Sage Journals: Discover world-class research

Abstract

Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the taxonomy of rhizobia has changed considerably over the last 30 year. Recently, several non-rhizobial species belonging to alpha and beta subgroup of Proteobacteria have been identified as nitrogen-fixing legume symbionts. Here we provide an overview of the history of the rhizobia and the widespread phylogenetic diversity of nitrogen-fixing legume symbionts.

Keywords

rhizobia taxonomy legumes gene-transfer root-nodules rhizobium

Introduction

Members of the Leguminosae, comprising about 19,000 species form the largest plant family on earth and play an important ecological role. Leguminous plants are very diverse in morphology, habitat, and ecology, ranging from Arctic annuals to tropical trees and their importance as food crops worldwide is large. Some 25% of the world's major crop production is derived from legumes, and more than one-third of humanity's nutritional nitrogen requirement comes from legumes. Besides, legumes are very important both ecologically and agriculturally because they are responsible for a substantial part of the global flux of nitrogen from atmospheric N₂ to fixed forms such as ammonia, nitrate, and organic nitrogen.

They probably evolved approximately 60 million years ago (Ma), early in the Tertiary period and their evolutionary success can be largely attributed to their ability to form symbiosis with specific bacteria known as rhizobia. The symbiotic relationship between nitrogen-fixing rhizobia and legume plants has been studied for over 100 years as a classic example of mutualistic associations. Rhizobia or sometimes Rhizobium is the general name given to a phylogenetically diverse group of soil bacteria that form nitrogenfixing symbioses with leguminous plants. These bacteria are environmental heterotrophs with great metabolic plasticity that may survive in many different environments, sometimes unassociated with plant hosts but they have significant interest because of their ability to form symbiotic associations with legumes and are able to elicit symbiotic association on the species of Leguminosae, forming nodules in roots or stems (Fig. 1).

Figure 1

Typical effective nodules formed by Rhizobium in Phaseolus.

Symbiosis between rhizobia and legumes is the result of millions of years of co-evolution being a process complex and exquisitely regulated that plays an important role because it offers the ability to convert atmospheric molecular nitrogen into forms useable by the plant, a process called biological nitrogen fixation. Whatever the true figure, this symbiosis represents the most important nitrogen input to many ecosystems and is among the most important ecological interactions to humans and ecosystems. Currently, the subject of biological nitrogen fixation is of great practical importance because the use of nitrogenous fertilizers has resulted in unacceptable levels of water pollution increasing concentrations of toxic nitrates in drinking water supplies and the eutrophication of lakes and rivers. Over the years, the term “rhizobia” has come to be used for all the bacteria that are capable of nodulation and nitrogen fixation in association with legumes but the rhizobial species described so far are very diverse and do not form an evolutionary homologous clade. In this article, we expose the widespread phylogenetic diversity of nitrogen-fixing legume symbionts and their taxonomic history.

From the Rhizobia Discovery until Bergey's Manual from 1974

The microorganisms able to establish nitrogen fixing symbiosis with legumes were discovered in XIX century, being Frank who firstly named them Rhizobium leguminosarum.¹ Since this date all bacteria able to nodulate legumes are called rhizobia and therefore they were involved in the history of the Bacteriology since the beginning of this science. Frank was contemporary of Ferdinand Cohn who published a bacterial code system for which is considered the father of the bacterial taxonomy, based at that time on the shape and general appearance of bacteria.² After, Orla-Jensen proposed the use of physiological characteristics as basic criterion in bacterial taxonomy.³ In addition to these, other criteria that include microbe interactions with higher organisms were used in some groups such as rhizobia although their taxonomic value was considered of doubtful since the beginning of Bacteriology.⁴

In the beginning of XX century, an American microbiologist, Bergey, initiated the publication named Bergey's Manual⁵ in which the bacteria were classified on basis of their phenotypic characteristics. In the case of rhizobia their classification as Gram negative, aerobic, non-sporulated and motile rods do not allow their differentiation from other soil bacteria with the same phenotypic characteristics. Therefore their ability to induce nodules in legumes was from this date the basic criteria for differentiation of rhizobia and their taxonomy reached lower development than that of other soil related bacteria whose taxonomy was much more developed just due to their inability to form plant nodules.

The Bergey's Manual played a fundamental role in rhizobial taxonomy since it recorded the history of the species of rhizobia from the beginning of the Bacteriology until 1980 in which they were officially validated.⁶ In the Bergey's Manual of Determinative Bacteriology edited in 1974 six species were included in the genus Rhizobium.⁷ Only few phenotypic characteristics of the species of this genus were included and the authors of this chapter indicated that the data about plant infection are essential for species classification.⁷ These characteristics were also essential to differentiate Rhizobium from genus Agrobacterium the second genus included in the family Rhizobiaceae. Whereas Rhizobium contained species nodulating legumes, Agrobacterium included species able to induce different pathogenic symptoms in plants.

The species of genus Rhizobium were divided into two groups containing the fast and slow growing species on YMA medium, respectively.⁸ The fast growing species were R. leguminosarum nodulating Pisum, R. trifolii nodulating Trifolium, R. phaseoli nodulating Phaseolus and R. meliloti nodulating Medicago (Fig. 2). The slow growing bacteria included R. lupini and R. japonicum nodulating Lupinus and Glycine, respectively. In contrast with the genus Rhizobium, the species of the genus Agrobacterium were differentiated on the basis of several phenotypic characteristics since two species of this genus, A. tumefaciens (Fig. 3) and A. rubi produced the same symptoms in plants, tumours. From the other two species of this genus A. rhizogenes produces hairy roots and A. radiobacter is not pathogenic for plants.

Figure 2

Typical effective nodules formed by Ensifer meliloti (formerly Sinorhizobium meliloti, formely Rhizobium meliloti) in Medicago sativa.

Figure 3

Tumours formed by A. tumefaciens in Nicotiana tabaccum.

The only molecular datum included in the 1974 edition of Bergey's Manual was the G + C content of the bacterial species although in the 60's decade techniques as DNA-DNA hybridization for species differentiation was reported in several works after the discovery of DNA renaturation by Marmur.^9–11

Taxonomy of Rhizobia between 1974 and 2000

In 70's decade it was discovered that the symbiosis and pathogenicity genes are harboured in plasmids, in many cases autoconjugative, in both Agrobacterium¹² and Rhizobium.¹³ The symbiotic genes included those involved in nodulation (nod) and nitrogen fixation (nif) and the pathogenicity genes those involved in tumour or hairy roots (vir). The nod genes are responsible for the synthesis of the nod factors (lipochitin-oligosaccharides) that are receptors for the plant favonoid signal.^14–18 The nodD is a regulatory gene of the operon nodABC^19–21 whose genes are determinants of the host range.^22–27 The nifH gene codifies a subunit of the enzyme nitrogenase involved in nitrogen fixation and is carried by rhizobia but also by free-living nitrogen fixers.^28–30

Although, the genes that are easily transferred among species are not useful in taxonomy, when the first edition of Bergey's Manual of Systematic Bacteriology was published in 1984, the symbiotic and pathogenic criteria not only were not eliminated from the rhizobial taxonomy but used to reclassify some species.³¹ This was the case of the species R. phaseoli and R. trifolii that were reclassified into R. leguminosarum and from this moment were considered by rhizobiologists as biovars from R. leguminosarum. Then, the genus Rhizobium contained only three species, the two old species R. leguminosarum and R. meliloti, and a new species named R. loti proposed by Jarvis et al³² to include rhizobia nodulating legumes other than those nodulated by R. leguminosarum and R. meliloti.³¹

It is necessary to take into account that in 1980 was published the valid list of bacterial species by Skerman et al⁶ that included R. leguminosarum, R. phaseoli, R. trifolii and R. meliloti. From this date all species must be described or validated in the International Journal of Systematic Bacteriology (IJSB) being not valid the proposal performed outside this Journal. As the proposal of Jordan in the Bergey's Manual was not validated in IJSB, the species R. phaseoli and R. trifolii were maintained in the list of the valid species. The species Rhizobium lupini disappeared from the Manual but as it was not reclassified in any species and neither was officially rejected it currently remains as valid species.

In the Bergey's Manual from 1984 two new genera were added to family Rhizobiaceae, the genus Bradyrhizobium (Fig. 4) with a single species, B. japonicum, that was originated by the segregation of the slow growing species from genus Rhizobium³³ and the genus Phyllobacterium isolated from plant leaves nodules with two species P. myrsinacearum and P. rubiacearum.³⁴ Whereas the species B. japonicum was described in the IJSB, those of genus Phyllobacterium did not, but were validated in the same year of the Bergey's publication.³⁵

Figure 4

Typical effective nodules formed by Bradyrhizobium in Lupinus albus.

In 1988 a new genus named Azorhizobium able to nodulate stems of Sesbania rostrata in Africa was added to family Rhizobiaceae³⁶ and the species R. fredii, a fast growing species nodulating soyabean, officially described in 1984³⁷ was reclassified into a new genus named Sinorhizobium on basis of phenotypic characteristics³⁸ and 16S rRNA gene sequences.³⁹

From 1984 ahead deep changes in the taxonomy of prokaryotes had been occurred from the Woese's proposal to classify them on basis of their 16S rRNA gene sequences⁴⁰ (Fig. 9). The analysis of this gene allowed the phylogenetic classification of bacteria with independence of their phenotypic or symbiotic characteristics. Nevertheless, during many years the symbiotic characteristics have a dominant role in the rhizobial taxonomy and the 16S rRNA gene was not included in the minimal standards for rhizobial species description until 1991.⁴¹ According to them the cultural and morphological characteristics, the 16S rRNA gene analysis, the hybridization of DNA-DNA or rRNA-DNA, the RFLP and MLEE analysis and the symbiotic characteristics are recommended to describe new species of rhizobia.

