云南高原程海湖沉积物中的细菌多样性研究
|
摘要
湖泊沉积物是一个由多种生物参与的、物质发生频繁交换的有机、无机混合体。外界营养物质的持续输入及环境条件的改变等因素都是造成沉积物中微生物群落变化原因。微生物在湖泊沉积物中的营养物质循环和化合物降解中起着至关重要的作用,同时沉积物也为微生物的各种代谢活动提供场所。沉积物的多种环境因子的变化都能影响其沉积物环境微生物群落的组成和结构。因此研究湖泊沉积物中的微生物群落结果及其多样性将会增强我们对湖泊生态系统的进一步认识。
本研究从云南高原程海湖中采集沉积物,用免培养法(DGGE指纹图谱技术,16S rRNA基因克隆测序和454测序技术)和纯培养法研究沉积物中细菌群落组成和分布。比较分析程海湖各沉积物样点细菌多样性异同,分析细菌多样性与环境非生物因子的相关性,以期较全面、系统的了解程海湖沉积物中细菌的多样性,从而为深入开展程海湖中微生物资源的研究、保护及开发利用奠定基础。
DGGE指纹图谱技术研究结果表明,程海湖沉积物中细菌有较高的丰度和丰富的多样性。以物种的丰度和多样性为依据,对沉积物中细菌DGGE指纹图谱聚类分析,结果表明14个程海沉积物样品聚成三簇。根据采样点周围生境和DGGE指纹图谱聚类分析结果,选出6个代表性沉积物样品,应用16S rRNA基因克隆序列分析法和纯培养分离方法,系统、深入的研究程海湖沉积物中细菌多样性及其与环境非生物因子的相关性。
基于16S rRNA基因分析法从程海湖6个沉积物获得2715条高质量克隆序列,进一步对其进行的系统发育分析结果显示：程海沉积物中存在丰富的细菌多样性,其中有15.2%(415条克隆序列)的细菌克隆序列经RDP分类工具不能确定其分类地位；程海沉积物中的2300条细菌克隆序列归属于细菌域的19个门(Phylum): Actinobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Acidobacteria, Verrucomcrobia, Planctomycetes, Bacteroidetes, Proteobacteria, Armatimonadetes, Caldiserica, Deferribacteres, Gemmatimonadetes, Spirochaetes, Chlorobi, Nitrospira, Elusimicrobia和两个候选门WS3和TM7；程海沉积物中细菌群落组成存在明显的空间分布差异,湖边沉积物的细菌多样性明显的高于湖泊中心沉积物的细菌多样性；2715条克隆序列代表666个OTU,仅有24个OTU是6个沉积物样品共有的。聚类分析和主相关性分析(PCoA)显示：6号沉积物样点与其它五个样点相比,细菌群落丰度和多样性差别较大,6号样点细菌多样性最高。Chloroflexi, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria和Firmicutes是程海湖沉积物中的主要细菌类群。程海湖沉积物样品中的细菌群落组成与环境非生物因子相关,Actinobacteria, Planctomycetes, Alphaproteobacteria和Chlorobi的丰度与程海沉积物样品中的总磷含量(TP)显著负相关,且.RDA分析结果显示程海沉积物中总磷的含量是影响其微生物群落组成的最主要的环境非生物因子。
454高通量测序研究程海沉积物细菌多样性及其与环境非生物因子的相关性,6个沉积物中共获得38977条有效序列,通过质量检测、嵌合体检测和Silva数据库比对,排除8471条序列,得到30506条高质量序列。去除barcode标签序列和前引物序列后,序列平均长度为433bp。以97%相似性划分OTU,30506条序列共划分为4802个OTU。通过与Silva数据库比对,其中有1076个OTU,不能分类到目前已知的任何细菌门级分类单元(unclassified Bacteria)。剩余3726个OTU归属于细菌域的24个系统发育类群,其中Proteobacteria和Chloroflexi是程海沉积物种主要的细菌类群。多样性统计分析,6号样点细菌多样性最高,5号沉积物中细菌多样性最低。Pearson相关性和RDA分析结果显示总磷(TP)的含量是影响程海微生物群落组成的主要环境非生物因子。
尽管454高通量测序获得的数据量要比克隆测序法高出一个数量级,然而这两种测序方法获得相似的主要的细菌类群及相似的与环境因子的相关性。
以免培养分析结果和湖泊沉积物中的理化因子为依据,选用或设计四种培养基,对程海湖6个沉积物样品中的可培养细菌进行分离、培养。基于16S rRNA基因序列的系统发育分析研究所分离菌株种群的多样性。
研究结果表明,从程海湖沉积物中共分离到148个细菌和典型放线菌物种,分属于细菌域的4个门(Actinobacteria, Proteobacteria, Firmicutes和Bacteriodetes),34个科,60个属。其中29个属(Micromonospora, Microbacterium, Micrococcus, Kocuria, Verrucosispora, Rhodococcus, Streptomyces, Citricoccus, Brachybacterium, Agromyces, Brevibacterium, Polymorphospora, Nocardioides, Corynebacterium,Kytococcus, Dietzia, Ornithinimicrobium, Arthrobacter, Cellulomonas, Jiangella, Agrococcus, Asanoa, Mycobacterium, Nocardia, Williamsia, Kribbella, Promicromonospora, Saccharopolyspora和Nonomuraea)属于Actinobacteria门；16个属(Pseudomonas, Acinetobacter, Brevundimonas, Porphyrobacter, Proteus, Sphingobium, Haematobacter, Amaricoccus, Erythromicrobium, Methylobacterium, Paracoccus, Pantoea, Alcaligenes, Enterobacter, Psychrobacter和Stenotrophomonas)属于Proteobacteria门；14个属(Bacillus, Planococcus, Paenibacillus, Staphylococcus, Jeotgalibacillus, Planomicrobium, Halobacillus, Oceanobacillus, Paenisporosarcina, Exiguobacterium, Aneurinibacillus, Lysinibacillus, Brevibacillus和Solibacillus)属于Firmicutes门；3个属(Myroides, Sphingobacterium和Aquiflexum)属于Bacteroidetes门。其中有11株细菌菌株代表11个潜在的新物种,其它大部分菌株与其系统发育关系密切的典型菌株之间的16SrRNA基因序列都有一定的差异。这些结果揭示了程海湖沉积物中存在丰富的可培养细菌多样性,同时程海沉积物中也蕴藏着较为丰富的新的微生物资源。
免培养分析法检测到细菌域的24个门,而纯培养法分离到的菌株归属于细菌域的4个门,甚至有些菌株是用免培养法未检测到的。纯培养分离到的菌株并不都是程海沉积物中主要的细菌类群,说明我们选用或设计的培养基、培养策略适合这些微生物的分离培养,同时也揭示免培养法有一定的局限性。因此,免培养分析法并不能代替纯培养法。既要重视免培养分析法,也要充分认识到纯培养分离方法的重要性。只有两种方法结合使用,才能全面、系统的了解程海湖沉积物中细菌的多样性。
Sediments of lakes are important habitats, in which, there are many kinds of microorganism's participation and substances frequently exchanged. Microbial communities play important roles in nutrient recycling and decomposition of chemical compounds in freshwater sediments. Sediment biogeochemical properties provide niches for metabolically diversity microorganisms. Changes of the environmental factors, can influence microbial community structure in the sediment environments。 Therefore, investigations of bacterial communities and their diversity in freshwater sediments will greatly enhance our understanding of the aquatic ecosystem.
The objective of this research was to study the bacterial community composition and diversity in Chenghai Lake sediments. An integrated approach was employed cultivation-independent approachs including DGGE fingerprint and16S rDNA clone sequencing and cultivation-dependent method. The abundant bacterial communities of six Chenghai Lake sediments were compared and discussed; at the same time, the relationships between bacterial community compositions and environmental factors were to be investigated. The results of this study expand our current understanding of microbial ecology in Yunnan Plateau Lakes.
The result of bacterial DGGE fingerprint shows that, there are high bacterial abundance and diversity in Chenghai Lake sediments. Cluster analysis based on abundances and diversity revealed that bacterial communities in the14sediment samples from Chenghai Lake could be clustered into three groups. Then, we selected6representative sediment samples to carry out further study on the bacteria diversity using an integrated approach including16S rDNA clone sequencing and cultivation method.
RDP classifier analysis based on16S rDNA clone sequences indicated that2715clone sequences from6sediment samples collected from Chenghai Lake could be classified as nineteen bacterial phyla:Actinobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Acidobacteria, Verrucomcrobia, Planctomycetes, Bacteroidetes, Proteobacteria, Armatimonadetes, Caldiserica, Deferribacteres, Gemmatimonadetes, Spirochaetes, Chlorobi, Nitrospira, Elusimicrobia, and two Candidates WS3and TM7Chloroflexi, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria and Firmicutes are dominant groups and present in all Chenghai Lake sediments. There are only24OTU of666OTU were present in all six sediment samples. the Cluster analysis and PCoA analysis based on abundances at the species-level revealed that bacterial communities differences in the6sediment samples from Chenghai Lake, the number six sediment samples has the highest bacteria abundance and diversity. The relative abundances of Actinobacteria Planctomycetes, Alphaproteobacteria and Chlorobi in Chenghai Lake sediments were significantly correlated with total phosphorus. RDA result demonstrated that the changes of TP could have significant effect on members of bacteria in Chenghai Lake.
The bacterial diversity and correlated with abiotic factors in the sediments of Chenghai Lake were also researched by using454pyrosequencing.The pyrosequencing analysis of16S rRNA gene amplicons from six sediment samples produced38977reads, leaving30506reads after quality filtering and removal of chimeric sequences. The average sequence length was of433nucleotides, excluding the adaptor and barcode primer sequences. The sequences could be assigned to4802operational taxonomic units. Of our filtered sequences, we found24different bacterial phyla across all sediment samples with the Silva alignment. Proteobacteria and Chloroflexi were the most abundant phylum across all samples.
The highest diversity was found in No.6sediment samples and the lowest diversity in No.5sediment sample by using species richness, coverage and diversity estimations. Pearson correlation and RDA result demonstrated that the changes of TP could have significant effect on bacterial communities in sediments of Chenghai Lake.
