紫花苜蓿内生和非内生根瘤菌多样性及共生差异

【背景】对根瘤菌多样性的研究有助于推进根瘤菌种质资源的利用。【目的】研究紫花苜蓿内生和非内生根瘤菌的表型和遗传多样性,比较菌株在5个苜蓿品种上的共生效应,验证根瘤菌群体共生效应由苜蓿品种决定的假设。【方法】从甘肃省白银会宁旱作区、兰州安宁灌区、武威凉州灌区3个栽培区域的陇中、清水、WL168HQ、甘农3号、甘农9号等紫花苜蓿品种中分离内生(植株种子、花、叶、茎、根表皮、根中柱和根瘤)和非内生(根际土壤和田间土壤)根瘤菌菌株,通过表型数值分类、 16SrRNA基因限制性片段长度多态性(Restrictionfragmentlengthpolymorphism,RFLP)、16S rRNA基因测序、持家基因多位点序列分型(Multilocus sequence typing,MLST),以及结瘤基因nodC和固氮基因nifH片段序列测定,研究紫花苜蓿根瘤菌的表型和遗传多样性,并采用主成分分析研究根瘤菌菌株在5个紫花苜蓿品种上的共生效应差异。【结果】共分离得到43株内生根瘤菌和10株非内生根瘤菌,叶片和花中没有分离到根瘤菌菌株。53株根瘤菌以及对照菌株R.GN5和S.12531表型特征数值分类聚为8个群,菌株表型多样性丰富。经16SrRNA-RFLP分析共形成22种RFLP分型组合,基因型Ⅰ分布最广泛(24),其次为基因型Ⅻ(5)、ⅩⅤ(5)和ⅩⅨ(3),其余16株菌各代表1种基因型,菌株遗传多样性丰富。16S rRNA基因测序和MLST分析将所有菌株划分为Rhizobiumradiobacter、R.rosettiformans和Ensifermeliloti。仅从7株E.meliloti代表菌株和对照菌株S.12531中扩增到nodC和nifH基因,说明E.meliloti菌株均能结瘤固氮。E.meliloti菌株G3L3接种甘农3号,LP3、LL1和LL2接种陇中,QL2接种清水,LL1、LL2和WLP2接种WL169HQ苜蓿均能显著促进植株的单株结瘤数、地上干重和粗蛋白含量。E.meliloti菌株接种甘农3号、甘农9号和清水苜蓿品种后所有参数值在PC1轴上分别聚在-1-1之间,在PC3轴上聚在-1.5-1.5之间;接种陇中和WL168HQ苜蓿的参数值较分散,PC1轴上分散在-1.5-4之间,PC3轴上分散在-3-4之间。【结论】紫花苜蓿内生和非内生根瘤菌菌株多样性丰富,表型和遗传多样性与其来源没有直接关系。菌株G3L3与甘农3号,LP3、LL1、LL2与陇中,QL2与清水、LL1、LL2、WLP2与WL169HQ苜蓿品种共生匹配和适应能力强。在甘农3号、甘农9号和清水紫花苜蓿品种上群体共生效应相似,在陇中和WL168HQ紫花苜蓿上共生效应差异明显。本研究内生和非内生根瘤菌菌株的群体共生效应根据苜蓿品种而定,根瘤菌菌株与苜蓿品种间的信号识别程度存在差异。     

毛乌素沙地中间锦鸡儿根瘤菌遗传多样性及16S rDNA全序列分析

野生豆科植物中间锦鸡儿是毛乌素沙地的优势种。从蛋白质和DNA水平分析与其共生的根瘤茵的遗传多样性。在蛋白质水平上,24株中间锦鸡儿根瘤菌和9株参比菌株分为2组,A组包含95．8％供试中间锦鸡儿根瘤菌,参比菌株聚为B组,菌株GH72不与其余供试根瘤菌聚类。应用16S　rDNA　PCR—RFLP方法将供试菌株分为22种基因型,中间锦鸡儿根瘤菌组成12种,其余10种由参比菌株构成。表明中间锦鸡儿根瘤菌具高水平遗传多样性。选取代表菌株GH2001进行16S　rDNA全序列测定。与已知相关根瘤菌菌株16S　rDNA进行同源性比较,构建系统发育树状图。GH2001位于Rhizobium分支,与且Agrobacterium radiobacter,Ag.rubi,Rhizobium giardinii,R.mongolense,R.yanglingense,R.galegae和R.huautlense的序列同源性分别达到99％、98．3％、96．3％、95．5％、95．6％、95．27％和95．7％。     