From 1984 until 1994, year in which was published the ninth edition of the Bergey's Manual of Determinative Bacteriology, only Bradyrhizobium elkanii, a new slow growing species nodulating soyabean, was described outside IJSB⁴² although was later validated in this journal.⁴³ Since this date a clear dichotomy was produced between Bergey's Manual and IJSB because the species published in IJSB were not completely recorded in the Manual. In this way in the edition of 1994 were included S. xinjiangensis,³⁸ whose name was later corrected as S. xinjiangense, a species nodulating soyabean, and R. galegae, a species nodulating Galega.⁴⁴ However, Agrobacterium vitis inducing tumours in Vitis vinifera⁴⁵ and two species of genus Rhizobium, R. huakuii and R. tropici, nodulating Astragalus and Phaseolus, respectively were not recorded.^46,47

Recent Changes in the Taxonomy of Rhizobia

From Woese's proposal, in the 90's decade and mainly from year 2000 significant changes were produced in the taxonomy of all bacteria since the sequencing of 16S rRNA gene was mandatory for bacterial species description. From this moment, although the nodulation of legumes was not excluded from rhizobial taxonomy, it became a secondary criterion in species description. This was a revolutionary change in rhizobia because the identification of these bacteria was possible with independence of the isolation source.

In the second edition of the Bergey's Manual of Systematic Bacteriology published in 2005 the bacteria were arranged in different phylogenetic groups obtained after the analysis of 16S rRNA gene. The rhizobia were included in the class alpha Proteobacteria and distributed in several families within the new order Rhizobiales belonging to alpha-Proteobacteria.⁴⁸ This new order was not validated in IJSEM because it is not rightful⁴⁹ since includes the genus Hyphomicrobium and this genus was previously included in a valid order named Hyphomicrobiales.⁶ In this way the Manual recovered the different taxonomic changes proposed in the taxonomy of this group of bacteria since the publication of the previous Manual of Systematic Bacteriology from year 1984. In this Manual the former family Rhizobiaceae includes the former genera Rhizobium, Sinorhizobium, Agrobacterium and the new genus Allorhizobium isolated from Neptunia nodules in Senegal,⁵⁰ together with a genus that does not was isolated from legumes nodules named Ensifer. The genus Azorhizobium was included in the family Hyphomicrobiaceae and the genus Bradyrhizobium in the family Bradyrhizobiaceae. This family is not valid because includes the genus Nitrobacter included in a previously validated family named Nitrobacteraceae.⁶ A new genus proposed in 1997 to include the species of intermediate growth named Mesorhizobium⁵¹ (Fig. 5) was included in the family Phyllobacteriaceae that also included the former genus Phyllobacterium.

Figure 5

Typical effective nodules formed by Mesorhizobium in Cicer arietinum.

In spite of the efforts of Bergey's Manual for the adaptation of its contents to the current taxonomy of rhizobia, we can affirm that the dichotomy between Manual of Bergey's and IJSEM is until more marked in the 2005 edition than in previous ones. In spite of the increasing of the number of rhizobial species recorded in the Bergey's Manual some species described several years before its publication are missing such as R. yanglingense,⁵² R. sullae⁵³ and R. indigoferae⁵⁴ within genus Rhizobium. In the case of genus Sinorhizobium, S. arboris and S. kostiense,⁵⁵ S. kummerowiae⁵⁴ and S. morelense⁵⁶ were not included. In the genus Agrobacterium it lacks A. larrymoreii.⁵⁷ Finally, in the case of genus Bradyrhizobium, B. yuanmingense⁵⁸ was not included. It is also surprisingly that in the Manual was not recorded the proposal to include the genera Agrobacterium and Allorhizobium into genus Rhizobium since the author responsible of the complete chapter from order Rhizobiales was one of the coauthors of the reclassification of Agrobacterium and Allorhizobium into genus Rhizobium.

Although the current classification of bacteria is based in the 16S rRNA gene that has allowed the description of non-nodulating species of rhizobia, it has limitations to differentiate among close species^59,60 and for this purpose several metabolic genes (housekeeping) have been proposed in several groups of bacteria.⁶¹ In rhizobia the two first genes analyzed were recA and atpD⁶² and currently they have been sequenced in many rhizobial species showing their usefulness in differentiation of species whose 16S rRNA genes are nearly identical.^59,60 In the last years new schemes for identification and phylogenetic analysis of bacteria named MLSA (Multilocus sequence analysis) and MLST (Multilocus sequence typing) based in the analysis of several housekeeping genes have been applied phylogenetic analyses of concrete groups of rhizobia as Ensifer^63–65 and Bradyrhizobium.^66,67 For instance, these studies indicate that housekeeping genes sequencing is superior to DNA–DNA hybridization for the assessment of genetic relatedness between Ensifer species and support the suggestion that Ensifer xinjiangensis is a later heterotypic synonym of Ensifer fredii.⁶⁴ The ad hoc committee for re-evaluation of the species definition suggested that ‘species should be identifiable by readily available methods (phenotypic, genomic)’ and that one promising approach towards this goal is the determination of a minimum of housekeeping genes⁶⁸ and Zeigler⁶⁹ suggested that analysis of less than five suitable housekeeping genes might be sufficient for a reliable classification. For this reason, in the last descriptions of new rhizobial species the analysis of at least two housekeeping genes have been included commonly to know the closest related species before to perform DNA-DNA hybridization experiments.

Besides the housekeeping genes also named “core” genes, some “auxiliary” or “accessory” genes involved in the legume symbiosis are commonly included in species description of rhizobia and in some MLST analysis.^70,71 The symbiotic genes from rhizobia are codified in plasmids in fast and some middle growing species and in symbiotic islands in the middle and slow growing ones.^72–85 From these genes, the most studied in rhizobia are nodD, nodA, nodC and nifH.^{25,70,86–90} Nevertheless, the symbiotic genes are not useful in taxonomy because due to their ability to be transferred in nature^91,92 from plasmids to islands,⁹³ from bacteria to plants⁹⁵ and among bacteria.⁹⁶ Therefore the analysis of symbiotic genes is overall useful to identify non-rhizobial species able to nodulate legumes (Fig. 10 and Fig. 11) and to carry out biogeography studies of legume endosymbionts.⁹⁷ Particularly the nodulation genes are useful to define biovars within rhizobial species.^26,98–100

Currently there are species from classic rhizobial genera in which the symbiotic genes nodD and nifH were not found as occurs in Bradyrhizobium betae isolated from roots of Beta vulgaris (Fig. 6) affected by tumour-like deformations.¹⁰¹ Also several species have been not isolated from nodules although they were able to nodulate Medicago sativa as Rhizobium daejeonense isolated from a cyanide-treatment biorreactor¹⁰² and R. cellulosilyticum isolated from a pulverized decaying wood of Populus alba.¹⁰³ Other species have been isolated from plant rhizosphere such as and R. alamii¹⁰⁴ and plant root inner tissues as R. oryzae.¹⁰⁵

Figure 6

Tumour-like formations in Beta vulgaris from which was isolated Bradyrhizobium betae.

The complete list of valid species of rhizobia is recorded in the List of Prokaryotic Names with Standing in Nomenclature that is performed and revised by Dr. Euzeby (http://www.bacterio.cict.fr). According to this list currently the genus Rhizobium contains 33 species and includes to the former genera Agrobacterium and Allorhizobium. The genus Sinorhizobium, currently named Ensifer, contains 12 species, the genus Mesorhizobium, 19 species, the genus Bradyrhizobium, 8 species, the genus Phyllobacterium, 7 species and the genus Azorhizobium, 2 species (http://www.bacterio.cict.fr). This high number of species able to nodulate legumes (Table 1) was unexpected only two decades ago and the previsions are that it will be increased in next times since currently there are eight new species in press in IJSEM.

Table 1

Traditionally considered rhizobia species and nodulating non-rhizobia species classification.

