北美大豆共生根瘤菌Bradyrhizobium群体的微进化关系及动态学分析
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摘要
大豆(Glycine max)是世界上最重要的豆科作物,是油和蛋白质的主要来源。慢生根瘤菌属(Bradyrhizobium)中的B. japonicum、 B. elkanii等能与大豆有效共生固氮,从而减低作物生产过程中对氮肥的需求。由于Bradyrhizobium群体代表了非常有用的遗传资源,加上大豆的经济价值,这让Bradyrhizobium属成为了研究的热点。加拿大的特殊地理位置,使它成为种植大豆的最北部地区,大豆产量居世界第七位。尽管大豆生产对加拿大的农业和经济有着非常重要的影响,但却没有关于大豆共生根瘤菌基因资源方面的信息,特别是缺乏代表性共生根瘤菌Bradyrhizobium种群多样性、动态学、群体结构或进化史方面的资料。研究Bradyrhizobium属的生物多样性,不仅有利于为可持续的农业生产开发新的根瘤菌资源,发掘新的根瘤菌基因资源,还可以进一步清楚地展示Bradyrhizobium属内的分类地位,揭示属内的遗传进化关系,同时还可以为大豆生产筛选高效的根瘤菌菌株。
本研究对从加拿大东部两个采样地(相距280公里,有显著不同大豆种植史和接种史)分离的Bradyrhizobium群体进行了系统的调查研究,结果如下：
1.通过植物诱捕,收集了220株共生细菌。同时,还收集了已知的在加拿大用于大豆接种的Bradyrhizobium接种菌。所有分离株具有共同的特点：在YEM培养基上生长缓慢：28℃培养7-14天后,菌落直径小于1mm：都能在大豆上结瘤。
2.成功扩增了所有供试菌株的6个看家基因,并进行了序列测定,获得了长度为435bp (atpD),555bp (glnll)、462bp (recA)、618bp (gyrB)、771bp (rpoB)和369bp (dnaK)的基因片段。各看家基因拥有的等位基因数从9(dnaK)到17(rpoB)变化,而单个基因座的遗传多样性(π)从00251(atpD)到0.0338(recA)变化。所有基因座的dN/dS平均值均小于1,表明这些基因座正处于稳定或净化选择。另外,phi test检验显示,gyrB和recA基因座存在显著的重组,而其他基因座没有检测到显著的重组。
3.220株分离株6个看家基因的合并序列组成了35个独特的多位点序列类型(ST)。其中,15个ST的分离株来源于采样地A,27个ST的分离株来源于采样地B,7个ST的分离株来源于A、B两地。其中,ST21含有最多的细菌,共有53株分离株,占所有分离株的24.1%,其次是ST15,共有36株分离株,占所有分离株的16.4%。
4.参比接种菌中,USDA136和USDA122拥有相同的ST,归入到ST4。而532C、USDA138和B. japonicum USDA6T也拥有同样的ST,归入到ST24。只有很少一部分分离株被鉴定为推定接种菌。其中,采样地A只获得了一株推定接种菌；采样地B中31%的分离株被鉴定为推定接种菌。采样地A、B均未获得与接种菌61A124相关的分离株。
5.多位点序列分析及微进化分析结果表明,与大豆共生的Bradyrhizobium群体高度结构化,并呈现出遗传多样性。所有的分析都支持将220株分离株分入5个系统分支,分别对应于是B.japonicum group1、 B.japonicum group1a以及Bradyrhizobium属内3个新的系统分支。
6. STRUCTURE分析显示,220株分离株起源于5个Ancestral Lineage。 Lineage I中的分离株全部来自采样地B,而Lineage III中的菌株全部来自采样地A,并且这两个Lineage中菌株的遗传物质都是100%来自各自的Ancestral Lineage,这为分离株的空间分布提供了有力的证据。20株分离株(分别来自Lineage Ⅱ、 Ⅳ、Ⅴ)呈现山不同程度的混合祖先,这表明Lineage (?)发生了基因漂流,但不频繁。被鉴定为推定接种菌的这些ST中,只有有ST24(532C)展现出了混合祖先,遗传物质分别来自Ancestral Lineage Ⅱ、Ⅲ、ⅠV和V,并且ST24是唯一一个来自采样地B且继承有Ancestral LineageIII遗传物质的ST。
7.一致网络图显示,220株分离株被分入了5个清晰地类群,这和STRUCTURE推断的5个Lineage完全一致。对应于LineageⅠ、Ⅱ和Ⅲ的3个类群中没有任何标准菌株,位于独立的系统分支上,表明它们是Bradyrhizobium属内新的演化谱系。 LineageⅣ和Ⅴ中观察到了中度复杂的网状结构,它们的存在及复杂程度反映了系统发育不确定性的程度,同时也暗示了重组的存在。
8. ClonalFrame分析发现,重组对系统发育的推断有显著影响。共鉴定了21个重组事件,其中,12个重组事件发生在gyrB基因座上。代表内部节点的祖先推断中,没有一个推定接种菌被鉴定为外部节点的最近祖先。所有Lineages的重组与突变比值的比率(p／0)是0.05,这表明发生重组的频率是发生突变的频率的二十分之一；重组相对于突变的作用(r／m)的值是0.59,说明突变大约2倍于重组引起核苷酸替换。 LineageⅡ的外部分支与内部分支长度比率高于预期值,说明该lineage最近经历了一次群体扩大。
