轮作对土壤养分、微生物活性及细菌群落结构的影响

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陈丹梅, 陈晓明, 梁永江, 霍新建, 张长华, 段玉琪, 杨宇虹, 袁玲. .轮作对土壤养分、微生物活性及细菌群落结构的影响. 草业学报, 2015,24(12): 56-65
CHEN Dan-Mei, CHEN Xiao-Ming, LIANG Yong-Jiang, HUO Xin-Jian, ZHANG Chang-Hua, DUAN Yu-Qi, YANG Yu-Hong, YUAN Ling. .Influence of crop rotation on soil nutrients, microbial activities and bacterial community structures. Acta Prataculturae Sinica,2015,24(12): 56-65 复制到剪切板

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轮作对土壤养分、微生物活性及细菌群落结构的影响

陈丹梅¹, 陈晓明², 梁永江², 霍新建², 张长华², 段玉琪³, 杨宇虹³, 袁玲^1,^*

1.西南大学资源环境学院,重庆400716

2.贵州省遵义市烟草公司,贵州遵义 563000

3.云南省烟草农业科学研究院,云南昆明 650031

*通信作者Corresponding author. E-mail:lingyuanh@aliyun.com

作者简介:陈丹梅(1992-),女,四川绵阳人,在读博士。E-mail:544328279@qq.com

收稿日期: 2015-01-05

基金项目:遵义市烟草公司(2010ZY),云南省烟草公司(2013YN11),国家烟草专卖局(110201302016)和科技部“973”课题(2013CB127405)资助

摘要

试验选择云南省具有代表性的烤烟-休闲-玉米(T-F-M)、烤烟-油菜-玉米(T-C-M)、烤烟-油菜-水稻(T-C-R)和烤烟-苕子-水稻(T-V-R)等4种轮作模式,通过测定土壤养分、酶活性及16S rDNA序列分析,研究了轮作对土壤养分、微生物活性及细菌群落结构的影响。结果表明,经过16年的不同轮作种植后,土壤pH值变化于6.2~7.1之间,有机质和有效氮、磷、钾提高或无显著变化,说明在高强度轮作种植条件下,辅以秸秆还田或冬季休闲均可保持或提高土壤肥力和生产力。土壤微生物量碳氮、蔗糖酶、脱氢酶、脲酶、磷酸酶和过氧化氢酶活性均以T-V-R最高,说明土壤生态环境改善,促进微生物繁衍,数量增加,活性增强。土壤细菌的16S rDNA读数依次为5395(T-F-M)、5864(T-C-M)、5528(T-C-R)和6614(T-V-R),分别代表885,973,969和987种(属)类的细菌,归属于变形菌、绿弯菌、放线菌、酸杆菌、拟杆菌等31个门,其中变形菌门的数量最多,占总量的24.69%~32.49%。此外,在4种轮作处理土壤中,前5种门类的细菌相同,15种优势菌株有6种(属)一样,均有较高的丰富度,但也因种植模式不同而变化,说明土壤是决定细菌组成的基本要素,种植模式可不同程度地改变它们的种群结构。从土壤有机质、有效养分、酶活性、微生物量碳氮、细菌种群结构和多样性等方面看,T-V-R 最佳,该种植模式具有潜在的推广应用价值。

关键词: 轮作; 养分; 土壤酶; 细菌; 多样性

Influence of crop rotation on soil nutrients, microbial activities and bacterial community structures

CHEN Dan-Mei¹, CHEN Xiao-Ming², LIANG Yong-Jiang², HUO Xin-Jian², ZHANG Chang-Hua², DUAN Yu-Qi³, YANG Yu-Hong³, YUAN Ling^1,^*

1.College of Resources and Environment, Southwest University, Chongqing 400716, China

2.Guizhou Zunyi Tobacco Company, Zunyi 563000, China

3.Yunnan Tobacco Agriculture Research Institute, Kunming 650031, China

Abstract

A 16-year field experiment has been carried out to investigate the influence of crop rotations on soil nutrients, microbial activities and bacterial community structures. The study includes 454 pyrosequencing analysis of bacterial 16S rDNA. The experiment investigated four crop rotation treatments: 1) flue-cured tobacco in summer, followed by winter fallowing and maize in summer (T-F-M); 2) flue-cured tobacco in summer, canola in winter and maize in summer (T-C-M); 3) flue-cured tobacco in summer, canola in winter and rice in summer (T-C-R); and 4) tobacco in summer, Vicia villosa in winter and rice in summer (T-V-R). After 16-years of crop rotation, soil pH had changed from 6.2 to 7.1. Compared with original soil levels, organic matter and available nutrients (such as nitrogen, phosphorus and potassium) either varied very little or significantly increased, suggesting the retention or growth of fertility under intensive rotations that return straw into soil and fallow during winter. There were higher microbial biomass carbon and nitrogen and enzyme activity (for example, sucrase, phosphatase, dehydrogenase, catalase and urease) in soils under the T-V-R treatment than in any of the other treatments. The readings of bacterial 16S rDNA sequences were 5395 for T-F-M soils, 5864 for T-C-M, 5528 for T-C-R and 6614 for T-V-R, representing 885, 973, 969 and 987 bacterial genera or species respectively, attributed to 31 phyla including Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and Bacteroidetes. Proteobacteria were the largest group, accounting for 24.69%-32.49% of soil bacteria. 5 of the 31 bacterial phyla and 6 of the 15 predominant bacteria were found in all the treatments’ soils. It seems reasonable to suggest that crop rotation was a fundamental determinant of the abundance of soil bacterial components and community structures. Taking into account variations in organic matter, available nutrients, enzyme activities, microbial biomass, bacterial community structures and biodiversity, our experiment suggests that T-V-R could be the best rotation model to promote in the flue-tobacco cultivation areas of Yunnan province.

Keyword: rotation; nutrients; soil enzymes; bacteria; diversity

Show Figures

连续种植同一或近缘作物容易发生“ 连作障碍” 。如土壤养分异常积累或过度消耗, 病原微生物迅速繁衍, 化感物质积累, 土壤微生物种群结构失衡, 作物产量品质降低等^{[1, 2]}。玉米(Zea mays)连作降低土壤有益微生物数量, 增加真菌的相对比例, 频繁发生作物病害^[3]。西瓜(Citrullus lanatus)根系能分泌酚类物质, 产生自毒作用, 抑制生长, 降低产量^[4]。烤烟(Nicotiana tabacum)长期连作, 提高黑胫病和赤星病的发病率, 降低烟叶产量和质量^[5]。相反, 轮作能合理利用土壤养分, 改变土壤理化和生物学性质, 保持地力, 增加产量, 提高经济效益^[6]。但是, 轮作模式不同, 对土壤理化和生物学性质的影响也不一样。连续5年实施水稻(Oryza sativa)-油菜(Brassica campestris)轮作, 土壤有机质含量显著高于水稻-小麦(Triticum aestivum)和水稻-黑麦草(Lolium perenne)轮作^[7]。从土壤酶活性看, 采用草莓(Fragaria ananassa)-休闲种植模式的土壤蔗糖酶活性最高, 草莓-水稻种植模式次之, 草莓-甜瓜(Cucumis melo)轮作最低, 最高比最低提高了94.1%^[8]; 但在草莓-休闲种植的土壤中, 酸性磷酸酶和过氧化氢酶活性分别比草莓-甜瓜种植模式降低22.9%和13.5%。在我国东北黑土上, 实施黄瓜(Cucumis sativus)连作、小麦-黄瓜和毛苕子(Vicia villosa)-黄瓜轮作, 轮作显著增加根际细菌种类, 减少结瓜后期的真菌种群, 尤以毛苕子-黄瓜轮作最为显著^[9]。

微生物是土壤的重要组成部分, 可释放多种酶类, 参与土壤有机质降解、腐殖质合成和养分循环等生物化学过程^[10]。细菌是数量最多和种群最丰富的土壤微生物, 人们通常采用分离培养、磷脂脂肪酸和PCR-DGGE等常规和分子生物学技术研究土壤微生物, 但获得的细菌数量种类有限, 不能充分反映土壤细菌多样化的组成和种群结构。454高通量测序技术是在PCR扩增的基础上, 分析细菌16S rDNA和真菌18S rDNA序列, 与基因库中的已知序列进行对比, 鉴别微生物种(属)类, 具有适用范围广、灵敏性高、可靠性好, 同时检测活性和休眠微生物等特点^[11]。

云南省是我国烤烟主产区, 烤烟轮作比例达80%以上, 烟地夏季主要轮作玉米和水稻, 分别占种植面积的64.7%和27.6%, 冬季一般种植油菜和绿肥或休闲, 轮作年限一般为2~3年^[12]。选择科学的轮作模式, 减轻连作障碍, 是保持整个农业生产健康和持续发展的重要措施^[13], 但相关研究较少。为了深入了解土壤细菌的数量、活性、组成结构和多样性, 建立科学合理的轮作模式, 本研究采用常规方法和454高通量测序技术, 研究了云南省烟区主要轮作模式对土壤养分、微生物活性与细菌群落结构的影响。