Class I. α-Proteobacteria. Order Hyphomicrobiales
Family	Genus	species	Host	References
Rhizobiaceae	Rhizobium	R. alamii	^*	104
		R. alkalisoli	Caragana intermedia	150
		R. cellulosilyticum	Medicago	103
		R. daejeonense	Medicago	102
		R. etli	Phaseolus	151
		R. fabae	Vicia faba	152
		R. galegae	Galegae	44
		R. gallicum	Phaseolus	153
		R. giardinii	Phaseolus	153
		R. hainanense	Desmodium	154
		R. huautlense	Sesbania	155
		R. indigoferae	Indigofera	54
		R. larrymooreii	^*	57,156
		R. leguminosarum	Pisum	1,60
		R. loessense	Astragalus	157
		R. lusitanum	Phaseolus	59
		R. mesosinicum	Chinese legumes	158
		R. miluonense	Lespedeza	159
		R. mongolense	Medicago	160
		R. multihospitium	Chinese legumes	161
		R. oryzae	Oryza alta	106
		R. phaseoli	Phaseolus	6,60
		R. pisi	Pisum	60
		R. radiobacter	^*	6,108
		R. rhizogenes	Phaseolus	6,108
		R. rubi	^*	6,108
		R. selenitireducens	^*	162,163
		R. sullae	Hedysarum	53
		R. tibeticum	Medicago archiduchis-nicolai	164
		R. tropici	Phaseolus	47
		R. undicola	^*	50,109
		R. vitis	^*	45,109
		R. yanglingense	Amphicarpaea	52
	Ensifer	E. americanus	Acacia	106,156,165,166
		E. arboris	Acacia	55,106,156
		E. fredii	Glycine max	37–39,106,156
		E. kostiense	Acacia	55,106,156
		E. kummerowiae	Kummerowia	54,106,156
		E. meliloti	Medicago	6,106,156,167
		E. medicae	Medicago	106,156,168
		E. morelense	Leucaena leucocephala	56,63
		E. saheli	Acacia	106,156,168
		E. terangae	Acacia	106,156,168
		E. xinjiangense	Glycine max	38,106,156,169
		E. adhaerens	^*	170
Phyllobacteriaceae	Mesorhizobium	M. albiziae	Albizia kalkora	171
		M. amorphae	Amorpha	172
		M. australianum	Biserrula pelecinus	173
		M. caraganae	Caragana spp.	174
		M. chacoense	Prosopis	17
		M. ciceri	Cicer	51,176
		M. gobiense	Chinese legumes	177
		M. huakuii	Astragalus	46,51
		M. loti	Lotus	32,51
		M. mediterraneum	Cicer	51,178
		M. metallidurans	Anthyllis vulneraria	179
		M. opportunistum	Biserrula pelecinus	173
		M. plurifarium	Acacia	180
		M. septentrionale	Astragalus	181
		M. shangrilense	Caragana spp.	182
		M. tarimense	Chinese legumes	177
		M. temperatum	Astragalus	181
		M. thiogangeticum	^*	183
		M. tianshanense	Sophora	51,184
	Phyllobacterium	P. trifolii ^#	Trifolium	122
Bradyrhizobiaceae	Bradyrhizobium	B. betae	^*	101
		B. canariense	Genisteae	185
		B. elkanii	Glycine	42,43
		B. japonicum	Glycine	6,33
		B. jicamae	Pachyrhizus erosus	186
		B. liaoningenese	Glycine	187
		B. pachyrhizi	Pachyrhizus erosus	186
		B. yuanmingense	Lespedeza	58
	Blastobacter	B. denitrificans ^#	Aeschynomene	118,188
	Azorhizobium	A. caulinodans	Sesbania rostrata	36
Hyphomicrobiaceae		A. doebereinerae	Sesbania virgata	190,191
	Devosia	D. neptuniae ^#	Neptunia natans	131,191
Brucellaceae	Ochrobactrum	O. lupini^# O. cytisi ^#	Lupinus Cytisus	120,191 121
Methylobacteriaceae	Methylobacterium	M. nodulans ^#	Crotalaria	116
Class II. β-Proteobacteria. Order Burkholderiales
Family	Genus	species	Host	References
Burkholderiaceae	Burkholderia	B. cepacia ^#	Dalbergia spp.	6,125
		B. mimosarum ^#	Mimosa ssp.	126
		B. nodosa ^#	Mimosa bimucronata; M. scabrella	127
		B. phymatum ^#	Machaerium lunatum	124,192
		B. sabiae ^#	Mimosa caesalpiniifolia	128
		B. tuberum ^#	Aspalathus carnosa	124,192
	Cupriavidus	C. taiwanensis ^#	Mimosa spp.	123,135

Non-rhizobia species able to establish symbiosis and form nodules in legumes.

Species with no described nodulation ability included in traditionally considered rhizobial genera.

Some Problems in Rhizobial Taxonomy

Along the rhizobial history some problems have been produced in the taxonomy of these microorganisms because rhizobiologists do not take into account the existence of general rules for species nomenclature. They do not consider that the species reclassifications carried out in the Bergey's Manual are not official and that while they are validated in the official journal of bacterial systematics the old names remain valid. This occurred in the case of R. phaseoli and R. trifolii, which were considered not valid from 1984 because Jordan reclassified these two species into R. leguminosarum in his chapter of Bergey's Manual.³¹ However, as this reclassification was never validated, all these species remain valid until 2008 in which our investigation group revised the taxonomic status of these species.⁶⁰ Our results showed that the valid species are R. leguminosarum and R. phaseoli, whereas R. trifolii is a later synonym of R. leguminosarum. Moreover, a problem with the type strains of R. leguminosarum deposited in different culture collections was detected and a new species named R. pisi was proposed to include one of these two strains deposited in DSMZ and NCIMB collections from Germany and United Kingdom, respectively.

Nomenclatural problems also affected to the order Rhizobiales and family Rhizobiaceae that as was already mentioned are illegitimate names because it was not considered the existence of previous valid names for these taxa. The same type of problems had occurred in the case of genus Sinorhizobium whose name has been recently changed to Ensifer.¹⁰⁶ This problem was originated because a species named Ensifer adhaerens described before than genus Sinorhizobium was not considered at the time of its description. Considering the rules of the Bacteriological Code, the name Ensifer has priority over Sinorhizobium since it was described before and thus it is clear that the proposal by Willems et al¹⁰⁷ to reclassify E. adhaerens into genus Sinorhizobium is not acceptable as was pointed out in the decision of the Judicial Commission of the International Committee on Systematics of Prokaryotes whose decision has been very recently published.¹⁰⁸

The use of virulence or symbiotic genes in taxonomy has also caused many problems such as that detected in the former genus Agrobacterium when Sawada et al¹⁰⁹ showed the total identity between the 16S rRNA gene sequences of the type strains from A. radiobacter and A. tumefaciens. Thus they proposed to reject the name A. tumefaciens since the name A. radiobacter has priority according to the nomenclature rules. Therefore the species A. radiobacter contains strains tumorigenic and non-tumorigenic strains depending on the presence of the plasmid pTi containing the virulence genes.^109,110 A second error affected to the former species A. rhizogenes (Fig. 7) that contains strains able to induce hairy-roots in plants.¹¹⁰ From the works of Willems and Collins¹¹¹ and Yanagi and Yamasato¹¹² it was found that this species phylogenetically belong to the genus Rhizobium and concretely it is close to R. tropici. This initial error was crucial in the later decision for reclassification of genus Agrobacterium into genus Rhizobium mainly based in the 16S rRNA gene sequences.¹⁰⁸

Figure 7

Atypical ineffective nodules formed by Rhizobium rhizogenes in Phaseolus vulgaris.

It is typical among the rhizobia researchers do not easily accept the official taxonomic changes in the systematics of these bacteria. They were reluctant to accept the change of the name Rhizobium meliloti to Sinorhizobium meliloti, also the proposal to reject the name Agrobacterium tumefaciens has not been until completely accepted and this name is currently used by some researchers. Also the reclassification of Agrobacterium and Allorhizobium into genus Rhizobium is subject of controversy and several letters to the editor have been published in IJSEM.^113,114 However, since this reclassification was accepted in this journal must be accepted. Finally, in the last meeting of the International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Agrobacterium and Rhizobium the members decided to do not accept the name Ensifer and proposed to use the name Sinorhizobium.

The Non-Rhizobia Nodulating Legumes

In the past eight years, several bacteria capable of forming nodules and fixing nitrogen in legume roots have been documented and grouped within alpha and beta Proteobacteria, which include Methylobacterium nodulans,^115,116 Burkholderia sp.,¹¹⁷ Blastobacter denitrificans,¹¹⁸ Devosia neptuniae,¹¹⁹ Ochrobactrum lupini¹²⁰ and O. cytisi,¹²¹ Phyllobacterium trifolii,¹²² Ralstonia taiwanensis (renamed as Cupriavidus taiwanensis),¹²³ Burkholderia tuberum, B. phymatum,¹²⁴ B. cepacia,¹²⁵ B. mimosarum,¹²⁶ B. nodosa¹²⁷ and B. sabiae.¹²⁸

As has been previously mentioned a common error in the rhizobial taxonomy was the use of symptoms in plants as a criterium for classification and identification of isolates. This lead to other error that was to consider the nodulation of legumes as an exclusive ability of rhizobia and thus the strains isolated from nodules that do not present the typical colonies on YMA plates are discarded. For instance, the colonies with this typical aspect are named Rhizobium even without further identification. This situation dramatically changed from 2001 ahead when the 16S rRNA gene sequencing was applied to the identification of the isolates. In this year was published in Nature the nodulation of legumes by Burkholderia, a genus that belong to beta-Proteobacteria.¹¹⁷ This genus contains diverse species with different physiological and ecological properties, is a common soil habitant bacterium, often associated with plant roots, but also has been isolated from animals and humans. Moulin et al¹¹⁷ isolated a strain of Burkholderia from nodules of the South African legume, Aspalathus carnosa. This isolate is also able to form nodules in the roots of Macroptilium atropurpureum, a tropical legume, confirming to have the ability of symbiotic nitrogen fixation. The Burkholderia strain carried nodulation (nodABC) genes phylogenetically related to those found in legume symbionts of the class alpha Proteobacteria (“classic” rhizobia) supporting the hypothesis of lateral gene transfer in the rhizosphere, crossing the boundary between class alpha Proteobacteria and beta Proteobacteria.

In the same year the nodulation of Crotalaria by a strain of genus Methylobacterium from alpha Proteobacteria¹¹⁵ later named M. nodulans¹¹⁶ was reported. Phylogenic analysis based on 16S rRNA of nodulating strains of Methylobacterium shows their close relationship to other species of Methylobacterium¹¹⁵ whereas it was confirmed that this species harbors the common nodulation nodABC genes and nifH gene encoding structural nitrogenase enzyme.^115,116 Phylogenic analysis based on nifH gene shows that it is related to Gluconacetobacter diazotrophicus, a sugarcane nitrogen fixing endophyte.¹²⁹

A typical case of bacteria classified into the genus Rhizobium by its morphology in YMA medium was that of Rhizobium neptuniae isolated from Neptunia natans nodules.¹³⁰ When we analyzed the LMW RNA profiles of these bacteria we proved that they are not typical of any rhizobial genera¹¹⁹ and the analysis of the 16S rRNA gene sequence confirmed that they belong to a new species of genus Devosia, named Devosia neptuniae.¹³¹ The strains of this species carry nodD and nifH genes closely related to those of R. tropici CIAT899^T indicating that they were transferred to D. neptuniae from R. tropici an American species nodulating Leucaena.⁴⁷ Later this hypothesis was supported by the finding that R. tropici nodulated Neptunia in America.¹³²

In the year 2002, besides that of Neptunia by Devosia, the nodulation of Aeschynomene indica by Blastobacer denitrificans was reported.¹¹⁸ Aschynomene indica is most frequently nodulated by Bradyrhizobium japonicum and Bradyrhizobium elkanii.¹³³ Nevertheless, Blastobacter denitrificans is able to form effective nodules in the roots of A. indica and reduce the atmospheric nitrogen¹¹⁸ which was again confirmed by presence of nifHDK genes by southern hybridization. Although the reclassification of Blastobacter denitrificans into genus Bradyrhizobium has been proposed¹³⁴ as this proposal has been not until validated in IJSEM it cannot be considered as official.

