Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae.

The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.

1. Introduction: Origin and Differentiation of the Tribe Genisteae

The Genisteae is one of the largest tribes within the legume family (Fabaceae) with ca. 618 species within 25 genera [1]. Most genera within the Genisteae show a preference for a temperate climate although several lupin (Lupinus spp.) species inhabit tropical areas in eastern Brazil [2,3,4]. These predominantly woody legumes thrive in a wide range of habitats, including coastal dunes, scrubland, sagebrush steppes, grasslands, mountain woodlands, and meadows. Genisteae (especially lupins) inhabit areas across a wide altitudinal range, extending from sea level to the upper elevation limit for plant growth, i.e., ca. 5,000 m [5]. Almost all of the Genisteae species tested can fix atmospheric nitrogen via symbiotic bacteria (general term ‘rhizobia’) in root nodules, and this gives them an advantage in low N soils if other factors are favourable for growth [6,7,8].

It has been estimated that the separation of the Genisteae and Crotalarieae took place in the Eocene ca. 41 million of years ago [9]. Evidence indicates that the formation of the two basal lineages, which later evolved into the extant genera Dichilus-Melolobium-Polhillia and Argyrolobium, occurred in southern Africa. Later, this tribe dispersed northward reaching the Mediterranean, where two other genera, Lupinus and Adenocarpus appeared. These events were followed by the emergence of the Cytisinae (nine genera) and Genistinae (eight genera) as predominant Genisteae groups in the Mediterranean [1,2,10]. Given that the time of separation of the genus Lupinus and the Cytisinae-Genistinae genera has been estimated at ca. 16 million years ago, the process of differentiation into the extant Genisteae genera may have been initiated in the Oligocene, albeit not later than in the early Miocene [11,12]. The environmental changes that are associated with the global climate cooling and growing aridification from the end of the Eocene may have played pivotal roles in the Genisteae speciation process [13,14]. Similarly, the mountain uplifts in the western parts of North and South America triggered replicate radiations in the genus Lupinus, resulting in the appearance of ca. 200 species with a great variety of morphological forms [12,15].

The amphi-Atlantic distribution of Genisteae species points to dispersal events having occurred across the Atlantic Ocean into the areas now comprising a distinct Fabaceae flora. The thesis of this review is that the complex evolutionary history of the Genisteae tribe is reflected by the diversity of rhizobium symbionts, with which it interacts. Indeed, seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species (Figure 1). Thus, the objective of this work is to present a comprehensive phylogenetic and phylogeographic data concerning the rhizobia that nodulate this legume tribe.

Figure 1

A Bayesian posterior probability consensus tree based on 1408 bps of 16S rRNA derived from 16 rhizobial and 4 related genera (the genera nodulating Genisteae are in bold case-underlined). The strains used for this construction and the 16S rRNA Genbank accession numbers were: Rhizobium leguminosarum ATCC 10004 (U29386), Sinorhizobium fredii ATCC 35423 (X67231), Allorhizobium undicola ATCC 700741 (Y17047), Pararhizobium capsulatum ATCC 43294 (X73042), Neorhizobium galegae ATCC 43677 (D11343), Shinella zoogloeoides ATCC 19623 (AB238789), Ciceribacter lividus MSSRFBL1 (NR 135717), Mesorhizobium loti ATCC 700743 (X67229), Aminobacter anthyllidis STM 4645(FR869633), Phyllobacterium brassicacearum LMG 22836 (AY785319), Ochrobactrum lupini LMG 22726 (AY457038), Methylobacterium marchantiae DSM 21328 (FJ157976), Bradyrhizobium lupini USDA 3051 (KM114861), Bosea lupini LMG 26383 (FR774992), Azorhizobium oxalatiphilum DSM 18749 (FR799325), Labrys okinawensis DSM 18385 (AB236169), Devosia honganensis ACCC 19737 (KP339871), Paraburkholderia caribensis CCUG 42847 (Y17009), Cupriavidus alkaliphilus LMG 26294 (HQ438078), and Microvirga lupini LMG 26460 (EF191408). The 16S rRNA sequences were aligned in MUSCLE [16] and implemented in MEGA 6.0 [17]. The Bayesian analyses were performed using BEAST 1.7 software [18]. The model of nucleotide evolution used in all of the analyses was GTR + I + G, as selected by the jModel Test software [19]. The Yule process was selected as a tree prior to Bayesian analysis, 10,000,000 generations were performed and the tree was visualized and edited using FigTree version 1.3.1 software [20].

2. The Genus Bradyrhizobium as a Predominant Group Infecting Genisteae Legumes

Bradyrhizobium strains were isolated from nodules of 30 out of the 33 lupin species listed in Table 1. Bradyrhizobium also occured in root nodules of 36 out of the 44 species of the remaining Genisteae genera (see Table 1). This indicates that Bradyrhizobium is a dominant rhizobium lineage nodulating this legume tribe although it is acknowledged that rhizobial symbionts have been characterized in only a fraction of Genisteae species [6,21], and nothing is known about rhizobial symbionts of 14, mostly monotypic genera.

Table 1

Genisteae species and their rhizobium symbionts.