1 材料与方法

1.1 试验地概况

云南省烟草农业科学研究院试验基地(N 24° 14', E 102° 30'), 海拔1680 m, 年均温度15.9℃, 年降雨量918 mm, 雨季(4-9月)降雨量占全年的79.5%, 年日照时数2072 h。供试土壤为云南省典型、具有代表性的砂质红壤, pH 6.4, 有机质10.70 g/kg, 全氮0.54 g/kg, 全磷0.11 g/kg, 全钾6.43 g/kg, 有效氮82.0 mg/kg, 有效磷 9.0 mg/kg, 有效钾160.0 mg/kg。

1.2 试验处理

试验始于1998年, 设置烤烟-休闲-玉米(flue cured tobacco-fallowness-maize, T-F-M)、烤烟-油菜-玉米(flue cured tobacco-canola-maize, T-C-M)、烤烟-油菜-水稻(flue cured tobacco-canola-rice, T-C-R)和烤烟-苕子-水稻(flue cured tobacco-vetch-rice, T-V-R)4种轮作模式。小区面积28 m², 重复3次, 随机区组排列。烤烟、玉米和水稻5月初移栽, 苕子和油菜秋末播种。根据当地大田生产情况, 油菜施用纯氮90 kg/hm², P₂O₅ 30 kg/hm²; 玉米和水稻施用纯氮112.5 kg/hm², P₂O₅ 40 kg/hm²; 苕子施用纯氮75 kg/hm²。此外, 水稻、玉米和油菜秸秆全部切碎还田; 绿肥收割多次, 未彻底收割的残桩全部翻压入土。在烤烟种植季节, 基肥由N∶ P₂O₅∶ K₂O=10∶ 10∶ 25烤烟专用肥提供, 施氮量占施肥总量的70%; 剩余30%的氮素由烤烟专用追肥(N∶ P₂O₅∶ K₂O=10∶ 0∶ 25)提供, 在移栽后7~10 d和30~40 d均分两次穴施。在玉米、油菜及苕子种植季节, 化学氮磷分别由尿素和过磷酸钙提供。其中, 玉米和油菜70%的氮和全部磷肥作基肥, 剩余30%的氮分别在油菜云苔期和玉米大喇叭口期作为追肥穴施, 苕子全施基肥。

1.3 土样采集与分析

在2014年油菜和苕子旺长期, 采集0~20 cm的耕层土壤(包括休闲处理), 拣去杂物, 取部分土壤晾干进行常规分析。采用电位法测定土壤pH; 重铬酸钾容量法测定土壤有机质; 碱解扩散法测定土壤碱解氮; NaHCO₃提取法测定土壤有效磷; NH₄Ac-火焰光度法测定土壤有效钾^[14]。土壤蔗糖酶活性采用3, 5-二硝基水杨酸比色法测定, 酶活性以24 h后1 g土壤中生成的葡萄糖(glucose)mg数表示^[15]; 磷酸酶活性用磷酸苯二钠比色法测定, 酶活性以24 h后1 g土中释放的酚mg数表示^[15]; 脲酶活性用苯酚钠-次氯酸钠显色法测定, 酶活性以24 h后1 g土中N $\begin{matrix} {H_{4}}^{+} \end{matrix}$ -N的mg数表示^[15]; 过氧化氢酶活性采用高锰酸钾滴定法测定, 酶活性以每h内1 g土消耗0.1 mol/L KMnO₄的mL数表示^[15]; 脱氢酶活性采用TTC比色法测定, 酶活性以24 h后1 g土中TPF(三苯基甲月替)的mg数表示^[15]。另取部分土壤立即液氮冷冻备测微生物碳氮量和细菌16S rRNA序列。微生物碳氮量采用氯仿熏蒸-0.5 mol/L K₂SO₄提取, 用K₂Cr₂O₇氧化法测碳和腚酚蓝比色法测氮^[16]。

在上海美吉生物科技有限公司进行细菌16S rDNA测序, 参照454高通量测序方法, 提取、扩增、纯化、定量和均一化细菌16S rDNA, 利用Roche Genome Sequencer FLX测序平台进行测序^[17]。然后, 对有效序列进行去杂、修剪、除嵌合体序列等过滤处理, 得到优化序列, 通过聚类分析形成分类单元(operational taxonomic units, OTUs), 采用BLAST程序对比GenBank(http://ncbi.nlm.nih.gov)中的已知序列, 根据97%的相似度确定16S rDNA序列所代表的细菌种(属)类。

1.4 数据处理

利用土壤细菌属(种)数(OTUs)和16S rDNA序列数(Reads)计算土壤细菌的种群特征值, 包括多样性指数和优势度指数。

Shannon-Wiener多样性指数(H)的计算公式为:

H=- $\begin{matrix} \overset{S_{obs}}{\sum_{i = 1}} \end{matrix} \begin{matrix} \frac{n_{i}}{N} \end{matrix}$ ln $\begin{matrix} \frac{n_{i}}{N} \end{matrix}$

Simpson优势度指数(D)的计算公式为:

D= $\begin{matrix} \frac{\overset{S_{obs}}{\sum_{i = 1}} n_{i} (n_{i} - 1)}{N (N - 1)} \end{matrix}$

其中, S_obs为获得OTUs的总数量; n_i为细菌i的OTUs数量; N为获得细菌的总数量^{[18, 19]}。

细菌丰富度为某种细菌的16S rDNA读数占细菌16S rDNA总读数的百分数^{[20, 21]}。

1.5 统计分析

用Excel进行基本计算, SPSS 16.0软件进行统计分析, 差异显著性水平为P< 0.05。

2 结果与分析

2.1 土壤pH、有机质与有效养分

在不同种轮作处理的土壤中, pH、有机质和有效养分的含量显著提高或无明显变化(表1)。与原始土壤相比, T-C-M和T-F-M显著提高土壤pH, 从pH 6.4提高到pH 6.9~7.1, 但T-C-R和T-V-R对土壤pH无显著影响。T-C-M、T-C-R和T-V-R不同程度地提高了土壤有机质含量, 增幅变化于16.26%~45.14%之间, 以T-V-R最为显著。T-C-R和T-V-R的有效氮较原始土壤分别提高10.0%和32.5%; 在4种轮作处理的土壤中, 有效磷含量是原始土壤的2.13~4.67倍; T-F-M使土壤有效钾增加64.06%。

表1 不同轮作模式对土壤pH、有机质和有效养分的影响 Table 1 Selected properties of the soil under different rotation treatments

2.2 土壤酶活性

土壤酶活性因轮作模式不同而异(表2)。在T-V-R处理的土壤中, 蔗糖酶、磷酸酶、脱氢酶、过氧化氢酶和脲酶活性最高。在T-F-M、T-C-M和T-C-R处理的土壤中, 蔗糖酶活性无显著差异; 脲酶活性的变化趋势同蔗糖酶。在T-C-M处理的土壤中, 磷酸酶和脱氢酶活性最低, 但脱氢酶活性与T-C-R处理无显著差异。在T-F-M和T-C-R处理的土壤中, 过氧化氢酶活性无显著差异, 但显著低于T-C-M和T-V-R。

表2 不同种植模式对土壤酶活性的影响 Table 2 Influence of rotation modals on enzyme activities in soil

轮作处理Rotation modals	蔗糖酶Sucrase	磷酸酶Phosphatase	脱氢酶Dehydrogenase	过氧化氢酶Catalase	脲酶Urease
烤烟-休闲-玉米T-F-M	35.50b	1.42b	5.27b	0.20b	0.59b
烤烟-油菜-玉米T-C-M	32.79b	0.65c	0.65c	0.21a	0.57b
烤烟-油菜-水稻T-C-R	34.78b	1.41b	4.02b	0.20b	0.58b
烤烟-苕子-水稻T-V-R	66.74a	2.01a	9.85a	0.21a	0.62a

* 蔗糖酶活性Sucrase activity:mg 葡萄糖Glucose/(g· h); 磷酸酶活性Phosphatase activity:mg pNP/(g· h); 脱氢酶活性Dehydrogenase activity:mg TPF/(g· h); 过氧化氢酶活性Catalase activity:mL(0.1 mol/L K₂MnO₄)/(h· g); 脲酶活性Urease activity:mg N $\begin{matrix} {H_{4}}^{+} \end{matrix}$ -N/(g· h).