Despite our454pyrosequencing reads being an order of magnitude larger than their corresponding clone sequences, similar dominant bacterial community and similar correlations with environmental abiotic factors were obtained.
Based on the analysis results of cultivation-independent approach and environmental factors, we selected or designed four media to isolate the bacterial strains from the6sediment samples of Chenghai Lake. Phylogenetic analysis based on16S rRNA gene sequence indicated that the isolates could be classified into one hundred and forty-eight genomic species, including eleven potential novel species, the16S rRNA gene sequence of most isolates are different from their phylogenetic neighbours. These isolates belong to sixty genera of thirty-four families(Aerococcaceae, Alcaligenaceae, Bacillaceae, Caulobacteraceae, Cellulomonadaceae, Corynebacteraceae, Rhodobacteriaceae, Cyclobacteriaceae, Dermabacteraceae, Dermacoccaceae, Dietziaceae, Enterobacteriaceae, Flavobacteraceae, Intrasporangiaceae, Jiangellaceae, Methylobacteraceae, Microbacteriaceae, Micrococcaceae, Micromonosporaceae, Moraxellaceae, Mycobacteraceae, Nocardiaceae, Nocardioidaceae, Paenibacillaceae, Promicromonosporaceae, Pseudomonadaceae, Pseudonocardiaceae, Rhodobacteriaceae, Sphingobacteriaceae, Sphingomonadaceae, Staphylococcaceae, Streptomycetaceae, Streptosporangiaceae and Xanthomonadaceae) in four bacteria phyla(Actinobacteria, Proteobacteria, Firmicutes and Bacteriodetes). The results presented above shown that there are abundant bacterial diversity and potential novel taxa in sediments of Chenghai Lake.
We detected24bacteria phyla using cultivation-independent approach and isolated4bacterial phyla strains using cultivation-dependent method. However, some isolates is not found using cultivation-independent method. The result proves that the strategies we selected were suitable for the cultivation of these microorganisms, but also reveals the sequencing depth our selected can not reflect the entire microorganism in the environment. In all, cultivation-independent method cannot replace cultivation-dependent method. Only using an integrated approach including cultivation-indpendent and cultivation-dependent methods, we can comprehensive and systematic understand the bacterial diversity in the sediments of Chenghai Lake.
本研究从云南高原程海湖中采集沉积物,用免培养法(DGGE指纹图谱技术,16S rRNA基因克隆测序和454测序技术)和纯培养法研究沉积物中细菌群落组成和分布。比较分析程海湖各沉积物样点细菌多样性异同,分析细菌多样性与环境非生物因子的相关性,以期较全面、系统的了解程海湖沉积物中细菌的多样性,从而为深入开展程海湖中微生物资源的研究、保护及开发利用奠定基础。
DGGE指纹图谱技术研究结果表明,程海湖沉积物中细菌有较高的丰度和丰富的多样性。以物种的丰度和多样性为依据,对沉积物中细菌DGGE指纹图谱聚类分析,结果表明14个程海沉积物样品聚成三簇。根据采样点周围生境和DGGE指纹图谱聚类分析结果,选出6个代表性沉积物样品,应用16S rRNA基因克隆序列分析法和纯培养分离方法,系统、深入的研究程海湖沉积物中细菌多样性及其与环境非生物因子的相关性。
基于16S rRNA基因分析法从程海湖6个沉积物获得2715条高质量克隆序列,进一步对其进行的系统发育分析结果显示：程海沉积物中存在丰富的细菌多样性,其中有15.2%(415条克隆序列)的细菌克隆序列经RDP分类工具不能确定其分类地位；程海沉积物中的2300条细菌克隆序列归属于细菌域的19个门(Phylum): Actinobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Acidobacteria, Verrucomcrobia, Planctomycetes, Bacteroidetes, Proteobacteria, Armatimonadetes, Caldiserica, Deferribacteres, Gemmatimonadetes, Spirochaetes, Chlorobi, Nitrospira, Elusimicrobia和两个候选门WS3和TM7；程海沉积物中细菌群落组成存在明显的空间分布差异,湖边沉积物的细菌多样性明显的高于湖泊中心沉积物的细菌多样性；2715条克隆序列代表666个OTU,仅有24个OTU是6个沉积物样品共有的。聚类分析和主相关性分析(PCoA)显示：6号沉积物样点与其它五个样点相比,细菌群落丰度和多样性差别较大,6号样点细菌多样性最高。Chloroflexi, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria和Firmicutes是程海湖沉积物中的主要细菌类群。程海湖沉积物样品中的细菌群落组成与环境非生物因子相关,Actinobacteria, Planctomycetes, Alphaproteobacteria和Chlorobi的丰度与程海沉积物样品中的总磷含量(TP)显著负相关,且.RDA分析结果显示程海沉积物中总磷的含量是影响其微生物群落组成的最主要的环境非生物因子。
454高通量测序研究程海沉积物细菌多样性及其与环境非生物因子的相关性,6个沉积物中共获得38977条有效序列,通过质量检测、嵌合体检测和Silva数据库比对,排除8471条序列,得到30506条高质量序列。去除barcode标签序列和前引物序列后,序列平均长度为433bp。以97%相似性划分OTU,30506条序列共划分为4802个OTU。通过与Silva数据库比对,其中有1076个OTU,不能分类到目前已知的任何细菌门级分类单元(unclassified Bacteria)。剩余3726个OTU归属于细菌域的24个系统发育类群,其中Proteobacteria和Chloroflexi是程海沉积物种主要的细菌类群。多样性统计分析,6号样点细菌多样性最高,5号沉积物中细菌多样性最低。Pearson相关性和RDA分析结果显示总磷(TP)的含量是影响程海微生物群落组成的主要环境非生物因子。
尽管454高通量测序获得的数据量要比克隆测序法高出一个数量级,然而这两种测序方法获得相似的主要的细菌类群及相似的与环境因子的相关性。
以免培养分析结果和湖泊沉积物中的理化因子为依据,选用或设计四种培养基,对程海湖6个沉积物样品中的可培养细菌进行分离、培养。基于16S rRNA基因序列的系统发育分析研究所分离菌株种群的多样性。
研究结果表明,从程海湖沉积物中共分离到148个细菌和典型放线菌物种,分属于细菌域的4个门(Actinobacteria, Proteobacteria, Firmicutes和Bacteriodetes),34个科,60个属。其中29个属(Micromonospora, Microbacterium, Micrococcus, Kocuria, Verrucosispora, Rhodococcus, Streptomyces, Citricoccus, Brachybacterium, Agromyces, Brevibacterium, Polymorphospora, Nocardioides, Corynebacterium,Kytococcus, Dietzia, Ornithinimicrobium, Arthrobacter, Cellulomonas, Jiangella, Agrococcus, Asanoa, Mycobacterium, Nocardia, Williamsia, Kribbella, Promicromonospora, Saccharopolyspora和Nonomuraea)属于Actinobacteria门；16个属(Pseudomonas, Acinetobacter, Brevundimonas, Porphyrobacter, Proteus, Sphingobium, Haematobacter, Amaricoccus, Erythromicrobium, Methylobacterium, Paracoccus, Pantoea, Alcaligenes, Enterobacter, Psychrobacter和Stenotrophomonas)属于Proteobacteria门；14个属(Bacillus, Planococcus, Paenibacillus, Staphylococcus, Jeotgalibacillus, Planomicrobium, Halobacillus, Oceanobacillus, Paenisporosarcina, Exiguobacterium, Aneurinibacillus, Lysinibacillus, Brevibacillus和Solibacillus)属于Firmicutes门；3个属(Myroides, Sphingobacterium和Aquiflexum)属于Bacteroidetes门。其中有11株细菌菌株代表11个潜在的新物种,其它大部分菌株与其系统发育关系密切的典型菌株之间的16SrRNA基因序列都有一定的差异。这些结果揭示了程海湖沉积物中存在丰富的可培养细菌多样性,同时程海沉积物中也蕴藏着较为丰富的新的微生物资源。
免培养分析法检测到细菌域的24个门,而纯培养法分离到的菌株归属于细菌域的4个门,甚至有些菌株是用免培养法未检测到的。纯培养分离到的菌株并不都是程海沉积物中主要的细菌类群,说明我们选用或设计的培养基、培养策略适合这些微生物的分离培养,同时也揭示免培养法有一定的局限性。因此,免培养分析法并不能代替纯培养法。既要重视免培养分析法,也要充分认识到纯培养分离方法的重要性。只有两种方法结合使用,才能全面、系统的了解程海湖沉积物中细菌的多样性。
Sediments of lakes are important habitats, in which, there are many kinds of microorganism's participation and substances frequently exchanged. Microbial communities play important roles in nutrient recycling and decomposition of chemical compounds in freshwater sediments. Sediment biogeochemical properties provide niches for metabolically diversity microorganisms. Changes of the environmental factors, can influence microbial community structure in the sediment environments。 Therefore, investigations of bacterial communities and their diversity in freshwater sediments will greatly enhance our understanding of the aquatic ecosystem.
The objective of this research was to study the bacterial community composition and diversity in Chenghai Lake sediments. An integrated approach was employed cultivation-independent approachs including DGGE fingerprint and16S rDNA clone sequencing and cultivation-dependent method. The abundant bacterial communities of six Chenghai Lake sediments were compared and discussed; at the same time, the relationships between bacterial community compositions and environmental factors were to be investigated. The results of this study expand our current understanding of microbial ecology in Yunnan Plateau Lakes.
The result of bacterial DGGE fingerprint shows that, there are high bacterial abundance and diversity in Chenghai Lake sediments. Cluster analysis based on abundances and diversity revealed that bacterial communities in the14sediment samples from Chenghai Lake could be clustered into three groups. Then, we selected6representative sediment samples to carry out further study on the bacteria diversity using an integrated approach including16S rDNA clone sequencing and cultivation method.
