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Genetic diversity of rhizobial strains isolated from the relict legumes Gueldenstaedtia monophylla and G. verna growing in the republics of Altai and Buryatia (Russia)
Abstract
For the first time, bacteria were isolated and identified from the root nodules of relict legumes Gueldenstaedtia monophylla Fisch. and G. verna (Georgi) Boriss. growing in the republics of Altai and Buryatia. The taxonomic position of the 29 obtained isolates was determined by sequencing the 16S rRNA gene (rrs). Showing a significant biodiversity, the isolates from G. monophylla and G. verna belonged to five genera of the order Rhizobiales: Mesorhizobium and Phyllobacterium (family Phyllobacteriaceae), Rhizobium (family Rhizobiaceae), Bosea (family Boseaceae), Bradyrhizobium (family Bradyrhizobiaceae). Three isolates which belonged to the species Bradyrhizobium valentinum and Rhizobium alamii showed 100 % of rrs-similarity with the type strains B. valentinum LmjM3T and R. alamii GBV016T, respectively. Six isolates of the genera Bosea and Rhizobium had a low level of rrs-similarity with the closest type strains (less than 99.5 %), which indicates that they may be assigned to new species. The data obtained can be used to itemise taxonomy within the order Rhizobiales, as well as to reveal the mechanisms of the formation of specific plant-microbial relationships during the evolution of symbiosis by studying the intermediate link between the extinct and modern rhizobia-legume symbiotic systems.
Метод газоразрядной визуализации (ГРВ, электрофотографии) позволяет регистрировать и количественно оценивать
свечение, возникающее вблизи поверхности объекта (семени), при помещении его в электромагнитное поле высокой напряжённости. Методом газоразрядной визуализации в сочетании с автоматическим анализом цифровых газоразрядных
изображений выявлены и проанализированы скрытые дефекты изученных семян. Обнаружена невыполненность образцов семян сосны кедровой сибирской (Pinus sibirica Du Tour) и биогенное повреждение бактериального происхождения семян кукурузы сахарной (Zea mays L.). Показано, что невыполненные (пустые) семена имеют пониженные значения
средней интенсивности цифровых газоразрядных изображений. Согласно полученным данным, методы газоразрядной
визуализации и микрофокусной рентгенографии показали высокую эффективность (> 90%) точности при выявлении
невыполненных (пустых) семян сосны кедровой сибирской. Проведена сравнительная оценка газоразрядных показателей
и всхожести семян как интегральных показателей для оценки биологической полноценности семян кукурузы сахарной.
Установлено, что образец семян кукурузы сахарной гибрида Краснодарский 194 МВ характеризовался сниженными
значениями средней интенсивности газоразрядных изображений, а также средней яркости цифровых рентгеновских
изображений по сравнению с тремя другими образцами семян. Образец гибрида Краснодарский 194 МВ характеризо-
вался худшими посевными качествами: энергией прорастания, всхожестью, длиной корня и длиной ростка. Показано,
что семена Краснодарский 194 MB были поражены фитопатогенными бактериями Pantoea ananatis. Обнаружена
средняя обратная корреляция ряда характеристик газоразрядного свечения (площадь, суммарная интенсивность) со среднеквадратическим отклонением яркости цифровых рентгеновских изображений, а также слабая достоверная связь большинства газоразрядных характеристик с посевными качествами. Исследованиями подтверждено, что метод газоразрядной визуализации в сочетании с автоматическим анализом цифровых газоразрядных изображений может служить
эффективным дополнительным инструментом для оперативного выявления дефектных семян.The gas-discharge visualization (GDV, electrophotography) method allows recording and quantifying the glow that occurs near the surface of the object (seed), when placing it in an electromagnetic field of high intensity. The hidden defects – emptiness of Pinus sibirica Du Tour seeds and biogenic damage (by phytopathogenic bacteria Pantoea ananatis) of Zea mays L. seeds were revealed and analyzed by the method of gas discharge visualization in combination with automatic analysis of digital gas-discharge images. It is shown that empty seeds have reduced values of the averaged intensity of digital gas discharge images. According to the data obtained, the methods of gas-discharge imaging (electrophotography) and microfocus radiography showed high efficiency (> 90%) of accuracy in the detection of empty
seeds of Pinus sibirica. It was found that the sample of Zea mays seeds (hybrid Krasnodarskiy 194 MV) was characterized
by reduced values of the average intensity of gas-discharge images, as well as the average brightness of digital X-ray images, compared with the other three seed samples. The seed sample of hybrid Krasnodarskiy 194 MB was characterized
by the worst sowing qualities: emergence rate, germination, root length and shoot length. It was shown that the Krasnodarskiy 194 MB seeds were affected by phytopathogenic bacteria Pantoea ananatis. The average inverse correlations
of a number of characteristics of gas-discharge glow (area, total intensity) with the standard deviation of brightness of
digital X-ray images, as well as weak reliable correlation of most gas-discharge characteristics with seeding qualities were found. Comparative assessment of gas discharge indices and seedlings germination as integral indices for evaluation
of biological completeness of Zea mays seeds was carried out. Research has confirmed that the method of gas discharge visualization in combination with automatic analysis of digital gas-discharge images can be used as an effective additional tool for rapid detection of defective seeds.
We present the latest version of the Molecular Evolutionary Genetics Analysis (MEGA) software, which contains many sophisticated
methods and tools for phylogenomics and phylomedicine. In this major upgrade, MEGA has been optimized for use on 64-bit computing
systems for analyzing bigger datasets. Researchers can now explore and analyze tens of thousands of sequences in MEGA. The
new version also provides an advanced wizard for building timetrees and includes a new functionality to automatically predict
gene duplication events in gene family trees. The 64-bit MEGA is made available in two interfaces: graphical and command line.
The graphical user interface (GUI) is a native Microsoft Windows application that can also be used on Mac OSX. The command
line MEGA is available as native applications for Windows, Linux, and Mac OSX. They are intended for use in high-throughput
and scripted analysis. Both versions are available from www.megasoftware.net free of charge.