In 2003 the nodulation of Mimosa by Ralstonia taiwanensis or Wautersia taiwanensis was published.¹²³ This species was isolated from nodules of Mimosa pudica and Mimosa diplotricha. In this case the strain was erroneously classified as Ralstonia and it has been later named Cupriavidus taiwanensis.¹³⁵ At present, Cupriavidus is a beta Proteobacteria, belonging to family Burkholderiaceae of order Burkholderiales. Several species of this genus were isolated from soil and human clinical specimens¹³⁵ but C. taiwanensis was the only species able to form effective nodules and fixes atmospheric nitrogen in legumes. C. taiwanensis carries ten nodulation genes nodBCIJHASUQ and one regulatory gene nodD on pRalta.¹³⁶ Next to nod genes, C. taiwanensis carries 19 genes, presumably arranged in five operons and covering 25 kb that are involved in nitrogenase synthesis and functioning. These operons are nifA, encoding a sigma 54-dependent regulator, nifENfdxBnifQ and a modified nifX, nifVWfixABCX, nifBfdxNnifZfixU and the nitrogenase structural genes nifHDK.¹³⁶

In year 2004 strains from genus Ochrobactrum from family Brucellaceae were found in nodules of Acacia mangium but no information on their symbiotic genes was reported.¹³⁷ Later a new species of this genus carrying symbiotic genes close to those of rhizobia was reported as endosymbiont of Lupinus honoratum nodules.¹²⁰ It harbors megaplasmids of 1500, 200 and 150 kb and the nodulation (nod) and nitrogen fixation (nif) genes were detected in all the sym plasmids using nifH and nodD probes. Besides, in 2007 a second new species of Ochrobactrum named O. cytisi was isolated from Cytisus scoparius nodules in Spain.¹²¹ O. cytisi strains contained nodD and nifH genes on megaplasmids that were related phylogenetically to those of rhizobial strains nodulating Phaseolus, Leucaena, Trifolium and Lupinus.

In the same year 2005 a new species named Phyllobacterium trifolii was isolated from Trifolium pratense nodules.¹²² Phyllobacterium species was originally proposed to accommodate bacteria isolated from leaf nodules of Rubiaceae and Myrsinaceae tropical plants³⁴ but the plasmid profile revealed that P. trifolii harbors symbiotic plasmids in which nodulation and nitrogen fixation genes are located and experiments with this species revealed that it forms atypical nodules in the roots of Trifolium repens and Lupinus albus¹²² (Fig. 8).

Figure 8

Atypical ineffective nodules formed by Phyllobacterium trifolii in Lupinus.

Figure 9

Neighbour-joining phylogram showing relatedness of partial 16S rDNA gene sequences of type strains from bacteria able to nodulate legumes. Bootstrap confidence values were estimated from 1000 replications of each sequence. Bar, 2 substitutions per 100 nucleotide positions.

Figure 10

Neighbour-joining phylogram showing relatedness of partial nodC gene sequences of representative type strains from bacteria able to nodulate legumes. Bootstrap confidence values were estimated from 1000 replications of each sequence. Bar, 5 substitution per 100 nucleotide positions.

Figure 11

Neighbour-joining phylogram showing relatedness of partial nifH gene sequences of representative type strains from bacteria able to nodulate legumes. Bootstrap confidence values were estimated from 1000 replications of each sequence. Bar, 2 substitutions per 100 nucleotide positions.

On the other hand in the same year we demonstrated the nodulation of Phaseolus vulgaris by two pathogenic strains of the former species Agrobacterium rhizogenes (currently Rhizobium radiobacter) and the presence in these strains. The nodD and nifH genes found in these strains were close to those nodulating Phaseolus vulgaris and together with the symbiotic plasmids the presence of tumourigenic or hairy-root inducing plasmids was shown.¹³⁸

From 2006 to 2008 several new species of Burkholderia have been isolated from Mimosa nodules, B. mimosarum,¹²⁶ B. nodosa¹²⁷ and B. sabiae.¹²⁸ B. mimosarum was isolated from root nodules of M. pigra and M. scabrella from Taiwan, Brazil and Venezuela and several isolates showed effective nodulation in Mimosa species. The presence of nif and nod genes in the genomes has been demonstrated.^139,140 B. nodosa was isolated from root nodules on Mimosa bimucronata and Mimosa scabrella from Brazil and produced N₂-fixing nodules on Mimosa pudica, M. diplotricha and M. pigra. Also the nodulation of Mimosa by B. phymatum have been reported.¹⁴¹ Although all the most reports are from mimosoid legumes, there is evidence that papilionoid legumes such as Cyclopia that is nodulate by B. tuberum¹⁴² and Dalbergia louveli¹²⁵ that is reported for the first time that a strain belonging to the Burkholderia cepacia complex are able to induce efficient nodules on these legume plants. Even very recently it has been shown that some strains of Burkholderia are more competitive than R. tropici for the nodulation of Mimosa.¹⁴³ Also, preliminary evidence suggests that nodulating strains of both Burkholderia may have obtained nod genes from local rhizobia.¹⁴⁰

The fact that the closest known relatives of these species in the 16S rRNA tree are nonsymbiotic taxa and presence of very similar and phylogenetically related nodABC genes in nodulating alpha and beta Proteobacteria strongly implies that the genes required for legume nodulation are thought to have been acquired subsequently by lateral transfer from undefined sources, thus converting soil saprophytes into symbionts.¹⁴³ This hypothesis has been supported by many works^125,144,145 but it is not clear whether a single transfer event was responsible for the spread of nodulation genes.

Finally, several studies reported the presence of gamma Proteobacteria in legume nodules but until now symbiotic genes have been not detected in these strains.^146–148 Nevertheless as Benhizia et al¹⁴⁶ say they could nodulate legumes since recently it has been reported the legume symbiosis may exist in absence of nod genes as occurs in the case of photosynthetic bradyrhizobia.¹⁴⁹

Anyway, all these findings showed that the legume symbiosis are until poorly understood and the needed of further studies on the legume endosymbionts in different ecosystems and geographical locations mainly of those remaining unexplored from a symbiotic point of view. The set of genes available, data from several genes as housekeeping genes and the availability of new set of tools can provide useful insights to unravel relationships in these groups. Today, with modern molecular techniques this is a realistic goal. Inclusion of such molecular information in future phylogenetic analyses could lead to a reassessment of the position of these species and help to resolve the taxonomic problems.

Publish with Libertas Academica and every scientist working in your field can read your article

“I would like to say that this is the most author-friendly editing process I have experienced in over 150 publications. Thank you most sincerely.”

“The communication between your staff and me has been terrific. Whenever progress is made with the manuscript, I receive notice. Quite honestly, I've never had such complete communication with a journal.”

“LA is different, and hopefully represents a kind of scientific publication machinery that removes the hurdles from free flow of scientific thought.”

Your paper will be:

•

Available to your entire community free of charge

•

Fairly and quickly peer reviewed

•

Yours! You retain copyright

http://www.la-press.com

Footnotes

The authors report no conflicts of interest.

References

Frank

Über die Pilzsymbiose der Leguminosen. Berichte Deutschen Botanischen Gesellschaft. 1889; 7: 332–46.

Cohn

Untersuchungen über Bakterien. Beitr Biol Pflanz. 1872; 1: 127–224.

Orla-Jensen

Die Hauptlinien der natürlichen Bakteriensystems. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt II. 1909; 22: 305–46.

Palleroni

N.J.

Prokaryote taxonomy of the 20th century and the impact of studies on the genus Pseudomonas: a personal view. Microbiology. 2003; 149: 1–7.

Bergey

D.H.

, Harrison

F.C.

, Breed

R.S.

, Hammer

B.W.

, Huntoon

F.M.

Bergey's Manual of Determinative Bacteriology, 1st edn. Baltimore, USA: Williams & Wilkins; 1923.

Skerman

V.B.D.

, Mcgowan

, Sneath

P.H.A.

Approved Lists of Bacterial Names. Int J Syst Bacteriol. 1980; 30: 225–420.

Jordan

D.C.

, Allen

O.N.

Family III. Rhizobiaceae Conn 1938, 321. In: Buchanan

R.E.

, Gibbons

N.E.

, eds. Bergey's Manual of Determinative Bacteriology. Baltimore, USA: Williams & Wilkins. 1974: 261–7.

Vincent

J.M.

The cultivation, isolation and maintenance of rhizobia. In: Vincent

J.M.

, ed. A Manual for the Practical Study of Root-Nodule. Oxford: Blackwell Scientific Publications. 1970: 1–13.

Marmur

Procedure for isolation of deoxyribonucleic acid from microorganisms. J Mol Biol. 1961; 3: 208.

10.

Marmur

, Doty

Procedure for isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol. 1961; 3: 585.

11.

Schildkraut

, Doty

, Marmur

Formation of hybrid DNA molecules and their use in studies of DNA homologies. J Mol Biol. 1961; 3: 595.

12.

Ledeboer

A.M.

, Krol

A.J.

, Dons

J.J.

On the isolation of TI-plasmid from Agrobacterium tumefaciens.

Nucleic Acids Res. 1976; 3: 449–63.

13.

Zurkowski

, Lorkiewicz

Plasmid deoxyribonucleic acid in Rhizobium trifolii.

J Bacteriol. 1976; 128: 481–4.

14.

Downie

Signalling strategies for nodulation of legumes by rhizobia. Trends Microbiol. 1994; 2: 318–24.

15.

Dénarié

, Debellé

, Rosenberg

Signaling and host range variation in nodulation. Annu Rev Microbiol. 1992; 46: 497–531.

16.

Pueppke

S.G.

The genetic and biochemical basis for nodulation of legumes by rhizobia. Crit Rev Biotechnol. 1996; 16: 1–51.

17.