RDP classifier analysis based on16S rDNA clone sequences indicated that2715clone sequences from6sediment samples collected from Chenghai Lake could be classified as nineteen bacterial phyla:Actinobacteria, Chloroflexi, Firmicutes, Cyanobacteria, Acidobacteria, Verrucomcrobia, Planctomycetes, Bacteroidetes, Proteobacteria, Armatimonadetes, Caldiserica, Deferribacteres, Gemmatimonadetes, Spirochaetes, Chlorobi, Nitrospira, Elusimicrobia, and two Candidates WS3and TM7Chloroflexi, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria and Firmicutes are dominant groups and present in all Chenghai Lake sediments. There are only24OTU of666OTU were present in all six sediment samples. the Cluster analysis and PCoA analysis based on abundances at the species-level revealed that bacterial communities differences in the6sediment samples from Chenghai Lake, the number six sediment samples has the highest bacteria abundance and diversity. The relative abundances of Actinobacteria Planctomycetes, Alphaproteobacteria and Chlorobi in Chenghai Lake sediments were significantly correlated with total phosphorus. RDA result demonstrated that the changes of TP could have significant effect on members of bacteria in Chenghai Lake.
The bacterial diversity and correlated with abiotic factors in the sediments of Chenghai Lake were also researched by using454pyrosequencing.The pyrosequencing analysis of16S rRNA gene amplicons from six sediment samples produced38977reads, leaving30506reads after quality filtering and removal of chimeric sequences. The average sequence length was of433nucleotides, excluding the adaptor and barcode primer sequences. The sequences could be assigned to4802operational taxonomic units. Of our filtered sequences, we found24different bacterial phyla across all sediment samples with the Silva alignment. Proteobacteria and Chloroflexi were the most abundant phylum across all samples.
The highest diversity was found in No.6sediment samples and the lowest diversity in No.5sediment sample by using species richness, coverage and diversity estimations. Pearson correlation and RDA result demonstrated that the changes of TP could have significant effect on bacterial communities in sediments of Chenghai Lake.
Despite our454pyrosequencing reads being an order of magnitude larger than their corresponding clone sequences, similar dominant bacterial community and similar correlations with environmental abiotic factors were obtained.
Based on the analysis results of cultivation-independent approach and environmental factors, we selected or designed four media to isolate the bacterial strains from the6sediment samples of Chenghai Lake. Phylogenetic analysis based on16S rRNA gene sequence indicated that the isolates could be classified into one hundred and forty-eight genomic species, including eleven potential novel species, the16S rRNA gene sequence of most isolates are different from their phylogenetic neighbours. These isolates belong to sixty genera of thirty-four families(Aerococcaceae, Alcaligenaceae, Bacillaceae, Caulobacteraceae, Cellulomonadaceae, Corynebacteraceae, Rhodobacteriaceae, Cyclobacteriaceae, Dermabacteraceae, Dermacoccaceae, Dietziaceae, Enterobacteriaceae, Flavobacteraceae, Intrasporangiaceae, Jiangellaceae, Methylobacteraceae, Microbacteriaceae, Micrococcaceae, Micromonosporaceae, Moraxellaceae, Mycobacteraceae, Nocardiaceae, Nocardioidaceae, Paenibacillaceae, Promicromonosporaceae, Pseudomonadaceae, Pseudonocardiaceae, Rhodobacteriaceae, Sphingobacteriaceae, Sphingomonadaceae, Staphylococcaceae, Streptomycetaceae, Streptosporangiaceae and Xanthomonadaceae) in four bacteria phyla(Actinobacteria, Proteobacteria, Firmicutes and Bacteriodetes). The results presented above shown that there are abundant bacterial diversity and potential novel taxa in sediments of Chenghai Lake.
We detected24bacteria phyla using cultivation-independent approach and isolated4bacterial phyla strains using cultivation-dependent method. However, some isolates is not found using cultivation-independent method. The result proves that the strategies we selected were suitable for the cultivation of these microorganisms, but also reveals the sequencing depth our selected can not reflect the entire microorganism in the environment. In all, cultivation-independent method cannot replace cultivation-dependent method. Only using an integrated approach including cultivation-indpendent and cultivation-dependent methods, we can comprehensive and systematic understand the bacterial diversity in the sediments of Chenghai Lake.
引文
Alain, K. & Querellou, J.(2009). Cultivating the uncultured:limits, advances and future challenge. Extremophiles 13,583-594.
Altmann, D., Stief, P., Amann, R., de Beer, D. (2004). Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms. Aquatic Microbial Ecology 36,73-81.
Alvarado, P., Manjon, J. L. (2009). Selection of enzymes for terminal restriction fragment length polymorphism analysis of fungal internally transcribed spacer sequences. Appl.Enviro.Microbiol 75, 4747.4752.
Amann, R. I., Ludwig, W. & Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of indivadual microbial cells without cultivation. Microbiol Rev,59,143-169.
Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J. & Weightman, A. J. (2006). New screening software shows most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol 72,5734-5741.
Auchtung, T. A., Takacs-Vesbach, C. D. & Cavanaugh C. M. (2006).16S rRNA phylogenetic investigation of the candidate division "Korarchaeota". Appl.Enviro.Microbiol 72,5077-5082.
Azam, F., T. Fenchel, J. G. Field, J. S. Gray, L. A. Meyer, and F. Thingstad. (1983). The ecological role of water column microbes in the sea. Mar. Ecol. Prog. Ser.10,257-263.
Bai, Y., Shi, Q., Wen, D., Li, Z., Jefferson, W. A., et al. (2012). Bacterial Communities in the Sediments of Dianchi Lake, a Partitioned Eutrophic Waterbody in China. PLoS ONE 7:e37796.
Bjornsson, L., Hugenholtz, P., Tyson, G.W. & Blackall, L.L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiol 148,2309-2318.
Brinkmeyer, R., Knittel, K., Jiirgens, J., Weyland, H., Amann, R., Helmke, E. (2003). Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl. Environ. Microbiol 69,6610-6619.
Bruce K D. (1997). Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl.Enviro.Microbiol 63,2647-2653.
Brulc, J. M., Antonopoulos, D. A., Berg Miller, M. E., Wilson, M. K. Yannarell, A. C., Dinsdale, E. A. et al. (2009). Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America 106,1948-1953.
Caron, D. A., E. R. Peele, E. L. Lim, and M. R. Dennett. (1999). Picoplankton and nanoplankton and their trophic coupling in the surface waters of the Sargasso Sea sOTUh of Bermuda. Limnol. Oceanogr 44,259-272.
Chandler, D. P., Kukhtin, A., Mokhiber, R., Knickerbocker, C., Ogles, D., Rudy, G., Golova, J., Long, P., Peacock, A. (2010). Monitoring microbial community structure and dynamics during in situ U(VI) bioremediation with a field-portable microarray analysis system. Enviro Sci & Technol 44, 5516-5522.
Cho, J. C. & Giovannoni, S. J. (2006). Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 56, 855-859.
Christensson, M., Blackall, L. L., Welander, T. (1998). Metabolic transformations and characterisation of the sludge community in an enhanced biological phosphorus removal system. Appl. Environ. Microbiol 49,226-234.
Collins, M. D. & Jones, D. (1980). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48,459-470.
Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977). Distribution of menaquinones in actinomycetes and corynebacteria. JGen Microbiol 100,221-230.
Cui, X. L., Mao, P. H., Zeng, M., Li, W. J., Zhang, L. P., Xu, L. H. & Jiang, C. L. (2001). Streptomonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51,357-363.
Curtis TP, Sloan WT, Scannell JW (2002). Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99,10494-10499
Deiglmayr, K., Philippot, L., Tscherko, D., Kandeler, E. (2006). Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Enviro Microbiol.8,1600-1612.
Deiglmayr, K., Philippot, L., Tscherko, D. & Kandeler, E. (2006). Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Enviro Microbiol.8,1600-1612.
Delong E. F., Wickham, G. S. & Pace N. R. (1989). Phylogenetic strains:ribosomal RNA based probes for the identification of the identification of single microbial cells. Science,243:1360-1363.
Demergasso, C., Casamayor, E. O., Chong, G., Galleguillos, P. & Escuder,0.(2004). Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile. FEMS Microbiol Ecol 48,57-69.
Dimitriu, P. A., Pinkart, H. C., Peyton, B. M.&Mormile M. R. (2008). Spatial and temporal patterns in the microbial diversity of a meromictic soda lake in washington state. Appl. Environ. Microbiol 74,4877-4888.
Dong, H. L., Zhang, G. X., Jiang, H. C., Yu, B. S., Chapman, L. R., Lucas, C. R., Fields, M.
W.(2006). Microbial Diversity in Sediments of Saline Qinghai Lake, China:Linking Geochemical Controls to Microbial Ecology. Microb Ecol 51,65-82.
Duckworth, A. W. Grant, W. D. Jones, B. E. & Steenbergen, R.V. (1996). Phylogenetic diversity of soda lake alkaliphiles, FEMS Microbiol. Ecol,19,181-191.
Edlund, A., Soule,T., Sjoling, S. & Jansson, J. K. (2006). Microbial community structure in polluted Baltic Sea sediments. Environ Microbiol 8,223-232.
Eilers, H., Pernthaler, J., Glockner, F. O., Amann, R. (2000). Culturability and In situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol 66,3044-3051.
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
Felske, A., Wolterink, A., VanLis, R., DeVos, W.M. & Akkermans, A.D. (2000). Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66,3998-4003.
Fisher, M. M., Triplett, E. W. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol 65.4630-4636.
Gaudette, H. E., Flight, W. R., Toner, L. & Folger, D. W. (1974). An inexpensive titration method for the determination of organic carbon in recent sediments. J Sediment Res 44,249-253.
Gentry, T.J. (2010). Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J A,829-838.
Gieseke, A., Purkhold, U., Wagner, M., Amann, R., Schramm, A. (2001). Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl. Environ. Microbiol 61,1351-1362.
Glissmann, K., Chin, K. J., Casper, P. & Conrad, R. (2004). Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow:effect of temperature. Microbial. Ecol 48.389-399.
Glockner, F. O., Fuchs, B. M., Amann, R. (1999). Bacterioplankton compositions of lakes and oceans:a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol 65, 3721-3726
Go, Y. S., Han, S. K., Lee, I.G. & Ahn, T. Y. (2000). Diversity of the domain Archaea as determined by 16S rRNA gene analysis in the sediments of Lake Soyang, Arch. Hydrobiol 149, 459-466.