Two bacterial strains Ach-343 and Opo-235 were isolated, respectively from nodules of Miocene-Pliocene relict legumes Astragalus chorinensis Bunge and Oxytropis popoviana Peschkova originated from Buryatia (Baikal Lake region, Russia). For identification of these strains the sequencing of 16S rRNA (rrs) gene was used. Strain Opo-235 belonged to the species Mesorhizobium japonicum, while the strain Ach-343 was identified as M. kowhaii (100 and 99.9% rrs similarity with the type strains MAFF 303099T and ICMP 19512T, respectively). Symbiotic genes of these strains as well as some genes that promote plant growth (acdS, gibberellin- and auxin-synthesis related genes) were searched throughout the whole genome sequences. The sets of plant growth-promoting genes found were almost identical in both strains, whereas the sets of symbiotic genes were different and complemented each other with several nod, nif, and fix genes. Effects of mono- and co-inoculation of Astragalus sericeocanus, Oxytropis caespitosa, Glycyrrhiza uralensis, Medicago sativa, and Trifolium pratense plants with the strains M. kowhaii Ach-343 and M. japonicum Opo-235 expressing fluorescent proteins mCherry (red) and EGFP (green) were studied in the gnotobiotic plant nodulation assay. It was shown that both strains had a wide range of host specificity, including species of different legume genera from two tribes (Galegeae and Trifolieae). The effects of co-microsymbionts on plants depended on the plant species and varied from decrease, no effect, to increase in the number of nodules, nitrogen-fixing activity and plant biomass. One of the reasons for this phenomenon may be the discovered complementarity in co-microsymbionts of symbiotic genes responsible for the specific modification of Nod-factors and nitrogenase activity. Localization and co-localization of the strains in nodules was confirmed by the confocal microscopy. Analysis of histological and ultrastructural organization of A. chorinensis and O. popoviana root nodules was performed. It can be concluded that the strains M. kowhaii Ach-343 and M. japonicum Opo-235 demonstrate lack of high symbiotic specificity that is characteristic for primitive legume-rhizobia systems. Further study of the root nodule bacteria having complementary sets of symbiotic genes will contribute to clarify the evolutionary paths of legume-rhizobia relationships and the mechanisms of effective integration between partners.
Genetic variability of the rare species Gueldenstaedtia monophylla from 7 natural populations in the central part of its range (Ongudai district, Altai Republic) was studied. To characterize the genetic diversity of this rare relict species at the population level, SDS-electrophoresis of seed storage proteins was used. Polypeptide spectra of seeds contained from 17 to 32 protein components, of which 28 were polymorphic. The populations of G. monophylla were revealed to have a sufficiently high level of genetic polymorphism, the genetic similarity index within the populations studied ranged from 0.673 to 0.813. The highest variability of seed storage proteins was found in the populations Inegen (0.673) and Malaya Inya (0.734). The lowest level of variability of the polypeptide spectra was in the population Bol’shoy Yaloman (0.813). The Nei genetic distance between the populations studied was 0.018–0.215, the greatest distance in the protein spectra was found between Inegen and Malaya Inya (0.215). Inegen was the most remote from the other populations, the Nei distance between this population and all other populations varying from 0.113 to 0.215. With AMOVA, it was found that the share of intra-population variability is 53 % and inter-population, 47 %. Perhaps this high genetic diversity in populations of G. monophylla is provided and maintained by such biological characteristics of the species as cross-pollination, high life expectancy and a long reproductive period. The results of our study suggest that some rare species are able to maintain high levels of genetic diversity, even in a small-size population. The relatively high level of genetic variability indicates that the current genetic drift and inbreeding do not pose a threat to the survival of the species.
Genetic variability of rare species G. monophylla of 7 natural populations in the central part of its range (Ongudai district of the Altai Republic) was studied. To characterize the genetic diversity that rare relict species as the species and on the population level SDS-electrophoresis seed storage protein was used. Polypeptide spectra seeds contain from 17 to 32 protein components, of which 28 were polymorphic. The populations of G. monophylla was revealed sufficiently high level of genetic polymorphism, genetic similarity index within populations studied ranged from 0.673- 0,813. The highest variability of seed storage proteins found in populations Inegen (S = 0,673) and Small Yin (S = 0,734). The lowest level of variability of the spectra of the polypeptide identified in a population of Big Yaloman S = 0,813. The genetic distance of Nei (D) between the studied populations was 0,018-0,215, the greatest distance in the protein spectra was found between populations Inegen and M. Yin – 0,215. Population Inegen most geographically isolated from other populations we studied, Nei distance between this population and all other populations varied from 0,113 to 0,215. With AMOVA was found that the share of intra-population variability account for 53 % and inter-population – 47 %. Perhaps quite high genetic diversity in populations of G. monophylla is provided and maintained by such biological characteristics of the species, as the cross-pollination, most of the life expectancy and long reproductive period. The results of our study suggest that some rare species are able to maintain high levels of genetic diversity, even with a small amount of the population. The relatively high level of genetic variability indicates that the current genetic drift and inbreeding does not pose a threat to the survival of the species.
Tibetia and Gueldenstaedtia are two morphologically similar and small genera in Fabaceae, with distributions largely corresponding to the Sino-Himalayan and Sino-Japanese subkingdoms in eastern Asia, respectively. These two genera have confusing relationships based on morphology; therefore, we aimed to provide a clear understanding of their phylogenetic and biogeographic evolution within eastern Asia. In our investigations we included 88 samples representing five Gueldenstaedtia species, five Tibetia species, and outgroup species were sequenced using five markers (nuclear: ITS; chloroplast: matK, trnL-F, psbA-trnH and rbcL). Our phylogenetic results support (1) the monophyly of Tibetia and of Gueldenstaedtia, respectively; and (2) that Tibetia and Gueldenstaedtia are sister genera. Additionally, our data identified that Tibetia species had much higher sequence variation than Gueldenstaedtia species. Our results suggest that the two genera were separated from each other about 17.23 million years ago, which is congruent with the Himalayan orogeny and the uplift of the Tibetan Plateau in the mid Miocene. The divergence of Tibetia and Gueldenstaedtia is strongly supported by the separation of the Sino-Himalayan and Sino-Japanese region within eastern Asia. In addition, the habitat heterogeneity may accelerate the molecular divergence of Tibetia in the Sino-Himalayan region.
Eleven extra-slow-growing strains were isolated from nodules of the relict legume Vavilovia
formosa growing in North Ossetia (Caucasus) and Armenia. All isolates formed a single rrs cluster together with the type strain Tardiphaga
robiniae LMG 26467T, while the sequencing of the 16S–23S rDNA intergenic region (ITS) and housekeeping genes glnII, atpD, dnaK, gyrB, recA and rpoB divided them into three groups. North Ossetian isolates (in contrast to the Armenian ones) were clustered separately from the type strain LMG 26467T. However, all isolates were classified as T. robiniae because the DNA–DNA relatedness between them and the type strain LMG 26467T was 69.6 % minimum. Two symbiosis-related genes (nodM and nodT) were amplified in all isolated Tardiphaga strains. It was shown that the nodM gene phylogeny is similar to that of ITS and housekeeping genes. The presence of the other symbiosis-related genes in described Tardiphaga strains, which is recently described genus of rhizobia, as well as their ability to form nodules on any plants are under investigation.
Based on sequence data of the nuclear ITS and plastid matK, trnL-F and psbA-trnH markers of 162 species (169 accessions), the relationships and monophyly of tribe Hedysareae and its close relatives were assessed, with special reference to the infrageneric phylogeny
of Hedysarum. The results showed that Hedysareae sensu Lock is not monophyletic, and its relationships with tribe Galegeae are unclear. Tribe Galegeae is polyphyletic. Hedysareae sensu Lock includes two strongly supported clades: the Caraganean clade and the Hedysaroid clade. Tribe
Caraganeae Ranjbar was supported to be recognized based on the Caraganean clade, but it is herein suggested to be re-circumscribed by excluding Chesneya and Gueldenstaedtia. Our results support treating the Hedysaroid clade as tribe Hedysareae, comprising nine genera: Alhagi,
Corethrodendron, Ebenus, Eversmannia, Greuteria, Hedysarum, Onobrychis, Sulla and Taverniera. Hedysarum as delimited here consists of three main clades: the first clade (the mesic group) corresponds to H. sect. Hedysarum;
the second clade (the xeric group) is the re-defined H. sect. Multicaulia, consisting of the core group of H. sect. Multicaulia plus the former genus Sartoria; and the third clade (the psychrophilic group) includes the monospecific H. sect. Stracheya
(with H. tibeticum) and two species previously placed in H. sect. Multicaulia (H. kumaonense, H. lehmannianum).
The Gram-negative, rod-shaped slow-growing strains Vaf-17, Vaf-18(T) and Vaf-43 were isolated from the nodules of Vavilovia formosa plants growing in the hard-to-reach mountainous region of the North Ossetian State Natural Reserve (north Caucasus, Russian Federation). The sequencing of 16S rDNA (rrs), ITS region and five housekeeping genes (atpD, dnaK, recA, gyrB and rpoB) showed that the isolated strains were most closely related to the species Bosea lathyri (class Alphaproteobacteria, family Bradyrhizobiaceae) which was described for isolates from root nodules of Lathyrus latifolius. However the sequence similarity between the isolated strains and the type strain B. lathyri LMG 26379(T) for the ITS region was 90 % and for the housekeeping genes it was ranged from 92 to 95 %. All phylogenetic trees, except for the rrs-dendrogram showed that the isolates from V. formosa formed well-separated clusters within the Bosea group. Differences in phenotypic properties of the B. lathyri type strain and the isolates from V. formosa were studied using the microassay system GENIII MicroPlate BioLog. Whole-cell fatty acid analysis showed that the strains Vaf-17, Vaf-18(T) and Vaf-43 had notable amounts of C16:0 (4.8-6.0 %), C16:0 3-OH (6.4-6.6 %), C16:1 ω5c (8.8-9.0 %), C17:0 cyclo (13.5-13.9 %), C18:1 ω7c (43.4-45.4 %), C19:0 cyclo ω8c (10.5-12.6 %) and Summed Feature (SF) 3 (6.4-8.0 %). The DNA-DNA relatedness between the strains Vaf-18(T) and B. lathyri LMG 26379(T) was 24.0 %. On the basis of genotypic and phenotypic analysis a new species Bosea vaviloviae sp. nov. (type strain RCAM 02129(T) = LMG 28367(T) = Vaf-18(T)) is proposed.
Two novel Gram-negative strains (CCBAU 03422T and CCBAU 03415) isolated from root nodules of Sophora flavescens were phylogenetically classified into the genus of Phyllobacterium based on the comparative analysis of 16S rRNA and atpD genes. They showed 99.8% rRNA gene sequence similarities to Phyllobacterium brassicacearum LMG 22836T, and CCBAU 03422T showed 91.2% and 88.6% atpD gene similarities to strains P. endophyticum LMG 26470T and P. brassicacearum LMG 22836T, respectively. Strain CCBAU 03422T contained Q-10 as its major quinone and showed cellular fatty acid profile, carbon source utilization and other phenotypic characteristics differing from type strains of the related species. DNA-DNA relatedness (lower than 48.8%) further confirmed the differences between the novel strains and the type strains of related species. Strain CCBAU 03422T could nodulate and fix nitrogen effectively on its original host plant, Sophora flavescens. Based upon the studies mentioned above, a novel species named as Phyllobacterium sophorae is proposed and the type strain is CCBAU 03422T (= A-6-3T = LMG 27899T = HAMBI 3508T).
Sixteen bacterial strains were isolated from root nodules of Vavilovia formosa plants originated from the North Ossetian State Natural Reserve (Caucasus, Russia). Phylogenetic analysis of these strains was performed using partial 16S rRNA gene and internally transcribed spacer (ITS) sequences. The results showed that the isolates belong to three families of root nodule bacteria. Twelve of them were related to the genus Rhizobium (family Rhizobiaceae) but four strains can be most probably identified as Phyllobacterium-related (family Phyllobacteriaceae), Bosea- and Rhodopseudomonas-related (family Bradyrhizobiaceae). Amplified fragment length polymorphism clustering was congruent with ITS phylogeny but displayed more variability for Rhizobium isolates, which formed a single group at the level of 30 % similarity. We expect that the isolates obtained can belong to new taxa at genus, species or subspecies levels. The results of PCR amplification of the nodulation genes nodC and nodX showed their presence in all Rhizobium isolates and one Rhodopseudomonas-related isolate. The nodC gene sequences of V. formosa isolates were closely related to those of the species Rhizobium leguminosarum bv. viciae but formed separate clusters and did not intermingle with any reference strains. The presence of the nodX gene, which is necessary for nodulation of Afghan peas (Pisum sativum L.) originated from the Middle East, allows the speculation that these wild-type pea cultivars may be the closest existing relatives of V. formosa. Thus, the studies of genetic diversity and symbiotic genes of V. formosa microsymbionts provide the primary information about their phylogeny and contribute to the conservation of this relict leguminous species.
A strain named S658T was isolated from a Lotus corniculatus nodule in a soil of Uruguay. The phylogenetic analyses of 16S rRNA and atpD genes showed that this strain clusters within genus Phyllobacterium. Its closest related species were in both cases P. trifolii PETP02T with 99.8% identity in the 16S rRNA gene and 96.1% in the atpD gene. The 16S rRNA gene contains an insert at the begining of the sequence that has no homologies with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. The strain S658T differed from its closest relatives in the growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a novel species of Phyllobacterium for which the name Phyllobacterium loti sp. nov. is proposed (type strain S658T= LMG 27289T = CECT 8230T).
A strain named PEPV15T was isolated from a Phaseolus vulgaris nodule in a soil of Northern Spain. The phylogenetic analyses of 16S rRNA and atpD genes showed that this strain belongs to the genus Phyllobacterium. The closest related species were in both cases P. brassicacearum, P. bourgognense and P. trifolii whose type strains presented 98.9, 98.6 and 98.4% identities, respectively, in the 16S rRNA gene and 88.1, 87.5 and 88.7%, respectively, in the atpD gene. The strain PEPV15T contained Q-10 as major quinone (88%) and low amounts of Q-9 (12%). It differed from its closest relatives in the growth in diverse culture conditions and in the assimilation of several carbon sources. The strain was not able to reproduce nodules in P. vulgaris. The results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain belongs to a new species of genus Phyllobacterium for which the name Phyllobacterium endophyticum sp. nov. is proposed (type strain PEPV15T= LMG 26470T = CECT 7949T).
Three chickpea rhizobial strains (CCBAU 83963T, CCBAU 83939 and CCBAU 83908) which were identified previously as a distinctive genospecies were further studied and compared taxonomically to the related species in the genus of Mesorhizobium in the current studies. Results from SDS-PAGE of whole-cell soluble proteins showed their differences from other closely related known Mesorhizobium species. Values of DNA-DNA hybridization varied from 15.28 to 50.97% between the representative strain CCBAU 83963T and the type strains of the defined Mesorhizobium species (except for M. thiogangeticum). Representative strain CCBAU 83963T contained characteristic fatty acids similar to the components of other Mesorhizobium species, but it possessed the highest concentrations (44.88%) of 19:0 cyclo ω8c and 17:0 iso (3.62%). Strain CCBAU 83963T had phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG) as its three major polar lipids, and ornithine-containing lipid (OL), phosphatidyl-N-dimethylethanolamine (DMPE) and cardiolipin (CL) as its three minor components. Nodulation tests demonstrated the distinct symbiotic character of strain CCBAU 83963T; only Cicer arietinum, its host plant, could be invaded to form effective nitrogen fixation nodules. Narrow spectrum on the utilization of sole carbon sources, lower resistance to antibiotics, NaCl, pH and temperature differentiated these novel rhizobia from other related Mesorhizobium species. Based upon all the comparative analyses, a novel species Mesorhizobium muleiense sp. nov. was proposed with CCBAU 83963T (=HAMBI 3264T =CGMCC 1.11022T) as the type strain.
Plant growth‐promoting bacteria (PGPB) have been reported to stimulate root morphogenesis. To improve our knowledge of the PGPB effect, the early modifications of Brassica napus root system architecture induced by the PGPB Phyllobacterium sp. (29‐15) were analysed. ________Plants were grown in Petri dishes on a vertical medium supplemented with variable doses of Phyllobacterium sp. in gnotobiotic conditions. Root system elementary variables were measured in a nondestructive manner and the distribution of the bacteria throughout the primary root was quantified. ________ Phyllobacterium sp. in doses from 3 × 107 to 3 × 108 colony‐forming units ml−1 significantly promoted B. napus total root length up to 50% by increasing both lateral root density throughout the primary root and growth rate of mature lateral roots. The primary root was progressively colonized by the bacteria from the tip to the base and the number of colonizing cells was positively correlated with the inoculum density.
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Relationships between inoculum density, root colonization and root system architecture emphasized the relevance of this approach to specify PGPB effects on plants.
A group of exopolysaccharide-producing bacteria was isolated from the root environment of Arabidopsis thaliana. The genetic diversity revealed by REP-PCR fingerprinting indicated that the isolates correspond to different strains. 16S rRNA gene sequence analysis showed that the isolates are closely related to the strains Rhizobium sp. YAS34 and USDA 1920, respectively isolated from sunflower roots and Medicago ruthenica nodules. These bacteria belong to the Rhizobium lineage of the Alphaproteobacteria, and the closest known species was Rhizobium sullae. DNA-DNA hybridization experiments and biochemical analysis demonstrated that the nine strains isolated from A. thaliana and Rhizobium strains YAS34 and USDA 1920 constitute a novel species within the genus Rhizobium, for which the name Rhizobium alamii sp. nov. is proposed. The type strain is GBV016(T) (=CFBP 7146(T) =LMG 24466(T)).
Root-adhering soil (RAS) forms the immediate environment where plants take up water and nutrients for their growth. We report
the effect of an exopolysaccharide (EPS)-producing rhizobacterium (strain YAS34) on the physical properties of sunflower (Helianthus annuus L.) RAS, associated with plant growth promotion, under both water stress and normal water supply conditions. Strain YAS34
was isolated as a major EPS-producing bacterium from the rhizoplane of sunflowers grown in a French dystric cambisol. Strain
YAS34 was assigned to the Rhizobium genus by 16S ribosomal DNA gene sequencing. Inoculation of sunflower seeds and soil with strain YAS34 caused a significant
increase in RAS per root dry mass (dm) (up to 100%) and a significant increase in soil macropore volume (12 to 60 μm in diameter).
The effect of inoculation on sunflower shoot dm (up to +50%) and root dm (up to +70%) was significant under both normal and
water stress conditions. Inoculation with strain YAS34 modified soil structure around the root system, counteracting the negative
effect of water deficit on growth. Using [15N]nitrate, we showed that inoculation made the use of fertilizer more effective by increasing nitrogen uptake by sunflower
plantlets.
Both root architecture and plant N nutrition are altered by inoculation with the plant growth-promoting rhizobacteria (PGPR) Phyllobacterium strain STM196. It is known that NO3- and N metabolites can act as regulatory signals on root development and N transporters. In this study, we investigate the possible interrelated effects on root development and N transport. We show that the inhibition of Arabidopsis lateral root growth by high external NO3- is overridden by Phyllobacterium inoculation. However, the leaf NO3- pool remained unchanged in inoculated plants. By contrast, the Gln root pool was reduced in inoculated plants. Unexpectedly, NO3- influx and the expression levels of AtNRT1.1 and AtNRT2.1 genes coding for root NO3- transporters were also decreased after 8 days of Phyllobacterium inoculation. Although the mechanisms by which PGPR exert their positive effects remain unknown, our data show that they can optimize plant development independently from N supply, thus alleviating the regulatory mechanisms that operate in axenic conditions. In addition, we found that Phyllobacterium sp. elicited a very strong induction of AtNRT2.5 and AtNRT2.6, both genes preferentially expressed in the shoots whose functions are unknown.
Bacterial strain PETP02(T) was isolated from nodules of Trifolium pratense growing in a Spanish soil. Phylogenetic analysis of the 16S rRNA gene sequence showed that this strain represents a member of the genus Phyllobacterium. However, divergence found with the 16S rRNA gene sequence of the single recognized species of this genus, Phyllobacterium myrsinacearum, indicated that strain PETP02(T) belongs to a different species. The results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium trifolii sp. nov. is proposed. The type strain is PETP02(T) (=LMG 22712(T)=CECT 7015(T)). This strain was strictly aerobic and used several carbohydrates as carbon source. It was not able to reduce nitrate. Aesculin hydrolysis was negative. It did not produce urease, arginine dihydrolase, gelatinase or beta-galactosidase. The DNA G+C content was 56.4 mol%. The nodD gene of this strain showed a sequence closely related to those of strains able to nodulate Lupinus. Infectivity tests showed that this strain is able to produce nodules in both Trifolium repens and Lupinus albus.
Gram-negative bacteria were isolated from the rhizoplane of Brassica napus in France and from root nodules of Argyrolobium uniflorum, Astragalus algerianus and Lathyrus numidicus growing in the infra-arid zone of southern Tunisia. Based on phylogenetic analysis of the 16S rRNA gene sequences, the seven isolates belong to the Alphaproteobacteria and are related to Phyllobacterium myrsinacearum strains. The isolates formed three clusters; clusters A and C consist of Tunisian strains, whereas cluster B consists of two strains from Brassica napus from France. Phylogenetic reconstruction based on the atpD gene strongly supports their affiliation to the genus Phyllobacterium. DNA-DNA hybridizations revealed that (i) none of the isolates belong to the species P. myrsinacearum, (ii) clusters A and C represent two distinct genomospecies and (iii) the two strains of cluster B represent two separate genomospecies. Distinctive phenotypic features were deduced from numerical analysis of phenotypic data. Based on this polyphasic approach, four novel species are proposed: Phyllobacterium leguminum sp. nov. (type strain ORS 1419T = CFBP 6745T = LMG 22833T), Phyllobacterium ifriqiyense sp. nov. (type strain STM 370T = CFBP 6742T = LMG 22831T), Phyllobacterium brassicacearum sp. nov. (type strain STM 196T = CFBP 5551T = LMG 22836T) and Phyllobacterium bourgognense sp. nov. (type strain STM 201T = CFBP 5553T = LMG 22837T). The description of the genus Phyllobacterium is emended accordingly.
The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2% similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1% similarity, respectively) and R. tropici IIB CIAT 899T (90.6% and 91.8% similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8% similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA-DNA hybridization showed means of 28 and 25% similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).
Two Gram-stain-negative strains, RCAM04680T and RCAM04685, were isolated from root nodules of the relict legume Caragana jubata (Pall.) Poir. originating from the south-western shore of Lake Khuvsgul (Mongolia). The 16S rRNA gene (rrs) sequencing data showed that these novel isolates belong to the genus Bosea and are phylogenetically closest to the type strains Bosea lathyri LMG 26379T, Bosea vaviloviae LMG 28367T, Bosea massiliensis LMG 26221T and Bosea lupini LMG 26383T (the rrs-similarity levels were 98.7-98.8 %). The recA gene of strain RCAM04680T showed the highest sequence similarity to the type strain B. lupini LMG 26383T (95.4 %), while its atpD gene was closest to that of B. lathyri LMG 26379T (94.4 %). The ITS, dnaK and gyrB sequences of this isolate were most similar to the B. vaviloviae LMG 28367T (86.8 % for ITS, 90.4 % for the other genes). The most abundant fatty acid was C18 : 1ω7c (40.8 %). The whole genomes of strains RCAM04680T and RCAM04685 were identical (100 % average nucleotide identity). The highest average nucleotide identity value (82.8 %) was found between the genome of strain RCAM04680T and B. vaviloviae LMG 28367T. The common nodABC genes required for legume nodulation were absent in both strains; however, some other symbiotic nol, nod, nif and fix genes were detected. Based on the genetic study, as well as analyses of the whole-cell fatty acid compositions and phenotypic properties, a new species, Boseacaraganae sp. nov. (type strain RCAM04680T (=LMG 31125T), is proposed.
Gram-negative strains Tri-36, Tri-38, Tri-48Tand Tri-53 were isolated from root nodules of the relict legume Oxytropis triphylla (Pall.) Pers. originating from Zunduk Cape (Baikal Lake region, Russia). 16S rRNA gene sequencing showed that the novel isolates were phylogenetically closest to the type strains Phyllobacterium sophorae LMG 27899T, Phyllobacterium brassicacearum LMG 22836T, Phyllobacterium endophyticum LMG 26470Tand Phyllobacterium bourgognense LMG 22837Twhile similarity levels between the isolates and the most closely related strain P. endophyticum LMG 26470Twere 98.8-99.5 %. The recA and glnII genes of the isolates showed highest sequence similarities with P. sophorae LMG 27899T(95.4 and 89.5 %, respectively) and P. brassicacearum LMG 22836T(91.4 and 85.1 %, respectively). Comparative analysis of phenotypic properties between the novel isolates and the closest reference strains P. sophorae LMG 27899T, P. brassicacearum LMG 22836Tand P. endophyticum LMG 26470Twas performed using a microassay system. Average nucleotide identities between the whole genome sequences of the isolates Tri-38 and Tri-48Tand P. sophorae LMG 27899T, P. brassicacearum LMG 22836Tand P. endophyticum LMG 26470Tranged from 79.23 % for P. endophyticum LMG 26470Tto 85.74 % for P. sophorae LMG 27899T. The common nodABC genes required for legume nodulation were absent from strains Tri-38 and Tri-48T, although some other symbiotic nod and fix genes were detected. On the basis of genotypic and phenotypic analysis, a novel species, Phyllobacterium zundukense sp. nov. (type strain Tri-48T=LMG 30371T=RCAM 03910T), is proposed.
Ten rhizobial strains were isolated from root nodules of a relict legume Oxytropis popoviana Peschkova. For identification of the isolates sequencing of rrs, ITS (internal transcribed spacer) region and housekeeping genes recA, glnII and rpoB was used. Nine fast-growing isolates were Mesorhizobium-related: eight strains were identified as M. japonicum and one isolate belonged to M. kowhaii. The only slow-growing isolate was identified as Bradyrhizobium sp. Two strains, M. japonicum Opo-242 and Bradyrhizobium sp. Opo-243, were isolated from the same nodule. Symbiotic genes of these isolates were searched throughout the whole genome sequences. The common nodABC genes and other symbiotic genes required for the plant nodulation and nitrogen fixation were present in the isolate Opo-242. The strain Opo-243 did not contain the principal nod, nif and fix genes, however five genes (nodPQ, nifL, nolK and noeL) affecting the specificity of plant-rhizobia interactions, but absent in the isolate Opo-242, were detected. The strain Opo-243 could not induce nodules, however significantly accelerated the root nodule formation after co-inoculation with the isolate Opo-242. Thus we demonstrated that taxonomically different strains of the archaic symbiotic system can be co-microsymbionts infecting the same nodule and promoting the nodulation process due to complementary sets of symbiotic genes.
Four pairs of strains were isolated from four individual root nodules collected from different plants of the Miocene-Pliocene relict legume Oxytropis triphylla growing in the Baikal region (one nodule – one pair of strains). Identification of these strains by the 16S rRNA gene sequencing showed that one strain of each pair was fast-growing and phylogenetically closest to the type strains Phyllobacterium endophyticum PEPV15T (98.8–99.5% 16S rDNA similarity) and Phyllobacterium bourgognense STM 201T (98.8–99.3% 16S rDNA similarity). The other strain was slow-growing and closely related to the type strains Bosea vestrisii 34635T and Bosea eneae 34614T (99.5–99.8% 16S rDNA similarity). Results of the atpD gene sequencing suggested that Phyllobacterium-related isolates most probably belong to a new species of Phyllobacterium. It is known that none of the currently described strains of P. endophyticum, P. bourgognense (family Phyllobacteriaceae), B. vestrisii and B. eneae (family Bradyrhizobiaceae) can induce root nodules, but several symbiotic genes were found in the representatives of these two genera. Thus we hypothesize that the pairs of strains isolated from O. triphylla root nodules can be co-microsymbionts having complementary sets of symbiotic genes and their simultaneous presence in roots is required for efficient nodulation of the host plant. The whole genome sequencing of the studied strains is in progress to find and compare symbiotic genes.
Many relict and endemic legumes are often rare and endangered species, located in remote and almost impenetrable areas. This makes it difficult to study their symbiosis with nodule bacteria. The aim of this work was to obtain root nodules under laboratory conditions of Hedysarum zundukii, Oxytropis popoviana, Oxytropis triphylla, Oxytropis tragacanthoides, Astragalus chorinensis and Glycyrrhiza uralensis belonging to the Miocene-Pliocene relicts, usually growing in restricted habitats of the Baikal Lake region. A pot experiment was conducted with soils and seeds collected in distribution areas of these legumes. The collected soils had low content of N and P, suggesting importance of nitrogen-fixing symbiosis for successful maintenance of plant populations. The symbiotic nodules were observed on roots of all plant species tested and 52 bacterial strains assumed as root nodule bacteria (rhizobia) were isolated from nodules. The proposed method avoids collection of native plants and prevents decrease in plant populations. The isolated bacteria will be used to search for ancestral genes responsible for the specificity and efficiency of rhizobia-legume symbiosis and can contribute to the conservation of rare and endangered species of relict legumes in the Baikal region.
Eight mesorhizobial symbiotic strains isolated from Anthyllis vulneraria root-nodules were studied and compared taxonomically with defined Mesorhizobium species. All strains presented identical 16S rDNA sequences but can be differentiated by multilocus sequence analysis of housekeeping genes (recA, atpD, glnII and dnaK). Matrix-Assisted Laser Desorption Ionization-Time-of-Flight mass spectrometry analyses separate these strains in two groups and a separate strain. Levels of DNA-DNA relatedness were less than 55% between representative strains and their closest Mesorhizobium reference relatives. The two groups containing four and three strains, respectively, originating from border mine and non-mining areas in Cévennes, were further phenotypically characterized. Groupings were further supported by average nucleotide identity values based on genome sequencing, which ranged from 80 to 92% with their close relatives and with each other, confirming these groups represent new Mesorhizobium species. Therefore, two novel species Mesorhizobium delmotii sp. nov. (type strain STM4623T = LMG 29640T = CFBP 8436T) and Mesorhizobium prunaredense sp. nov. (type strain STM4891T = LMG 29641T = CFBP 8437T) are proposed. Type strains of the two proposed species share accessory common nodulation genes within the new symbiovar anthyllidis as found in the Mesorhizobium metallidurans type strain.
Liconic Instruments’ automated −80°C Tube Store becomes an extremely useful, simple and intuitive system for a long-term storage of microorganisms at optimum conditions without the loss of their valuable properties. This ultra low temperature store is based on the chest freezer principle. Samples are loaded into the chamber via special interface unit (-20°C). This ensures a stable temperature and dry conditions into the storage compartment. Computer passwords used by depositors during the sample load operation ensure an authorized access to commercial strains of microorganisms. Unique “real time” online database of microorganisms has been organized on basis of the STC Tube Store Sample management software, which contains all information about the strains deposited: description, location in the store and movements of each sample. Such kind of store gives possibilities to intensify the search of new microbial cultures, keeping in mind the huge soil microbe’s biodiversity and a necessity to mobilize genetic resources of microorganisms for an agricultural production. © 2012 by World Scientific Publishing Co. Pte. Ltd. All rights reserved.
A strictly aerobic, mesophilic bacterium, strain AMX 51 T , was isolated from anaerobic digester sludge. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum. The isolate had phenotypic traits of the genus Bosea, including cellular fatty acid and substrate utilization profiles. Physiological characteristics and antibiotic susceptibility were determined. Phylogenetic analysis revealed that strain AMX 51 T was a member of the α-Proteobacteria, most closely related to Bosea thiooxidans DSM 9653 T (similarity of 98.88 %). Methylobacterium organophilum JCM 2833 T , Methylobacterium mesophilicum JCM 2829 T , Afipia clevelandensis DSM 7315 T , Afipia felis DSM 7326 T , Afipia broomeae DSM 7327 T , Blastobacter denitrificans LMG 8443 T and Bradyrhizobium japonicum DSM 30131 T showed significant 1 6S rRNA gene sequence similarities to strain AMX 51 T . The DNA G + C composition of strain AMX 51 T was 68.5 mol%. DNA-DNA hybridization analysis revealed 44.2 and 15.1 % relatedness between strain AMX 51 T and the respective type strains of Bosea thiooxidans and A. felis. Overall results suggest that strain AMX 51 T (= DSM 13099 T = ATCC 700918 T = CIP 106457 T ) represents a novel species of the genus Bosea; the name Bosea minatitlanensis sp. nov. is proposed.
This paper provides a taxonomic revision of Gueldenstaedtia (Fabaceae). Four spe-cies and one form are recognized. The revision is based on herbarium material and includes pollen and seed morphological observations. I treat the genus as distinct from the closely related Tibetia based on pollen and seed morphology, other morphological characters and chromosome data. A number of names in Gueldenstaedtia are reduced to synonyms. A key to all species of the genus is provided. For each taxon, its description, ecology, phenology, notes and an illustration and distribution map are also provided.
Bacterial strains isolated from nitrogen-fixing nodules of Lupinus mariae-josephae have been characterized following genetic, phenotypic and symbiotic approaches. Analysis of 16S rRNA genes placed them in a group together with Bradyrhizobium elkanii USDA 76(T), B. pachyrhizi PAC48(T), B. jicamae PAC68(T), 'B. retamae' Ro19(T) and B. lablabi CCBAU 23086(T) with over 99.0% identity. Phylogenetic analysis of concatenated housekeeping genes, recA, atpD and glnII, suggested that L. mariae-josephae strains represent a new Bradyrhizobium species, closely related to B. lablabi CCBAU 23086(T), B. jicamae PAC68(T) and 'B. retamae' Ro19(T) with 92.1, 91.9 and 90.8% identity, respectively. These results are consistent with overall genomic identities calculated as Average Nucleotide Identity (ANIm) using draft genomic sequences obtained for relevant strains. While L. mariae-josephae strains LmjM3(T)/LmjM6 exhibited a 99.2% ANIm value, they were significantly distant (<93% ANIm) from type strains of their closest species ('B. retamae' Ro19(T), B. lablabi CCBAU 23086(T) and B. jicamae PAC68(T)). Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (WC-MALDI-TOF-MS) analysis of proteomic patterns of the same strains was consistent with these results. The symbiosis-related genes nodC, nodA and nifH genes from strains nodulating L. mariae-josephae were phylogenetically related to those from 'B. retamae' Ro19(T), but divergent from those of strains that nodulate other lupine species. Based on genetic, genomic, proteomic and phenotypic data presented in this study, L. mariae-josephae nodulating strains LmjM3(T), LmjM6 and LmjM2 should be grouped within a new species for which the name Bradyrhizobium valentinum sp. nov. is proposed (type strain LmjM3(T)=CECT 8364(T), LMG 2761(T)).