Tribes and Genera	Geographical Origin	Rhizobium Symbionts and Sources
Genisteae
Adenocarpus
Adenocarpus decorticans	Morocco	Rhizobium [22]
Adenocarpus foliolosus	Spain-Canary Islands	Bradyrhizobium [23,24]
Adenocarpus hispanicus	Spain	Phyllobacterium [25]; Bradyrhizobium [26]
Argyrolobium
Argyrolobium lunare	South Africa	Mesorhizobium [27]
Argyrolobium rupestre	South Africa	Bradyrhizobium [28]
Argyrolobium sericeum	South Africa	Bradyrhizobium [28]
Argyrolobium velutinum	South Africa	Mesorhizobium [27]
Argyrolobium uniflorum	Senegal, Tunisia	Rhizobium, Sinorhizobium (=Ensifer) [29,30]; Sinorhizobium [31,32]; Rhizobium [33]
Calicotome
Calicotome infesta	Italy	Bradyrhizobium [34]
Calicotome spinosa	Italy	Bradyrhizobium, Rhizobium [34]
Chamaecytisus
Chamaecytisus proliferus	Morocco, Spain-Canary Islands, New Zealand	Bradyrhizobium [23,24,35,36,37,38]
Chamaecytisus ratisbonensis	Poland	Bradyrhizobium [39]
Chamaecytisus ruthenicus	Russia	Bradyrhizobium [40]
Cytisus
Cytisus aeolicus	Italy	Bradyrhizobium [34]
Cytisus arboreus	Morocco	Rhizobium [22]
Cytisus balansae	Spain	Bradyrhizobium [41,42,43]
Cytisus grandiflorus	Portugal	Bradyrhizobium [21,44]
Cytisus laburnum	Spain	Bradyrhizobium [25]
Cytisus multiflorus	Spain	Bradyrhizobium [41,42,43]
Cytisus proliferus	Spain-Canary Islands	Bradyrhizobium [21,44]
Cytisus purgans	Spain	Agrobacterium, Rhizobium [25]
Cytisus scoparius	Belgium, Ireland, Poland, Spain, UK, USA; Australia, New Zealand	Bradyrhizobium [21,37,38,39,41,44,45]; Bradyrhizobium, Mesorhizobium, Rhizobium [46]; Ochrobactrum cytisi [47]; Bradyrhizobium, Ensifer, Rhizobium, Phyllobacterium [48]
Cytisus striatus	Spain	Bradyrhizobium [39,42]
Cytisus triflorus	Algeria, Morocco	Bradyrhizobium [49,50]
Cytisus villosus	Algeria, Morocco	Bradyrhizobium [49,50,51,52,53]
Genista
Genista aspalathoides	Italy	Bradyrhizobium Clade II and Clade IV [34]
Genista germanica	Poland	Bradyrhizobium [39]
Genista hystrix	Spain	Bradyrhizobium [41,42]
Genista linifolia	Spain	Bradyrhizobium [54]
Genista monspessulana	Spain	Bradyrhizobium [54]
Genista saharae	Algeria, Tunisia	Ensifer, Phyllobacterium, Mesorhizobium, Rhizobium [55]; Ensifer [31]; Ensifer, Mesorhizobium, Neorhizobium [56]
Genista stenopetala	Spain-Canary Islands	Bradyrhizobium [21,44]
Genista sylvestris	Croatia	Bradyrhizobium [21]
Genista tinctoria	Poland, Russia, Slovenia	Bradyrhizobium [21,57,58]; Phyllobacterium, Rhizobium, Bradyrhizobium [40]
Genista versicolor	Spain	Bradyrhizobium [59]
Laburnum
Laburnum anagyroides	Belgium, Croatia	Bradyrhizobium [21,25]; Bradyrhizobium [48]
Lupinus
Lupinus albescens	Brazil	Bradyrhizobium [60,61]
Lupinus albus	Poland, Spain	Mesorhizobium [62,63]; Bradyrhizobium [44,60,64,65,66,67]
Lupinus angustifolius	Australia, Poland, South Africa, Spain	Bradyrhizobium [60,64,65,68,69]
Lupinus arboreus	USA-California, New Zealand	Bradyrhizobium [37,70,71]
Lupinus bandelierae	Bolivia	Bradyrhizobium [60]
Lupinus bicolor	USA-California	Bradyrhizobium [71]
Lupinus bracteolaris	Brazil	Bradyrhizobium [60]
Lupinus breviscapus	Bolivia	Bradyrhizobium [60]
Lupinus campestris	Mexico	Bradyrhizobium [60]
Lupinus cosentinii	Australia, Spain	Bradyrhizobium [64,68]
Lupinus hispanicus	Spain	Bradyrhizobium [64]
Lupinus honoratus	Argentina	Ochrobactrum [72]
Lupinus lepidus	USA-Washington	Bradyrhizobium [53,70]
Lupinus leucophyllus	USA-Washington	Bradyrhizobium [70]
Lupinus luteus	Poland, Spain, USA	Bradyrhizobium, Mesorhizobium [73]; Bradyrhizobium [64,65,69]
Lupinus mariae-josephae	Spain	Bradyrhizobium [64,74,75,76,77]
Lupinus micranthus	Algeria, Spain, Tunisia	Bradyrhizobium [64,78]; Bradyrhizobium, Microvirga, Phyllobacterium [79,80]
Lupinus misticola	Peru	Bradyrhizobium [60]
Lupinus montanus	Mexico-Morelos	Bradyrhizobium [24]
Lupinus mutabilis	Ecuador	Bradyrhizobium [60]
Lupinus nootkatensis	USA-Alaska	Bradyrhizobium [60,70]
Lupinus paraguariensis	Brazil	Bradyrhizobium [60]
Lupinus paranensis	Brazil	Bradyrhizobium [60]
Lupinus perennis	USA	Bradyrhizobium [81,82]
Lupinus polyphyllus	Belgium, Germany, New Zealand, Poland	Bosea [83]; Bradyrhizobium [24,60,84,85]; Bradyrhizobium, Rhizobium [48]
Lupinus pycnostachys	Bolivia	Bradyrhizobium [60]
Lupinus rubriflorus	Brazil,	Bradyrhizobium [60]
Lupinus sericeus	USA-Washington	Bradyrhizobium [70]
Lupinus simulans	Mexico-Oaxaca	Bradyrhizobium [53,70]; Bradyrhizobium [53]
Lupinus succulentus	USA-California	Mesorhizobium [86]
Lupinus texensis	USA-Texas	Microvirga [87]
Lupinus tominensis	Bolivia	Bradyrhizobium [60]
Lupinus uleanus	Brazil	Bradyrhizobium [60]
Retama
Retama monosperma	Algeria, Morocco, Spain	Bradyrhizobium [88,89]
Retama raetam	Algeria, Tunisia	Agrobacterium, Mesorhizobium, Rhizobium, Sinorhizobium (Ensifer) [90,91]; Bradyrhizobium [92]; Sinorhizobium [31]
Retama sphaerocarpa	Algeria, Morocco, Spain	Bradyrhizobium [21,41,88,92,93]; Bradyrhizobium, Phyllobacterium [25]
Spartium
Spartium junceum	Croatia, Italy, Slovenia, Spain	Bradyrhizobium [21,34,50,94]; Bradyrhizobium, Phyllobacterium [25]
Teline
Teline canariense	Spain	Bradyrhizobium [23,24,35]
Teline monspessulana	Italy	Mesorhizobium [34]
Teline stenopetala	Spain	Bradyrhizobium [34]
Ulex
Ulex europaeus	New Zealand, Portugal	Bradyrhizobium [38,44,48,95,96]