Schultze

, Kondorosi

Regulation of symbiotic root nodule development. Annu Rev Genet. 1998; 32: 33–57.

18.

Broughton

W.J.

, Jabbouri

, Perret

Keys to symbiotic harmony. J Bacteriol. 2000; 182: 5641–52.

19.

Winsor

B.A.

A nod at differentiation: the nodD gene product and initiation of Rhizobium nodulation. Trends Genet. 1989; 5: 199–201.

20.

Györgypal

, Kiss

G.B.

, Kondorosi

Transduction of plant signal molecules by the Rhizobium NodD proteins. Bioessays. 1991; 13: 575–81.

21.

Fellay

, Hanin

, Montorzi

nodD2 of Rhizobium sp. NGR234 is involved in the repression of the nodABC operon. Mol Microbiol. 1998; 27: 1039–50.

22.

Relic

, Perret

, Estrada-García

M.T.

Nod factors of Rhizobium are a key to the legume door. Mol Microbiol. 1994 Jul; 13: 171–8.

23.

Roche

, Maillet

, Plazanet

The common nodABC genes of Rhizobium meliloti are host-range determinants. Proc Natl Acad Sci USA. 1996; 93: 15305–10.

24.

Perret

, Staehelin

, Broughton

W.J.

Molecular basis of symbiotic promiscuity. Microbiol Mol Biol Rev. 2000; 64: 180–201.

25.

Laguerre

, Nour

S.M.

, Macheret

, Sanjuan

, Drouin

, Amarger

Classification of rhizobia based on nodC and nifH gene analysis reveals a close phylogenetic relationship among Phaseolus vulgaris symbionts. Microbiology. 2001; 147: 981–93.

26.

Rivas

, Laranjo

, Velázquez

, Mateos

P.F.

, Oliveira

, Martínez-Molina

Strains of Mesorhizobium amorphae and M. tianshanense carrying symbiotic genes of common chickpea endosymbiotic species constitute a novel biovar (ciceri) able to nodulate Cicer arietinum.

Lett Appl Microbiol. 2007; 44: 412–8.

27.

Iglesias

, Rivas

, García-Fraile

Genetic characterization of fast-growing rhizobia able to nodulate Prosopis alba in North Spain. FEMS Microbiol Lett. 2000; 277: 210–6.

28.

Fischer

H.M.

Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev. 1994; 58: 352–86.

29.

Zehr

J.P.

, Jenkins

B.D.

, Short

S.M.

, Steward

G.F.

Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environ Microbiol. 2003; 5: 539–54.

30.

, Fay

A.W.

, Lee

C.C.

, Yoshizawa

, Ribbe

M.W.

Assembly of nitrogenase MoFe protein. Biochemistry. 2008; 47: 3973–81.

31.

Jordan

D.C.

Family III. Rhizobiaceae. In: Krieg

N.R.

, Holt

J.G.

, eds. Bergey's Manual of Systematic Bacteriology. Vol. I. Baltimore: Williams & Wilkins; Baltimore. 1984; 234–42.

32.

Jarvis

B.D.W.

, Pankhurst

, Patel

J.J.

Rhizobium loti, a new species of legume root nodule bacteria. Int J Syst Bacteriol. 1982; 32: 378–80.

33.

Jordan

D.C.

Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing, root nodule bacteria from leguminous plants. Int J Syst Bacteriol. 1982; 32: 136–9.

34.

Knösel

D.H.

Genus IV. Phyllobacterium nom. rev. In: Krieg

N.R.

, Holt

J.G.

, eds. Bergey's Manual of systematic Bacteriology Vol. I. Baltimore: Williams & Wilkins; 1984; 254–6.

35.

Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 15. Int J Syst Bacteriol. 1984; 34: 355–7.

36.

Dreyfus

, Garcia

, Gillis

Characterization of Azorhizobium caulinodans gen. nov., sp. nov., a Stem-Nodulating Nitrogen-Fixing Bacterium Isolated from Sesbania rostrata.

Int J Syst Bacteriol. 1988; 38: 89–98.

37.

Scholla

M.H.

, Elkan

G.H.

Rhizobium fredii sp. nov., a Fast-Growing Species That Effectively Nodulates Soybeans. Int J Syst Bacteriol. 1984; 34: 484–6.

38.

Chen

W.X.

, Yan

G.H.

, Li

J.L.

Numerical taxonomic study of fast-growing soybean rhizobia and a proposal that Rhizobium fredii be assigned to Sinorhizobium gen. nov. Int J Syst Bacteriol. 1988; 38: 392–7.

39.

Jarvis

B.D.

, Downer

H.L.

, Young

J.P.

Phylogeny of fast-growing soybeannodulating rhizobia support synonymy of Sinorhizobium and Rhizobium and assignment to Rhizobium fredii.

Int J Syst Bacteriol. 1992; 42: 93–6.

40.

Woese

C.R.

, Stackebrandt

, Weisburg

W.G.

The phylogeny of purple bacteria: The alpha subdivision. System Appl Microbiol. 1984; 5: 315–26.

41.

Graham

P.H.

, Sadowsky

M.J.

, Keyser

H.H.

Proposed Minimal Standards for the Description of New Genera and Species of Root- and Stem-Nodulating Bacteria. Int J Syst Bacteriol. 1991; 41: 582–7.

42.

Kuykendall

L.D.

, Saxena

, Devine

T.E.

, Udell

S.E.

Genetic diversity in Bradyrhizobium japonicum Jordan 1982 and a proposal for Bradyrhizobium elkanii sp. nov. Can J Microbiol. 1992; 38: 501–5.

43.

Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 45. Int J Syst Bacteriol. 1993; 43: 398–9.

44.

Lindström

Rhizobium galegae, a new species of legume root nodule bacteria. Int J Syst Bacteriol. 1989; 39: 365–7.

45.

Ophel

, Kerr

Agrobacterium vitis sp. nov. for Strains of Agrobacterium biovar 3 from Grapevines. Int J Syst Bacteriol. 1990; 40: 236–41.

46.

Chen

, Li

, Qi

, Wang

, Yuan

, Li

Rhizobium huakuii sp. nov. Isolated from the Root Nodules of Astragalus sinicus.

Int J Syst Bacteriol. 1991; 41: 275–80.

47.

Martínez-Romero

, Segovia

, Mercante

F.M.

, Franco

A.A.

, Graham

, Pardo

M.A.

Rhizobium tropici, a novel species nodulating Phaseolus vulgaris L. beans and Leucaena sp. trees. Int J Syst Bacteriol. 1991; 41: 417–26.

48.

Kuykendall

L.D.

Family I. Rhizobiaceae Conn 1938, 321AL. In: Brenner

D.J.

, Krieg

N.R.

, Stanley

J.T.

eds. Bergey's Manual of Systematic Bacteriology. Vol. 2, part C. Springer, New York; 2005: 324–61.

49.

Validation List no. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2006; 56: 1–6.

50.

de Lajudie

, Laurent-Fulele

, Willems

Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal. Int J Syst Bacteriol. 1992; 42: 93–6.

51.

Jarvis

B.D.W.

, Van Berkum

, Chen

W.X.

Transfer of Rhizobium loti, Rhizobium huakuii, Rhizobium ciceri, Rhizobium mediterraneum, and Rhizobium tianshanense to Mesorhizobium gen. nov. Int J Syst Bacteriol. 1997; 47: 895–8.

52.

Tan

Z.Y.

, Kan

F.L.

, Peng

G.X.

, Wang

E.T.

, Reinhold-Hurek

, Chen

W.X.

Rhizobium yanglingense sp. nov., isolated from arid and semi-arid regions in China. Int J Syst Evol Microbiol. 2001; 51: 909–14.

53.

Squartini

, Struffi

, Döring

Rhizobium sullae sp. nov. (formerly ‘Rhizobium hedysari’), the root-nodule microsymbiont of Hedysarum coronarium L. Int J Syst Evol Microbiol. 2002; 52: 1267–76.

54.

Wei

G.H.

, Wang

E.T.

, Tan

Z.Y.

, Zhu

M.E.

, Chen

W.X.

Rhizobium indigoferae sp. nov. and Sinorhizobium kummerowiae sp. nov., respectively isolated from Indigofera spp. and Kummerowia stipulacea.

Int J Syst Evol Microbiol. 2002; 52: 2231–9.

55.

Nick

, de Lajudie

, Eardly

B.D.

Sinorhizobium arboris sp. nov. and Sinorhizobium kostiense sp. nov., isolated from leguminous trees in Sudan and Kenya. Int J Syst Bacteriol. 1999; 49: 1359–68.

56.

Wang

E.T.

, Tan

Z.Y.

, Willems

, Fernández-López

, Reinhold-Hurek

, Martínez-Romero

Sinorhizobium morelense sp. nov., a Leucaena leucocephala-associated bacterium that is highly resistant to multiple antibiotics. Int J Syst Evol Microbiol. 2002; 52: 1683–7.

57.

Bouzar

, Jones

J.B.

Agrobacterium larrymoorei sp. nov., a pathogen isolated from aerial tumours of Ficus benjamina.

Int J Syst Evol Microbiol. 2001; 51: 1023–6.

58.

Yao

Z.Y.

, Kan

F.L.

, Wang

E.T.

, Wei

G.H.

, Chen

W.X.

Characterization of rhizobia that nodulate legume species of the genus Lespedeza and description of Bradyrhizobium yuanmingense sp. nov. Int J Syst Evol Microbiol. 2002; 52: 2219–30.

59.

Valverde

, Igual

J.M.

, Peix

, Cervantes

, Velázquez

Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris.

Int J Syst Evol Microbiol. 2006; 56: 2631–7.

60.

Ramírez-Bahena

M.H.

, García-Fraile

, Peix

Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov. Int J Syst Evol Microbiol. 2008; 58: 2484–90.

61.

Maiden

M.C.J.

Multilocus sequence typing of Bacteria. Annu Rev Microbiol. 2006; 60: 561–88.

62.

Gaunt

M.W.