表2 不同种植模式对土壤酶活性的影响 Table 2 Influence of rotation modals on enzyme activities in soil

2.3 微生物生物量

由图1可知, 微生物量碳T-V-R处理最高, 达到154.70 mg/kg; T-C-M和T-C-R次之; T-F-M最低, 仅56.33 mg/kg。但是, 微生物量氮的变化趋势与微生物量碳有所不同, T-V-R最高, T-C-M和T-F-M次之, T-C-R最低。在4种不同轮作模式处理中, 微生物碳氮比差异显著。

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	图1 种植模式对土壤微生物量碳氮的影响Fig.1 Influence of rotation treatments on microbial C and N in soil不同小写字母表示差异显著, 下同。The different small letters mean the significant differences at P< 0.05, the same below.

2.4 土壤细菌

2.4.1 稀释曲线

随机抽取测序样品中的16S rDNA读数(reads), 以细菌种(属)类数(OTUs)为纵坐标, 16S rDNA读数为横坐标, 获得稀释曲线(图2)^[22]。结果表明, 抽样读数大约在1500以下时, 细菌种(属)类数迅速增加; 读数在1500~4000之间, 细菌种(属)数缓慢增加; 读数超过4000之后, 其种(属)类数的增长逐渐趋于平缓。此外, 细菌稀释曲线的最高值因轮作处理不同而异, T-V-R最高, T-C-M和T-C-R次之, T-F-M最低。

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	图2 不同轮作处理的土壤中细菌稀释性曲线Fig.2 Bacteria rarefaction curves in soil under different rotation treatments

2.4.2 细菌门类

在T-F-M、T-C-M、T-C-R和T-V-R处理的土壤中, 细菌16S rDNA读数依次为5395, 5864, 5528和6614, 分别代表885, 973, 969和987种(属)类的细菌, 其中62.21%~69.72%的细菌读数小于5。土壤细菌分别归属于变形菌(Proteobacteria)、绿弯菌(Chloroflexi)、放线菌(Actinobacteria)、酸杆菌(Acidobacteria)、拟杆菌(Bacteroidetes)、浮霉菌(Planctomycetes)、芽单胞菌(Gemmatimonadetes)及厚壁菌(Firmicutes)等31个门, 约有1%的细菌尚待确定所归属的门类(表3, 图3)。其中, 变形菌门的丰富度最高, 占总量的24.69%~32.49%, 平均29.51%。此外, 在各处理的土壤中, 前5种门类的细菌相同, 依次为变形菌门、绿弯菌门、放线菌门、酸杆菌门和拟杆菌门, 其丰富度因种植模式不同而异。

2.4.3 优势菌株

在各处理的土壤中, 前15种优势菌株的丰富度合计占总量的45.91%~48.58%。其中, 以两种待定细菌(unclassified bacteria)的丰富度最高, 平均占总量的26.68%和11.52%; 第15种优势菌株的丰富度占总量的0.24%~0.44%。

	Figure Option View Download New Window
	图3 不同种植处理的土壤中, 前10个门类细菌16S rDNA序列数及其丰富度Fig.3 The 16S rDNA reads and abundance of top 10 bacterial phyla in soil with different cropping treatments

由表3可知, 在15种优势菌株中, 待定细菌-1、待定细菌-2、酸杆菌、芽单胞菌、放线菌和绿弯菌共存于4种轮作模式的土壤中。其中, 待定细菌-1和待定细菌-2的丰富度合计高达42.62%~45.68%, 且不因轮作处理而发生改变; 酸杆菌、放线菌和芽单孢菌属于已鉴定的前5种优势菌株。此外, 伯克氏菌(Burkholderiaceae)共存于T-F-M、T-C-M和T-V-R处理的土壤; 黏球菌、α -变形菌和酸微菌是T-F-M、T-C-R和T-V-R的共有细菌; β -变形菌同时存在于T-C-M、T-C-R和T-V-R处理的土壤。

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	表 3

在15种优势菌株中, 梭菌仅发现于T-F-M处理的土壤; 链霉菌、终极腐霉菌和黄杆菌为T-C-M处理土壤的独有菌株; 在T-C-R处理的土壤中, 独有菌株包括变形菌、假单胞菌、浮霉状菌和根瘤菌; 在T-V-R处理的土壤中, 中慢生型天山根瘤菌和贪噬菌为独有菌株。

2.4.4 细菌群落特征值在T-V-R的土壤中, 细菌多样性指数最高, 达到3.925; T-C-M次之, 为3.756; T-F-M和T-C-R最低。但是, 优势度指数T-F-M最高, 达0.711, T-V-R最低, 仅0.583(表4)。

表4 各轮作处理土壤细菌群落特征值 Table 4 Characteristic values of bacterial communities in soil under different rotation treatments

3 讨论

经过16年的轮作种植, 有机质和有效养分提高或无显著变化, 土壤pH变化于6.2~7.1之间, 仍然在粮、油、经、蔬等多种作物种植的适合范围之内, 说明在高强度轮作种植条件下, 辅以秸秆还田或冬季休闲均可保持或提高土壤肥力和生产力。此外, 在各轮作处理的土壤中, 有效磷高达19.2~42.0 mg/kg, 是原始土壤 9.0 mg/kg的2.13~4.67倍, 可以适量减施磷肥。综合土壤pH、有机质和有效养分的变化, 以T-V-R种植模式最佳。

土壤有机质是微生物的碳源和氮源^[23]。秸秆还田和轮作向土壤提供大量的、丰富多样的有机质, 可满足不同微生物对碳源和养分的需要。在实施T-V-R轮作的过程中, 水旱轮作, 嫌/好气交替, 创造了适合多种微生物繁衍的不同土壤环境; 烤烟、水稻和苕子的近缘性小, 有机成分差异较大, 有益于不同微生物的繁殖生长。因此, T-V-R土壤中的微生物量碳氮最高, 16S rDNA读数最大, 细菌种(属)类最多。从土壤酶活性看, T-V-R轮作的蔗糖酶、脱氢酶、磷酸酶、过氧化氢酶和脲酶活性最强, 推测微生物分泌的酶较多^[24], 土壤酶活性强促进有机质分解、腐殖质合成、养分转化、生物固氮、污染物清除等^[25]。

在不同轮作处理的土壤中, 土壤微生物量碳氮比高低相差约2.5倍, 意味着它们的群落结构也发生了显著变化。本文采用454高通量测序方法, 揭示了细菌从门类到种(属)的组成、优势菌株、丰富度和多样性特征等。结果表明, 稀释性曲线呈迅速增加-缓慢增加-逐渐平缓的变化趋势, 说明16S rDNA的样本量和测序数据合理, 准确地反映了样本中的细菌数及组成情况; 稀释曲线的峰值高低不一, 意味着轮作处理影响细菌的多样性。一般认为, 多样性指数表示生物群落中的物种多寡, 数值愈大表示群落中的物种越丰富; 优势度指数越大, 生物群落内的奇异度越高, 优势种群突出^[26]。在健康稳定的生态环境中, 生物多样性指数较高, 优势度指数较低。T-V-R显著提高细菌群落的多样性指数, 但降低优势度指数。因此, T-V-R处理的土壤生态环境较好, 有益于细菌生长繁殖, 数量增多, 种群增加, 密度增大。此外, 在不同种植模式的土壤中, 细菌的丰富度因轮作和它们的门、属、种不同而异, 存在885~987种(属)的细菌, 远远超过了目前的常规培养、磷脂脂肪酸和PCR-DGGE能达到的水平。因此, 更能深入研究土壤细菌的组成和群落结构。值得注意的是, 16S rDNA读数和细菌OTUs以T-V-R最高, T-F-M最低, 说明T-V-R土壤中的细菌数和种(属)类最多。

在4种轮作处理的土壤中, 前5种门类的细菌相同, 但因种植模式不同而影响其丰富度。在前15种优势细菌中, 有 6种(属)共同存在于各轮作处理的土壤中, 均有较高的丰富度, 也因种植模式不同而发生变化; 其中待定细菌-1和待定细菌-2的丰富度合计高达42.62%~45.68%, 居绝对优势地位。说明土壤是决定细菌组成的基本要素, 种植模式可不同程度地改变细菌的种群结构。从优势菌株的功能看, 丰富度最高的待定细菌-1和待定细菌-2尚待鉴定分类, 需要明确其生物学功能; 酸杆菌广泛存在于自然界的各种环境中, 具有丰富的遗传和代谢多样性, 对稳定生态系统贡献极大^{[27, 28]}; 放线菌也是自然界分布最广泛的微生物类群之一, 参与土壤有机质转化, 土壤结构形成, 植物生长素和抗生素分泌^[29]; 绿弯菌是活性污泥的组成成分之一^[30], 生活在好氧环境下, 有利于土壤中有毒物质的降解。除T-C-R之外, 其他3种轮作处理的土壤都存在伯克氏菌, 且丰富度较高, 它们能分泌生长素、ACC脱氨酶和铁载体, 溶解矿物态无机磷, 促进番茄(Lycopersicon esculentum)、美洲商陆(Phytolacca Americana)和籽粒苋(Amaranthus hypochondriacus)生长, 提高植物抗(耐)重金属的能力^{[31, 32]}。此外, T-V-R处理的土壤中还存在贪噬菌和中慢生型天山根瘤菌, 前者参与有机磷、硝基酪氨酸、除草剂、三氯乙烯等的生物降解^{[33, 34]}, 中慢生型天山根瘤菌明显与苕子结瘤固氮有关。因此, 优势细菌的作用与土壤功能密切相关。

总之, 不同轮作方式均有益于保持或提高土壤肥力和土地生产力。从土壤有机质、有效养分、酶活性、微生物量、细菌种群结构和多样性等方面看, T-V-R最佳, 是值得推广的一种种植模式。

The authors have declared that no competing interests exist.