Grant, S., Sorokin, D. y., Grant, W.D., Jones B.E. & Heaphy, S. (2004). A phylogenetic analysis of Wadiel Natrun soda Lake cellulose enrichment cultures and identification of cellulose genes from these cultures. Extremephiles 8,421-429.
Hollister, E.B, Engledow, A.S, Hammett, A.J.M., Provin, T. L., Wilkinson, H.H. & Gregersen, T. (1978). Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5.123-127.
Hansen, G. H. & S(?)rheim, R. (1991). Improved method for phenotypical characterization of marine bacteria. JMicrobiol Methods 13,231-241
Hollister, E.B, Engledow, A.S, Hammett, A.J.M., Provin, T. L., Wilkinson, H. H. & Gentry, T.J. (2010). Shifts in microbial community structure along an ecological gradient of hypersaline
soils and sediments. ISME J 4,829-838.
Hori, T., Haruta, S., Ueno, Y., Ishii, M., Igarashi, Y. (2006). Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl. Environ. Microbiol 72,1623-1630
Huber, J.A., Johnson, H.P., Butterfield, D.A. & Baross, J.A. (2006). Microbial life in ridge flank crustal fluids. Environ Microbiol 8,88-99.
Huggenholtz, P., Goebel, B. M.& Pace N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol.180,4765-4774.
Humayoun, S. B., Bano, N. & Hollibaugh, J. T. (2003). Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Appl Environ Microbiol 69,1030-1042
Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A.& Sogin, M.L. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4(11), e1000255.
Ikeda, S., Rallos, L. E. E., Okubo, T., Eda, S., Inaba, S., Mitsui, H., Minamisawa, K. (2008). Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Appl. Environ. Microbiol 74,5704-5709.
Jiang, H., Dong, H., Zhang, G., Yu, B., Chapman, L.R. and Fields, M.W. (2006). Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China. Appl Environ Microbiol 72,3832-3845.
Jurgens, G., Glockner, F., Amann, R., Saano, A., Montonen, L., Likolammi, M & Munster, U. (2000). Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34,45-56.
Kampfer, P., Young, C. C., Chen, W. M., Rekha, P. D., Fallschissel, K., Lodders, N., et al. (2010). Fontibacter flavus gen. nov., sp. nov., a member of the family 'Cyclobacteriaceae', isolated from a hot spring. Int J Syst Evol Microbiol 60,2066-2070.
Knittel, K., Losekann, T., Boetius, A., Kort, R., Amann, R. (2005). Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol 71,467-479
Kovacs, N. (1956). Identification of Pseudomonas pyocyanea by oxidase reaction. Nature 178, 703-704.
Kreader, C. A. (1996). Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol.62,1102-1106.
Kvennefors, E. C. E., Sampayo, E., Ridgway, T., Barnes, A. C., Hoegh-Guldberg, O. (2010).
Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates. PLOS ONE 5,1-14
Lane, D. J. (1991).16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. and Goodfellow, M. pp.115-175. Chichester, UK:John Wiley & Sons.
Lee, Z. M. P., Bussema, C., Schmidt, T. M. (2009). rrnDB:documenting the number of rRNA and tRNA genes in bacteria and Archaea. Nucleic Acids Res 37, D489-D493.
Lefranc, M., Aurelie T., Lepere, C. & Debroas D. (2005). Genetic Diversity of Small Eukaryotes in lakes differing by their trophic status. Appl. Environ. Microbiol 71,5935-5942
Lepere, C., Boucher, D., Jardillier, L., Domaizon, I. & Debroas, Di. (2006). Succession and Regulation Factors of Small Eukaryote Community Composition in a Lacustrine Ecosystem (Lake Pavin). Appl. Environ. Microbiol 72,2971-2981.
Llobet-Brossa, E., Rabus, R., Bottcher, M. E., Konneke, M., Finke, N., Schramm, A., Meyer, R. L. et al. (2002). Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment:a multi-method approach. Aquatic Microbial Ecology 29,211-226.
Liu, F. H., Lin, G. H., Gao, G., Qin, B. Q., Zhang, J. S., et al. (2009). Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis. J Appl Microbiol 106,1022-1032.
Liu, W. T., Marsh, T. L., Cheng, H. et al. (1997). Characterization of microbial diversity by determing terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl.Enviro.Microbiol 63,3616-3620.
Lu, Y., Rosencrantz, D., Liesack, W. & Conrad, R. (2006). Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environ Microbiol 8,1351-1360.
Mardis, E. R. (2008). The impact of next-generation sequencing technology on genetics. Trends Genetics.24.133-141.
Martins, R. F., Davids, W., Abu Al-Soud, W., Levander, F., Radstrom, P. & Hatti-Kaul R. (2001). Starch-hydrolyzing bacteria from Ethiopian soda lakes. Extremophiles 5,135-144.
McLellan, S., Huse, S., Mueller Spitz, S., Andreishcheva, E. & Sogin, M. (2010). Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12,378-392.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39,159-167.
Mesbah, N. M., Abou-EI-Ela, S. H. & Wiegel, J. (2007). Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microb.Ecol.54,598-617.
Mesbah, N. M. & Wiegel, J. (2009a). Natronovirga wadinatrunensis gen. nov., sp. nov. and Natranaerobius trueperi sp. nov., halophilic, alkalithermophilic micro-organisms from soda lakes of the Wadi An Natrun, Egypt. Int J Syst Evol Microbiol.59,2042-2048
Mesbah, N. M. & Wiegel, J. (2009b). Natronovirga wadinatrunensis gen. nov., sp. nov. and Natranaerobius trueperi sp. nov.. halophilic. alkalithermophilic micro-organisms from soda lakes of the Wadi An Natrun. Egypt. Int J Syst Evol Microbiol.59,2042-2048
Meyer, M., Stenzel, U., Hofreiter, M. (2008). Parallel tagged sequencing on the 454 platform. Nature Protocols.3,267-278.
Mikkelsen, D., Kappler, U., McEwan, A. G., Sly, L. I. (2009). Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH. Systematic and Applied Microbiology 32.501-513
Mou, X. Z., Sun, S. L., Edwards, R. A., Hodson, R. E., Moran, M. A. (2008). Bacterial carbon processing by generalist species in the coastal ocean. Nature 451,708-711.
Muyzer, G., De Waal, E. & Uitterlinden, A. G (1993). Profiling of complex microbial population by gradient gel electrophoresis analysis (DGGE) of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol,59,695-700.
Myers, R.M., Fisher, S.G., Delerman, L.S. et al. (1985). Nearly all single base substitution in DNA fragments joined to a GC-clamp can be detected by Denaturing Gradient Gel Electrophoresis. Nucleic Acid Res.13,3131-3145.
Nealson, K. H. (1997). Sediment bacteria:Who's there, what are they doing, and what's new? Annu Rev Earth Pl Sc 25,403-434.
Nelson, D. M, Ohene-Adjei, S., Hu, F. S., Cann, I. K. & Mackie, R. I. (2007). Bacterial diversity and distribution in the holocene sediments of a northern temperate lake. Microb Ecol 54,252-263.
Olsen, S. R. & Sommers, L.E. (1982). Phosphorus. In Methods of Soil Analyses, Part 2, Chemical and Microbiological Properties ed. Page, A.L., Miller, R.H. and Keeney, D.R. pp.
Paerl, H. W., & Paul V. J. (2012). Climate change:Links to global expansion of harmful cyanobacteria. Water Research.46,1349-1363.
Parkes, R. J., Webster, G., Cragg, B. A., Weightman, A. J., Newberry, C. J., Ferdelman, T. G. et al. (2005). Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436,390-394.
Percent, S.F., Frischer, M.E., Vescio, P.A., Duffy, E.B., Milano, V. et al. (2008). Bacterial community structure of acid-impacted lakes:what controls diversity? Appl Environ Microbiol 74, 1856-1868.
Poitelon, J. B., Joyeux, M., Welte, B., Duguet, J. P., Prestel, E., Lespinet, O., DuBow, M.
S.(2009). Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags. Water Research 43,4197-4206.
Qian, P., Wang, Y., Lee, O., Lau, S., Yang, J., Lafi, F. et al. (2010). Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J5,507-518.
Quail, M.A., Kozarewa, I., Smith, F., Scally,A., Stephens,P.J., Durbin, R., Swerdlow, H. & Turner, D.J. (2008). A large genome center's improvements to the Illumina sequencing system. Nature Methods.5,1005-1010.
Rappe, MS & Giovannoni, SJ. (2003). The uncultured microbial majority. Annu.Rev. Microbiol. 57,369-394.
Ravenschlag, K., Sahm, K., Knoblauch, C., J(?)rgensen, B. B., Amann, R. (2000). Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol 66,3592-3602.
Rees, H. C., Grant,W. D., Jones, B. E. & Heaphy, S. (2004). Diversity of Kenyan soda lake alkaliphiles. Extremophiles 8,63-71.
Rodas, A. M., Ferrer, S., Pardo, I. (2003).16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Systematic and Applied Microbiology.26,412-422
Saitou, N. & Nei, M. (1987). The neighbor-joining method:a new method for reconstructing phylogenetic trees. Mol Biol Evol 4,406-425.
Sanz, J. L., Kochling, T. (2007). Molecular biology techniques used in wastewater treatment:an overview. Process Biochemistry 42,119-133.
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20,16.
Schloss, P. D. & Handelsman, J. (2004). Status of the microbial census. Microbiol Mol Biol Rev 68, 686-691.
Schramm, A., de Beer, D., van den Heuvel, J. C., Ottengraf, S., Amann, R. (1999). Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor:quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol 65,3690-3696.
Schwarz, J. I. K., Eckert, W., & Conrad, R. (2007). Community structure of Archaea an Bacteria in a profundal lake sediment Lake Kinneret (Isreal). Systematic and Applied Microbiology 30, 239-240.