, Turner

S.L.

, Rigottier-Gois

, Lloyd-Macgilp

S.A.

, Young

J.P.

Phylogenies of atpD and recA support the small subunit rRNA-based classification of rhizobia. Int J Syst Evol Microbiol. 2001; 51: 2037–48.

63.

Martens

, Delaere

, Coopman

, de Vos

, Gillis

, Willems

Multilocus sequence analysis of Ensifer and related taxa. Int J Syst Evol Microbiol. 2007; 57: 489–503.

64.

Martens

, Dawyndt

, Coopman

, Gillis

, de Vos

, Willems

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium). Int J Syst Evol Microbiol. 2008; 58: 200–14.

65.

van Berkum

, Elia

, Eardly

B.D.

Multilocus sequence typing as an approach for population analysis of Medicago-nodulating rhizobia. J Bacteriol. 2006; 188: 5570–7.

66.

Vinuesa

, Rojas-Jiménez

, Contreras-Moreira

Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the Asiatic continent. Appl Environ Microbiol. 2008; 74: 6987–96.

67.

Rivas

, Martens

, de Lajudie

, Willems

Multilocus sequence analysis of the genus Bradyrhizobium.

Syst Appl Microbiol. 2009; 32: 101–10.

68.

Stackebrandt

, Frederiksen

, Garrity

G.M.

Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol. 2002; 52: 1043–7.

69.

Zeigler

D.R.

Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int J Syst Evol Microbiol. 2003; 53: 1893–900.

70.

Silva

, Vinuesa

, Eguiarte

L.E.

, Souza

, Martínez-Romero

Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumes. Mol Ecol. 2005; 14: 4033–50.

71.

Vinuesa

, Silva

, Lorite

M.J.

, Izaguirre-Mayoral

M.L.

, Bedmar

E.J.

, Martínez-Romero

Molecular systematics of rhizobia based on maximum likelihood and Bayesian phylogenies inferred from rrs, atpD, recA and nifH sequences, and their use in the classification of Sesbania microsymbionts from Venezuelan wetlands. Syst Appl Microbiol. 2005; 28: 702–16.

72.

Barnett

M.J.

, Fisher

R.F.

, Jones

Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc Natl Acad Sci USA. 2001; 98: 9883–8.

73.

Moriguchi

, Maeda

, Satou

The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae. J Mol Biol. 2001; 307: 771–84.

74.

Wood

D.W.

, Setubal

J.C.

, Kaul

The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science. 2001; 294: 2317–23.

75.

Flores

, Morales

, Avila

Diversification of DNA sequences in the symbiotic genome of Rhizobium etli.

J Bacteriol. 2005 Nov; 187: 7185–92.

76.

Young

J.P.

, Crossman

L.C.

, Johnston

A.W.

The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol. 2006; 7: R34.

77.

Crossman

L.C.

, Castillo-Ramírez

, McAnnula

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria. PLoS ONE. 2008; 2–3: e2567. Erratum in: PLoS ONE. 2008.

78.

Lee

K.B.

, de Backer

, Aono

The genome of the versatile nitrogen fixer Azorhizobium caulinodans ORS571. BMC Genomics. 2008; 9: 271.

79.

Yang

, Li

, Wei

, Cheng

, Zhou

The function of three indigenous plasmids in Mesorhizobium huakuii 2020 and its symbiotic interaction with Sym pJB5JI of Rhizobium leguminosarum.

Sci China C Life Sci. 2008; 51: 353–61.

80.

Sullivan

J.T.

, Trzebiatowski

J.R.

, Cruickshank

R.W.

Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol. 2002; 184: 3086–95.

81.

Kaneko

, Nakamura

, Sato

Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 2002; 31; 9: 189–97.

82.

Sullivan

J.T.

, Ronson

C.W.

Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc Natl Acad Sci USA. 1998 Apr 28;95(9): 5145–9. Erratum in: Proc Natl Acad Sci USA. 1998; 95: 9059.

83.

Uchiumi

, Ohwada

, Itakura

Expression islands clustered on the symbiosis island of the Mesorhizobium loti genome. J Bacteriol. 2004; 186: 2439–48.

84.

Nandasena

K.G.

, O'Hara

G.W.

, Tiwari

R.P.

, Sezmis

, Howieson

J.G.

In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L. Environ Microbiol. 2007; 9: 2496–511.

85.

Itakura

, Saeki

, Omori

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members. ISME J. 2009; 3: 326–39.

86.

Stepkowski

, Hughes

C.E.

, Law

I.J.

Diversification of lupine Bradyrhizobium strains: evidence from nodulation gene trees. Appl Environ Microbiol. 2007; 73: 3254–64.

87.

Laranjo

, Alexandre

, Rivas

, Velázquez

, Young

J.P.

, Oliveira

Chickpea rhizobia symbiosis genes are highly conserved across multiple Mesorhizobium species. FEMS Microbiol Ecol. 2008; 66: 391–400.

88.

Steenkamp

E.T.

, Stepkowski

, Przymusiak

, Botha

W.J.

, Law

I.J.

Cowpea and peanut in southern Africa are nodulated by diverse Bradyrhizobium strains harboring nodulation genes that belong to the large pantropical clade common in Africa. Mol Phylogenet Evol. 2008; 48: 1131–44.

89.

Zhao

C.T.

, Wang

E.T.

, Chen

W.F.

, Chen

W.X.

Diverse genomic species and evidences of symbiotic gene lateral transfer detected among the rhizobia associated with Astragalus species grown in the temperate regions of China. FEMS Microbiol Lett. 2008; 286: 263–73.

90.

Estrella

M.J.

, Muñoz

, Soto

M.J.

, Ruiz

, Sanjuán

Genetic diversity and host range of rhizobia nodulating Lotus tenuis in typical soils of the Salado River Basin (Argentina). Appl Environ Microbiol. 2009; 75: 1088–98.

91.

Mergaert

, Van Montagu

, Holsters

Molecular mechanisms of Nod factor diversity. Mol Microbiol. 1997; 25: 811–7.

92.

Finan

T.M.

Evolving insights: symbiosis islands and horizontal gene transfer. J Bacteriol. 2002; 184: 2855–6.

93.

Nakatsukasa

, Uchiumi

, Kucho

, Suzuki

, Higashi

, Abe

Transposon mediation allows a symbiotic plasmid of Rhizobium leguminosarum bv. trifolii to become a symbiosis island in Agrobacterium and Rhizobium.

J Gen Appl Microbiol. 2008; 54: 107–18.

94.

Boisson-Dernier

, Chabaud

, Garcia

, Bécard

, Rosenberg

, Barker

D.G.

Agrobacterium rhizogenes-transformed roots of Medicago truncatula for the study of nitrogen-fixing and endomycorrhizal symbiotic associations. Mol Plant Microbe Interact. 2001; 14: 695–700.

95.

Broothaerts

, Mitchell

H.J.

, Weir

Gene transfer to plants by diverse species of bacteria. Nature. 2005; 433: 629–33.

96.

Rogel

M.A.

, Hernández-Lucas

, Kuykendall

L.D.

, Balkwill

D.L.

, Martinez-Romero

Nitrogen-fixing nodules with Ensifer adhaerens harboring Rhizobium tropici symbiotic plasmids. Appl Environ Microbiol. 2001 Jul; 67(7): 3264–8.

97.

Wei

, Chen

, Zhu

, Chen

, Young

J.P.

, Bontemps

Invasive Robinia pseudoacacia in China is nodulated by Mesorhizobium and Sinorhizobium species that share similar nodulation genes with native American symbionts. FEMS Microbiol Ecol. 2009. In press.

98.

Villegas

M.C.

, Rome

, Mauré

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

Syst Appl Microbiol. 2006; 29: 526–38.

99.

Mnasri

, Mrabet

, Laguerre

, Aouani

M.E.

, Mhamdi

Salt-tolerant rhizobia isolated from a Tunisian oasis that are highly effective for symbiotic N2-fixation with Phaseolus vulgaris constitute a novel biovar (bv. mediterranense) of Sinorhizobium meliloti.

Arch Microbiol. 2007; 187: 79–85.

100.

León-Barrios

, Lorite

M.J.

, Donate-Correa

, Sanjuán

Ensifer meliloti bv. lancerottense establishes nitrogen-fixing symbiosis with Lotus endemic to the Canary Islands and shows distinctive symbiotic genotypes and host range. Syst Appl Microbiol. 2009. In press.

101.

Rivas

, Willems

, Palomo

J.L.

Bradyrhizobium betae sp. nov. isolated from roots of Beta vulgaris affected by tumour-like deformations. Int J Syst Evol Microbiol. 2004; 54: 1271–5.

102.

Quan

Z.X.

, Bae

H.S.

, Baek

J.H.

, Chen

W.F.

, Im

W.T.

, Lee

S.T.

Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor. Int J Syst Evol Microbiol. 2005; 55: 2543–9.

103.

García-Fraile

, Rivas

, Willems

Rhizobium cellulosilyticum sp. nov., isolated from sawdust of Populus alba.

Int J Syst Evol Microbiol. 2007; 57: 844–8.

104.

Berge

, Lodhi

, Brandelet

Rhizobium alamii sp. nov., an exopolysaccharide-producing species isolated from legume and non-legume rhizospheres. Int J Syst Evol Microbiol. 2009; 59: 367–72.

105.

Peng

, Yuan

, Li

, Zhang

, Tan

Rhizobium oryzae sp. nov., isolated from the wild rice Oryza alta.

Int J Syst Evol Microbiol. 2008; 58: 2158–63.

106.

Judicial Commission of the International Committee on Systematics of Prokaryotes. The genus name Sinorhizobium Chen, et al. 1988 is a later synonym of Ensifer Casida 1982 and is not conserved over the latter genus name, and the species name ‘Sinorhizobium adhaerens’ is not validly published. Opinion 84. Int J Syst Evol Microbiol. 2008; 58: 1973.

107.