江汉平原及其周边地区花生根瘤菌的遗传多样性

采用RAPD分析技术和16S－23S rRNA间隔区段（IGS）RFLP分析,分别对分离自江汉平原及其周缘地区的花生根瘤菌进行了遗传多样性和系统发育研究。结果表明,全部供试验菌分别在48％和50％的相似性水平分为Ⅰ、Ⅱ两群,供试花生根瘤菌与参比菌株B.japonicum和B.elkanii聚在群I,参比菌株Rhizobium Sinorhizobium,Mesorhizobium和Agrobacterium聚在群Ⅱ。供试花生根瘤菌的遗传多样性及其在系统发育中的地位主要受地域因素的影响,来自江汉平原中心地带天门和潜江的菌株在76％以上的相似性水平上聚在一起,处于周边地带的武汉和荆州,由于其特定的地理因素的影响。菌株的多样性更为丰富,部分菌株在分类上与其它地域的菌株相互融合,并在较高的相似水平存在一定摆动性,来自外缘随州的菌株,表现了明显的地理分隔作用,其在系统演化中的地位相对独立,总体上从平原腹地到外缘地区。根瘤菌地理分隔作用逐渐明显,在平原外缘的交接地带,根瘤菌的多样性最为丰富。     

花生根瘤菌群体遗传多样性和系统发育研究

利用16S rRNA RFLP,16S rRNA序列分析和16S－23S IGS PCR RFLP技术对43株花生根瘤菌和来自其他种属的15个参比菌株进行了群体遗传多样性和系统分析。16S rRNA PCR RFLP分析结果表明,所有供试花生根瘤菌均属于慢生根瘤菌属,在系统发育上与B.japonicum的亲缘关系最近,具有相同的16S rRNA RFLP基因型,而与B.elkanii相对较远。16S rRNA 序列分析结果表明,供试花生根瘤菌在系统发育上更接近于B.liaoningense,序列间差异小于1％,而B.liaoningense在系统发育上与B.japonicum相距很近,其序列间差异小于1％,16S－23S rRNA IGS RFLP分析结果表明,尽管花生根瘤菌与B.japonicum和B.elkanii的亲缘关系很近,但在71％的相似性水平上供试花生根瘤菌仍各自聚为一群,并可进一步分为A、B、C和D4个亚群,该分群还明显反映了地理因素对群体遗传多样性和系统发育的影响。     

黄土高原地区大豆根瘤菌的遗传多样性和系统发育

【目的】研究黄土高原地区大豆根瘤菌的遗传多样性和系统发育。【方法】采用BOX-PCR、16S rDNAPCR-RFLP、16S-23S IGS PCR-RFLP和16S rRNA基因序列分析方法对分离自我国黄土高原地区4个省的15个地区的130株大豆根瘤菌及部分参比菌株进行了遗传多样性和系统发育分析。【结果】BOX-PCR反映的菌株多样性最丰富,形成的遗传群最多,16S rDNA PCR-RFLP方法在属、种水平上聚群较好,16S-23S IGSPCR RFLP反映的多样性介于BOX-PCR和16S rDNA PCR-RFLP之间,能够较好地反映出属、种和亲缘关系很近的菌株间的差异,3种方法聚类分析结果基本一致,可将所有供试菌株分为两大类群,中华根瘤菌属(Sinorhizobium)和慢生根瘤菌属(Bradyrhizobium)。从系统发育来看,供试的快生大豆根瘤菌为费氏中华根瘤菌(Sinorhizobium fredii),慢生大豆根瘤菌为日本慢生大豆根瘤菌(Bradyrhizobium japonicum)和辽宁慢生根瘤菌(Bradyrhizobium liaoningense)。【结论】我国黄土高原地区大豆根瘤菌具有较丰富的遗传多样性,S.fredii优势种,慢生大豆根瘤菌仅占10%,同时,分离到2株B.liaoningense。     

华北及西北地区岩黄芪根瘤菌的表型及遗传多样性

选用分离自河北、内蒙古等5省区的岩黄芪根瘤菌30株及17株已知参比菌株,进行了营养利用、抗生素抗性、耐逆性及生理生化反应等12 5项表型性状研究,所得数值分类树状图表明不同宿主及不同地域的岩黄芪根瘤菌的表型多样性。通过对其中部分菌株进行16 S r DNA PCR- RFL P及BOX- PCR指纹图谱分析,聚类结果表明供试岩黄芪根瘤菌具有遗传多样性。     

陕西太白尾矿废弃地豆科植物根瘤菌16S rDNA PCR-RFLP及全序列分析

应用16S rDNA-RFLP和16S rDNA全序列测定方法,对分离自陕西太白金矿尾矿废弃地的55株根瘤菌和12株参比菌株进行了遗传多样性和系统发育地位研究。采用平均连锁法(UPMGA)对16S rDNA PCR-RFLP聚类,结果显示所有菌株在72%的水平上聚到一起。根据参比菌株的种属关系,将供试菌株初步分成6个遗传发育群。群Ⅰ为根瘤菌属,群Ⅱ为中华根瘤菌属,群Ⅲ是中慢生根瘤菌属,群Ⅳ为土壤杆菌属,群V为一未知群,群Ⅵ为慢生根瘤菌属。分离自天蓝苜蓿的根瘤菌主要分布在群Ⅱ,截叶胡枝子根瘤菌在各个群内均有分布,表现出丰富的遗传多样性。选取群Ⅰ、Ⅱ的代表菌株TB17-1、TB50-1进行16S rDNA全序列测定分析,结果显示TB17-1与Rhizonbium leguminosarumUSDA2370的同源性高达99.7%,TB50-1与Sinorhizobium melilotiLMG6133的同源性为100%。全序列测定结果与RFLP分析结果基本一致。     

商洛多花胡枝子根瘤菌16S rDNA-RFLP分析及系统发育研究

利用16S rDNA-RFLP和全序列测定方法,对分离自商洛地区5个分布点的59株多花胡枝子根瘤菌进行了RFLP分析和系统发育研究.结果表明:(1)42株供试菌株归属根瘤菌属(Rhizobium)、11株归属中华根瘤菌属(Sinorhizobium).其余6株非根瘤菌中3株是嗜麦芽黄单胞菌(Stenotrophomonas maltophilia)、3株是解淀粉类芽孢杆菌(Paenibacillus amylolyticus),说明胡枝子根瘤内生菌较为丰富且类型多样.(2)结合供试菌株的地理生境分析,发现来自不同采集点的菌株有些具有同样的遗传类型,而来自同一采集点的菌株遗传类型却有差异,证明胡枝子根瘤菌在分群类别上与地理环境之间没有明确的对应关系,地理环境并非根瘤菌多样性形成的主要因素.建议今后对根瘤菌多样性研究应从根瘤菌与寄主植物物之间的共生选择进化,特别是对共生体系中基因的横向转移方面进行深入探讨.     

安徽地区大豆根瘤菌遗传多样性研究

采用RAPD技术对分离自安徽地区的大豆根瘤菌和部分参比菌株进行了遗传多样性和系统发育研究.结果表明:来自山东即墨、宿州灵壁、凤阳小溪河和六安金寨的菌株归为慢生型根瘤菌、来自安庆宿松、凤阳中都城、巢湖含山、滁州天长、淮北杜集、蚌埠淮上的菌株归为S.xinjiangensis,来自滁州全椒和风阳韭山洞的菌株是与花生根瘤菌和苜蓿根瘤菌更接近的快生型根瘤菌.而1株来自巢湖庐江的大豆根瘤菌和其它菌株的遗传距离较远,单独归为一类,其遗传地位特殊.     

斜茎黄芪根瘤菌结瘤基因nodA PCR扩增及PCR-RFLP分析

对采自我国北方地区的16株斜茎黄芪根瘤菌代表菌株的共同结瘤基因nodA进行了PCR扩增及PCR-RFLP分析研究。来自Mesorhizobium和Rhizobium系统发育分支的代表菌株都得到了nodA PCR扩增产物;而来自Agrobacterium系统发育分支的代表菌株都没有得到nodA PCR扩增产物。进一步的nodAPCR-RFLP分析结果表明斜茎黄芪根瘤菌具有很大的nodA基因遗传多样性,具有4种不同的16S rDNAPCR-RFLP遗传图谱类型的12株斜茎黄芪根瘤菌具有8种不同的nodA PCR-RFLP遗传图谱类型。但是斜茎黄芪根瘤菌nodA基因遗传多样性随种群而变化,来自M.septentrionale的具有相同的16S rDNA PCR-RFLP遗传图谱类型的4个代表菌株具有4种不同的nodA PCR-RFLP遗传图谱类型;而来自M.tempera-tum的具有相同的16S rDNA PCR-RFLP遗传图谱类型3个代表菌株则具有相同的nodA PCR-RFLP遗传图谱类型。此外,来自不同种的具有不同16S rDNA PCR-RFLP遗传图谱类型的菌株却具有相同的nodA PCR-RFLP遗传图谱类型,说明nodA基因可能在根瘤菌的不同种间发生了水平转移。     

Identification and cloning of the bacterial nodulation specificity gene in the Sinorhizobium meliloti--Medicago laciniata symbiosis

Medicago laciniata (cut-leaf medic) is an annual medic that is highly nodulation specific, nodulating only with a restricted range of Sinorhizobium meliloti. e.g., strain 102L4, but not with most strains that nodulate Medicago sativa (alfalfa), e.g., strains RCR2011 and Rm41. Our aim was to identify and clone the S. meliloti 102L4 gene implicated in the specific nodulation of M. laciniata and to characterize the adjacent nodulation (nod) region. An 11-kb EcoRI DNA fragment from S. meliloti 102L4 was shown to complement strain RCR2011 for nodulation of M. laciniata. Nucleotide sequencing revealed that this fragment contained nodABCIJ genes whose overall arrangement was similar to those found in strains RCR2011 and Rm41, which do not nodulate M. laciniata. Data for Tn5 mutagenesis of the nodABCIJ region of strain 102L4 suggested that the nodC gene was involved in the specific nodulation of M. laciniata. Tn5 insertions in the nodIJ genes gave mutants with nodulation delay phenotypes on both M. laciniata and M. sativa. Only subclones of the 11-kb DNA fragment containing a functional nodC gene from strain 102L4 were able to complement strain RCR2011 for nodulation of M. laciniata. The practical implications of these findings are discussed in the context of the development of a specific M. sativa - S. meliloti combination that excludes competition for nodulation by bacterial competitors resident in soil.     

Nitrogen-fixing sinorhizobia with Medicago laciniata constitute a novel biovar (bv. medicaginis) of S. meliloti

Sixty-eight new rhizobial isolates were obtained from root-nodules of Medicago laciniata and from Mediterranean soils in Tunisia and France. All of them were identified as Sinorhizobium meliloti on the basis of PCR-RFLP analyses of 16S rDNA and the intergenic spacer sequence between 16S and 23S rDNAs. DNA/DNA hybridization, phenotypic characterization and 16S rRNA gene sequencing led to the conclusion that they belong the same taxon. All new isolates shared the ability to nodulate and fix nitrogen with M. laciniata except 11 of them not capable of fixing nitrogen with this plant and originating from French soils containing no efficiently adapted symbionts with M. laciniata. The nitrogen-fixing rhizobia on M. laciniata differed markedly from the other S. meliloti or Sinorhizobium medicae isolates and references in their symbiotic traits such as nifDK RFLP diversity, nodA sequences and nitrogen effectiveness with tree other different annual Medicago species (M. truncatula, M. polymorpha and M. sauvagei). Two infrasubspecific (biovar) divisions are therefore proposed within S. meliloti: bv. medicaginis for Sinorhizobium efficient on M. laciniata and bv. meliloti for the classically known S. meliloti group represented by the strains ATCC9930(T) and RCR 2011 efficient on M. sativa.     

Effect of primers hybridizing to different evolutionarily conserved regions of the small-subunit rRNA gene in PCR-based microbial community analyses and genetic profiling

Genetic profiling techniques of microbial communities based on PCR-amplified signature genes, such as denaturing gradient gel electrophoresis or single-strand-conformation polymorphism (SSCP) analysis, are normally done with PCR products of less than 500-bp. The most common target for diversity analysis, the small-subunit rRNA genes, however, are larger, and thus, only partial sequences can be analyzed. Here, we compared the results obtained by PCR targeting different variable (V) regions (V2 and V3, V4 and V5, and V6 to V8) of the bacterial 16S rRNA gene with primers hybridizing to evolutionarily conserved flanking regions. SSCP analysis of single-stranded PCR products generated from 13 different bacterial species showed fewer bands with products containing V4-V5 (average, 1.7 bands per organism) than with V2-V3 (2.2 bands) and V6-V8 (2.3 bands). We found that the additional bands (>1 per organism) were caused by intraspecies operon heterogeneities or by more than one conformation of the same sequence. Community profiles, generated by PCR-SSCP from bacterial-cell consortia extracted from rhizospheres of field-grown maize (Zea mays), were analyzed by cloning and sequencing of the dominant bands. A total of 48 sequences could be attributed to 34 different strains from 10 taxonomical groups. Independent of the primer pairs, we found proteobacteria (alpha, beta, and gamma subgroups) and members of the genus Paenibacillus (low G+C gram-positive) to be the dominant organisms. Other groups, however, were only detected with single primer pairs. This study gives an example of how much the selection of different variable regions combined with different specificities of the flanking "universal" primers can affect a PCR-based microbial community analysis.     

Effect of Primers Hybridizing to Different Evolutionarily Conserved Regions of the Small-Subunit rRNA Gene in PCR-Based Microbial Community Analyses and Genetic Profiling

Genetic profiling techniques of microbial communities based on PCR-amplified signature genes, such as denaturing gradient gel electrophoresis or single-strand-conformation polymorphism (SSCP) analysis, are normally done with PCR products of less than 500-bp. The most common target for diversity analysis, the small-subunit rRNA genes, however, are larger, and thus, only partial sequences can be analyzed. Here, we compared the results obtained by PCR targeting different variable (V) regions (V2 and V3, V4 and V5, and V6 to V8) of the bacterial 16S rRNA gene with primers hybridizing to evolutionarily conserved flanking regions. SSCP analysis of single-stranded PCR products generated from 13 different bacterial species showed fewer bands with products containing V4-V5 (average, 1.7 bands per organism) than with V2-V3 (2.2 bands) and V6-V8 (2.3 bands). We found that the additional bands (>1 per organism) were caused by intraspecies operon heterogeneities or by more than one conformation of the same sequence. Community profiles, generated by PCR-SSCP from bacterial-cell consortia extracted from rhizospheres of field-grown maize (Zea mays), were analyzed by cloning and sequencing of the dominant bands. A total of 48 sequences could be attributed to 34 different strains from 10 taxonomical groups. Independent of the primer pairs, we found proteobacteria (α, β, and γ subgroups) and members of the genus Paenibacillus (low G+C gram-positive) to be the dominant organisms. Other groups, however, were only detected with single primer pairs. This study gives an example of how much the selection of different variable regions combined with different specificities of the flanking “universal” primers can affect a PCR-based microbial community analysis.     

Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes

Operational taxonomic units (OTUs) are conventionally defined at a phylogenetic distance (0.03—species, 0.05—genus, 0.10—family) based on full-length 16S rRNA gene sequences. However, partial sequences (700 bp or shorter) have been used in most studies. This discord may affect analysis of diversity and species richness because sequence divergence is not distributed evenly along the 16S rRNA gene. In this study, we compared a set each of bacterial and archaeal 16S rRNA gene sequences of nearly full length with multiple sets of different partial 16S rRNA gene sequences derived therefrom (approximately 440-700 bp), at conventional and alternative distance levels. Our objective was to identify partial sequence region(s) and distance level(s) that allow more accurate phylogenetic analysis of partial 16S rRNA genes. Our results showed that no partial sequence region could estimate OTU richness or define OTUs as reliably as nearly full-length genes. However, the V1-V4 regions can provide more accurate estimates than others. For analysis of archaea, we recommend the V1-V3 and the V4-V7 regions and clustering of species-level OTUs at 0.03 and 0.02 distances, respectively. For analysis of bacteria, the V1-V3 and the V1-V4 regions should be targeted, with species-level OTUs being clustered at 0.04 distance in both cases.     

Concurrent evolution of human immunodeficiency virus type 1 in patients infected from the same source: rate of sequence change and low frequency of inactivating mutations.

Direct sequencing of segments of the envelope gene of human immunodeficiency virus type 1 proviruses in peripheral blood mononuclear cells has revealed that a cohort of hemophiliacs who were infected after exposure to a single common batch of factor VIII share closely related virus strains. Seventy-four sequences extending from hypervariable regions V4 through V5 from nine patients yielded a mean intrapatient nucleotide distance of 5.5%, while a mean of 4.2% was observed in 39 sequences of the V3 loop (six patients). Phylogenetic analysis revealed that sequences of six Edinburgh patients were particularly closely related and those from a patient infected in the United States were very distinct. The mean nucleotide distance among these six was 8.3%, while the mean distance from the U.S.-derived sequences was 25.5% in the V4-V5 region. The rate of sequence change across this patient group has been estimated to be 0.4% per year in the V4-V5 region and 0.5% per year in the V3 region, with at least a twofold range across patients. Only two inactivating nucleotide substitutions have been observed in a total of 42 kb of sequence obtained from the env and gag genes during this study.     

Comparison of nucleotide diversity and symbiotic properties of Rhizobium meliloti populations from annual Medicago species

Abstract: Forty-three isolates of Rhizobium meliloti were trapped from soil with five annual species of Medicago (M. polymorpha, M. truncatula, M. rigidula, M. orbicularis and M. minima ) and one perennial species of Medicago (M. sativa) . The annual species were growing naturally near the soil sampling site, and the commonly studied perennial species was used for comparison. Each R. meliloti was characterized by PCR-RFLP methods applied to two DNA regions nested between 16S rRNA and 23S rRNA genes and between nif D and nif K genes. They fell into two highly divergent groups (groups I and II), separated at a genetic distance of 0.024 by rDNA-amplified pattern analysis (profiles R1 and R2) and at 0.029 by nif -amplified pattern analysis (profiles N1-N2 and N3). These two groups were consistent with some cross-nodulation and -fixation results: rhizobia with the R1 genetic background elicited rudimentary nodules and could not fix nitrogen on M. polymorpha , while they were able to nodulate the five other species of Medicago . In contrast, rhizobia with an R2 profile were highly effective on M. polymorpha and poorly nodulated M. rigidula species, but were able to nodulate efficiently the other species. The striking phenotypic traits on M. polymorpha were also shared by reference strains: strains genetically closed to R2 type triggered typical and efficient nodules on M. polymorpha while those close to R1 type elicited rudimentary and non-efficient ones. Our results suggest that the presence of R. meliloti with R2 genetic backgrounds could be favoured by the distribution of M. polymorpha species.     

A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria

Bacterial 16S ribosomal RNA (rRNA) genes contain nine "hypervariable regions" (V1-V9) that demonstrate considerable sequence diversity among different bacteria. Species-specific sequences within a given hypervariable region constitute useful targets for diagnostic assays and other scientific investigations. No single region can differentiate among all bacteria; therefore, systematic studies that compare the relative advantage of each region for specific diagnostic goals are needed. We characterized V1-V8 in 110 different bacterial species including common blood borne pathogens, CDC-defined select agents and environmental microflora. Sequence similarity dendrograms were created for hypervariable regions V1-V8, and for selected combinations of regions or short segments within individual hypervariable regions that might be appropriate for DNA probing and real-time PCR. We determined that V1 best differentiated among Staphylococcus aureus and coagulase negative Staphylococcus sp. V2 and V3 were most suitable for distinguishing all bacterial species to the genus level except for closely related enterobacteriaceae. V2 best distinguished among Mycobacterium species and V3 among Haemophilus species. The 58 nucleotides-long V6 could distinguish among most bacterial species except enterobacteriaceae. V6 was also noteworthy for being able to differentiate among all CDC-defined select agents including Bacillus anthracis, which differed from B. cereus by a single polymorphism. V4, V5, V7 and V8 were less useful targets for genus or species-specific probes. The hypervariable sequence-specific dendrograms and the "MEGALIGN" files provided online will be highly useful tools for designing specific probes and primers for molecular assays to detect pathogenic bacteria, including select agents.     

Comparative analysis of the intergenic spacer regions and population structure of the species complex of the pathogenic yeast Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic basidiomycete responsible for the high incidence of cryptococcosis in patients with AIDS and in other immune-compromised individuals. This study, which focused on the molecular structure and genetic variability of the two varieties in the C. neoformans and Cryptococcus gattii species complex, employed sequence analysis of the intergenic spacer regions, IGSI and IGSII. The IGS region is the most rapidly evolving region of the rDNA families. The IGSI displayed the most genetic variability represented by nucleotide base substitutions and the presence of long insertions/deletions (indels). In contrast, the IGSII region exhibited less heterogeneity and the indels were not as extensive as those displayed in the IGSI region. Both intergenic spacers contained short, interspersed repeat motifs, which can be related to length polymorphisms observed between sequences. Phylogenetic analysis undertaken in the IGSI, IGSII and IGSI +5S rRNA + IGSII regions revealed the presence of six major phylogenetic lineages, some of which segregated into subgroups. The major lineages are represented by genotypes 1 (C. neoformans var. grubii), genotype 2 (C. neoformans var. neoformans), and genotypes 3, 4, 5 and 6 represented by C. gattii. Genotype 6 is a newly described IGS genotypic group within the C. neoformans species complex. With the inclusion of IGS subgenotypic groups, our sequence analysis distinguished 12 different lineages. Sequencing of clones, which was performed to determine the presence of multiple alleles at the IGS locus in several hybrid strains, yielded a single IGS sequence type per isolate, thus suggesting that the selected group of cloned strains was mono-allelic at this locus. IGS sequence analyses proved to be a powerful technique for the delineation of the varieties of C. neoformans and C. gattii at genotypic and subgenotypic levels.     

Genetic structure of natural populations of the nitrogen-fixing bacterium Rhizobium meliloti.

The genetic structure of populations of the symbiotic nitrogen-fixing soil bacterium Rhizobium meliloti was examined by analysis of electrophoretically demonstrable allelic variation in 14 metabolic, presumably chromosomal, enzyme genes. A total of 232 strains were examined, most of which were isolated from southwest Asia, where there is an unsurpassed number of indigenous host species for R. meliloti. The collection consisted of 115 isolates recovered from annual species of Medicago in Syria, Turkey, and Jordan; 85 isolates cultured from two perennial species of Medicago (M. sativa [alfalfa] and M. falcata) in northern Pakistan and Nepal; and 32 isolates collected at various localities in North and South America, Europe, South Africa, New Zealand, and Australia, largely from M. sativa. Fifty distinctive multilocus genotypes (electrophoretic types [ETs]) were identified, and cluster analysis revealed two primary phylogenetic divisions separated at a genetic distance of 0.83. By the criterion of genetic differentiation conventionally applied in defining species limits among members of the family Enterobacteriaceae and certain other bacteria, the two primary divisions of R. meliloti represent distinct evolutionary species. Division A included 35 ETs represented by 209 strains from the eastern Mediterranean basin, northern Pakistan, Nepal, and various other localities worldwide. This division contained the nine commercial alfalfa inoculant strains examined. Division B included 15 ETs represented by 23 isolates, 21 of which were isolated from annual medic species growing in previously uninoculated soils in the eastern Mediterranean basin. The two remaining strains in division B, both representing the same ET, were isolated in the United States and Australia.(ABSTRACT TRUNCATED AT 250 WORDS)