土壤细菌的影响.土壤细菌多样性分析结果表明:复垦20年组,榆树最高,杏树最低,其余3个植被无显著差异;复垦15年组,云杉显著高于刺槐;刺槐随复垦年限延长,其土壤细菌多样性显著增高,而云杉却反之.相似性系数分析、聚类分析和PCA均显示,相同复垦年限的土样细菌群落结构相似性高.相关性分析表明细菌多样性指数和土壤pH显著正相关.优势和差异条带测序鉴定出Nitrospira、Sphingomonas、Arthrobacter、Brachybacterium、Rhizobium以及Mesorhizobium等或参与氮循环、或降解多环芳烃及杂环有机物的细菌属.本研究说明榆树和云杉有利于土壤细菌多样性的恢复;复垦区土壤的优势菌群多为有利于污染土壤的生态修复和肥力恢复的功能细菌属.