Shao, K. Q., Gao, G., Wang, Y.P., Tang, X. M., Qin, B.Q. (2013).Vertical diversity of sediment bacterial communities in two different trophic states of the eutrophic Lake Taihu, China. J Environ Sci.25,1186-1194.
Sorokin, D. Y., Tourova, T. P., Sjollema, K. A. & Kuenen, J. G. (2003). Thialkalivibrio nitratireducens sp. nov., a nitrate-reducing member of an autotrophic denitrifying consortium from a soda lake. Int J Syst Evol Microbiol 53,1779-1783.
Spring, S., Schulze, R., Overmann, J. & Schleifer, K. (2000). Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes:molecular and cultivation studies. FEMS Microbiol Rev 24,573-590.
Song, H., Li, Z., Du, B., Wang, G. & Ding, Y. (2011). Bacterial communities in sediments of the shallow Lake Dongping in China. J Appl Microbiol 112,79-89.
Spring S, Schulze R, Overmann J & Schleifer K (2000). Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes:molecular and cultivation studies. FEMS Microbiol Rev 24:573-590.
Stockner, J. G., and N. J. Antia. (1986). Algal picoplankton from marine and freshwater ecosystems:a multidisciplinary perspective. Can. J. Fish. Aquat. Sci 43,2472-2503.
Strous, M., Kuenen, J. G., Jetten, M. S. M. (1999). Key physiology of anaerobic ammonium oxidation. Appl. Environ. Microbiol 65,3248-3250.
Suzuki, M., Rappe, M. S., Giovannoni, S. J. (1998). Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol 64,4522-4529.
Switzer, B. J., Burns, B. A., Buzzelli, J., Stolz, J.F. & Oremland, R.S. (1998). Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.:two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Arch Microbiol 171,19-30.
Talbot, G., Roy, C. S., Topp, E., Beaulieu, C., Palin, M. F., Masse, D. I. (2009). Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure. FEMS Microbiol Ecol 70,540-552.
Tamaki, H., Sekiguchi, Y., Hanada, S., Nakamura, K., Nomura, N., et al. (2005). Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71,2162-2169.
Tamaoka, J., Katayama-Fujimura, Y. & Kuraishi, H. (1983). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54,31-36.
Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4:molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24,1596-1599.
Tebbe, C.C. & Vahjen, W. (1993). Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinantDNA from bacteria and a yeast. Applied andEnvironmentalMicrobiology 59,2657-2665.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTALX windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25,4876-4882.
Tran, H. T. Park, Y. J., Cho, M. K., Kim, D. J., Ahn, D. H. (2006). Anaerobic ammonium oxidation process in an upflow anaerobic sludge blanket reactor with granular sludge selected from an anaerobic digestor. Biotechnology and Bioprocess Engineering 11,199-204.
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E.et al. (2009). A core gut microbiome in obese and lean twins. Nature,457:480-484.
Vargas, V. A., Delgado, O. D., Hatti-Kaul, R. & Mattiasson, B. (2004). Lipase-producing microorganisms from a Kenyan alkaline soda lake. Biotechnol Lett.26,81-86.
von Wintzingerode, F., Gobel, U.B., Stackebrandt, E. (1997). Determination of microbial diversity in environmental samples:pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21, 213-229.
Wani, A. A., Surakasi, V. P., Siddharth, J., Raghavan, R. G., Patole, M. S., Ranade, D. & Shouche, Y. S. (2006). Molecular analysis of microbial diversity associated with the Lonar soda lake in India:an impact crater in a basalt area. Res Microbiol 157,928-93.
White, D. C., Davis, W. M., Nickels, J. S., King, J. D., Bobbie, R. J. (1979). Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40,51-62
Whittaker, R. H. (1960). Vegetation of the Siskiyou Mountains, Oregon and California. Ecol. Monogr 30,279-338.
Whittaker, R. H. (1965). Dominance and diversity in land plant communities. Science 147, 250-6070.
Whittaker, R. H. (1969). Evolution of diversity in plant communities. Brook-haven Symp. Biol 22, 178-9671.
Whittaker, R. H. (1972). Evolution and measurement of species diversity. Taxon 21,213-5172.
Whittaker, R. H., Woodwell, G. M. (1969). Structure, production and diversity of the oak-pine forest at Brook
Winderl, C., Anneser, B., Griebler, C., Meckenstock, R.U., Lueders, T. (2008). Depth-resolved quantification of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl. Environ. Microbiol 74,792-801.
Wood, S. A., Rueckert, A., Cowan, D. A., Cary, S. C. (2008). Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME J,2,308-320.
Wu, Q. L L., Zwart, G., Schauer, M., Kamst-van Agterveld M. P.& Hahn, M. W. (2006). Bacterioplankton community composition along a salinity gradient of sixteen high mountain lakes located on the Tibetan Plateau, China. Appl. Environ. Microbiol.72,5478-5485.
Xue, D. W., Feng, S. G., Zhao, H. Y., Jiang, H., Shen, B., Shi, N. N., Lu, J. J., Liu, J. J., Wang, H. Z. (2010).The linkage maps of Dendrobium species based on RAPD and SRAP markers. Journal of Genetics and Genomics 37,197-204
Yamada, T. & Sekiguchi, Y. (2009). Cultivation of uncultured Chloroflexi subphyla:significance and ecophysiology of formerly uncultured Chloroflexi'subphylum I'with natural and biltechnological relevance. Microbes Environ.24,205-216
Yannarell, A. C. & Kent, A. D. (2009). Bacteria, Distribution and Community Structure. Encyclopedia of inland waters 3,201-210.
Yannarell, A. C., Kent, A.D., Lauster, G.H., Kratz, T. K.&Triplett, E.W. (2003). Temporal Patterns in Bacterial Communities in Three Temperate Lakes of Different Trophic Status. Microb Ecol 46,391-405
Ye, W. J., Liu, X. L., Lin, S. Q., Tan, J., Pan, J. L., Li, D.T.&Yang, H. (2009). The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol Ecol 70,263-276.
Zeng, J., Yang, L.Y., Liang, Y., Li, J. Y., Xiao, L., Jiang, L. J. & Zhao, D. Y. (2008). Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis. Can J. Microbiol 54,1053-1063.
Zepp-Falz, K., Holliger,C., Grosskopf, R., Liesack, W., Nozhevnikova, A.N., Muller, B., Wehrli, B. & Hahn, D. (1999). Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland), Appl. Environ. Microbiol 65,2402-2408.
Zhao, D.Y., Huang, R., Zeng, J., Yan, W.M., Wang, J.Q., Ma, T., Wang, M. & Wu, Q. L. L. (2012). Diversity analysis of bacterial community compositions in sediments of urban lakes by terminal restriction fragment length polymorphism (T-RFLP). World J Microbiol Biotechnol 28, 3159-3170.
Zwart, G., Crump, B. C., Kamst-van Agterveld, M. P., Hagen, F. & Han, S. K. (2002). Typical freshwater bacteria:an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28,141-155.
陈敬安,万国江.云南程海现在沉积物理环境记录研究[J].矿物学报,2000,20,112-115.
陈瑞银,李再云,陈宜瑜.程海鱼类区系的来源和物种分化[J].动物学研究,1983,4,227-234.
程占冰,杨江科.富营养化湖泊武汉东湖沉积物细菌多样性和系统发育研究.硕士学位论文,华中科技大学.2011.
崔晓龙,徐丽华,姜成林.分子生态学.pp161-12.放线菌现代生物学与生物技术[M],刘志恒,姜成林主编.北京：科学出版社2004.
单振光,李加联。程海水生植被研究[J]。云南师范大学学报：自然科学版,1994,14,667-671.
董云仙,邹锐等.程海湖生态系统研究[M].昆明：云南科技出版社,2011.
张民,于洋等.云贵高原湖泊夏季浮游植物组成及多样性[J].湖泊科学.2010,22,829-836.
董云仙,洪雪花等.程海冬季水花爆发期间氮、磷营养元素的形态与分布[J].生态环境学报2010,19,2675-2679.
董云仙,谭志卫等.程海藻类植物种群结构和数量的周年变化特征[J].生态环境学报.2012,21,1289-1295.
龚世杰,吴兰,李四光.湖泊微生物多样性研究进展[J].生物技术通报,2008,4,54-57.
胡文英,季江.程海水质状况及咸化趋势[J].湖泊科学,1992,4,60-66.
李德斌,杨洪一,卢磊.变性梯度凝胶电泳在微生物生态学中的应用[J].生物技术通报,2010,12,88-92.
李开源,丁明.云南程海蓝藻毒素研究[J].云南大学学报：自然科学版,1998,20,193-196.
马晓亮,崔晓龙.云南高原湖泊泸沽湖细菌多样性研究.硕士学位论文,云南大学.2013.
屈建航,曹书娟,袁红莉.不同营养湖／库沉积物中细菌群落差异分析[J].中国农业大学学报.2011,16,49-53.
田时平,崔晓龙.云南高原程海碱性湖泊细菌多样性研究.硕士学位论文,云南大学.2011.
晋方佑,杨丽源.程海湖可培养淡水真菌多样性及其抗菌、产酶活性评价.硕士学位论文,云南大学.2013.
王若南,钱澄宇.程海的蓝藻[J].云南大学学报：自然科学版,1987,9,87-88.
王若南,钱澄宇.程海藻类植物调查研究[J].云南大学学报：自然科学版,1988,10,250-258.
王苏民,窦鸿身等.中国湖泊志[M].北京：科学出版社,1998.
吴敬禄,王苏民.云南程海富营养化过程的碳氧同位素示踪[J].第四纪研究,2003,23,557-564.
吴伦祥.云南省第四大湖泊——程海移植滇池高背鲫鱼增养殖技术试验研究[J].水产学杂志, 1995,8,58-62.
张钰,朱瑞卫.湖泊沉积物中微生物多样性和厌氧氨氧化菌鉴别研究.硕士学位论文,华中农业大学.2012.
周新丽,李绍兰.云南三种极端环境酵母菌多样性研究.硕士学位论文,云南大学.2012.
周欣.螺旋藻开发对程海水质的影响及对策[J].云南环境科学,1997,16,35-37.