9. Unifrac分析显示,Lineage间分离株频率的差异存在于采样地间(P<=0.01)和栽培种间(P<=0.01)。代表Lineage的分离株和代表单个ST的分离株在采样地间及大豆栽培种间的频率也有显著差异。这些都为群体的空间结构提供了证据。10.共生基因nodC序列由7个等位基因类型组成,遗传多样性(π)为0.0167,GC含量为57.3%；dN/dS平均值为0.076,说明该基因正处于稳定或净化选择;phi检验没有检测到显著的重组。一致网络图中nodC序列分入了2个明显区分的群：nod I和nod II,并且几乎没有明显的网状结构,说明nodC基因座的重组很少见。Chi-square检验结果显示,nod I中分离株的频率在采样地间存在显著差异,而nod II中分离株的频率在采样地间不显著。nod I和nod II中分离株的频率在栽培种间都没有显著差异。
11.供试菌株间的固氮有效性存在相当大的差异。一些推定接种菌的固氮效率很低,这说明这些分离株正经历固氮基因的遗传变化或它们本来就存在于土壤中,只是碰巧与接种菌拥有同样的多位点基因型(ST)。
Soybean (Glycine max) is the most important grain legume on a production basis in the world and is a major source of oil and protein. The genus Bradyrhizobium includes species of economically important soil bacteria that fix atmospheric nitrogen in symbiotic association with soybeans and thereby minimize the requirement for nitrogen fertilizer inputs in crop production. Populations of Bradyrhizobium were widely studied for its valuable genetic resources and economic values of soybean. Canada represents the northern-most limit for soybean cultivation and ranks as the world's seventh largest producer. Despite the importance of soybeans to Canada, no information is available on the genetic resource represented by populations of symbiotic Bradyrhizobium associated with this legume with regard to their diversity, dynamics, structure or micro-evolutionary history. The research on biodiversity of Bradyrhizobium will benefit exploitation of new Rhizobium resources and novel gene resources for the sustainable agricultural production, provide further insight into taxonomy and evolutionary relationship within Bradyrhizobium genus and assist in selection of bacteria with desirable traits as inoculants for soybean production.
This study presented a systematic investigation of Bradyrhizobium populations that were isolated from two field sites (A and B, about280km apart in Eastern Canada) with contrasting histories of Bradyrhizobium inoculation and soybean cultivation. The results are listed below.
1. A collection of symbiotic bacteria (220isolates) was made by plant trap. At the same time, we assembled a reference collection of Bradyrhizobium strains known to have been used in inoculants for soybeans in Canada. All isolates were slow growing on YEM agar (colony diameter＜1mm after7to14days at28℃) and elicited nodules on soybeans.