Willems

, Fernández-López

, Muñoz-Adelantado

Description of new Ensifer strains from nodules and proposal to transfer Ensifer adhaerens Casida 1982 to Sinorhizobium as Sinorhizobium adhaerens comb. nov. Request for an opinion. Int J Syst Evol Microbiol. 2003; 53: 1207–17.

108.

Young

J.M.

, Kuykendall

L.D.

, Martínez-Romero

, Kerr

, Sawada

A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie, et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis.

Int J Syst Evol Microbiol. 2001; 51: 89–103.

109.

Sawada

, Ieki

, Oyaizu

, Matsumoto

Proposal for rejection of Agrobacterium tumefaciens and revised descriptions for the genus Agrobacterium and for Agrobacterium radiobacter and Agrobacterium rhizogenes.

Int J Syst Bacteriol. 1993; 43: 694–702.

110.

Kersters

, de Ley

Genus III. Agrobacterium. In: Krieg Holt

H.G.

, eds. Bergey's Manual of Systematic Bacteriology. Baltimore: Williams & Wilkins; 1984: 244–54.

111.

Willems

, Collins

M.D.

Phylogenetic analysis of rhizobia and agrobacteria based on 16S rRNA gene sequences. Int J Syst Bacteriol. 1993; 43: 305–13.

112.

Yanagi

, Yamasato

Phylogenetic analysis of the family Rhizobiaceae and related bacteria by sequencing of 16S rRNA gene using PCR and DNA sequencer. FEMS Microbiol Lett. 1993; 107: 115–20.

113.

Farrand

S.K.

, Van Berkum

P.B.

, Oger

Agrobacterium is a definable genus of the family Rhizobiaceae.

Int J Syst Evol Microbiol. 2003; 53: 1681–7.

114.

Young

J.M.

, Kuykendall

L.D.

, Martínez-Romero

, Kerr

, Sawada

Classification and nomenclature of Agrobacterium and Rhizobium—a reply to Farrand, et al. Int J Syst Evol Microbiol. 2003; 53: 1689–95.

115.

, Giraud

, Jourand

, Garcia

Methylotrophic Methylobacterium bacteria nodulate and fix nitrogen in symbiosis with legumes. J Bacteriol. 2001; 183: 214–20.

116.

Jourand

, Giraud

, Béna

Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria. Int J Syst Evol Microbiol. 2004; 54: 2269–73.

117.

Moulin

, Munive

, Dreyfus

, Boivin-Masson

Nodulation of legumes by members of the beta-subclass of Proteobacteria. Nature. 2001; 411: 948–50. Erratum in: Nature. 2001; 412: 926.

118.

van Berkum

, Eardly

B.D.

The aquatic budding bacterium Blastobacter denitrificans is a nitrogen-fixing symbiont of Aeschynomene indica.

Appl Environ Microbiol. 2002; 68: 1132–6.

119.

Rivas

, Velázquez

, Willems

A new species of Devosia that forms a unique nitrogen-fixing root-nodule symbiosis with the aquatic legume Neptunia natans (L.f.) druce. Appl Environ Microbiol. 2002; 68: 5217–22.

120.

Trujillo

M.E.

, Willems

, Abril

Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol. 2005; 71: 1318–27.

121.

Zurdo-Piñeiro

J.L.

, Rivas

, Trujillo

M.E.

Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol. 2007; 57: 784–8.

122.

Valverde

, Velázquez

, Fernández-Santos

Phyllobacterium trifolii sp. nov., nodulating Trifolium and Lupinus in Spanish soils. Int J Syst Evol Microbiol. 2005; 55: 1985–9.

123.

Chen

W.M.

, James

E.K.

, Prescott

A.R.

, Kierans

, Sprent

J.I.

Nodulation of Mimosa spp. by the beta-proteobacterium Ralstonia taiwanensis.

Mol Plant Microbe Interact. 2003; 16: 1051–61.

124.

Vandamme

, Goris

, Chen

W.M.

, de Vos

, Willems

Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes. Syst Appl Microbiol. 2002; 25: 507–12.

125.

Rasolomampianina

, Bailly

, Fetiarison

Nitrogen-fixing nodules from rose wood legume trees (Dalbergia spp.) endemic to Madagascar host seven different genera belonging to alpha- and beta-Proteobacteria. Mol Ecol. 2005; 14: 4135–46.

126.

Chen

W.M.

, James

E.K.

, Coenye

Burkholderia mimosarum sp. nov., isolated from root nodules of Mimosa spp. from Taiwan and South America. Int J Syst Evol Microbiol. 2006; 56: 1847–51.

127.

Chen

W.M.

, de Faria

S.M.

, James

E.K.

Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella.

Int J Syst Evol Microbiol. 2007; 57: 1055–9.

128.

Chen

W.M.

, de Faria

S.M.

, Chou

J.H.

Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia.

Int J Syst Evol Microbiol. 2008; 58: 2174–9.

129.

Lee

, Reth

, Meletzus

, Sevilla

, Kennedy

Characterization of a major cluster of nif, fix, and associated genes in a sugarcane endophyte, Acetobacter diazotrophicus.

J Bacteriol. 2000; 182: 7088–91.

130.

Subba-Rao

N.S.

, Mateos

P.F.

, Baker

The unique root-nodule symbiosis between Rhizobium and the aquatic legume Neptunia natans (L.f.) Druce. Planta. 1995; 196: 311–20.

131.

Rivas

, Willems

, Subba-Rao

N.S.

Description of Devosia neptuniae sp. nov. that nodulates and fixes nitrogen in symbiosis with Neptunia natans, an aquatic legume from India. Syst Appl Microbiol. 2003; 26: 47–53.

132.

Zurdo-Piñeiro

J.L.

, Velázquez

, Lorite

M.J.

Identification of fast-growing rhizobia nodulating tropical legumes from Puerto Rico as Rhizobium gallicum and Rhizobium tropici.

Syst Appl Microbiol. 2004; 27: 469–77.

133.

van Berkum

, Tully

R.E.

, Keister

D.L.

Nonpigmented and Bacteriochlorophyll-Containing Bradyrhizobia Isolated from Aeschynomene indica.

Appl Environ Microbiol. 1995; 61: 623–9.

134.

van Berkum

, Leibold

J.M.

, Eardly

B.D.

Proposal for combining Bradyrhizobium spp. (Aeschynomene indica) with Blastobacter denitrificans and to transfer Blastobacter denitrificans (Hirsch and Muller, 1985) to the genus Bradyrhizobium as Bradyrhizobium denitrificans (comb. nov.). Syst Appl Microbiol. 2006; 29: 207–15.

135.

Vandamme

, Coenye

Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol. 2004; 54: 2285–9.

136.

Amadou

, Pascal

, Mangenot

Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 2000; 18: 1472–83.

137.

Ngom

, Nakagawa

, Sawada

A novel symbiotic nitrogen-fixing member of the Ochrobactrum clade isolated from root nodules of Acacia mangium.

J Gen Appl Microbiol. 2004; 50: 17–27.

138.

Velázquez

, Peix

, Zurdo-Piñeiro

J.L.

The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Mol Plant Microbe Interact. 2005; 18: 1325–32.

139.

Chen

W.M.

, de Faria

S.M.

, Straliotto

Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America. Appl Environ Microbiol. 2005; 71: 7461–71.

140.

Chen

W.M.

, James

E.K.

, Chou

J.H.

, Sheu

S Y.

, Yang

S.Z.

, Sprent

J.I.

Beta-Rhizobia from Mimosa pigra, a newly discovered invasive plant in Taiwan. New Phytol. 2005; 168: 661–75.

141.

Elliott

G.N.

, Chen

W.M.

, Chou

J.H.

Burkholderia phymatum is a highly effective nitrogen-fixing symbiont of Mimosa spp. and fixes nitrogen ex planta. New Phytol. 2007; 173: 168–80.

142.

Elliott

G.N.

, Chen

W.M.

, Bontemps

Nodulation of Cyclopia spp. (Leguminosae, Papilionoideae) by Burkholderia tuberum.

Ann Bot (Lond). 2007; 100: 1403–11.

143.

Elliott

G.N.

, Chou

J.H.

, Chen

W.M.

Burkholderia spp. are the most competitive symbionts of Mimosa, particularly under N-limited conditions. Environ Microbiol. 2009; 11: 762–78.

144.

Barrett

C.F.

, Parker

M.A.

Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp nodule bacteria on two Mimosa spp. in Costa Rica. Appl Environ Microbiol. 72: 1198–206.

145.

Zakhia

, Jeder

, Willems

, Dreyfus

, de Lajudie

Diverse bacteria associated with root nodules of spontaneous legumes in Tunisia and first report for nifH-like gene within the genera Microbacterium and Starkeya.

Microb Ecol. 2006; 51: 375–93.

146.

Benhizia

, Benhizia

, Benguedouar

, Muresu

, Giacomini

, Squartini

Gamma proteobacteria can nodulate legumes of the genus Hedysarum.

Syst Appl Microbiol. 2004; 27: 462–8.

147.

Muresu

, Polone

, Sulas

Coexistence of predominantly nonculturable rhizobia with diverse, endophytic bacterial taxa within nodules of wild legumes. FEMS Microbiol Ecol. 2008; 63: 383–400.

148.

Ibáñez

, Angelini

, Taurian

, Tonelli

M.L.

, Fabra

Endophytic occupation of peanut root nodules by opportunistic Gammaproteobacteria. Syst Appl Microbiol. 2009; 32: 49–55.

149.

Giraud

, Moulin

, Vallenet

Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science. 2007 Jun 1; 316(5829): 1307–12.

150.

Y.L.

, Chen

W.F.

, Han

L.L.

, Wang

E.T.

, Chen

W.X.

Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China. Int J Syst Evol Microbiol. In press.

151.

Segovia

, Young

J.P.

, Martínez-Romero

Reclassification of American Rhizobium leguminosarum biovar phaseoli type I strains as Rhizobium etli sp. nov. Int J Syst Bacteriol. 1993; 43: 374–7.

152.