Altmann, D., Stief, P., Amann, R., de Beer, D. (2004). Distribution and activity of nitrifying bacteria in natural stream sediment versus laboratory sediment microcosms. Aquatic Microbial Ecology 36,73-81.
Alvarado, P., Manjon, J. L. (2009). Selection of enzymes for terminal restriction fragment length polymorphism analysis of fungal internally transcribed spacer sequences. Appl.Enviro.Microbiol 75, 4747.4752.
Amann, R. I., Ludwig, W. & Schleifer, K. H. (1995). Phylogenetic identification and in situ detection of indivadual microbial cells without cultivation. Microbiol Rev,59,143-169.
Ashelford, K. E., Chuzhanova, N. A., Fry, J. C., Jones, A. J. & Weightman, A. J. (2006). New screening software shows most recent large 16S rRNA gene clone libraries contain chimeras. Appl. Environ. Microbiol 72,5734-5741.
Auchtung, T. A., Takacs-Vesbach, C. D. & Cavanaugh C. M. (2006).16S rRNA phylogenetic investigation of the candidate division "Korarchaeota". Appl.Enviro.Microbiol 72,5077-5082.
Azam, F., T. Fenchel, J. G. Field, J. S. Gray, L. A. Meyer, and F. Thingstad. (1983). The ecological role of water column microbes in the sea. Mar. Ecol. Prog. Ser.10,257-263.
Bai, Y., Shi, Q., Wen, D., Li, Z., Jefferson, W. A., et al. (2012). Bacterial Communities in the Sediments of Dianchi Lake, a Partitioned Eutrophic Waterbody in China. PLoS ONE 7:e37796.
Bjornsson, L., Hugenholtz, P., Tyson, G.W. & Blackall, L.L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiol 148,2309-2318.
Brinkmeyer, R., Knittel, K., Jiirgens, J., Weyland, H., Amann, R., Helmke, E. (2003). Diversity and structure of bacterial communities in Arctic versus Antarctic pack ice. Appl. Environ. Microbiol 69,6610-6619.
Bruce K D. (1997). Analysis of mer gene subclasses within bacterial communities in soils and sediments resolved by fluorescent-PCR-restriction fragment length polymorphism profiling. Appl.Enviro.Microbiol 63,2647-2653.
Brulc, J. M., Antonopoulos, D. A., Berg Miller, M. E., Wilson, M. K. Yannarell, A. C., Dinsdale, E. A. et al. (2009). Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences of the United States of America 106,1948-1953.
Caron, D. A., E. R. Peele, E. L. Lim, and M. R. Dennett. (1999). Picoplankton and nanoplankton and their trophic coupling in the surface waters of the Sargasso Sea sOTUh of Bermuda. Limnol. Oceanogr 44,259-272.
Chandler, D. P., Kukhtin, A., Mokhiber, R., Knickerbocker, C., Ogles, D., Rudy, G., Golova, J., Long, P., Peacock, A. (2010). Monitoring microbial community structure and dynamics during in situ U(VI) bioremediation with a field-portable microarray analysis system. Enviro Sci & Technol 44, 5516-5522.
Cho, J. C. & Giovannoni, S. J. (2006). Pelagibaca bermudensis gen. nov., sp. nov., a novel marine bacterium within the Roseobacter clade in the order Rhodobacterales. Int J Syst Evol Microbiol 56, 855-859.
Christensson, M., Blackall, L. L., Welander, T. (1998). Metabolic transformations and characterisation of the sludge community in an enhanced biological phosphorus removal system. Appl. Environ. Microbiol 49,226-234.
Collins, M. D. & Jones, D. (1980). Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48,459-470.
Collins, M. D., Pirouz, T., Goodfellow, M. & Minnikin, D. E. (1977). Distribution of menaquinones in actinomycetes and corynebacteria. JGen Microbiol 100,221-230.
Cui, X. L., Mao, P. H., Zeng, M., Li, W. J., Zhang, L. P., Xu, L. H. & Jiang, C. L. (2001). Streptomonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51,357-363.
Curtis TP, Sloan WT, Scannell JW (2002). Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99,10494-10499
Deiglmayr, K., Philippot, L., Tscherko, D., Kandeler, E. (2006). Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Enviro Microbiol.8,1600-1612.
Deiglmayr, K., Philippot, L., Tscherko, D. & Kandeler, E. (2006). Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps. Enviro Microbiol.8,1600-1612.
Delong E. F., Wickham, G. S. & Pace N. R. (1989). Phylogenetic strains:ribosomal RNA based probes for the identification of the identification of single microbial cells. Science,243:1360-1363.
Demergasso, C., Casamayor, E. O., Chong, G., Galleguillos, P. & Escuder,0.(2004). Distribution of prokaryotic genetic diversity in athalassohaline lakes of the Atacama Desert, Northern Chile. FEMS Microbiol Ecol 48,57-69.
Dimitriu, P. A., Pinkart, H. C., Peyton, B. M.&Mormile M. R. (2008). Spatial and temporal patterns in the microbial diversity of a meromictic soda lake in washington state. Appl. Environ. Microbiol 74,4877-4888.
Dong, H. L., Zhang, G. X., Jiang, H. C., Yu, B. S., Chapman, L. R., Lucas, C. R., Fields, M.
W.(2006). Microbial Diversity in Sediments of Saline Qinghai Lake, China:Linking Geochemical Controls to Microbial Ecology. Microb Ecol 51,65-82.
Duckworth, A. W. Grant, W. D. Jones, B. E. & Steenbergen, R.V. (1996). Phylogenetic diversity of soda lake alkaliphiles, FEMS Microbiol. Ecol,19,181-191.
Edlund, A., Soule,T., Sjoling, S. & Jansson, J. K. (2006). Microbial community structure in polluted Baltic Sea sediments. Environ Microbiol 8,223-232.
Eilers, H., Pernthaler, J., Glockner, F. O., Amann, R. (2000). Culturability and In situ abundance of pelagic bacteria from the North Sea. Appl. Environ. Microbiol 66,3044-3051.
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle, USA.
Felske, A., Wolterink, A., VanLis, R., DeVos, W.M. & Akkermans, A.D. (2000). Response of a soil bacterial community to grassland succession as monitored by 16S rRNA levels of the predominant ribotypes. Appl Environ Microbiol 66,3998-4003.
Fisher, M. M., Triplett, E. W. (1999). Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl. Environ. Microbiol 65.4630-4636.
Gaudette, H. E., Flight, W. R., Toner, L. & Folger, D. W. (1974). An inexpensive titration method for the determination of organic carbon in recent sediments. J Sediment Res 44,249-253.
Gentry, T.J. (2010). Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J A,829-838.
Gieseke, A., Purkhold, U., Wagner, M., Amann, R., Schramm, A. (2001). Community structure and activity dynamics of nitrifying bacteria in a phosphate-removing biofilm. Appl. Environ. Microbiol 61,1351-1362.
Glissmann, K., Chin, K. J., Casper, P. & Conrad, R. (2004). Methanogenic pathway and archaeal community structure in the sediment of eutrophic Lake Dagow:effect of temperature. Microbial. Ecol 48.389-399.
Glockner, F. O., Fuchs, B. M., Amann, R. (1999). Bacterioplankton compositions of lakes and oceans:a first comparison based on fluorescence in situ hybridization. Appl. Environ. Microbiol 65, 3721-3726
Go, Y. S., Han, S. K., Lee, I.G. & Ahn, T. Y. (2000). Diversity of the domain Archaea as determined by 16S rRNA gene analysis in the sediments of Lake Soyang, Arch. Hydrobiol 149, 459-466.
Grant, S., Sorokin, D. y., Grant, W.D., Jones B.E. & Heaphy, S. (2004). A phylogenetic analysis of Wadiel Natrun soda Lake cellulose enrichment cultures and identification of cellulose genes from these cultures. Extremephiles 8,421-429.
Hollister, E.B, Engledow, A.S, Hammett, A.J.M., Provin, T. L., Wilkinson, H.H. & Gregersen, T. (1978). Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5.123-127.
Hansen, G. H. & S(?)rheim, R. (1991). Improved method for phenotypical characterization of marine bacteria. JMicrobiol Methods 13,231-241
Hollister, E.B, Engledow, A.S, Hammett, A.J.M., Provin, T. L., Wilkinson, H. H. & Gentry, T.J. (2010). Shifts in microbial community structure along an ecological gradient of hypersaline
soils and sediments. ISME J 4,829-838.
Hori, T., Haruta, S., Ueno, Y., Ishii, M., Igarashi, Y. (2006). Dynamic transition of a methanogenic population in response to the concentration of volatile fatty acids in a thermophilic anaerobic digester. Appl. Environ. Microbiol 72,1623-1630
Huber, J.A., Johnson, H.P., Butterfield, D.A. & Baross, J.A. (2006). Microbial life in ridge flank crustal fluids. Environ Microbiol 8,88-99.
Huggenholtz, P., Goebel, B. M.& Pace N. R. (1998). Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol.180,4765-4774.
Humayoun, S. B., Bano, N. & Hollibaugh, J. T. (2003). Depth distribution of microbial diversity in Mono Lake, a meromictic soda lake in California. Appl Environ Microbiol 69,1030-1042
Huse, S.M., Dethlefsen, L., Huber, J.A., Welch, D.M., Relman, D.A.& Sogin, M.L. (2008). Exploring microbial diversity and taxonomy using SSU rRNA hypervariable tag sequencing. PLoS Genet. 4(11), e1000255.
Ikeda, S., Rallos, L. E. E., Okubo, T., Eda, S., Inaba, S., Mitsui, H., Minamisawa, K. (2008). Microbial community analysis of field-grown soybeans with different nodulation phenotypes. Appl. Environ. Microbiol 74,5704-5709.
Jiang, H., Dong, H., Zhang, G., Yu, B., Chapman, L.R. and Fields, M.W. (2006). Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China. Appl Environ Microbiol 72,3832-3845.
Jurgens, G., Glockner, F., Amann, R., Saano, A., Montonen, L., Likolammi, M & Munster, U. (2000). Identification of novel Archaea in bacterioplankton of a boreal forest lake by phylogenetic analysis and fluorescent in situ hybridization. FEMS Microbiol Ecol 34,45-56.