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2013

0.0

. 2013, 5:6-12 DOI:doi:10.11838/sfsc.20130502

连作障碍发生机制研究进展

王飞, 李世贵, 徐凤花

摘　要：连作障碍是农业生产中经常发生的一种病害,各种作物或轻或重都会发生,已成为世界性难题,给农业生产造成了严重损失.近年来,国内外学者从多方面、多角度对连作障碍进行分析.本文从土壤生物学环境的恶化、化感作用和土壤理化性状改变等角度阐述了连作障碍发生机制的研究进展.

... 如土壤养分异常积累或过度消耗,病原微生物迅速繁衍,化感物质积累,土壤微生物种群结构失衡,作物产量品质降低等^[1,2] ...

2014

0.0

. 2014, 23(2):340-345 DOI:doi:10.11686/cyxb20140240

不同种植年限人工苜蓿草地植物和土壤化学计量特征

杨菁, 谢应忠, 吴旭东

Through measuring and analyzing carbon (C),nitrogen (N),phosphorus (P),and its stoichiometry ratios of leaf,stem and 0-20 cm soil under different plant ages (1,3,4,5 to 8 years) of alfalfa at the foot of Helan Mountain in Ningxia,the influence of planting-age on nutrient content and stoichiometry of soil and plant in alfalfa grassland were researched. 1)With the increase of plant time,0-20 cm soil C and N firstly increase and then descend,but the P is contrary. There were significant differences between different planting-age ( P

通过测定并分析不同种植年限(种植1,3,4,5及8年)人工苜蓿草地苜蓿叶片、茎秆及0~20 cm土壤中C、N、P含量及其化学计量比,研究了种植年限对人工苜蓿草地土壤及植物养分含量及其化学计量比的影响。结果表明,1)0~20 cm土壤C、N含量随种植年限的增加,呈先增后减的趋势,P含量与之相反,各年限间有显著差异( P

... 如土壤养分异常积累或过度消耗,病原微生物迅速繁衍,化感物质积累,土壤微生物种群结构失衡,作物产量品质降低等^[1,2] ...

2011

0.0

. 2011, 28(10):1777-1780

玉米连作对土壤微生物和土壤主要养分的影响

邢会琴, 肖占文, 闫吉智

A field survey was carried out to investigate the effect of continuous cropping of maize with different years on soil microbes (bacteria, fungus, actinomyces) and main soil nutrients for finding the main obstacle factors of continuous cropping of maize in the Hexi area. This study showed that the quantity of bacteria in 0-20 cm soil layer significantly decreased and the number of fungus increased as the cropping years increased (P

为确定河西地区玉米（Zea mays）连作的主要障碍因子，对不同连作年限的玉米田土壤微生物种群和土壤主要养分进行了常规分析。结果表明，在0～20 cm土层深处，细菌随连作年限增加呈递减趋势，与速效磷和有机质含量呈显著正相关，即速效磷和有机质均随连作年限的增加而显著减少（P

... 玉米(Zea mays)连作降低土壤有益微生物数量,增加真菌的相对比例,频繁发生作物病害^[3] ...

2013

0.0

. 2013, 24:10-15 DOI:doi:10.3969/j.issn.1000-6346.2013.24.003

西瓜化感作用研究进展

张小红, 赵依杰

The continuous cropping of watermelon〔 Citrullus lanatus （Thunb.）Matsum. et Nakai〕leads to the accumulation of allelochemicals，and causes the decrease of yield．It is of important significance to reveal the obstacle mechanism of allelopathic on watermelon continuous cropping，and overcome this obstacle．The paper reviewed the research progress on watermelon allelopathy， including the current research status on watermelon allelopathy，the allelochemicals and their releasing way，and the function characteristics of allelochemicals，and allelopathy application in production． The paper also prospected the future research directions on watermelon allelopathy，aiming at providing theoratical references for developing a scientific way to enhance watermelon resistance，and improving the yield and quality of watermelon.

西瓜连作引起化感物质积累，导致产量下降，研究西瓜化感作用对揭示西瓜连作障碍机理、克服西瓜连作障碍具有重要的意义。本文对西瓜化感作用的研究进展进行了综述，包括西瓜化感现象的研究现状、化感物质及其释放途径、化感物质的作用特点、以及化感作用在西瓜生产实践中的应用，并提出西瓜化感作用未来的研究方向，旨在为制定增强西瓜抗逆性能和提高西瓜产量、品质的科学途径提供一定理论参考。

... 西瓜(Citrullus lanatus)根系能分泌酚类物质, 产生自毒作用,抑制生长,降低产量^[4] ...

2004

0.0

. 2004, 17:267-271 DOI:doi:10.3969/j.issn.1001-4829.2004.z1.063

烤烟轮作、连作对烟叶产量质量的影响

晋艳, 杨宇虹, 段玉琪

烤烟连作、轮作的4年定位比较试验结果表明:连作烟株的田间长相长势、产量、产值、外观质量均低于轮作;连作的产量仅有轮作的59.12%;产值仅有轮作的29.93%;中上等烟比例仅有轮作的52.07%;均价仅有50.6%.烟叶的致香物质检测结果表明:轮作烟叶中致香物质含量大多数高于连作烟叶.连作与轮作土壤养分对比结果表明:连作田土壤中的有效磷和有效钾含量明显地高于轮作田;轮作土壤的pH值、有机质、全钾、速效硼、速效锌、CEC、交换性镁均高于连作.连作与轮作土壤中微生物总量差异不明显.与轮作相比,烤烟连作后黑胫病和赤星病的发病率升高.

... 烤烟(Nicotiana tabacum)长期连作,提高黑胫病和赤星病的发病率,降低烟叶产量和质量^[5] ...

2010

0.0

. 2010, 2:108- DOI:doi:10.3969/j.issn.1007-5739.2010.02.071

关于轮作的探讨

王玉琴

以大豆为例,论述了轮作的作用,分析了非合理轮作对大豆产量的影响,并提出合理的轮作方式,以期为轮作的推广提供参考.

... 相反,轮作能合理利用土壤养分,改变土壤理化和生物学性质,保持地力,增加产量,提高经济效益^[6] ...

2003

0.0

. 2003, 6:9-10 DOI:doi:10.3969/j.issn.1008-2239.2002.06.004

稻田不同轮作方式对培肥地力的作用

王先华

通过不同轮作方式的长期试验，研究土壤有机质，结合态腐殖质、养分变化和水稻产量影响，阐明油菜、一年生黑麦草、小麦秸秆翻压还田对土壤肥力的影响。试验表明，3种作物连作5年土壤有机质积累增加，其中油—稻增加最多达0.15％，平均每年增加0.03％；0.25～0.55mm微团聚体数量增加量最多。土壤全氮量以饲—稻处理增加多达0.04％；土壤有机磷和速效磷含量以饲—稻增加较多，有机磷提高11.6mg／kg。水稻产量以饲—稻最高。从而为农牧结合和用养结合增加农民收入找到了一条最佳的种植模式。

... 连续5年实施水稻(Oryza sativa)-油菜(Brassica campestris)轮作,土壤有机质含量显著高于水稻-小麦(Triticum aestivum)和水稻-黑麦草(Lolium perenne)轮作^[7] ...

2010

0.0

. 2010, 18(2):312-315 DOI:doi:10.3724/SP.J.1011.2010.00312

不同轮作方式下大棚草莓产量及土壤生物学特性

杨祥田, 周翠, 李建辉

A 4-year experiment was conducted in plastic greenhouse to determine the effect of three different cropping systems [strawberry-solarization (strawberry monoculture with solarization to inhibit pathogens), strawberry-rice rotation, and straw-berry-melon rotation] on the yield of strawberry, soil microbes and soil enzyme activity. The results show that both the yield and economic output of strawberry increase under strawberry-solarization and strawberry-rice rotation compared with strawberry-melon rotation. Soil pH increases but salt accumulation and wilting disease declines under the two cropping systems. Compared with strawberry-melon rotation, both strawberry-solarization and strawberry-rice rotation increase soil microbial amount. And the microbe composition changes in two systems with 95.92%～96.21% bacteria population, while bacteria population proportion is 89.91% under strawberry-melon rotation. The ratio of bacteria to fungi under strawberry-solarization and strawberry-rice rotation is 9 times higher than that under strawberry-melon rotation. Soil invertase activity is also enhanced under strawberry-rice rotation and strawberry -solarization. The findings of the study suggest that "wet-drought" crop rotation such as strawberry-solarization and strawberry-rice rotation can eliminate soil restrictions to realize sustainability of production.