Tian

C.F.

, Wang

E.T.

, Wu

L.J.

Rhizobium fabae sp. nov., a bacterium that nodulates Vicia faba.

Int J Syst Evol Microbiol. 2008; 58: 2871–5.

153.

Amarger

, Macheret

, Laguerre

Rhizobium gallicum sp. nov. and Rhizobium giardinii sp. nov., from Phaseolus vulgaris nodules. Int J Syst Bacteriol. 1997; 47: 996–1006.

154.

Chen

W.X.

, Tan

Z.Y.

, Gao

J.L.

, Li

, Wang

E.T.

Rhizobium hainanense sp. nov., isolated from tropical legumes. Int J Syst Bacteriol. 1997; 47: 870–3.

155.

Wang

E.T.

, van Berkum

, Beyene

Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae.

Int J Syst Bacteriol. 1998; 48: 687–99.

156.

Young

J.M.

The genus name Ensifer Casida 1982 takes priority over Sinorhizobium Chen, et al. 1988, and Sinorhizobium morelense Wang, et al. 2002 is a later synonym of Ensifer adhaerens Casida 1982. Is the combination “Sinorhizobium adhaerens” (Casida 1982) Willems, et al. 2003 legitimate? Request for an Opinion. Int J Syst Evol Microbiol. 2003; 53: 2107–10.

157.

Wei

G.H.

, Tan

Z.Y.

, Zhu

M.E.

, Wang

E.T.

, Han

S.Z.

, Chen

W.X.

Characterization of rhizobia isolated from legume species within the genera Astragalus and Lespedeza grown in the Loess Plateau of China and description of Rhizobium loessense sp. nov. Int J Syst Evol Microbiol. 2003; 53: 1575–83.

158.

Lin

D.X.

, Chen

W.F.

, Wang

F.Q.

Rhizobium mesosinicum sp. nov., isolated from root nodules of three different legumes. Int J Syst Evol. Microbiol. In press.

159.

C.T.

, Wang

E.T.

, Tian

C.F.

Rhizobium miluonense sp. nov., a symbiotic bacterium isolated from Lespedeza root nodules. Int J Syst Evol Microbiol. 2008; 58: 1364–8.

160.

van Berkum

, Beyene

, Bao

, Campbell

T.A.

, Eardly

B.D.

Rhizobium mongolense sp. nov. is one of three rhizobial genotypes identified which nodulate and form nitrogen-fixing symbioses with Medicago ruthenica [(L.) Ledebour]. Int J Syst Bacteriol. 1998; 48: 13–22.

161.

Han

T.X.

, Wang

E.T.

, Wu

L.J.

Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China. Int J Syst Evol Microbiol. 2008; 58: 1693–9.

162.

Hunter

W.J.

, Kuykendall

L.D.

, Manter

D.K.

Rhizobium selenireducens sp. nov.: a selenite-reducing alpha-Proteobacteria isolated from a bioreactor. Curr Microbiol. 2007; 55: 455–60.

163.

List of new names and new combinations previously effectively, but not validly, published. Validation List No. 121. Int J Syst Evol. Microbiol. 2008; 58: 1057.

164.

Hou

B.C.

, Wang

E.T.

, Li

Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Medicago archiducis-nicolai Vassilcz grown in Tibet, China. Int J Syst Evol Microbiol. In press.

165.

Toledo

, Lloret

, Martínez-Romero

Sinorhizobium americanus sp. nov., a new sinorhizobium species nodulating native Acacia spp. in Mexico. Syst Appl Microbiol. 2003; 26: 54–64.

166.

Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 100. Int J Syst Evol. Microbiol. 2004; 54: 1909–10.

167.

de Lajudie

, Willems

, Pot

Polyphasic taxonomy of Rhizobia: emendation of the genus Sinorhizobium and description of Sinorhizobium meliloti comb. nov., Sinorhizobium saheli sp. nov., and Sinorhizobium teranga sp. nov. Int J Syst Bacteriol. 44: 715–33.

168.

Rome

, Fernandez

M.P.

, Brunel

, Normand

, Cleyet-Marel

J.C.

Sinorhizobium medicae sp. nov., isolated from annual Medicago spp. Int J Syst Bacteriol. 1996; 46: 972–80.

169.

Euzéby

J.P.

Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int J Syst Bacteriol. 1998; 48: 1073–5.

170.

Casida

L.E.J.

Ensifer adhaerens gen nov. sp. nov.: a bacterial predator of bacteria in soil. Int J Syst Bacteriol. 1982; 32: 339–45.

171.

Wang

F.Q.

, Wang

E.T.

, Liu

Mesorhizobium albiziae sp. nov., a novel bacterium that nodulates Albizia kalkora in a subtropical region of China. Int J Syst Evol Microbiol. 2007; 57: 1192–9.

172.

Wang

E.T.

, van Berkum

, Sui

X.H.

, Beyene

, Chen

W.X.

, Martínez-Romero

Diversity of rhizobia associated with Amorpha fruticosa isolated from Chinese soils and description of Mesorhizobium amorphae sp. nov. Int J Syst Bacteriol. 1999; 49: 51–65.

173.

Nandasena

, O'Hara

G.W.

, Tiwari

R.P.

, Willems

, Howieson

J.G.

Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov. isolated from Biserrula pelecinus L. growing in Australia. Int J Syst Evol Microbiol. In press.

174.

Guan

S.H.

, Chen

W.F.

, Wang

E.T.

Mesorhizobium caraganae sp. nov., a novel rhizobial species nodulated with Caragana spp. in China. Int J Syst Evol Microbiol. 2008; 58: 2646–53.

175.

Velázquez

, Igual

J.M.

, Willems

Mesorhizobium chacoense sp. nov., a novel species that nodulates Prosopis alba in the Chaco Arido region (Argentina). Int J Syst Evol Microbiol. 2001; 51: 1011–21.

176.

Nour

S.M.

, Fernandez

M.P.

, Normand

, Cleyet-Marel

J.C.

Rhizobium ciceri sp. nov., consisting of strains that nodulate chickpeas (Cicer arietinum L.). Int J Syst Bacteriol. 1994; 44: 511–22.

177.

Han

T.X.

, Han

L.L.

, Wu

L.J.

Mesorhizobium gobiense sp. nov. and Mesorhizobium tarimense sp. nov., isolated from wild legumes growing in desert soils of Xinjiang, China. Int J Syst Evol Microbiol. 2008; 58: 2610–8.

178.

Nour

S.M.

, Cleyet-Marel

J.C.

, Normand

, Fernandez

M.P.

Genomic heterogeneity of strains nodulating chickpeas (Cicer arietinum L.) and description of Rhizobium mediterraneum sp. nov. Int J Syst Bacteriol. 1995; 45: 640–8.

179.

Vidal

, Chantreuil

, Berge

Mesorhizobium metallidurans sp. nov., a metal-resistant symbiont of Anthyllis vulneraria growing on metallicolous soil in Languedoc, France. Int J Syst Evol Microbiol. 2009; 59: 850–5.

180.

de Lajudie

, Willems

, Nick

Characterization of tropical tree rhizobia and description of Mesorhizobium plurifarium sp. nov. Int J Syst Bacteriol. 1998; 48: 369–82.

181.

Gao

J.L.

, Turner

S.L.

, Kan

F.L.

Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China. Int J Syst Evol Microbiol. 2004; 54: 2003–12.

182.

Y.L.

, Chen

W.F.

, Han

L.L.

Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana spp. growing in Yunnan Province of China. Int J Syst Evol Microbiol. In press.

183.

Ghosh

, Roy

Mesorhizobium thiogangeticum sp. nov., a novel sulfur-oxidizing chemolithoautotroph from rhizosphere soil of an Indian tropical leguminous plant. Int J Syst Evol Microbiol. 2006; 56: 91–7.

184.

Chen

, Wang

, Li

, Chen

, Li

Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People's Republic of China. Int J Syst Bacteriol. 1995; 45: 153–9.

185.

Vinuesa

, León-Barrios

, Silva

Bradyrhizobium canariense sp. nov., an acid-tolerant endosymbiont that nodulates endemic genistoid legumes (Papilionoideae: Genisteae) from the Canary Islands, along with Bradyrhizobium japonicum bv. genistearum, Bradyrhizobium genospecies alpha and Bradyrhizobium genospecies beta. Int J Syst Evol Microbiol. 2005; 55: 569–75.

186.

Ramírez-Bahena

M.H.

, Peix

, Rivas

Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus. Int J Syst Evol Microbiol. In press.

187.

L.M.

, Ge

, Cui

, Li

, Fan

Bradyrhizobium liaoningense sp. nov., isolated from the root nodules of soybeans. Int J Syst Bacteriol. 1995; 45: 706–11.

188.

Validation of the Publication of New Names and New Combinations Previously Effectively Published Outside the IJSB: List No. 20. Int J Syst Bacteriol. 1986; 36: 354–6.

189.

List of new names and new combinations previously effectively, but not validly, published. Validation List No. 92. Int J Syst Evol Microbiol. 2003; 53: 935–7.

190.

Moreira

F.M.S.

, Cruz

, de Faria

S.M.

Azorhizobium doebereinerae sp. nov. microsymbiont of Sesbania virgata (Caz.) Pers. Syst Appl Microbiol. 2006; 29: 197–206.

191.

List of new names and new combinations previously effectively, but not validly, published. Validation List No. 110. Int J Syst Evol Microbiol. 2006; 56: 1459–60.

192.

List of new names and new combinations previously effectively, but not validly, published. Validation List No. 91. Int J Syst Evol Microbiol. 2003; 53: 627–8.

Taxonomy of Bacteria Nodulating Legumes

Abstract

Keywords

Introduction

From the Rhizobia Discovery until Bergey's Manual from 1974

Taxonomy of Rhizobia between 1974 and 2000

Recent Changes in the Taxonomy of Rhizobia

Some Problems in Rhizobial Taxonomy

The Non-Rhizobia Nodulating Legumes

Footnotes

References