Kampfer, P., Young, C. C., Chen, W. M., Rekha, P. D., Fallschissel, K., Lodders, N., et al. (2010). Fontibacter flavus gen. nov., sp. nov., a member of the family 'Cyclobacteriaceae', isolated from a hot spring. Int J Syst Evol Microbiol 60,2066-2070.
Knittel, K., Losekann, T., Boetius, A., Kort, R., Amann, R. (2005). Diversity and distribution of methanotrophic archaea at cold seeps. Appl. Environ. Microbiol 71,467-479
Kovacs, N. (1956). Identification of Pseudomonas pyocyanea by oxidase reaction. Nature 178, 703-704.
Kreader, C. A. (1996). Relief of amplification inhibition in PCR with bovine serum albumin or T4 gene 32 protein. Appl. Environ. Microbiol.62,1102-1106.
Kvennefors, E. C. E., Sampayo, E., Ridgway, T., Barnes, A. C., Hoegh-Guldberg, O. (2010).
Bacterial communities of two ubiquitous Great Barrier Reef corals reveals both site- and species-specificity of common bacterial associates. PLOS ONE 5,1-14
Lane, D. J. (1991).16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics ed. Stackebrandt, E. and Goodfellow, M. pp.115-175. Chichester, UK:John Wiley & Sons.
Lee, Z. M. P., Bussema, C., Schmidt, T. M. (2009). rrnDB:documenting the number of rRNA and tRNA genes in bacteria and Archaea. Nucleic Acids Res 37, D489-D493.
Lefranc, M., Aurelie T., Lepere, C. & Debroas D. (2005). Genetic Diversity of Small Eukaryotes in lakes differing by their trophic status. Appl. Environ. Microbiol 71,5935-5942
Lepere, C., Boucher, D., Jardillier, L., Domaizon, I. & Debroas, Di. (2006). Succession and Regulation Factors of Small Eukaryote Community Composition in a Lacustrine Ecosystem (Lake Pavin). Appl. Environ. Microbiol 72,2971-2981.
Llobet-Brossa, E., Rabus, R., Bottcher, M. E., Konneke, M., Finke, N., Schramm, A., Meyer, R. L. et al. (2002). Community structure and activity of sulfate-reducing bacteria in an intertidal surface sediment:a multi-method approach. Aquatic Microbial Ecology 29,211-226.
Liu, F. H., Lin, G. H., Gao, G., Qin, B. Q., Zhang, J. S., et al. (2009). Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis. J Appl Microbiol 106,1022-1032.
Liu, W. T., Marsh, T. L., Cheng, H. et al. (1997). Characterization of microbial diversity by determing terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl.Enviro.Microbiol 63,3616-3620.
Lu, Y., Rosencrantz, D., Liesack, W. & Conrad, R. (2006). Structure and activity of bacterial community inhabiting rice roots and the rhizosphere. Environ Microbiol 8,1351-1360.
Mardis, E. R. (2008). The impact of next-generation sequencing technology on genetics. Trends Genetics.24.133-141.
Martins, R. F., Davids, W., Abu Al-Soud, W., Levander, F., Radstrom, P. & Hatti-Kaul R. (2001). Starch-hydrolyzing bacteria from Ethiopian soda lakes. Extremophiles 5,135-144.
McLellan, S., Huse, S., Mueller Spitz, S., Andreishcheva, E. & Sogin, M. (2010). Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent. Environ Microbiol 12,378-392.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39,159-167.
Mesbah, N. M., Abou-EI-Ela, S. H. & Wiegel, J. (2007). Novel and unexpected prokaryotic diversity in water and sediments of the alkaline, hypersaline lakes of the Wadi An Natrun, Egypt. Microb.Ecol.54,598-617.
Mesbah, N. M. & Wiegel, J. (2009a). Natronovirga wadinatrunensis gen. nov., sp. nov. and Natranaerobius trueperi sp. nov., halophilic, alkalithermophilic micro-organisms from soda lakes of the Wadi An Natrun, Egypt. Int J Syst Evol Microbiol.59,2042-2048
Mesbah, N. M. & Wiegel, J. (2009b). Natronovirga wadinatrunensis gen. nov., sp. nov. and Natranaerobius trueperi sp. nov.. halophilic. alkalithermophilic micro-organisms from soda lakes of the Wadi An Natrun. Egypt. Int J Syst Evol Microbiol.59,2042-2048
Meyer, M., Stenzel, U., Hofreiter, M. (2008). Parallel tagged sequencing on the 454 platform. Nature Protocols.3,267-278.
Mikkelsen, D., Kappler, U., McEwan, A. G., Sly, L. I. (2009). Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH. Systematic and Applied Microbiology 32.501-513
Mou, X. Z., Sun, S. L., Edwards, R. A., Hodson, R. E., Moran, M. A. (2008). Bacterial carbon processing by generalist species in the coastal ocean. Nature 451,708-711.
Muyzer, G., De Waal, E. & Uitterlinden, A. G (1993). Profiling of complex microbial population by gradient gel electrophoresis analysis (DGGE) of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol,59,695-700.
Myers, R.M., Fisher, S.G., Delerman, L.S. et al. (1985). Nearly all single base substitution in DNA fragments joined to a GC-clamp can be detected by Denaturing Gradient Gel Electrophoresis. Nucleic Acid Res.13,3131-3145.
Nealson, K. H. (1997). Sediment bacteria:Who's there, what are they doing, and what's new? Annu Rev Earth Pl Sc 25,403-434.
Nelson, D. M, Ohene-Adjei, S., Hu, F. S., Cann, I. K. & Mackie, R. I. (2007). Bacterial diversity and distribution in the holocene sediments of a northern temperate lake. Microb Ecol 54,252-263.
Olsen, S. R. & Sommers, L.E. (1982). Phosphorus. In Methods of Soil Analyses, Part 2, Chemical and Microbiological Properties ed. Page, A.L., Miller, R.H. and Keeney, D.R. pp.
Paerl, H. W., & Paul V. J. (2012). Climate change:Links to global expansion of harmful cyanobacteria. Water Research.46,1349-1363.
Parkes, R. J., Webster, G., Cragg, B. A., Weightman, A. J., Newberry, C. J., Ferdelman, T. G. et al. (2005). Deep sub-seafloor prokaryotes stimulated at interfaces over geological time. Nature 436,390-394.
Percent, S.F., Frischer, M.E., Vescio, P.A., Duffy, E.B., Milano, V. et al. (2008). Bacterial community structure of acid-impacted lakes:what controls diversity? Appl Environ Microbiol 74, 1856-1868.
Poitelon, J. B., Joyeux, M., Welte, B., Duguet, J. P., Prestel, E., Lespinet, O., DuBow, M.
S.(2009). Assessment of phylogenetic diversity of bacterial microflora in drinking water using serial analysis of ribosomal sequence tags. Water Research 43,4197-4206.
Qian, P., Wang, Y., Lee, O., Lau, S., Yang, J., Lafi, F. et al. (2010). Vertical stratification of microbial communities in the Red Sea revealed by 16S rDNA pyrosequencing. ISME J5,507-518.
Quail, M.A., Kozarewa, I., Smith, F., Scally,A., Stephens,P.J., Durbin, R., Swerdlow, H. & Turner, D.J. (2008). A large genome center's improvements to the Illumina sequencing system. Nature Methods.5,1005-1010.
Rappe, MS & Giovannoni, SJ. (2003). The uncultured microbial majority. Annu.Rev. Microbiol. 57,369-394.
Ravenschlag, K., Sahm, K., Knoblauch, C., J(?)rgensen, B. B., Amann, R. (2000). Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol 66,3592-3602.
Rees, H. C., Grant,W. D., Jones, B. E. & Heaphy, S. (2004). Diversity of Kenyan soda lake alkaliphiles. Extremophiles 8,63-71.
Rodas, A. M., Ferrer, S., Pardo, I. (2003).16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Systematic and Applied Microbiology.26,412-422
Saitou, N. & Nei, M. (1987). The neighbor-joining method:a new method for reconstructing phylogenetic trees. Mol Biol Evol 4,406-425.
Sanz, J. L., Kochling, T. (2007). Molecular biology techniques used in wastewater treatment:an overview. Process Biochemistry 42,119-133.
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20,16.
Schloss, P. D. & Handelsman, J. (2004). Status of the microbial census. Microbiol Mol Biol Rev 68, 686-691.
Schramm, A., de Beer, D., van den Heuvel, J. C., Ottengraf, S., Amann, R. (1999). Microscale distribution of populations and activities of Nitrosospira and Nitrospira spp. along a macroscale gradient in a nitrifying bioreactor:quantification by in situ hybridization and the use of microsensors. Appl. Environ. Microbiol 65,3690-3696.
Schwarz, J. I. K., Eckert, W., & Conrad, R. (2007). Community structure of Archaea an Bacteria in a profundal lake sediment Lake Kinneret (Isreal). Systematic and Applied Microbiology 30, 239-240.
Shao, K. Q., Gao, G., Wang, Y.P., Tang, X. M., Qin, B.Q. (2013).Vertical diversity of sediment bacterial communities in two different trophic states of the eutrophic Lake Taihu, China. J Environ Sci.25,1186-1194.
Sorokin, D. Y., Tourova, T. P., Sjollema, K. A. & Kuenen, J. G. (2003). Thialkalivibrio nitratireducens sp. nov., a nitrate-reducing member of an autotrophic denitrifying consortium from a soda lake. Int J Syst Evol Microbiol 53,1779-1783.
Spring, S., Schulze, R., Overmann, J. & Schleifer, K. (2000). Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes:molecular and cultivation studies. FEMS Microbiol Rev 24,573-590.
Song, H., Li, Z., Du, B., Wang, G. & Ding, Y. (2011). Bacterial communities in sediments of the shallow Lake Dongping in China. J Appl Microbiol 112,79-89.
Spring S, Schulze R, Overmann J & Schleifer K (2000). Identification and characterization of ecologically significant prokaryotes in the sediment of freshwater lakes:molecular and cultivation studies. FEMS Microbiol Rev 24:573-590.