试验研究了不同轮作方式下大棚草莓产量、土壤微生物区系和土壤4种酶活性的变化, 结果表明：草莓闷棚、草莓水稻轮作方式草莓产量及效益明显比草莓甜瓜旱地轮作方式高, 且土壤pH值高, 盐分积累少, 黄萎病发生率低。草莓闷棚、草莓水稻轮作方式的草莓土壤微生物总数比草莓甜瓜旱地轮作多, 其中细菌所占比例达95.92%～96.21%, 高于草莓甜瓜旱地轮作的89.91%, 细菌与真菌之比达649～787, 为草莓甜瓜旱地轮作的10倍左右。草莓闷棚、草莓水稻轮作明显提高了土壤转化酶的活性。实行草莓闷棚和草莓水稻水旱轮作方式, 可让大棚草莓的土壤障碍得到缓解或消除, 实现可持续生产。

... 1%^[8] ...

2011

0.0

. 2011, 48(1):175-184

小麦、毛苕子与黄瓜轮作对土壤微生态环境及产量的影响

于高波, 吴凤芝, 周新刚

Soil available nutrients, soil enzyme activity, soil microbial diversity and cucumber yield in a field under crop rotations of cucumber with wheat and hairy vetch with conventional methods and PCR-DGGE to study effect of the rotation on soil micro-ecological environment and yield of cucumber. Results indicate that the rotations significantly increased cucumber yield and effectively improved the soil micro-ecological environment. The rotation of wheat-cucumber increased the yield of cucumber the most significantly (p<0.01), by 28.04%, and improved the overall activity of polyphenol oxidase, catalase and urease. The rotation of hairy vetch-cucumber increased the yield of cucumber by 16.78% and improved the content of soil available nutrients, and the invertase activity significantly over CK (p<0.01) DGGE analysis shows that the rotation helped increase the diversity of bacterial species in the rhizosphere, while decreasing that of fungi at the late fruit-bearing stage. The effect of the rotation of hairy vetch-cucumber was more significant. The rotation of wheat-cucumber showed certain effect on rhizospheric soil fungi as well as the bacterial community structure 30 days after transplanting of cucumber. To sum up, the rotations of cucumber with wheat and with hairy vetch help mitigate the hazard of consecutive cropping of cucumber, improve the soil microbial eco-environment and raise the yield of cucumber.

采用常规方法及PCR-DGGE技术对土壤速效养分含量、土壤酶活性和微生物群落结构多样性以及黄瓜产量进行分析，以探究小麦、毛苕子与黄瓜轮作对黄瓜土壤微生态环境及产量的影响。结果表明，不同轮作处理均显著地提高了黄瓜产量，有效地改善了土壤微生态环境。其中小麦-黄瓜轮作黄瓜产量极显著高于对照 (p<0.01)，增产28.04%，其多酚氧化酶、过氧化氢酶及脲酶活性总体较高。毛苕子-黄瓜处理增产16.78%，并增加了土壤养分含量，转化酶活性较高，极显著高于对照 (p<0.01)。DGGE结果表明，轮作有助于根际土壤细菌种类的增多，结瓜后期真菌种类的减少，其中毛苕子-黄瓜处理的影响更为明显。小麦-黄瓜轮作对土壤真菌与定植后30 d土壤细菌群落结构具有一定的影响。总之，小麦、毛苕子与黄瓜轮作有利于缓解黄瓜连作障碍，改善土壤微生态环境，提高黄瓜产量。

... 在我国东北黑土上,实施黄瓜(Cucumis sativus)连作、小麦-黄瓜和毛苕子(Vicia villosa)-黄瓜轮作,轮作显著增加根际细菌种类,减少结瓜后期的真菌种群,尤以毛苕子-黄瓜轮作最为显著^[9] ...

1995

0.0

... 微生物是土壤的重要组成部分,可释放多种酶类,参与土壤有机质降解、腐殖质合成和养分循环等生物化学过程^[10] ...

2012

0.0

. 2012, 28(30):171-176 DOI:doi:10.3969/j.issn.1000-6850.2012.30.032

高通量测序技术及其在农业科学研究中的应用

闫绍鹏, 杨瑞华, 冷淑娇

High-throughput sequencing is a major breakthrough in DNA sequencing technology development, the emergence of high-throughput sequencing technology provided an unprecedented opportunity to modern agricultural scientific research. This paper summarized the principle of the 454, Solexa and SOLiD second-generation high-throughput sequencing technology and the latest progress of the HeliScope and Pacific Biosciences SMRT, as represented by the single-molecule sequencing technology. On this basis, the high-throughput sequencing technology was summed up in genome sequencing, transcriptome sequencing, small RNA molecules and digital gene expression profiles and other research areas in agricultural research. Finally, the characteristics and development prospect of high-throughput sequencing technology was noticed.

高通量测序是DNA测序技术发展中的重大突破，它的出现为现代农业科学的研究提供了前所未有的机遇。总结了以454、Solexa和SOLiD为代表的第二代高通量测序技术的原理以及HeliScope和Pacific Biosciences SMRT为代表的单分子测序技术的最新进展。在此基础上，归纳了高通量测序技术在基因组测序、转录组测序、小分子RNA及数字化基因表达谱等研究领域在农业研究中的应用。最后，指出了当前高通量测序技术的特点并对其在今后研究中的发展方向进行了展望。

... 454高通量测序技术是在PCR扩增的基础上,分析细菌16S rDNA和真菌18S rDNA序列,与基因库中的已知序列进行对比,鉴别微生物种(属)类,具有适用范围广、灵敏性高、可靠性好,同时检测活性和休眠微生物等特点^[11] ...

2006

0.0

. 2006, 2:211-217

云南烤烟轮作现状与对策分析

李天福, 王树会, 王彪

本文阐述了烤烟轮作与连作的研究进展，结合云南烤烟轮作现状与存在问题，提出了烤烟轮作的保障措施。根据烤烟种植规模与轮作现状，将云南省烤烟种植区分为稳定调整区、适度发展区、加快发展区和待开发区等四种区域类型。

... 6%,冬季一般种植油菜和绿肥或休闲,轮作年限一般为2~3年^[12] ...

2011

0.0

. 2011, 16:60-

轮作对土壤肥力的影响

郁飞燕, 李友军

轮作是在一定年限内在同一地块上有顺序地轮换种植不同的农作物,通过协调作物与土壤的关系,实现持续增产的一项具体有效措施.本文概述了轮作对土壤有机质、土壤养分利用、土壤结构等的作用,提出了合理轮作对土壤肥力的影响.

... 选择科学的轮作模式,减轻连作障碍,是保持整个农业生产健康和持续发展的重要措施^[13],但相关研究较少 ...

2008

0.0

... NH₄Ac-火焰光度法测定土壤有效钾^[14] ...

1986

0.0

... 土壤蔗糖酶活性采用3,5-二硝基水杨酸比色法测定,酶活性以24 h后1 g土壤中生成的葡萄糖(glucose)mg数表示^[15] ...

... 磷酸酶活性用磷酸苯二钠比色法测定,酶活性以24 h后1 g土中释放的酚mg数表示^[15] ...

... 脲酶活性用苯酚钠-次氯酸钠显色法测定,酶活性以24 h后1 g土中N H4+-N的mg数表示^[15] ...

... 1 mol/L KMnO₄的mL数表示^[15] ...

... 脱氢酶活性采用TTC比色法测定,酶活性以24 h后1 g土中TPF(三苯基甲月替)的mg数表示^[15] ...

1993

0.0

. 1993, 59:3605-3617

Phospholipid fatty acid composition, biomass, and activity of microbial communities from two soil types experimentally exposed to different heavy metals

Frostegard A , Tunlid A , Baat I E

Department of Microbial Ecology, Lund University, Helgonavägen 5, S-223 62 Lund, Sweden.