The predominance of Bradyrhizobium strains among the rhizobia nodulating Genisteae spp. could be due to different factors, including their symbiotic potential that is responsible for their nodulation of a wide spectrum of Fabaceae spp. and their adaptability to various edaphic and climatic conditions, resulting in this genus having a broad geographical range [21,97]. Bradyrhizobia are common in soils in places where legumes are absent, which may explain the loss of nodulating ability by portions of rhizobial communities [98,99,100]. Indeed, Bradyrhizobium communities comprise both nodulating and non-nodulating bacteria, and the latter may even lack the capacity to fix nitrogen [101]. In phylogenetic trees, these non-nodulating, non-diazotrophic bradyrhizobia are often indistinguishable from symbiotic strains [100]. The lack of symbiotic properties may, however, be compensated by other attributes as revealed in bradyrhizobia inhabiting forest soil habitats that are rich in organic matter, whose genomes are enriched in loci involved in the catabolism of aromatic compounds [102].

The colonization of terrestrial environments by land plants had a profound impact on soil microbiota [103]. It is likely that Bradyrhizobium benefited from the expansion of land plants, developing a range of, mainly, mutualistic associations, which had been formed prior to the emergence of nitrogen-fixing symbiosis with Fabaceae. This explains the persistence of this genus in soils regardless of the presence of legumes [104,105,106]. Remarkably, members of this genus also play important roles in the nitrogen and sulphur cycles [64,107] and are also involved in a range of, mainly, mutualistic interactions with animals [108,109,110].

3. Bradyrhizobium japonicum and Related Species

Currently, the genus Bradyrhizobium comprises 50 species that have been proposed for strains originating from Europe, Northern Africa, South America, and Asia (see Supplementary Table S1). Despite recent efforts that were centred on the characterization of nonsymbiotic bradyrhizobia, type strains of 45 species are bacteria isolated directly from root or stem nodules of Fabaceae plants. Importantly, phylogenies of the 16S rRNA gene and several other core (nonsymbiotic) gene markers that are commonly used in MLSA (multiple locus sequence analysis) studies reveal two major branches in the genus Bradyrhizobium [111]. One of the branches, referred to as the B. japonicum supergroup or Bradyrhizobium group I, currently comprises 29 species, in addition to B. japonicum [112,113] (Figure 2 and Figures S1 and S2). The remaining B. elkanii supergroup or group II contains B. elkanii and 17 other species (Supplementary Table S1). Bradyrhizobium denitrificans and Bradyrhizobium oligotrophicum tend to group separately from the two supergroups. Apart from the 50 recognized species, Bradyrhizobium core gene phylogenies uncover many unnamed groups and single-strain lineages [28,114].

Figure 2

Maximum likelihood (ML) phylogeny of concatenated recA and glnII partial gene sequences (425 bp + 519 bp), comprising type strains of Bradyrhizobium species with the exception of species, in which recA sequences were missing: Bradyrhizobium betae LMG 21987, Bradyrhizobium guangdongense CCBAU 51649, Bradyrhizobium guangxiense CCBAU 53363, Bradyrhizobium icense LMTR 13 and Bradyrhizobium ingae BR 10250. The scale bar indicates the number of substitutions per site. Bootstrap values >70% (percentage of 500 replicates calculated under distance criteria) are given at the branching nodes. The sequences of Rhodopseudomonas boonkerdii NS23, M. loti NZP2213, Sinorhizobium meliloti 1021 and R. leguminosarum 3841 were used as outgroups. The sequences were aligned using ClustalW software and ML phylogenies were inferred with Mega 6 [17] using the best-fit nucleotide substitution models as indicated by jModelTest 2.1.4. [115]. The distances were calculated according to the GTR+I+G model. Arrows indicate Bradyrhizobium species that nodulate Genisteae plants. Asterisk denotes Bradyrhizobium algeriensis, which has not been formally recognized.

Earlier studies suggested that lupin bradyrhizobia are related to, or are often indistinguishable from, many soybean isolates in core gene phylogenetic trees [23,24,35,73,116]. Given that soybean and lupin bradyrhizobia belong to different cross-inoculation groups, two symbiovars (symbiovar genistearum for strains nodulating Genisteae and symbiovar glycinearum for microsymbionts of soybean) were proposed [35,117]. This division enabled the differentiation of related Bradyrhizobium strains by referring to their distinct symbiotic properties.

Studies that followed the publication of Barrera et al. [116] suggested that Bradyrhizobium isolates of Genisteae spp. showed phylogenetic affinity to B. japonicum, i.e., all of the isolates belonged to the Bradyrhizobium japonicum supergroup. This observation concerned the isolates originating from Genisteae plants growing in acidic or neutral soils in the Mediterranean and the Andes, the regions encompassing the principal centres of Genisteae differentiation [34,51,60,63,64,79,80]. Also, related Bradyrhizobium strains were detected among Genisteae isolates at the northern margin of this tribe’s geographical range in Belgium and Poland [48,58,65]. Likewise, B. japonicum-related strains were described in the western part of the United States among Bradyrhizobium isolates that were recovered from lupin and Acmispon spp. [70,118].