Stockner, J. G., and N. J. Antia. (1986). Algal picoplankton from marine and freshwater ecosystems:a multidisciplinary perspective. Can. J. Fish. Aquat. Sci 43,2472-2503.
Strous, M., Kuenen, J. G., Jetten, M. S. M. (1999). Key physiology of anaerobic ammonium oxidation. Appl. Environ. Microbiol 65,3248-3250.
Suzuki, M., Rappe, M. S., Giovannoni, S. J. (1998). Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Appl. Environ. Microbiol 64,4522-4529.
Switzer, B. J., Burns, B. A., Buzzelli, J., Stolz, J.F. & Oremland, R.S. (1998). Bacillus arsenicoselenatis, sp. nov., and Bacillus selenitireducens, sp. nov.:two haloalkaliphiles from Mono Lake, California that respire oxyanions of selenium and arsenic. Arch Microbiol 171,19-30.
Talbot, G., Roy, C. S., Topp, E., Beaulieu, C., Palin, M. F., Masse, D. I. (2009). Multivariate statistical analyses of rDNA and rRNA fingerprint data to differentiate microbial communities in swine manure. FEMS Microbiol Ecol 70,540-552.
Tamaki, H., Sekiguchi, Y., Hanada, S., Nakamura, K., Nomura, N., et al. (2005). Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques. Appl Environ Microbiol 71,2162-2169.
Tamaoka, J., Katayama-Fujimura, Y. & Kuraishi, H. (1983). Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54,31-36.
Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007). MEGA4:molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24,1596-1599.
Tebbe, C.C. & Vahjen, W. (1993). Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinantDNA from bacteria and a yeast. Applied andEnvironmentalMicrobiology 59,2657-2665.
Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTALX windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25,4876-4882.
Tran, H. T. Park, Y. J., Cho, M. K., Kim, D. J., Ahn, D. H. (2006). Anaerobic ammonium oxidation process in an upflow anaerobic sludge blanket reactor with granular sludge selected from an anaerobic digestor. Biotechnology and Bioprocess Engineering 11,199-204.
Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E.et al. (2009). A core gut microbiome in obese and lean twins. Nature,457:480-484.
Vargas, V. A., Delgado, O. D., Hatti-Kaul, R. & Mattiasson, B. (2004). Lipase-producing microorganisms from a Kenyan alkaline soda lake. Biotechnol Lett.26,81-86.
von Wintzingerode, F., Gobel, U.B., Stackebrandt, E. (1997). Determination of microbial diversity in environmental samples:pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21, 213-229.
Wani, A. A., Surakasi, V. P., Siddharth, J., Raghavan, R. G., Patole, M. S., Ranade, D. & Shouche, Y. S. (2006). Molecular analysis of microbial diversity associated with the Lonar soda lake in India:an impact crater in a basalt area. Res Microbiol 157,928-93.
White, D. C., Davis, W. M., Nickels, J. S., King, J. D., Bobbie, R. J. (1979). Determination of the sedimentary microbial biomass by extractible lipid phosphate. Oecologia 40,51-62
Whittaker, R. H. (1960). Vegetation of the Siskiyou Mountains, Oregon and California. Ecol. Monogr 30,279-338.
Whittaker, R. H. (1965). Dominance and diversity in land plant communities. Science 147, 250-6070.
Whittaker, R. H. (1969). Evolution of diversity in plant communities. Brook-haven Symp. Biol 22, 178-9671.
Whittaker, R. H. (1972). Evolution and measurement of species diversity. Taxon 21,213-5172.
Whittaker, R. H., Woodwell, G. M. (1969). Structure, production and diversity of the oak-pine forest at Brook
Winderl, C., Anneser, B., Griebler, C., Meckenstock, R.U., Lueders, T. (2008). Depth-resolved quantification of anaerobic toluene degraders and aquifer microbial community patterns in distinct redox zones of a tar oil contaminant plume. Appl. Environ. Microbiol 74,792-801.
Wood, S. A., Rueckert, A., Cowan, D. A., Cary, S. C. (2008). Sources of edaphic cyanobacterial diversity in the Dry Valleys of Eastern Antarctica. ISME J,2,308-320.
Wu, Q. L L., Zwart, G., Schauer, M., Kamst-van Agterveld M. P.& Hahn, M. W. (2006). Bacterioplankton community composition along a salinity gradient of sixteen high mountain lakes located on the Tibetan Plateau, China. Appl. Environ. Microbiol.72,5478-5485.
Xue, D. W., Feng, S. G., Zhao, H. Y., Jiang, H., Shen, B., Shi, N. N., Lu, J. J., Liu, J. J., Wang, H. Z. (2010).The linkage maps of Dendrobium species based on RAPD and SRAP markers. Journal of Genetics and Genomics 37,197-204
Yamada, T. & Sekiguchi, Y. (2009). Cultivation of uncultured Chloroflexi subphyla:significance and ecophysiology of formerly uncultured Chloroflexi'subphylum I'with natural and biltechnological relevance. Microbes Environ.24,205-216
Yannarell, A. C. & Kent, A. D. (2009). Bacteria, Distribution and Community Structure. Encyclopedia of inland waters 3,201-210.
Yannarell, A. C., Kent, A.D., Lauster, G.H., Kratz, T. K.&Triplett, E.W. (2003). Temporal Patterns in Bacterial Communities in Three Temperate Lakes of Different Trophic Status. Microb Ecol 46,391-405
Ye, W. J., Liu, X. L., Lin, S. Q., Tan, J., Pan, J. L., Li, D.T.&Yang, H. (2009). The vertical distribution of bacterial and archaeal communities in the water and sediment of Lake Taihu. FEMS Microbiol Ecol 70,263-276.
Zeng, J., Yang, L.Y., Liang, Y., Li, J. Y., Xiao, L., Jiang, L. J. & Zhao, D. Y. (2008). Spatial distribution of bacterial communities in sediment of a eutrophic lake revealed by denaturing gradient gel electrophoresis and multivariate analysis. Can J. Microbiol 54,1053-1063.
Zepp-Falz, K., Holliger,C., Grosskopf, R., Liesack, W., Nozhevnikova, A.N., Muller, B., Wehrli, B. & Hahn, D. (1999). Vertical distribution of methanogens in the anoxic sediment of Rotsee (Switzerland), Appl. Environ. Microbiol 65,2402-2408.
Zhao, D.Y., Huang, R., Zeng, J., Yan, W.M., Wang, J.Q., Ma, T., Wang, M. & Wu, Q. L. L. (2012). Diversity analysis of bacterial community compositions in sediments of urban lakes by terminal restriction fragment length polymorphism (T-RFLP). World J Microbiol Biotechnol 28, 3159-3170.
Zwart, G., Crump, B. C., Kamst-van Agterveld, M. P., Hagen, F. & Han, S. K. (2002). Typical freshwater bacteria:an analysis of available 16S rRNA gene sequences from plankton of lakes and rivers. Aquat Microb Ecol 28,141-155.
陈敬安,万国江.云南程海现在沉积物理环境记录研究[J].矿物学报,2000,20,112-115.
陈瑞银,李再云,陈宜瑜.程海鱼类区系的来源和物种分化[J].动物学研究,1983,4,227-234.
程占冰,杨江科.富营养化湖泊武汉东湖沉积物细菌多样性和系统发育研究.硕士学位论文,华中科技大学.2011.
崔晓龙,徐丽华,姜成林.分子生态学.pp161-12.放线菌现代生物学与生物技术[M],刘志恒,姜成林主编.北京：科学出版社2004.
单振光,李加联。程海水生植被研究[J]。云南师范大学学报：自然科学版,1994,14,667-671.
董云仙,邹锐等.程海湖生态系统研究[M].昆明：云南科技出版社,2011.
张民,于洋等.云贵高原湖泊夏季浮游植物组成及多样性[J].湖泊科学.2010,22,829-836.
董云仙,洪雪花等.程海冬季水花爆发期间氮、磷营养元素的形态与分布[J].生态环境学报2010,19,2675-2679.
董云仙,谭志卫等.程海藻类植物种群结构和数量的周年变化特征[J].生态环境学报.2012,21,1289-1295.
龚世杰,吴兰,李四光.湖泊微生物多样性研究进展[J].生物技术通报,2008,4,54-57.
胡文英,季江.程海水质状况及咸化趋势[J].湖泊科学,1992,4,60-66.
李德斌,杨洪一,卢磊.变性梯度凝胶电泳在微生物生态学中的应用[J].生物技术通报,2010,12,88-92.
李开源,丁明.云南程海蓝藻毒素研究[J].云南大学学报：自然科学版,1998,20,193-196.
马晓亮,崔晓龙.云南高原湖泊泸沽湖细菌多样性研究.硕士学位论文,云南大学.2013.
屈建航,曹书娟,袁红莉.不同营养湖／库沉积物中细菌群落差异分析[J].中国农业大学学报.2011,16,49-53.
田时平,崔晓龙.云南高原程海碱性湖泊细菌多样性研究.硕士学位论文,云南大学.2011.
晋方佑,杨丽源.程海湖可培养淡水真菌多样性及其抗菌、产酶活性评价.硕士学位论文,云南大学.2013.
王若南,钱澄宇.程海的蓝藻[J].云南大学学报：自然科学版,1987,9,87-88.
王若南,钱澄宇.程海藻类植物调查研究[J].云南大学学报：自然科学版,1988,10,250-258.
王苏民,窦鸿身等.中国湖泊志[M].北京：科学出版社,1998.
吴敬禄,王苏民.云南程海富营养化过程的碳氧同位素示踪[J].第四纪研究,2003,23,557-564.
吴伦祥.云南省第四大湖泊——程海移植滇池高背鲫鱼增养殖技术试验研究[J].水产学杂志, 1995,8,58-62.
张钰,朱瑞卫.湖泊沉积物中微生物多样性和厌氧氨氧化菌鉴别研究.硕士学位论文,华中农业大学.2012.
周新丽,李绍兰.云南三种极端环境酵母菌多样性研究.硕士学位论文,云南大学.2012.
周欣.螺旋藻开发对程海水质的影响及对策[J].云南环境科学,1997,16,35-37.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |