长江口九段沙湿地盐沼植物根围细菌群落结构和多样性的研究
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摘要
土壤微生物群落的结构常常反映其所处生态系统的特点，如植被类型，所以植被类型的变化可能引起微生物群落结构和多样性的变化。为研究湿地生态系统植物快速演替过程中微生物群落的变化以及评价植物入侵对土著微生物群落的影响，本论文利用变性梯度电泳(denaturing gradient gel electrophoresis，DGGE)和克隆测序等分子手段分析了长江口九段沙湿地中芦苇、海三棱藨草和互花米草的根围细菌群落结构特征及动态变化，主要研究结果如下：
1．芦苇、海三棱藨草和互花米草根围细菌16S rDNA扩增片断[引物为8f(GC-clamp)和534r]的DGGE电泳结果表明，尽管Enterobacter、Serratia、Rhodobacter等属的一些细菌在植物不同生长时期的根围均存在，但有些细菌类群则会随植物生长时期的不同而出现或消失。三种植物不同生长时期根围细菌群落的变化呈现出明显的差异，这可能意味着不同植物在不同生长时期为根围细菌提供的生境条件是不同的，从而造成了细菌群落会随着植物生长时期的不同而发生变化。
2．通过建立了三种植物根围细菌群落16S rDNA的克隆文库，并对所获得序列的系统发育进行了分析，结果表明主要的细菌类群包括以下几个大的类群：Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria、Deltaproteobacteria、Epsilonproteobacteria、Acidobacteria、Bacteroidetes、Chloroflexi、Nitrospira、Planctomycetes、Spirochaetes、Verrucomicrobia和Gram positives(包括Actinobateria、Firmicutes)以及一些未分类的序列(unclassified sequence)；从三种植物根围中所获得的序列大部分属于Proteobacteria。虽然三种植物根围细菌群落所包含的许多大的细菌类群相同，但通过对所得序列的系统发育分析表明这些大类群的组成并不完全一致，即芦苇、海三棱藨草和互花米草的根围细菌群落结构都比较复杂，且不完全相同，这说明不同植物根围的物理和化学环境可能不同，致使不同的细菌选择在不同植物的根围定殖。
3．在大于97％的序列相似度水平上将克隆序列归为不同的OTUs，计算三种植物根围细菌群落16S rDNA克隆文库的OTUs丰度和均匀度，并以此估计Chao1无参数多样性，结果表明，芦苇根围细菌群落的OTUs丰度为200；海三棱藨草根围细菌群落的OTUs丰度最高(668 OTUs)；互花米草根围细菌群落的OTUs丰度为382。芦苇和互花米草根围细菌群落存在着明显的优势种，而海三棱藨草根围细菌群落中物种的多度分布相对比较均匀。这些差异在某种程度上可能反映了处在不同高程的宿主植物和不同土壤环境的选择压力共同作用于根围细菌群落的结果。
4．利用类群特异性引物的PCR扩增结合DGGE电泳分析了三种植物根围的硫酸盐还原菌群落和亚硝化细菌群落，研究发现三种植物根围亚硝化菌群落结构都比较简单，本论文已有数据显示亚硝化菌群落并不随三种植物不同的生长时期而呈现明显的变化。一些可以归为Desulfovibrio和Desulfuromonas的序列在三种植物根围不同的生长时期都可以检测到；另外一些可以归为Desulfobulbus、Desulfosarcina、Desulfocapsa的序列随不同植物及植物不同的生长时期而出现或消失。硫酸盐还原菌群落所表现的空间和时间变化也同样表明植物对根围细菌的影响；另外，这种变化有可能与硫酸盐还原速率相关联。
综上所述，植物可以影响根围细菌群落的结构和多样性；湿地生态系统中细菌群落的组成非常复杂，而且细菌的多样性随植物群落的演替而发生变化。该研究同时也表明，互花米草的入侵所带来的植物群落分布格局的变化已影响到土著微生物群落的结构和多样性。本研究结果为研究湿地生态系统中微生物的重要性以及评价互花米草入侵造成的生态后果提供了理论依据。
Soil microbial communities often reflect the biotic and abiotic properties of ecosystems such as plant community composition and plant traits, and thus any shifts in plant composition may lead to the changes in soil microbial communities. The objective of this study was to investigate the effects of marsh succession and plant invasion on the composition of bacterial communities. A combined use of DGGE (denaturing gradient gel electrophoresis) and cloning / sequencing was applied in this study to characterize bacterial community structure and dynamic changes in the rhizospheric soils of three marsh plants in Jiuduansha wetlands located in the Yangtze River estuary. The main results are summarized as follows:
1. The 16S rDNA fragments were amplified by PCR from total community DNA extracted from the rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora with primers 8f (GC-clamp) and 534r. We analyzed the rhizosphere DGGE patterns for all sampling times corresponding to major plant phonological stages (dormancy, vegetative growth, reproduction, senescence). Although some sequences, such as those similar to Enterobacter, Serratia and Rhodobacter, were detected at all sampling times, considerable shifts in the bacterial communities were found, which might have resulted from differences in the microenvironments that were specific to the rhizospheric soils of three plants
2. In this study, the composition of bacterial communities of rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora in Jiuduansha wetlands was investigated by constructing 16S ribosomal DNA clone libraries. A variety of bacterial taxa were identified, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Acidobacteria, Epsilonproteobacteria, Bacteroidetes, Chloroflexi, Nitrospira, Planctomycetes, Spirochaetes, Verrucomicrobia, Actinobateria, Firmicutes and some sequences ascribed to unclassified bacteria. The members of Proteobacteria were the most abundant in all rhizospheric soils. The rhizobacterial communities of three marsh plants contained similar major bacterial taxa, but phylogenetic analysis showed that the composition of these taxa was different among the plant species. This suggests that different bacteria might have selected the specific rhizospheric environments that
different plants have created.
3. Clones were placed into operational taxonomic unit (OTU) groups at the level of sequence similarity of >97% in order to quantify bacterial diversity. Chao 1 non-parametric diversity estimator coupled with the reciprocal of Simpson's index (1/D) was applied to sequence data obtained from each library to evaluate total sequence diversity and to quantitatively compare the level of dominance. Nonparametric estimations of bacterial richness showed that the rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora contained 200, 668 and 382 OTUs, respectively. The reciprocal of Simpson's index showed that bacterial communities in the Spartina alterniflora and Phragmites australis rhizospheric soils displayed species dominance, while those in Scirpus mariqueter rhizospheric soil had uniform distributions of species abundance. The differences in the observed OTU richness and evenness index, to some extent, are expected to reflect the combined effects of host plant and edaphic environmental selection pressures on bacteria in root microenvironments.
4. The 16S rDNA fragments were amplified by PCR with group-specific primers. Sulfate-reducing bacterial communities and ammonia-oxidizing bacterial communities of rhizospheric soils were investigated via PCR-DGGE approach. The results showed that the composition of ammonia-oxidizing bacterial communities in rhizosphere of three plants was relatively simple. According to the data obtained in this study, ammonia-oxidizing bacterial community structure showed little change at different stages of plant growth and development. Some sequences ascribed to Desulfovibrio and Desulfuromonas were detected at all sampling times, but sequences ascribed to Desulfobulbus、 Desulfosarcina、 Desulfocapsa were present or absent in rhizosphere soils of different plants and at different stages of plant growth. Temporal and spatial shifts in the sulfate-reducing bacterial communities are also expected to reflect the effects of plants rhizospheric bacteria, and might indicate an association with SO_4~(2-) reduction rates.
In conclusion, the results obtained in this study suggest that plants are capable of altering the structure and diversity of rhizobacterial communities. Phylogenetic analysis of the resultant sequences indicates that the salt marshes have a great diversity of bacteria, and that the bacterial diversity changes as the plant community experiences a rapid succession in wetlands. In addition, Spartina invasions might have
affected the composition of native bacterial communities. Our results provide valuable information for better understanding the important roles of bacteria in wetland ecosystem functioning and evaluating the ecological impacts of plant invasions on native ecosystems.
1．芦苇、海三棱藨草和互花米草根围细菌16S rDNA扩增片断[引物为8f(GC-clamp)和534r]的DGGE电泳结果表明，尽管Enterobacter、Serratia、Rhodobacter等属的一些细菌在植物不同生长时期的根围均存在，但有些细菌类群则会随植物生长时期的不同而出现或消失。三种植物不同生长时期根围细菌群落的变化呈现出明显的差异，这可能意味着不同植物在不同生长时期为根围细菌提供的生境条件是不同的，从而造成了细菌群落会随着植物生长时期的不同而发生变化。
2．通过建立了三种植物根围细菌群落16S rDNA的克隆文库，并对所获得序列的系统发育进行了分析，结果表明主要的细菌类群包括以下几个大的类群：Alphaproteobacteria、Betaproteobacteria、Gammaproteobacteria、Deltaproteobacteria、Epsilonproteobacteria、Acidobacteria、Bacteroidetes、Chloroflexi、Nitrospira、Planctomycetes、Spirochaetes、Verrucomicrobia和Gram positives(包括Actinobateria、Firmicutes)以及一些未分类的序列(unclassified sequence)；从三种植物根围中所获得的序列大部分属于Proteobacteria。虽然三种植物根围细菌群落所包含的许多大的细菌类群相同，但通过对所得序列的系统发育分析表明这些大类群的组成并不完全一致，即芦苇、海三棱藨草和互花米草的根围细菌群落结构都比较复杂，且不完全相同，这说明不同植物根围的物理和化学环境可能不同，致使不同的细菌选择在不同植物的根围定殖。
3．在大于97％的序列相似度水平上将克隆序列归为不同的OTUs，计算三种植物根围细菌群落16S rDNA克隆文库的OTUs丰度和均匀度，并以此估计Chao1无参数多样性，结果表明，芦苇根围细菌群落的OTUs丰度为200；海三棱藨草根围细菌群落的OTUs丰度最高(668 OTUs)；互花米草根围细菌群落的OTUs丰度为382。芦苇和互花米草根围细菌群落存在着明显的优势种，而海三棱藨草根围细菌群落中物种的多度分布相对比较均匀。这些差异在某种程度上可能反映了处在不同高程的宿主植物和不同土壤环境的选择压力共同作用于根围细菌群落的结果。
4．利用类群特异性引物的PCR扩增结合DGGE电泳分析了三种植物根围的硫酸盐还原菌群落和亚硝化细菌群落，研究发现三种植物根围亚硝化菌群落结构都比较简单，本论文已有数据显示亚硝化菌群落并不随三种植物不同的生长时期而呈现明显的变化。一些可以归为Desulfovibrio和Desulfuromonas的序列在三种植物根围不同的生长时期都可以检测到；另外一些可以归为Desulfobulbus、Desulfosarcina、Desulfocapsa的序列随不同植物及植物不同的生长时期而出现或消失。硫酸盐还原菌群落所表现的空间和时间变化也同样表明植物对根围细菌的影响；另外，这种变化有可能与硫酸盐还原速率相关联。
综上所述，植物可以影响根围细菌群落的结构和多样性；湿地生态系统中细菌群落的组成非常复杂，而且细菌的多样性随植物群落的演替而发生变化。该研究同时也表明，互花米草的入侵所带来的植物群落分布格局的变化已影响到土著微生物群落的结构和多样性。本研究结果为研究湿地生态系统中微生物的重要性以及评价互花米草入侵造成的生态后果提供了理论依据。
Soil microbial communities often reflect the biotic and abiotic properties of ecosystems such as plant community composition and plant traits, and thus any shifts in plant composition may lead to the changes in soil microbial communities. The objective of this study was to investigate the effects of marsh succession and plant invasion on the composition of bacterial communities. A combined use of DGGE (denaturing gradient gel electrophoresis) and cloning / sequencing was applied in this study to characterize bacterial community structure and dynamic changes in the rhizospheric soils of three marsh plants in Jiuduansha wetlands located in the Yangtze River estuary. The main results are summarized as follows:
1. The 16S rDNA fragments were amplified by PCR from total community DNA extracted from the rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora with primers 8f (GC-clamp) and 534r. We analyzed the rhizosphere DGGE patterns for all sampling times corresponding to major plant phonological stages (dormancy, vegetative growth, reproduction, senescence). Although some sequences, such as those similar to Enterobacter, Serratia and Rhodobacter, were detected at all sampling times, considerable shifts in the bacterial communities were found, which might have resulted from differences in the microenvironments that were specific to the rhizospheric soils of three plants
2. In this study, the composition of bacterial communities of rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora in Jiuduansha wetlands was investigated by constructing 16S ribosomal DNA clone libraries. A variety of bacterial taxa were identified, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Acidobacteria, Epsilonproteobacteria, Bacteroidetes, Chloroflexi, Nitrospira, Planctomycetes, Spirochaetes, Verrucomicrobia, Actinobateria, Firmicutes and some sequences ascribed to unclassified bacteria. The members of Proteobacteria were the most abundant in all rhizospheric soils. The rhizobacterial communities of three marsh plants contained similar major bacterial taxa, but phylogenetic analysis showed that the composition of these taxa was different among the plant species. This suggests that different bacteria might have selected the specific rhizospheric environments that
different plants have created.
3. Clones were placed into operational taxonomic unit (OTU) groups at the level of sequence similarity of >97% in order to quantify bacterial diversity. Chao 1 non-parametric diversity estimator coupled with the reciprocal of Simpson's index (1/D) was applied to sequence data obtained from each library to evaluate total sequence diversity and to quantitatively compare the level of dominance. Nonparametric estimations of bacterial richness showed that the rhizospheric soils of Phragmites australis, Scirpus mariqueter and Spartina alterniflora contained 200, 668 and 382 OTUs, respectively. The reciprocal of Simpson's index showed that bacterial communities in the Spartina alterniflora and Phragmites australis rhizospheric soils displayed species dominance, while those in Scirpus mariqueter rhizospheric soil had uniform distributions of species abundance. The differences in the observed OTU richness and evenness index, to some extent, are expected to reflect the combined effects of host plant and edaphic environmental selection pressures on bacteria in root microenvironments.
4. The 16S rDNA fragments were amplified by PCR with group-specific primers. Sulfate-reducing bacterial communities and ammonia-oxidizing bacterial communities of rhizospheric soils were investigated via PCR-DGGE approach. The results showed that the composition of ammonia-oxidizing bacterial communities in rhizosphere of three plants was relatively simple. According to the data obtained in this study, ammonia-oxidizing bacterial community structure showed little change at different stages of plant growth and development. Some sequences ascribed to Desulfovibrio and Desulfuromonas were detected at all sampling times, but sequences ascribed to Desulfobulbus、 Desulfosarcina、 Desulfocapsa were present or absent in rhizosphere soils of different plants and at different stages of plant growth. Temporal and spatial shifts in the sulfate-reducing bacterial communities are also expected to reflect the effects of plants rhizospheric bacteria, and might indicate an association with SO_4~(2-) reduction rates.
In conclusion, the results obtained in this study suggest that plants are capable of altering the structure and diversity of rhizobacterial communities. Phylogenetic analysis of the resultant sequences indicates that the salt marshes have a great diversity of bacteria, and that the bacterial diversity changes as the plant community experiences a rapid succession in wetlands. In addition, Spartina invasions might have
affected the composition of native bacterial communities. Our results provide valuable information for better understanding the important roles of bacteria in wetland ecosystem functioning and evaluating the ecological impacts of plant invasions on native ecosystems.
引文
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