Although the prevalence of B. japonicum-related strains among Genisteae isolates was highlighted in earlier work, a closer examination revealed that a number of strains originating from more acid soils (pH <6) clustered separately with respect to B. japonicum species. Some strains infecting genistoid legumes in the Canary Islands were subsequently delineated as Bradyrhizobium canariense species [35]. It was then shown that B. canariense is widespread in the Mediterranean among Genisteae isolates, including several lupin species, Cytisus aeolicus, Genista aspalathoides, Retama sphaerocarpa, and Spartium junceum [25,34]. Further studies revealed that this species is also common in the western United States [118,119]. The western part of the United States constitutes a major centre of differentiation of the genus Lupinus, moreover, it is also inhabited by multiple Loteae species [12,120,121,122]. Also, B. canariense strains were reported in Poland and Iceland as well as in Western Australia in areas where lupin and serradella crops were cultivated [60,65,68]. The identification of B. canariense in areas located outside a Mediterranean climate appeared to be associated with acidic soils and suggested that soil pH is a primary factor determining the range of this species.

In the following years, Cytisus villosus was found to be infected by B. canariense and strains that belonged to two other species, which were broadly related to B. japonicum groups. These strains were formally described as Bradyrhizobium cytisi and Bradyrhizobium rifense [49,52]. This indicated that C. villosus, like most Genisteae so far studied, is nodulated by a broad range of Bradyrhizobium lineages. B. cytisi strains were also identified among both symbiotic and nonsymbiotic isolates which inhabit the rhizosphere of Acmispon strigosus (tribe Loteae) sampled across California [118].

Finally, a new species, B. lupini was proposed for strain USDA3051 that occupied a sister position with respect to B. canariense isolates in 16S rRNA and glnII-recA phylogenies [69]. This species seems to be common among Genisteae symbionts in the Mediterranean, which could be deduced from its presence together with B. canariense among recently recovered Bradyrhizobium symbionts of Lupinus micranthus and Lupinus luteus in Spain, Algeria, and Tunisia [78,79,80]. In addition to the dominant B. canariense–B. lupini group, the report of Msaddak et al. [79] unveiled two other, yet unnamed groups within the B. japonicum supergroup, one of which (Group II) showed an affinity to B. betae, a nonsymbiotic bacterium isolated from sugar beet root [123], while the other (Group V), depending on markers used (recA or glnII-recA-rrs) clustered with either B. rifense or Bradyrhizobium diazoefficiens spp.

It appears that B. canariense, B. cytisi, B. lupini, and B. rifense spp. prevail among the microsymbionts of Genisteae spp. in acidic and neutral soils. All of these species are probably adapted to poor, oligotrophic soils formed in a semi-arid-mediterranean climate. It is, thus, hardly surprising that these species were detected in regions that are known for a high diversity of Genisteae spp., i.e., in the Mediterranean, and in the western part of the United States. On the other hand, B. japonicum seems to be more common in temperate and subtropical climate, associating with legumes that are growing in more neutral soils [24,35,49,51,52,60,65,118,119].

4. Genisteae Isolates Related to Bradyrhizobium elkanii

Although most Bradyrhizobium isolates from Genisteae species belong to the B. japonicum supergroup, some cluster in the B. elkanii supergroup. Among Bradyrhizobium strains isolated from lupins native to Brazil, a strain originating from Lupinus paraguariensis aligned within the B. elkanii supergroup [60]. Related Bradyrhizobium strains were later described among root-nodule isolates that were recovered from Lupinus albescens plants [61]. L. albescens belongs to the same lupin group as L. paraguariensis, showing a similar range encompassing the northern part of Argentina, but also Uruguay, Paraguay, and southern Brazil [4,124]. Like other lupins, Lupinus albescens is adapted to poor, sandy soils, although it also inhabits more fertile soils. Out of the three major groups uncovered in core gene phylogenies, one group (Cluster III) [61], comprised strains from non-arenized-non-sandy soils that clustered in proximity to Bradyrhizobium pachyrhizi-B. elkanii spp. However, the remaining strains, referred to as Cluster I (contained strains from non-arenized soils) and Cluster II (contained strains from arenized-sandy soils) grouped separately within the B. japonicum superclade [61].

A considerable effort was centred on the investigation of rhizobial symbionts of Lupinus mariae-josephae. Unlike other lupins, most of which prefer acidic or neutral soils, L. mariae-josephae grows in alkaline, calcareous soils. This lupin species is also highly endemic—its geographic range is limited to small populations, scattered across the Valencia province in Eastern Spain [125]. The characterization of L. mariae-josephae rhizobium isolates originating from soil samples collected at a single location revealed a substantial level of diversity. All Bradyrhizobium strains isolated in this work grew very slowly, and clustered within the B. elkanii supergroup [64]. In a subsequent study, a much larger number of L. mariae-josephae isolates (103 strains) were characterized, from plants sampled at four principal locations of its natural occurrence. Phylogenies based on combined sequences of atpD, glnII, and recA genes uncovered six major groups (group I-VI), all were confined to the B. elkanii supergroup [75]. Three closely related L. mariae-josephae isolates (each belonging to group I) were then subjected to detailed molecular and phenotypic analyses, which resulted in the description of a new species, Bradyrhizobium valentinum [76]. The systematic status of isolates representing the remaining groups (groups II-VI) is unclear, however, these strains do not group together with known Bradyrhizobium species, and thus likely represent separate species within this genus.

Lupin is not the only Genisteae genus infected by strains within the B. elkanii supergroup. In fact, strains showing phylogenetic affinity to B. elkanii were previously reported in Sicily, among the isolates nodulating Calicotome spinosa and G. aspalathoides [34]. In addition, B. elkanii-related strains were detected in nodules of Retama raetam and R. sphaerocarpa, in seven distinct ecological-climatic areas of north-eastern Algeria [92]. In another study, all of the Bradyrhizobium strains isolated in Morocco and Spain from R. sphaerocarpa and Retama monosperma clustered in the B. elkanii supergroup. Here, isolates were classified as a new species, Bradyrhizobium retamae. In the phylogenetic tree based on concatenated sequences of recA, atpD, and glnII genes, B. retamae occupied a sister albeit distinct position with respect to Bradyrhizobium lablabi and Bradyrhizobium jicamae species [88]. Notably, B. retamae was the first Bradyrhizobium species nodulating Genisteae plants with an affinity to the B. elkanii supergroup. Later, for Bradyrhizobium isolates that were recovered from R. sphaerocarpa plants growing in different soil and climatic conditions in Spain, roughly one-third of the isolates clustered in the B. japonicum supergroup, whereas the remaining strains grouped in the B. elkanii cluster [93]. Strains belonging to these two major groups of Bradyrhizobium were also detected among the symbionts of Genista versicolor, which is endemic to the Sierra Nevada National Park in Spain [59]. It is emphasized that a significant proportion of the strains that were isolated in the studies described formed phylogenetic lines clearly distinct from the known Bradyrhizobium species, which indicates a very high level of diversity within Genisteae symbionts in the Mediterranean.

5. Phylogeny of Symbiotic Loci of Genisteae-Nodulating Bradyrhizobium Strains

The analysis of nodA, nodC, as well as nifD and nifH gene sequences revealed a high level of diversity within the genus Bradyrhizobium [21,60,70,82,114,126,127,128,129,130,131]. In recently published phylogenies of nodA and nifD symbiotic genes, Bradyrhizobium strains formed 16 major groups, referred to as Clade I–Clade XVI [28]. Following this classification scheme, Bradyrhizobium strains nodulating Genisteae spp. cluster in the nodA tree in Clade I, Clade II, Clade III, Clade IV, Clade VII, Clade XI, Clade XIII, Clade XV, and Clade XVI [60,61,65,76,114,132]. In the current work, in phylogenies that were based on sequences of nodA and nifD genes, Clade V is formed solely by strains originating from Australian native legumes [114]. Some South American strains that previously were assigned to Clade V were transferred to subclade III.4 of Clade III, which in symbiotic gene trees cluster separately with respect to the Australian strains (Figure 3 and Figure S3).

Figure 3

Maximum likelihood (ML) tree based on bradyrhizobial nifD gene sequences (759 bp). The significance of each branch is indicated by the bootstrap percentage calculated for 500 bootstraps. The bootstrap values greater than 70% are indicated at nodes. The sequences were aligned using ClustalW software and ML phylogenies were inferred with Mega 6 [17] using the best-fit nucleotide substitution models, as indicated by jModelTest 2.1.4. [115]. The distances were calculated according to the HKY+I+G model. Because of the substitution saturation that is associated with the third codon position in the nifD dataset, as estimated using DAMBE 5 [133] these positions were excluded from further analysis. The number of sequences used in the construction of this phylogenetic tree is given in brackets: Bradyrhizobium: (640); Rhodopseudomonas (29); Paraburkholderia/Burkholderia (19); Mesorhizobium (22); Microvirga (3); Azorhizobium (2). The number of Bradyrhizobium sequences included in a particular clade or branch is also shown in brackets: Clade I (54), Clade II (106), Clade III(III.1) (2), Clade III(III.2) (33), Clade III(III.3A) (31), Clade III(III.3B) (22), Clade III(III.3C) (87), Clade III(III.3D) (54), Clade III(III.3E) (9), Clade III(III.3F) (8), Clade III(III.3G) (3), Clade III(III.3H) (12), Clade III(III.4) (33), Clade IV (41), Clade V (14), Clade VI (7), Clade VII (64), Clade X (9), Clade XI (2), Clade XVI (10), Clade XVIII (6), Clade XIX (7), Clade XX (15). Black arrows indicate Bradyrhizobium species nodulating Genisteae plants.

Clade II, also referred to as the lupin clade, was the first described symbiotic nodA gene group comprising Bradyrhizobium isolates from Genisteae spp. [132]. Further work revealed that Clade II is a dominant group among Genisteae bradyrhizobia in Europe and the Mediterranean [21,39,65,73,78,79,80]. Strains belonging to this group were also detected among Bradyrhizobium isolates that were recovered from Lupinus spp. endemic to the Andes, but not in lupin species that are native to the eastern part of Brazil [60,61]. Clade II strains also prevail among lupin isolates in North America, especially, in the western part of the United States [70,71,82,134].

The geographical range of Clade II overlaps with the distribution of Genisteae genera in the Mediterranean and the western part of the Americas. The exception is southern Africa where the four basal genera (Argyrolobium, Dichilus, Melolobium, and Polhillia) have their centres of divergence [2]. Presumably, these South-African genera are not nodulated by Clade II bradyrhizobia, as suggested by two recent studies [27,28]. However, this opinion should be taken with caution, given that only a limited number of Genisteae isolates from these four genera have so far been characterized in South Africa. Thus, we cannot exclude the possibility that early stages of Clade II differentiation took place in southern Africa, being connected to the divergence of the basal Genisteae genera [135]. In South Africa, Clade II bradyrhizobia have been detected as symbionts of Lupinus angustifolius which is exotic to this region. However, these strains were similar to European bradyrhizobia and it was assumed that they had been accidentally brought from Europe together with soil-contaminated lupin seeds [68].

Notably, the geographic range of Clade II to a large extent overlaps with the range of the Loteae tribe (Table S2). This legume tribe has its major centre of divergence in the Mediterranean, extending to western Asia, while the secondary centre of divergence is in the western part of the United States [120,121]. Although the Loteae plants are infected, primarily, by Mesorhizobium strains, at least some genera, e.g., the genus Acmispon in the western part of the United States, and the genus Ornithopus (serradella) in Europe show preference for Clade II bradyrhizobia [65,71,118,134]. Actually, Serradella species that are known to establish highly specific symbiosis with their rhizobial partners have, for a long time, been used as surrogate hosts for isolation of effective strains nodulating lupins and other Genisteae spp. [136,137]. Out of the five Ornithopus species, four are native to the Mediterranean and/or western and central Europe, whereas Ornithopus micranthus is endemic to south-eastern Brazil, north-eastern Argentina and Uruguay [121]. Evidently, Clade II bradyrhizobia are the preferred symbionts of pink (Ornithopus sativus) and yellow serradella (Ornithopus compressus) species [35,64,65,68]. Much less is known about rhizobia nodulating Ornithopus perpusillus and Ornithopus pinnatus, and the south American O. micranthus sp., although the two European species seem to be also nodulated by Clade II Bradyrhizobium symbionts [48,65,138]. Like the four European species, O. micranthus is infected by Bradyrhizobium strains, however, nothing is known about the phylogenetic affinities of symbiotic loci in these strains [139].

It has been assumed that Clade II Bradyrhizobium has evolved in the Mediterranean and that this process has been somehow connected to the diversification of Genisteae [60]. In fact, when considering the number of Genisteae genera, the Mediterranean is the major (although not primary) centre of divergence of this tribe [10,140,141]. The idea of coevolution of bradyrhizobia with Genisteae diversifying in the Mediterranean seems plausible as bradyrhizobia originating from this region occupy the outermost position within the nifD tree shown in Figure S4. However, the majority of Clade II nifD sequences form two internal branches, one of which comprises the “European” while the other the “American” isolates (Figure S4). It has to be mentioned that the “European” branch also includes bradyrhizobia that were recovered in the United States [44] and all American strains in this branch originate from Cytisus scoparius and are indistinguishable from European Clade II isolates. This is in line with a recent study [134], which revealed that European Genisteae legumes introduced to the United States show preference for “European” Clade II bradyrhizobia even in areas inhabited by native legumes nodulated by “American” Clade II strains.

Importantly, this branching pattern corroborates the assumption that the Mediterranean is the initial centre of Clade II divergence whereas the western part of the United States is a secondary centre of divergence (Figure 3 and Figure S4). The higher specificity of symbiosis with the Loteae and the fact that geographic ranges of these two tribes largely overlap indicate that the Loteae may have been a major driver in Clade II evolution. According to the “Jack-of-all-trades is master of none” hypothesis, one can assume that a specialist (in this case Clade II strains) shows much better ‘fitness’ with respect to a “generalist” group nodulating Genisteae [71]. Thus, the ability to form highly effective symbiosis with the two legume tribes (one of which is more restrictive) could explain the dissemination of Clade II bradyrhizobia across the Mediterranean and temperate parts of the Americas.

Clade III is the most heterogeneous and cosmopolitan group and it also shows the broadest host range amongst Bradyrhizobium major clades (see Table S2). In the nifD phylogenetic tree, this branch forms four, well supported inner branches referred to as III.1, III.2, III.3, and III.4 (see Figure 3 and Figure S3). Subclade III.1 comprises only two isolates from Senegal, while the remaining three subgroups are more numerous, containing bradyrhizobia originating from Genisteae (from American lupins) (Table S2). Unlike the cosmopolitan subclade III.3, Bradyrhizobium strains belonging to subclades III.2 and III.4 were detected solely in the Americas. Nevertheless, several independent reports indicate that these two groups are probably common among rhizobia infecting lupins that are native to South and North America [21,60,61,70,82]. In III.2 and III.4 subclades, bradyrhizobia originate from legumes belonging to 10 and 9 tribes, respectively, which implies that, although they have diversified in the Americas, there is a lack of evidence supporting a lasting co-evolution with Genisteae spp. (Table S2).

The largest and most cosmopolitan subclade III.3 comprises eight internal branches (III.3A-III.3H) (Figure 3). Bradyrhizobium strains originating from Genisteae are confined to branches III.3B, III.3C, and III.3G. The small branch III.3G contains identical nifD sequences from C. scoparius isolates originating from Spain and the United States, which suggests that this group may have a Mediterranean origin. In the predominantly Australian branch III.3B, four isolates originating from Spain (two strains from R. sphaerocarpa) and Portugal (two strains, one from introduced Acacia longifolia and one from native Cytisus grandiflorus) form an outer group. It cannot, however, be excluded that these strains, albeit originally from Australia, have extended their host range to the native Mediterranean genera [95]. On the other hand, the diverse branch III.C contains a single isolate from Argyrolobium rupestre (strain Arg105), originating from South Africa [28]. The branch III.C comprises the isolates from sub-Saharan Africa, southern Asia, Australia, as well as from Central and North Americas, therefore it can rightly be regarded as a cosmopolitan group.

Bradyrhizobium Clade IV strains nodulating Genisteae have been reported in the Mediterranean (in Algeria, Croatia, Italy, and Spain), among rhizobial symbionts of C. spinosa, G. aspalathoides, Laburnum anagyroides, L. mariae-josephae, R. monosperma, R. sphaerocarpa, and S. junceum [21,34,75,76]. Some of the isolates from L. mariae-josephae and Retama spp. belong to B. valentinum and B. retamae. Moreover, Clade IV bradyrhizobia were assigned to Bradyrhizobium icense, B. lablabi, Bradyrhizobium namibiense, Bradyrhizobium paxllaeri, and some as yet unnamed lineages (see Supplementary data Tables S1 and S2). This group shows a broad geographic range encompassing mainly arid and semi-arid parts of Africa, Asia, Australia, Europe, and the Americas [68,114,129,130,142].

Highly differentiated Clade VII comprises B. americanum, Bradyrhizobium ingae, B. iriomotense, B. manausense, and B. stylosanthis spp. (Supplementary data Table S1). The majority of Clade VII strains originate from North and South America, while some were isolated in south-east Asia (southern China, the Island of Okinawa, Thailand, and the Philippines) [143,144,145,146,147]. Given that Clade VII bradyrhizobia from south-east Asia occupy internal positions relative to the American strains, it can be assumed that this cluster has evolved in the Americas, possibly, in an area of hot and humid tropical climate. This can be deduced from the fact that this clade is common in tropical-humid (but not arid) parts of Central and South America, and the Caribbean [21,53,60,70,82]. Clade VII strains nodulate a broad range of, mainly, tropical legumes (Table S1), however, some strains originate from lupins that are endemic to south-eastern Brazil [60,61]. Like Clade VII, Clade XVI seems to be an American group. So far, Bradyrhizobium strains belonging to Clade XVI have been described among legume isolates from Costa Rica, Honduras, the Caribbean (the Island of Guadeloupe), and the United States [53,148,149,150]. Unlike Clade XVI strains that were isolated in Central America and the Caribbean which do not originate from Genisteae spp., all Clade XVI strains from the United States originate from Lupinus lepidus, Lupinus perennis, and A. strigosus [70].

In the nodA tree (Figure S3), Bradyrhizobium strains Arg62, Arg68, and Arg33 from the South African Argyrolobium sericeum cluster in Clade XV. This clade also comprises the isolates from Lotononis and Pearsonia spp.—the Crotalarieae genera endemic to southern Africa [1,28,151]. The grouping of these strains in the same cluster is not surprising considering the overlapping geographical ranges of the southern Genisteae genera and the Crotalarieae tribe in South Africa [27]. However, in the nifD tree (Figure 3), strain Arg62 groups within Clade III.3, while Arg33 has been included in Clade IV. This indicates that although nodA and nifD phylogenies are essentially congruent, there are some differences, most likely reflecting distinct evolutionary histories of these two symbiotic genes in particular clades.

Clade I has been described as a predominant group in temperate and tropical Australia, where this group of bradyrhizobia nodulate native legumes, primarily, members of the endemic Bossiaeeae-Mirbelieae tribes and the genus Acacia [68,114,132]. In addition, Clade I strains have been isolated outside this continent, usually from the introduced Australian Acacia species [95,152,153]. This implies that Clade I bradyrhizobia may have been co-introduced with Acacia spp. and that in their new habitats they out-competed the indigenous rhizobia in the process of nodulation of their native hosts. Importantly, Clade I bradyrhizobia were also reported in nodules of C. grandiflorus, L. micranthus, and Ulex europaeus (gorse), which can be regarded as an extension of Clade I strains’ range on native-Mediterranean hosts. This phenomenon of rapid adaptation to new legume hosts may be widespread in the genus Bradyrhizobium [80,95,154]. This can be concluded from the identification of other, presumably Australian groups, e.g. group III.3B (which has been mentioned above) as well as an enigmatic Clade XVIII (Figure 3). Clade XVIII is a phylogenetically distinct group, comprising nifD sequences (there is a lack of nod gene sequences for Clade XVIII in the GenBank database) which originate from Bradyrhizobium strains isolated from A. longifolia and A. saligna in Australia and A. saligna and Cytisus sp. in Portugal [155]. Although the Mediterranean origin of this group cannot be excluded, the association with Australian Acacia spp. in both Australia and in areas in Portugal that are infested by these mimosoid spp. strongly suggests that Clade XVIII has an Australian origin.

6. Fast-Growing Rhizobium Genera

In comparison to the genus Bradyrhizobium, much less is known about members of the fast-growing rhizobial genera that infect Genisteae plants. Nonetheless, work over the last 10 years has shown that Genisteae legumes are nodulated by both highly cosmopolitan genera as well as genera that occur rarely among rhizobial isolates.

The genera Mesorhizobium, Rhizobium, and Ensifer (=Sinorhizobium), along with Bradyrhizobium are regarded as the most cosmopolitan rhizobium groups due to their ability to nodulate a broad range of Fabaceae spp. [156]. However, available data indicate that these genera are not common symbionts of Genisteae species [156]. Mesorhizobium strains classified as M. loti nodulate with lupins, although they show a preference for Lotus spp., which, presumably, are their primary hosts. It seems, however, that M. loti is not the only Mesorhizobium species that is involved in root-nodule symbiosis with Genisteae. Recently, two Mesorhizobium strains isolated from North American lupins, one from Lupinus densiflorus, and the other from L. succulentus, were shown to have a phylogenetic affinity to Mesorhizobium ciceri—a species that until now has not been implicated in the symbiosis with genistoid legumes [157]. In the Mediterranean, Mesorhizobium strains nodulate with native Genisteae spp, including Genista saharae, R. raetam, Teline monspessulana, and three lupin species (see Table 1). However, only limited information is available about these strains especially their symbiotic loci [34,55,56,62]. Mesorhizobium strains were also recovered from root nodules of Argyrolobium lunare and A. velutinum in the Core Cape Subregion (the Fynbos) of South Africa. Interestingly, these isolates formed discrete branches on core gene and nodA phylogenetic trees, grouping together with strains nodulating Asphalathus spp. (tribe Crotalarieae), which indicates that these two genera are nodulated by closely related bacteria that may potentially form a single cross-inoculation group [27].

Although the isolation of Rhizobium strains from lupin nodules has been reported in a number of studies, to our knowledge the symbiotic effectiveness of these isolates on lupins has not been confirmed. Usually, strains described as Rhizobium, have not been sufficiently characterised at the molecular level or authentication tests on their original host have not been performed or proved negative [157,158,159]. For example, strain H 13-3 originally described as Rhizobium lupini, following more detailed analysis was reclassified as Agrobacterium sp. [160]. Also, two strains recently isolated from lupin species native to Morocco have been assigned to the genus Rhizobium based on the ARDRA analysis [161]. These strains require further characterization of selected core and symbiotic marker genes [111]. Nonetheless, there are reports indicating that members of the genus Rhizobium nodulate other Genisteae genera, including Adenocarpus spp., Argyrolobium uniflorum, C. spinosa, Cytisus spp. Genista spp., and R. raetam (see Table 1). However, as in the case of the lupin isolates, more detailed molecular characterization and authentication tests are needed to confirm their phylogenetic affinity and their symbiotic properties.