2. Fragments of6housekeeping genes were obtained by PCR amplifications and sequenced. The length of individual gene sequences ranged from369bp (dnaK) to771bp (rpoB). The genetic diversity (π) of individual loci ranged from0.0251(atpD) to0.0338(recA) with the number of allelic types ranging from9(dnaK) to17(rpoB). The mean values of dN/dS were all＜1indicating that these loci were subject to stabilizing or purifying selection. The phi test on sequences of individual loci detected significant recombination at gyrB and recA loci, but not at the remaining loci.
3. The concatenated sequences (six housekeeping genes) of220isolates were classified into35unique STs. Isolates representing totals of15and27STs were recovered from sites A and B whereas isolates of7STs were common to both sites. Isolates of ST21(53isolates) was most abundant and accounted for24.1%of all isolates. Isolates of ST15(36isolates) accounted for16.4%of the isolates.
4. Among reference strains, USD A136was found to have the same multilocus genotype (ST4) as USDA122;532C and USDA138also have an identical multilocus genotype (ST24) to B. japonicum USDA6T. A minority of all isolates were identified as putative inoculant strains. At site A, only one isolate was a putative inoculant strain. At site B, about31%of the isolates were putative inoculant strains. Isolates corresponding to reference inoculant strain61A124were not recovered at either site.
5. Multilocus sequence typing and microevolutionary analyses indicated that the Bradyrhizobium populations associated with soybeans were highly structured and genetically diverse. All analyses supported the division of220isolates into five lineages corresponding either to B. japonicum groups1and1a or to one of three novel lineages within the genus Bradyrhizobium.
6. STRUCTURE analysis indicated that220isolates originated from five ancestral lineages. Evidence for spatial structuring was provided by lineage Ⅰ and Ⅲ isolates that were encountered only at one of two sites and had100%of their genetic material derived from the respective ancestral lineage.20isolates in lineages Ⅱ, Ⅳ and Ⅴ showed evidence of mixed ancestry indicating that inter-lineage gene flow had infrequently taken place. Of these STs identified as putative inoculant strains, only ST24(532C) exhibited mixed ancestry with genetic material inherited from ancestral lineages Ⅱ, Ⅲ, Ⅳ and Ⅴ. ST24was the only ST from site B to possess genetic material derived from ancestral lineage III.
7. The network graph showed well defined clusters of isolates corresponding to the five lineages inferred by STRUCTURE. Clusters corresponding to lineages Ⅰ, Ⅱ and have no type strain indicating that they are novel evolutionary lineages within the genus Bradyrhizobium. Moderate reticulation was evident in Lineage Ⅳ and Ⅴ. Reticulation reflects extent of phylogenetic uncertainty and indicates recombination.
8. ClonalFrame analysis indicated that recombination has significant effect on phylogenetic inference. A total of21recombination events were found and twelve events were found at the gyrB locus. Analyses were done to infer ancestors representing internal nodes and did not identify any putative inoculant strains as MRCAs of external nodes. The ratio of rates of recombination relative to mutation (ρ/θ) for all five lineages was0.05indicating that recombination was about twenty times less frequent than mutation. The effect of recombination relative to mutation (r/m) was0.59indicating that recombination introduced almost two times fewer substitutions than mutation. Lineage Ⅱ may have been subject to a recent expansion in population size based on external to internal branch length ratio tests.
9. Unifrac analysis showed that there were overall differences in the frequency of lineages between sites A and B (P＜=0.01) and between cultivars M and O (P＜=0.01). It was also found that significant differences in frequencies of isolate representing lineages and individual STs between field sites and soybean cultivars. All data indicated spatial structuring of the populations.
10. Sequences of the symbiotic nodC gene were divided into7allelic types with genetic diversity (π) of0.0167and GC content of57.3%; the mean value of dnlds was0.076suggesting that this gene is subject to stabilizing or purifying selection. The phi test did not detect significant recombination at the nodC locus. nodC sequences were placed in two well defined groups (nod Ⅰ and nod Ⅱ) in the consensus network. It was almost complete absence of reticulation, suggesting that recombination was rare at the nodC locus. Chi-square tests of independence indicate that the frequency of nod Ⅰ isolates differed between sites whereas the relative frequencies of nod Ⅱ isolates group were not significantly different. The frequency of isolates representing nod Ⅰ and nod Ⅱ groups did not differ significantly between soybean cultivars.
11. Relative effectiveness test showed that there was considerable variation in the effectiveness of isolates tested. Several putative inoculant strains were poorly effective in nitrogen-fixation suggesting that these isolates may have undergone genetic exchange of nitrogen fixation genes or were soil residents that co-incidentally possessed the same multilocus genotype (ST) as an inoculant.
本研究对从加拿大东部两个采样地(相距280公里,有显著不同大豆种植史和接种史)分离的Bradyrhizobium群体进行了系统的调查研究,结果如下：
1.通过植物诱捕,收集了220株共生细菌。同时,还收集了已知的在加拿大用于大豆接种的Bradyrhizobium接种菌。所有分离株具有共同的特点：在YEM培养基上生长缓慢：28℃培养7-14天后,菌落直径小于1mm：都能在大豆上结瘤。
2.成功扩增了所有供试菌株的6个看家基因,并进行了序列测定,获得了长度为435bp (atpD),555bp (glnll)、462bp (recA)、618bp (gyrB)、771bp (rpoB)和369bp (dnaK)的基因片段。各看家基因拥有的等位基因数从9(dnaK)到17(rpoB)变化,而单个基因座的遗传多样性(π)从00251(atpD)到0.0338(recA)变化。所有基因座的dN/dS平均值均小于1,表明这些基因座正处于稳定或净化选择。另外,phi test检验显示,gyrB和recA基因座存在显著的重组,而其他基因座没有检测到显著的重组。
3.220株分离株6个看家基因的合并序列组成了35个独特的多位点序列类型(ST)。其中,15个ST的分离株来源于采样地A,27个ST的分离株来源于采样地B,7个ST的分离株来源于A、B两地。其中,ST21含有最多的细菌,共有53株分离株,占所有分离株的24.1%,其次是ST15,共有36株分离株,占所有分离株的16.4%。
4.参比接种菌中,USDA136和USDA122拥有相同的ST,归入到ST4。而532C、USDA138和B. japonicum USDA6T也拥有同样的ST,归入到ST24。只有很少一部分分离株被鉴定为推定接种菌。其中,采样地A只获得了一株推定接种菌；采样地B中31%的分离株被鉴定为推定接种菌。采样地A、B均未获得与接种菌61A124相关的分离株。
5.多位点序列分析及微进化分析结果表明,与大豆共生的Bradyrhizobium群体高度结构化,并呈现出遗传多样性。所有的分析都支持将220株分离株分入5个系统分支,分别对应于是B.japonicum group1、 B.japonicum group1a以及Bradyrhizobium属内3个新的系统分支。
6. STRUCTURE分析显示,220株分离株起源于5个Ancestral Lineage。 Lineage I中的分离株全部来自采样地B,而Lineage III中的菌株全部来自采样地A,并且这两个Lineage中菌株的遗传物质都是100%来自各自的Ancestral Lineage,这为分离株的空间分布提供了有力的证据。20株分离株(分别来自Lineage Ⅱ、 Ⅳ、Ⅴ)呈现山不同程度的混合祖先,这表明Lineage (?)发生了基因漂流,但不频繁。被鉴定为推定接种菌的这些ST中,只有有ST24(532C)展现出了混合祖先,遗传物质分别来自Ancestral Lineage Ⅱ、Ⅲ、ⅠV和V,并且ST24是唯一一个来自采样地B且继承有Ancestral LineageIII遗传物质的ST。
7.一致网络图显示,220株分离株被分入了5个清晰地类群,这和STRUCTURE推断的5个Lineage完全一致。对应于LineageⅠ、Ⅱ和Ⅲ的3个类群中没有任何标准菌株,位于独立的系统分支上,表明它们是Bradyrhizobium属内新的演化谱系。 LineageⅣ和Ⅴ中观察到了中度复杂的网状结构,它们的存在及复杂程度反映了系统发育不确定性的程度,同时也暗示了重组的存在。
8. ClonalFrame分析发现,重组对系统发育的推断有显著影响。共鉴定了21个重组事件,其中,12个重组事件发生在gyrB基因座上。代表内部节点的祖先推断中,没有一个推定接种菌被鉴定为外部节点的最近祖先。所有Lineages的重组与突变比值的比率(p／0)是0.05,这表明发生重组的频率是发生突变的频率的二十分之一；重组相对于突变的作用(r／m)的值是0.59,说明突变大约2倍于重组引起核苷酸替换。 LineageⅡ的外部分支与内部分支长度比率高于预期值,说明该lineage最近经历了一次群体扩大。
9. Unifrac分析显示,Lineage间分离株频率的差异存在于采样地间(P<=0.01)和栽培种间(P<=0.01)。代表Lineage的分离株和代表单个ST的分离株在采样地间及大豆栽培种间的频率也有显著差异。这些都为群体的空间结构提供了证据。10.共生基因nodC序列由7个等位基因类型组成,遗传多样性(π)为0.0167,GC含量为57.3%；dN/dS平均值为0.076,说明该基因正处于稳定或净化选择;phi检验没有检测到显著的重组。一致网络图中nodC序列分入了2个明显区分的群：nod I和nod II,并且几乎没有明显的网状结构,说明nodC基因座的重组很少见。Chi-square检验结果显示,nod I中分离株的频率在采样地间存在显著差异,而nod II中分离株的频率在采样地间不显著。nod I和nod II中分离株的频率在栽培种间都没有显著差异。
11.供试菌株间的固氮有效性存在相当大的差异。一些推定接种菌的固氮效率很低,这说明这些分离株正经历固氮基因的遗传变化或它们本来就存在于土壤中,只是碰巧与接种菌拥有同样的多位点基因型(ST)。
Soybean (Glycine max) is the most important grain legume on a production basis in the world and is a major source of oil and protein. The genus Bradyrhizobium includes species of economically important soil bacteria that fix atmospheric nitrogen in symbiotic association with soybeans and thereby minimize the requirement for nitrogen fertilizer inputs in crop production. Populations of Bradyrhizobium were widely studied for its valuable genetic resources and economic values of soybean. Canada represents the northern-most limit for soybean cultivation and ranks as the world's seventh largest producer. Despite the importance of soybeans to Canada, no information is available on the genetic resource represented by populations of symbiotic Bradyrhizobium associated with this legume with regard to their diversity, dynamics, structure or micro-evolutionary history. The research on biodiversity of Bradyrhizobium will benefit exploitation of new Rhizobium resources and novel gene resources for the sustainable agricultural production, provide further insight into taxonomy and evolutionary relationship within Bradyrhizobium genus and assist in selection of bacteria with desirable traits as inoculants for soybean production.
This study presented a systematic investigation of Bradyrhizobium populations that were isolated from two field sites (A and B, about280km apart in Eastern Canada) with contrasting histories of Bradyrhizobium inoculation and soybean cultivation. The results are listed below.
1. A collection of symbiotic bacteria (220isolates) was made by plant trap. At the same time, we assembled a reference collection of Bradyrhizobium strains known to have been used in inoculants for soybeans in Canada. All isolates were slow growing on YEM agar (colony diameter＜1mm after7to14days at28℃) and elicited nodules on soybeans.
2. Fragments of6housekeeping genes were obtained by PCR amplifications and sequenced. The length of individual gene sequences ranged from369bp (dnaK) to771bp (rpoB). The genetic diversity (π) of individual loci ranged from0.0251(atpD) to0.0338(recA) with the number of allelic types ranging from9(dnaK) to17(rpoB). The mean values of dN/dS were all＜1indicating that these loci were subject to stabilizing or purifying selection. The phi test on sequences of individual loci detected significant recombination at gyrB and recA loci, but not at the remaining loci.
3. The concatenated sequences (six housekeeping genes) of220isolates were classified into35unique STs. Isolates representing totals of15and27STs were recovered from sites A and B whereas isolates of7STs were common to both sites. Isolates of ST21(53isolates) was most abundant and accounted for24.1%of all isolates. Isolates of ST15(36isolates) accounted for16.4%of the isolates.
4. Among reference strains, USD A136was found to have the same multilocus genotype (ST4) as USDA122;532C and USDA138also have an identical multilocus genotype (ST24) to B. japonicum USDA6T. A minority of all isolates were identified as putative inoculant strains. At site A, only one isolate was a putative inoculant strain. At site B, about31%of the isolates were putative inoculant strains. Isolates corresponding to reference inoculant strain61A124were not recovered at either site.
5. Multilocus sequence typing and microevolutionary analyses indicated that the Bradyrhizobium populations associated with soybeans were highly structured and genetically diverse. All analyses supported the division of220isolates into five lineages corresponding either to B. japonicum groups1and1a or to one of three novel lineages within the genus Bradyrhizobium.
6. STRUCTURE analysis indicated that220isolates originated from five ancestral lineages. Evidence for spatial structuring was provided by lineage Ⅰ and Ⅲ isolates that were encountered only at one of two sites and had100%of their genetic material derived from the respective ancestral lineage.20isolates in lineages Ⅱ, Ⅳ and Ⅴ showed evidence of mixed ancestry indicating that inter-lineage gene flow had infrequently taken place. Of these STs identified as putative inoculant strains, only ST24(532C) exhibited mixed ancestry with genetic material inherited from ancestral lineages Ⅱ, Ⅲ, Ⅳ and Ⅴ. ST24was the only ST from site B to possess genetic material derived from ancestral lineage III.
7. The network graph showed well defined clusters of isolates corresponding to the five lineages inferred by STRUCTURE. Clusters corresponding to lineages Ⅰ, Ⅱ and have no type strain indicating that they are novel evolutionary lineages within the genus Bradyrhizobium. Moderate reticulation was evident in Lineage Ⅳ and Ⅴ. Reticulation reflects extent of phylogenetic uncertainty and indicates recombination.
8. ClonalFrame analysis indicated that recombination has significant effect on phylogenetic inference. A total of21recombination events were found and twelve events were found at the gyrB locus. Analyses were done to infer ancestors representing internal nodes and did not identify any putative inoculant strains as MRCAs of external nodes. The ratio of rates of recombination relative to mutation (ρ/θ) for all five lineages was0.05indicating that recombination was about twenty times less frequent than mutation. The effect of recombination relative to mutation (r/m) was0.59indicating that recombination introduced almost two times fewer substitutions than mutation. Lineage Ⅱ may have been subject to a recent expansion in population size based on external to internal branch length ratio tests.
9. Unifrac analysis showed that there were overall differences in the frequency of lineages between sites A and B (P＜=0.01) and between cultivars M and O (P＜=0.01). It was also found that significant differences in frequencies of isolate representing lineages and individual STs between field sites and soybean cultivars. All data indicated spatial structuring of the populations.
10. Sequences of the symbiotic nodC gene were divided into7allelic types with genetic diversity (π) of0.0167and GC content of57.3%; the mean value of dnlds was0.076suggesting that this gene is subject to stabilizing or purifying selection. The phi test did not detect significant recombination at the nodC locus. nodC sequences were placed in two well defined groups (nod Ⅰ and nod Ⅱ) in the consensus network. It was almost complete absence of reticulation, suggesting that recombination was rare at the nodC locus. Chi-square tests of independence indicate that the frequency of nod Ⅰ isolates differed between sites whereas the relative frequencies of nod Ⅱ isolates group were not significantly different. The frequency of isolates representing nod Ⅰ and nod Ⅱ groups did not differ significantly between soybean cultivars.
11. Relative effectiveness test showed that there was considerable variation in the effectiveness of isolates tested. Several putative inoculant strains were poorly effective in nitrogen-fixation suggesting that these isolates may have undergone genetic exchange of nitrogen fixation genes or were soil residents that co-incidentally possessed the same multilocus genotype (ST) as an inoculant.
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