The phospholipid fatty acid (PLFA) pattern was analyzed in a forest humus and in an arable soil experimentally polluted with Cd, Cu, Ni, Pb, or Zn at different concentrations. In both soil types, there were gradual changes in the PLFA patterns for the different levels of metal contamination. The changes in the forest soil were similar irrespective of which metal was used, while in the arable soil the changes due to Cu contamination differed from those due to the other metals. Several PLFAs reacted similarly to the metal amendments in the two soil types, while others showed different responses. In both soils, the metal pollution resulted in a decrease in the iso-branched PLFAs i15:0 and i17:0 and in the monounsaturated 16:1omega5 and 16:1omega7c fatty acids, while increases were found for i16:0, the branched br17:0 and br18:0, and the cyclopropane cy17:0 fatty acids. In the forest soil, the methyl branched PLFAs 10Me16:0, 10Me17:0, and 10Me18:0 increased in metal-polluted soils, indicating an increase in actinomycetes, while in the arable soil a decrease was found for 10Me16:0 and 10Me18:0 in response to most metals. The bacterial PLFAs 15:0 and 17:0 increased in all metal-contaminated samples in the arable soil, while they were unaffected in the forest soil. Fatty acid 18:2omega6, which is considered to be predominantly of fungal origin, increased in the arable soil, except in the Cu-amended samples, in which it decreased instead. Effects on the PLFA patterns were found at levels of metal contamination similar to or lower than those at which effects on ATP content, soil respiration, or total amount of PLFAs had occurred.

PMID: 16349080

... 5 mol/L K₂SO₄提取,用K₂Cr₂O₇氧化法测碳和腚酚蓝比色法测氮^[16] ...

2013

0.0

... 在上海美吉生物科技有限公司进行细菌16S rDNA测序,参照454高通量测序方法,提取、扩增、纯化、定量和均一化细菌16S rDNA,利用Roche Genome Sequencer FLX测序平台进行测序^[17] ...

1989

0.0

... N为获得细菌的总数量^[18,19] ...

2011

0.0

. 2011, 6(12):1-14 DOI:10.1371/journal.pone.0027310

Reducing the effects of PCR amplification and sequencing artifacts on 16S rDNA-based studies

Patrick D S , Dirk G , Sarah L W

Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, United States of America. pschloss@umich.edu

The advent of next generation sequencing has coincided with a growth in interest in using these approaches to better understand the role of the structure and function of the microbial communities in human, animal, and environmental health. Yet, use of next generation sequencing to perform 16S rRNA gene sequence surveys has resulted in considerable controversy surrounding the effects of sequencing errors on downstream analyses. We analyzed 2.7×10(6) reads distributed among 90 identical mock community samples, which were collections of genomic DNA from 21 different species with known 16S rRNA gene sequences; we observed an average error rate of 0.0060. To improve this error rate, we evaluated numerous methods of identifying bad sequence reads, identifying regions within reads of poor quality, and correcting base calls and were able to reduce the overall error rate to 0.0002. Implementation of the PyroNoise algorithm provided the best combination of error rate, sequence length, and number of sequences. Perhaps more problematic than sequencing errors was the presence of chimeras generated during PCR. Because we knew the true sequences within the mock community and the chimeras they could form, we identified 8% of the raw sequence reads as chimeric. After quality filtering the raw sequences and using the Uchime chimera detection program, the overall chimera rate decreased to 1%. The chimeras that could not be detected were largely responsible for the identification of spurious operational taxonomic units (OTUs) and genus-level phylotypes. The number of spurious OTUs and phylotypes increased with sequencing effort indicating that comparison of communities should be made using an equal number of sequences. Finally, we applied our improved quality-filtering pipeline to several benchmarking studies and observed that even with our stringent data curation pipeline, biases in the data generation pipeline and batch effects were observed that could potentially confound the interpretation of microbial community data.

PMID: 22194782

... N为获得细菌的总数量^[18,19] ...

2007

0.0

. 2007, (4):283-290

Pyrosequencing enumerates and contrasts soil microbial diversity

Roesch L F W , Fulthorpe R R , Riva A

Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611-0700, USA.

Estimates of the number of species of bacteria per gram of soil vary between 2000 and 8.3 million (Gans et al., 2005; Schloss and Handelsman, 2006). The highest estimate suggests that the number may be so large as to be impractical to test by amplification and sequencing of the highly conserved 16S rRNA gene from soil DNA (Gans et al., 2005). Here we present the use of high throughput DNA pyrosequencing and statistical inference to assess bacterial diversity in four soils across a large transect of the western hemisphere. The number of bacterial 16S rRNA sequences obtained from each site varied from 26,140 to 53,533. The most abundant bacterial groups in all four soils were the Bacteroidetes, Betaproteobacteria and Alphaproteobacteria. Using three estimators of diversity, the maximum number of unique sequences (operational taxonomic units roughly corresponding to the species level) never exceeded 52,000 in these soils at the lowest level of dissimilarity. Furthermore, the bacterial diversity of the forest soil was phylum rich compared to the agricultural soils, which are species rich but phylum poor. The forest site also showed far less diversity of the Archaea with only 0.009% of all sequences from that site being from this group as opposed to 4%-12% of the sequences from the three agricultural sites. This work is the most comprehensive examination to date of bacterial diversity in soil and suggests that agricultural management of soil may significantly influence the diversity of bacteria and archaea.

PMID: 18043639

... 细菌丰富度为某种细菌的16S rDNA读数占细菌16S rDNA总读数的百分数^[20,21] ...

2010

0.0

. 2010, 48(3):284-289 DOI:10.1007/s12275-010-9369-5

Assessment of soil fungal communities using pyrosequencing

Lim Y M , Kim B K , Kim C

National Institute of Biological Resource, Incheon, 404-708, Republic of Korea.

Pyrosequencing, a non-electrophoretic method of DNA sequencing, was used to investigate the extensive fungal community in soils of three islands in the Yellow Sea of Korea, between Korea and China. Pyrosequencing was carried out on amplicons derived from the 5' region of 18S rDNA. A total of 10,166 reads were obtained, with an average length of 103 bp. The maximum number of fungal phylotypes in soil predicted at 99% similarity was 3,334. The maximum numbers of phylotypes predicted at 97% and 95% similarities were 736 and 286, respectively. Through phylogenetic assignment using BLASTN, a total of 372 tentative taxa were identified. The majority of true fungal sequences recovered in this study belonged to the Ascomycota (182 tentative taxa in 2,708 reads) and Basidiomycota (172 tentative taxa in 6,837 reads). The predominant species of Ascomycota detected have been described as lichen-forming fungi, litter/wood decomposers, plant parasites, endophytes, and saprotrophs: Peltigera neopolydactyla (Lecanoromycetes), Paecilomyces sp. (Sordariomycetes), Phacopsis huuskonenii (Lecanoromycetes), and Raffaelea hennebertii (mitosporicAscomycota). The majority of sequences in the Basidiomycota matched ectomycorrhizal and wood rotting fungi, including species of the Agaricales and Aphyllophorales, respectively. A high number of sequences in the Thelephorales, Boletales, Stereales, Hymenochaetales, and Ceratobasidiomycetes were also detected. By applying high-throughput pyrosequencing, we observed a high diversity of soil fungi and found evidence that pyrosequencing is a reliable technique for investigating fungal communities in soils.

PMID: 20571944

... 细菌丰富度为某种细菌的16S rDNA读数占细菌16S rDNA总读数的百分数^[20,21] ...

2013

0.0

. 2013, 7:1344-1353 DOI:10.1038/ismej.2013.16

Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes

Amato K R , Yeoman C J , Kent A

Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana, IL, USA.

The gastrointestinal (GI) microbiome contributes significantly to host nutrition and health. However, relationships involving GI microbes, their hosts and host macrohabitats remain to be established. Here, we define clear patterns of variation in the GI microbiomes of six groups of Mexican black howler monkeys (Alouatta pigra) occupying a gradation of habitats including a continuous evergreen rainforest, an evergreen rainforest fragment, a continuous semi-deciduous forest and captivity. High throughput microbial 16S ribosomal RNA gene sequencing indicated that diversity, richness and composition of howler GI microbiomes varied with host habitat in relation to diet. Howlers occupying suboptimal habitats consumed less diverse diets and correspondingly had less diverse gut microbiomes. Quantitative real-time PCR also revealed a reduction in the number of genes related to butyrate production and hydrogen metabolism in the microbiomes of howlers occupying suboptimal habitats, which may impact host health.

PMID: 23486247

... 随机抽取测序样品中的16S rDNA读数(reads),以细菌种(属)类数(OTUs)为纵坐标,16S rDNA读数为横坐标,获得稀释曲线(图2)^[22] ...

2002

0.0

... 土壤有机质是微生物的碳源和氮源^[23] ...

2012

0.0

. 2012, 32(1):1-6 DOI:doi:10.3969/j.issn.1009-5500.2012.01.001

围封年限对典型草原土壤微生物及酶活性的影响

单贵莲, 初晓辉, 罗富成

选取不同围封年限的生长季围封恢复草地为研究对象，开展典型草原恢复演替过程中土壤微生物及酶活性变化规律的研究，探讨土壤微生物及酶活性与草地植被及土壤养分的相关性，结果表明：（1）与自由放牧草地相比，围封7、 10、13、20年，土壤0-30cm土层细菌、放线茵、真菌数量显著增加，土壤转化酶、脲酶活性增强，土壤微生物量碳、氮含量显著增加（P 〈0．05），且随围封年限的延长呈增加的变化趋势。（2）典型草原恢复演替过程中土壤微生物及酶活性与草地植被及土壤养分呈基本一致的变化规律，三者呈密切的正相关关系，以土壤真菌数量、微生物量碳、氮含量与草地植被及土壤养分含量间的相关关系最为显著，其相关系数均达显著水平（P〈0．05）。

... 从土壤酶活性看,T-V-R轮作的蔗糖酶、脱氢酶、磷酸酶、过氧化氢酶和脲酶活性最强,推测微生物分泌的酶较多^[24],土壤酶活性强促进有机质分解、腐殖质合成、养分转化、生物固氮、污染物清除等^[25] ...

2006

0.0

. 2006, 72(2):1040-1044

Biodegradation of 3-nitrotyrosine by Burkholderia sp. strain JS165 and Variovorax paradoxus JS171

Nishino S F , Spain J C

Air Force Research Laboratory, Tyndall Air Force Base, Florida 32403-5323, USA.

The cascade of reactive nitrogen species generated from nitric oxide causes modification of proteins, lipids, and nucleic acids in a wide range of organisms. 3-Nitrotyrosine is one of the most common products of the action of reactive nitrogen species on proteins. Although a great deal is known about the formation of 3-nitrotyrosine, the subsequent metabolism of this compound is a mystery. Variovorax paradoxus JS171 and Burkholderia sp. strain JS165 were isolated from soil slurries when 3-nitrotyrosine was provided as the sole carbon, nitrogen, and energy source. During growth on 3-nitrotyrosine stoichiometric amounts of nitrite were released along with approximately one-half of the theoretically available ammonia. The catabolic pathway involving oxidative denitration is distinct from the pathway for tyrosine metabolism. The facile isolation and the specific, regulated pathway for 3-nitrotyrosine degradation in natural ecosystems suggest that there is a significant flux of 3-nitrotyrosine in such environments.

PMID: 16461647

1988

0.0

. 1988, 26(11):2465-2466

Numerical index of the discriminatory ability of typing systems-An application of Simpsons index of diversity

Hunter P R , Gaston M A

Division of Hospital Infection, Central Public Health Laboratory, London, England.

An index of discrimination for typing methods is described, based on the probability of two unrelated strains being characterized as the same type. This index may be used to compare typing methods and select the most discriminatory system.

PMID: 3069867

... 优势度指数越大,生物群落内的奇异度越高,优势种群突出^[26] ...

1997

0.0

. 1997, 63(4):1505-1514

Bacterial diversity of a carolina bay as determined by 16S rRNA gene analysis: confirmation of novel taxa

Wise M G , Mcarthur J V , Shimkets L J

Department of Microbiology, University of Georgia, Athens 30602-2605, USA.

Carolina bays are naturally occurring shallow elliptical depressions largely fed by rain and shallow ground water. To identify members of the domain Bacteria which inhibit such an environment, we used PCR to construct a library of 16S rRNA genes (16S rDNAs) cloned from DNA extracted from the sediments of Rainbow bay, located on the Savannah River Site, near Aiken, S.C. Oligonucleotides complementary to conserved regions of 16S rDNA were used as primers for PCR, and gel-purified PCR products were cloned into vector pGEM-T. Partial sequencing of the cloned 16S rDNAs revealed an extensive amount of phylogenetic diversity within this system. Of the 35 clones sequenced, 32 were affiliated with five bacterial groups: 11 clustered with the Proteobacteria division (including members of the alpha, beta, and delta subdivisions), 8 clustered with the Acidobacterium subdivision of the Fibrobacter division (as categorized by the Ribosomal Database Project's taxonomic scheme, version 5.0), 7 clustered with the Verrucomicrobium subdivision of the Planctomyces division, 3 clustered with the gram-positive bacteria (Clostridium and relatives subdivision), and 3 clustered with the green nonsulfur bacteria. One sequence branched very deeply from the Bacteria and was found not to be associated with any of the major divisions when phylogenetic trees were constructed. Two clones did not consistently cluster with specific groups and may be chimeric sequences. None of the clones exhibited an exact match to any of the 16S rDNA sequences deposited in the databases, suggesting that most of the bacteria in Rainbow Bay are novel species. In particular, the clones related to the Acidobacterium subdivision and the Verrucomicrobium subdivision confirm the presence of novel taxa discovered previously in other molecular surveys of this type.

PMID: 9097448

... 酸杆菌广泛存在于自然界的各种环境中,具有丰富的遗传和代谢多样性,对稳定生态系统贡献极大^[27,28] ...

1999

0.0

. 1999, 65(4):1731-1737

Wide distribution and diversity of members of the bacterial kingdom Acidobacterium in the environment

Barns S M , Takala S L , Kuske C R

Environmental Molecular Biology Group, Life Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA. sbarns@lanl.gov

To assess the distribution and diversity of members of the recently identified bacterial kingdom Acidobacterium, members of this kingdom present in 43 environmental samples were surveyed by PCR amplification. A primer designed to amplify rRNA gene sequences (ribosomal DNAs [rDNAs]) from most known members of the kingdom was used to interrogate bulk DNA extracted from the samples. Positive PCR results were obtained with all temperate soil and sediment samples tested, as well as some hot spring samples, indicating that members of this kingdom are very widespread in terrestrial environments. PCR primers specific for four phylogenetic subgroups within the kingdom were used in similar surveys. All four subgroups were detected in most neutral soils and some sediments, while only two of the groups were seen in most low-pH environments. The combined use of these primers allowed identification of a novel lineage within the kingdom in a hot spring environment. Phylogenetic analysis of rDNA sequences from our survey and the literature outlines at least six major subgroups within the kingdom. Taken together, these data suggest that members of the Acidobacterium kingdom are as genetically and metabolically diverse, environmentally widespread and perhaps as ecologically important as the well-known Proteobacteria and gram-positive bacterial kingdoms.

PMID: 10103274

... 酸杆菌广泛存在于自然界的各种环境中,具有丰富的遗传和代谢多样性,对稳定生态系统贡献极大^[27,28] ...

2011

0.0

. 2011, :- DOI:doi:10.7666/d.y1973520

土壤放线菌的筛选、鉴定及其活性代谢产物的研究[D]

朱兆香

放线菌由于其产生抗生素、酶及其抑制剂等有用生物活性物质,具有巨大经济价值,至今发现的两万种生物活性物质中,约70%是由放线菌产生的。而土壤又是放线菌含量最丰富的地方,因此开发土壤放线菌具有十分重要的意义。本研究旨在土壤中分离出对多种植物病原真菌具有强烈拮抗作用的放线菌,对菌株进行鉴定,并对其抑菌活性物质进行分离,寻找新型农用抗生素的产生菌来源,具体研究内容如下: (1)放线菌的分离。对来自黑龙江省、湖北省、山东省、贵州省、河北省五个省份的九份土样进行自然干燥等预处理后,采用选择性分离培养基腐殖酸培养基加 50μg/mL的重铬酸钾进行放线菌的选择性分离。共分离得到101株放线菌。 (2)高活性菌株的筛选。采用管碟法测定了101株放线菌发酵液对细菌的抑菌活性,其中有31株放线菌对枯草芽孢杆菌和藤黄微球菌的抑菌圈直径≥15 mm,其中W2、W13、B5、Q5、Q10这5株放线菌的抑菌圈直径都在20 mm以上。 (3)放线菌的分类学研究。结合经典分类和分子生物学中16SrRNA分类,对W2、W13、Q1、Q2、Q7这5株放线菌的分类研究表明:其形态特征、培养特征、生理生化特征均与链霉菌属一致;其中W2号放线菌同链霉菌Streptomyces neyagawaensis ATCC 27449的相似性达到99 %;Q1号放线菌同链霉菌Streptomyces corchorusii 088-68-1的相似性达到99 %;Q2号放线菌同链霉菌Streptomyces lavendulae ZGO429的相似性达到99 %;Q7号放线菌同链霉菌Streptomyces sp. VTT E-99-1333 (B306)的相似性达到99 %;W13号放线菌同链霉菌Streptomyces thermocarboxydus AT37的相似性达到99 %。进一步确定这5株放线菌均属于链霉菌属(Streptomyces)。 (4)发酵粗提物对真菌的抑制研究。对细菌有较好抑菌活性的W2、W13、B5、Q5、Q10这5株放线菌发酵粗提物,进行了对9种致病真菌的抑菌活性研究,结果表明,其发酵粗提物至少对4种真菌有抑菌作用,对6种以上真菌有抑制作用的菌株有2株,分别为W2和Q5,其中W2菌株对7种真菌都有抑菌作用, 并且抑制率都在50%以上。 (5)发酵粗提物的分离。将这5株放线菌的发酵粗提物进行了分离、纯化及结构鉴定。结果显示,从W2中分离出了2种化合物,其中化合物7- prenylindole具有抑制真菌的作用,化合物borrelidin具有抗癌,抑菌,除草活性等多种用途;从W13中分离出了1种新的化合物;从 B5中分离出了2种化合物conglobatin和anastrien B;从Q5中分离出1种化合物;从Q10中分离出2种化合物 (6)化合物的活性验证。进行了化合物7-prenylindole和borrelidin的抑真菌活性测定,结果表明:化合物7- prenylindole在浓度为100μg/mL时,对6种致病真菌都有抑制活性。borrelidin在浓度为100μg/mL对5种致病真菌都具有很强的抑制真菌活性。

... 放线菌也是自然界分布最广泛的微生物类群之一,参与土壤有机质转化,土壤结构形成,植物生长素和抗生素分泌^[29] ...