Ensifer (Sinorhizobium) strains have not been described in lupin nodules, which contrasts with several other Genisteae spp. that are nodulated by rhizobia belonging to this genus (see Table 1). For instance, Argyrolobium uniflorum and Genista saharae are infected exclusively by fast-growing rhizobium genera, in particular, Ensifer [29,30,31,55,56,91]. In the case of these two species, the predominance of Ensifer as symbiont may be caused by specific requirements of these particular Genisteae species, favouring this rhizobium genus. However, it may be related to the high salt and arid habitat of the legumes, which may favour Ensifer in comparison to other rhizobial genera [162].

In addition, to the four genera described above, Genisteae spp. are infected by three other fast-growing rhizobial genera. In 2005, Trujillo and co-workers described rhizobia classified as Ochrobactrum lupini, which were isolated in Argentina from native Lupinus honoratus [72]. Prior to this finding, this genus was assumed to comprise opportunistic pathogens and saprophytes living in soil and animal faeces [163]. Subsequently, Ochrobactrum strains were isolated in Spain from nodules of C. scoparius (Scotch broom) plants [47]. Also, Ochrobactrum rhizobia were described in root nodules of Acacia mangium in the Philippines and Thailand [164], as well as in nodules of Cicer arietinum in Pakistan [165].

The genus Microvirga which comprises soil and water saprophytes was included in the alpha-proteobacterial lineage of root-nodule bacteria only in 2012, although the first symbiotic strains were detected in nodules of Lupinus texensis in 2007 [87,166,167]. Recently, Microvirga strains were isolated from L. micranthus and L. luteus spp. in Tunisia, as well as from L. subcarnosus in the United States [79,80,157]. This indicates that Microvirga may be rather common among lupin isolates in both the Mediterranean and North America. It is unclear if Microvirga can nodulate Genisteae spp. other than lupins, however, aside from lupins, rhizobia belonging to this genus were also isolated from Listia angolensis in Zambia, Vigna sp. in Brazil, and from Vicia alpestris in the Caucasus, Russia [87,168,169].

The Phyllobacterium genus comprises bacteria that are well-known for their epiphytic and endophytic associations with plants [170]. Some phyllobacteria fix nitrogen, therefore, the occurrence of root-nodule bacteria in this genus is not unexpected [161]. Indeed, an isolate classified as Phyllobacterium trifolii was found nodulating white lupin (Lupinus albus) in addition to its original white clover (Trifolium repens) host. However, P. trifolii strains formed ineffective nodules on white lupins, which indicated that lupins are not their natural hosts [171]. Nonetheless, Phyllobacterium rhizobia were described in Tunisia, in the nodules of L. micranthus [79]. Prior to this finding, Phyllobacterium strains were identified as symbionts of Adenocarpus hispanicus, Genista saharae and G. tinctoria, R. sphaerocarpa, and S. junceum (see Table 1). This genus may be specialized in the nodulation of genistoid legumes, however, it cannot be excluded that some of the Phyllobacterium isolates are endophytic bacteria that are lacking the ability to form nodules [172].

The data discussed indicate that although members of the genera Microvirga, Ochrobactrum, and Phyllobacterium nodulate various legume-hosts (including some members of the tribe Genisteae), and show broad geographical range, they most likely prevail among root-nodule bacteria in only discrete environments [156]. While all the Genisteae isolates characterised so far are α–rhizobia, this may change if authentication tests confirm symbiotic-nitrogen-fixing properties of recently described lupin isolates belonging to the genus Burkholderia [157].

7. Summary

The high level of diversity shown by Genisteae microsymbionts most likely reflects the complex evolutionary history of this legume tribe, which can be linked to long-distance dispersal and radiation events in southern Africa, the Mediterranean, and the Americas. One can assume that following the dispersal, rhizobial communities which were encountered in newly colonized areas often differed from rhizobial symbionts in the areas of Genisteae primary occurrence. The lack of appropriate rhizobial symbionts is often perceived as an obstacle that is impeding the dispersal of particular Fabaceae spp. [173]. However, Fabaceae spp. may interact with indigenous rhizobia forming less efficient symbiosis [174,175]. This “opportunistic” strategy of the two symbiotic partners results in a broader range of rhizobial symbionts, and may explain why certain rhizobial genera cannot be regarded as optimal partners of their legume hosts. In the case of Genisteae spp., the necessity of adaptation to local rhizobia is manifested by the formation of symbiotic associations with members of at least seven rhizobial genera, out of the 16 genera that are known for their symbiotic nitrogen-fixation ability.

Despite the progress that has been made in the last ten years in research focused on the fast-growing genera nodulating Genisteae spp., the current knowledge concerning this diverse group of rhizobia lags significantly behind the understanding of the symbiosis that is established between Genisteae spp. and their Bradyrhizobium symbionts. Nonetheless, these efforts revealed three new genera, out which Microvirga appears to comprise effective symbionts of at least some lupin species in North America and the Old World [79,80,167].

Unlike the fast-growing rhizobia, the genus Bradyrhizobium appears to be a dominant group nodulating the majority of Genisteae species. Genisteae-nodulating bradyrhizobia cluster within both B. japonicum and B. elkanii superclades, belonging to seven distinct species, and a large number of partially characterized lineages. In symbiotic gene phylogenies, Bradyrhizobium symbionts are scattered in several distinct groups, each comprising strains originating from phylogenetically distinct legumes. This indicates that the capacity for nodulation of Genisteae spp. appeared independently in various symbiotic gene clades, and that the adaptation towards nodulation of this tribe was not a multi-step process. We assume that this process could be related to the loss of the noeI gene, which is involved in the methylation of the fucose moiety at the Nod factor reducing end [176], and which seems to be in a form of pseudogene in Bradyrhizobium strains nodulating Genisteae whose genomic sequences are available [60,73,86,177]. The exception could be Bradyrhizobium Clade II, which unlike other clusters comprises strains that appear to be specialized in the nodulation of Genisteae, but also Loteae species. It can be presumed that Clade II is an example of the long co-evolution process of Genisteae and their bradyrhizobial symbionts, although the tribe Loteae also may have played an important role.