1994

0.0

. 1994, 140(10):2849-2858

In situ probing of gram-positive bacteria with high DNA G+C content using 235-ribosomal-RNA-targeted oligonucleotides

Roller C , Wagner M , Amann R

Lehrstuhl für Mikrobiologie, Technische Universität München, Germany.

23S-rRNA-targeted oligonucleotide probes were designed for the phylogenetic group 'Gram-positive bacteria with high G + C content of DNA' (GPBHGC). A sequence idiosyncrasy in two adjacent base pairs in the stem of helix 69 in domain IV of the 23S rRNA is present in all hitherto analysed strains of GPBHGC. An oligonucleotide probe targeted to this region hybridized only with strains of GPBHGC and was successfully used for in situ monitoring of these cells in activated sludge. Another unique feature of the 23S rRNA molecules of GPBHGC is a large insertion in domain III. Fluorescent oligonucleotides targeted to the highly variable regions of the rRNA within the insertions of Corynebacterium glutamicum DSM 20300, Aureobacterium testaceum DSM 20166 and Brevibacterium sp. DSM 20165 hybridized specifically to their target strains, whereas probing with oligonucleotides complementary to the rRNA-coding strand of the 23S rDNA and to the spacer between 16S and 23S rRNA of C. glutamicum did not result in detectable fluorescence. This confirmed that the large 23S insertions are indeed present in 23S rRNAs of GPBHGC and provide potential target sites for highly specific nucleic acid probes.

PMID: 8000548

... 绿弯菌是活性污泥的组成成分之一^[30],生活在好氧环境下,有利于土壤中有毒物质的降解 ...

2011

0.0

... 除T-C-R之外,其他3种轮作处理的土壤都存在伯克氏菌,且丰富度较高,它们能分泌生长素、ACC脱氨酶和铁载体,溶解矿物态无机磷,促进番茄(Lycopersicon esculentum)、美洲商陆(Phytolacca Americana)和籽粒苋(Amaranthus hypochondriacus)生长,提高植物抗(耐)重金属的能力^[31,32] ...

2012

0.0

. 2012, 32(1):213-223

美洲商陆和籽粒苋对接种伯克氏菌的生理生化响应及其对富集铯的影响

廖上强, 郭军康, 王芳丽

To investigate the effect of bacteria Burkholderia sp. D54 on Cs uptake by P. americana Linn and A. crenentus L., a pot experiment with different concentrations of Cs was conducted. It was found that inoculation of Burkholderia sp. D54 on P. americana Linn. and A. crenentus L. enhanced total biomass of P. americana and A. crenentus by 19.8%~33.4% and 22.9%~76.6%, respectively. Shoot Cs concentration of P. americana and A. crenentus increased by 4.9%~22.4% and 8.1%~19.4%, while root Cs concentration increased by 6.8%~15.7% and 1.1%~10.8%, respectively. We also concluded that inoculated Burkholderia sp. D54, increased potassium uptake by two types of plants, enhanced net assimilation rate, stomatal conduction, transpiration and water use efficiency of photosynthesis of the two types of plants, increased the activity of antioxidant enzymes CAT, POD and SOD under Cs stress, and reduced plants MDA content in leaves.

利用盆栽试验研究一株具有重金属耐性的伯克霍尔德氏菌( Burkholderia sp. D54)对美洲商陆和籽粒苋生长及对铯富集的影响.结果表明,接种菌株D54,美洲商陆和籽粒苋总干物重分别比对照处理增加19.8%~33.4%和22.9%~76.6%,美洲商陆和籽粒苋地上部铯含量分别增加4.9%~22.4%和8.1%~19.4%,根中铯含量分别增加6.8%~15.7%和1.1%~10.8%.同时,接种微生物还增加了植物对钾的吸收,提高供试植物的光合反应速率、气孔导度、蒸腾速率和水分利用率,增加铯胁迫条件下植物的抗氧化酶CAT、POD、SOD的活性,降低了MDA的含量.

2005

0.0

. 2005, 71(2):904-911

Uniquekinetic properties of phenol-degrading Variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture

Futamata H , Nagano Y , Watanabe K

Department of Ecological Engineering, Toyohashi University of Technology, Tenpakutyo 1-1, Toyohashi, Aichi 441-8580, Japan. futamata@eco.tut.ac.jp

A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities. To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter(-1) day(-1)) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter(-1) day(-1) (enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a Variovorax ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus Variovorax and were shown to have high-affinity-type LmPHs. The LmPH of the Variovorax strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the Variovorax strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information, mechanisms accounting for the way the Variovorax population overgrew the chemostat enrichment are discussed.

PMID: 15691947

... 此外,T-V-R处理的土壤中还存在贪噬菌和中慢生型天山根瘤菌,前者参与有机磷、硝基酪氨酸、除草剂、三氯乙烯等的生物降解^[33,34],中慢生型天山根瘤菌明显与苕子结瘤固氮有关 ...

2008

0.0

. 2008, 74(8):2332-2340 DOI:10.1128/AEM.02687-07

Rapid mineralization of the phenyl urea herbicide diuron by Variovorax sp. strain SRS16 in pure culture and within a two-member consortium

S#cod#x000d8;rensen S R , Albers C N , Aamand J

Department of Geochemistry, Geological Survey of Denmark and Greenland, Øster Voldgade 10, DK-1350 Copenhagen K, Denmark. srs@geus.dk.

The phenylurea herbicide diuron [N-(3,4-dichlorophenyl)-N,N-dimethylurea] is widely used in a broad range of herbicide formulations, and consequently, it is frequently detected as a major water contaminant in areas where there is extensive use. We constructed a linuron [N-(3,4-dichlorophenyl)-N-methoxy-N-methylurea]- and diuron-mineralizing two-member consortium by combining the cooperative degradation capacities of the diuron-degrading organism Arthrobacter globiformis strain D47 and the linuron-mineralizing organism Variovorax sp. strain SRS16. Neither of the strains mineralized diuron alone in a mineral medium, but combined, the two strains mineralized 31 to 62% of the added [ring-U-(14)C]diuron to (14)CO(2), depending on the initial diuron concentration and the cultivation conditions. The constructed consortium was used to initiate the degradation and mineralization of diuron in soil without natural attenuation potential. This approach led to the unexpected finding that Variovorax sp. strain SRS16 was able to mineralize diuron in a pure culture when it was supplemented with appropriate growth substrates, making this strain the first known bacterium capable of mineralizing diuron and representatives of both the N,N-dimethyl- and N-methoxy-N-methyl-substituted phenylurea herbicides. The ability of the coculture to mineralize microgram-per-liter levels of diuron was compared to the ability of strain SRS16 alone, which revealed the greater extent of mineralization by the two-member consortium (31 to 33% of the added [ring-U-(14)C]diuron was mineralized to (14)CO(2) when 15.5 to 38.9 mug liter(-1) diuron was used). These results suggest that the consortium consisting of strains SRS16 and D47 could be a promising candidate for remediation of soil and water contaminated with diuron and linuron and their shared metabolite 3,4-dichloroaniline.

PMID: 18296530

2013

0.0

. 2013, 5:6-12 DOI:doi:10.11838/sfsc.20130502

连作障碍发生机制研究进展

王飞, 李世贵, 徐凤花

... 如土壤养分异常积累或过度消耗,病原微生物迅速繁衍,化感物质积累,土壤微生物种群结构失衡,作物产量品质降低等^[1,2] ...

2014

0.0

. 2014, 23(2):340-345 DOI:doi:10.11686/cyxb20140240

不同种植年限人工苜蓿草地植物和土壤化学计量特征

杨菁, 谢应忠, 吴旭东