Beneficial plant–microbe symbioses are based on the integration of genetic material from diverse organisms resulting in formation of superorganism genetic systems. Analysis of their functions and evolution requires the establishment of a new biological discipline, proposed to be called symbiogenetics, which provides a basis for fundamental and applied research of the genetic control over different (symbiotic and biocenotic) biotic interactions. In ecology and agrobiology, the approaches of symbiogenetics are indispensable for optimising the interactions between the plants and the beneficial microbes to be used in ecosystem management and in sustainable crop production in which hazardous fertilisers and pesticides should be replaced by environmentally friendly microbial inoculants.
Thirteen of the most abundant Gram-negative bacteria which are able to grow in N-depleted culture conditions were isolated
from the rhizoplane and endorhizosphere of canola (Brassica napus) and identified by 16S rDNA sequence analysis. Eight of these bacteria induced a significant increase in root dry weight
ranging from 11 to 52%. Phylogenetic positioning based on 16S rDNA sequences indicated that at least four genera are represented,
Pseudomonas, Variovorax, Agrobacterium and Phyllobacterium. The most important direct plant growth-promoting-rhizobacteria effect was found with both isolates belonging to the Phyllobacterium.
Gram-negative, rod-shaped bacteria were isolated from root nodules of Lupinus polyphyllus, Lathyrus latifolius and Robinia pseudoacacia. Based on the 16S rRNA gene phylogeny, they were closely related to Bosea species (100-97 % similarity), belonging to the class Alphaproteobacteria, family Bradyrhizobiaceae. The closest relatives of LMG 26383(T), LMG 26379(T) and LMG 26381(T) were respectively the type strains of Bosea thiooxidans (99.6 %), B. eneae (98.3 %) and B. minatitlanensis (99.0 %). Chemotaxonomic data, including major fatty acid profiles, supported the assignment of our strains to the genus Bosea. Analysis of the concatenated sequences of five housekeeping genes (atpD, dnaK, gyrB, recA and rpoB) and the results of DNA-DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from each other and from the five Bosea species with validly published names. No nodA or nodC genes could be amplified, while nifH PCR gave non-specific products. On the basis of genotypic and phenotypic data, three novel species, Bosea lupini sp. nov. (type strain LMG 26383(T) = CCUG 61248(T) = R-45681(T)), Bosea lathyri sp. nov. (type strain LMG 26379(T) = CCUG 61247(T) = R-46060(T)) and Bosea robiniae sp. nov. (type strain LMG 26381(T) = CCUG 61249(T) = R-46070(T)), are proposed.
Mathematical simulation of the evolution of polymorphic legume-rhizobium symbiosis showed that co-evolution of the partners for an improved ecological efficiency of symbiosis is greatly stimulated when low-active N2-fixing and non-N2-fixing strains of nodule bacteria are prohibited from colonizing nodules. The results of analysis of the model were collated with the comparative morphology of the infection process in various legumes, and its was assumed that mechanisms controlling bacterial reproduction in nodules arose in early evolution of symbiosis in primitive legumes owing to a transition from mixed to clonal infection. The development of such mechanisms was associated with adaptively valuable macroevolutionary transformations of symbiosis and directed its microevolution towards a parallel increase in the specificity and efficiency of mutualism. The increase was due to a reorganization of selective processes in endosymbiotic bacterial populations, which was based on changes in their genetic and spatial structures and optimized metabolic feedbacks between the partners (preferential allocation of photosynthesis products to the most active N2-fixing strains).
It is known that the Rhizobium galegae genomes contain megaplasmids. The suicide vector pSUP2111 with nifH gene of R. meliloti was introduced into the strains CIAM 0703 and CIAM 0711 of R. galegae inducing effective nodules on Galega orientalis plants. The formation of self-transmissible megaplasmids was observed. The megaplasmid transfer into non-nodulating R. meliloti mutants resulted in partial complementation of the nodulation defect in recipient strains though only one transconjugant showed the nitrogen-fixing activity in symbiosis with alfalfa and another one in symbiosis with G. orientalis plants. Among the Agrobacterium strains harbouring R. galegae megaplasmids there were four classes of transconjugants: (1) Nod+ Fix- in symbiosis with goat's rue plants (three strains); (2) Nod+ Fix- on Medicago sativa (two strains); (3) Nod+ Fix+ on M. sativa (five strains); (4) Nod- with both plant hosts (11 strains).
A set of oligonucleotide primers capable of initiating enzymatic amplification (polymerase chain reaction) on a phylogenetically and taxonomically wide range of bacteria is described along with methods for their use and examples. One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the additional primers are useful for various exceptional sequences. Methods for purification of amplified material, direct sequencing, cloning, sequencing, and transcription are outlined. An obligate intracellular parasite of bovine erythrocytes, Anaplasma marginale, is used as an example; its 16S rDNA was amplified, cloned, sequenced, and phylogenetically placed. Anaplasmas are related to the genera Rickettsia and Ehrlichia. In addition, 16S rDNAs from several species were readily amplified from material found in lyophilized ampoules from the American Type Culture Collection. By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them. In theory, any gene segment for which polymerase chain reaction primer design is possible can be derived from a readily obtainable lyophilized bacterial culture.
On the basis of phenotypic and DNA relatedness data, three novel species of the genus Bosea are proposed, Bosea massiliensis (63287T =CIP 106336T =CCUG 43117T), Bosea vestrisii (34635T =CIP 106340T =CCUG 43114T) and Bosea eneae (34614T =CIP 106338T =CCUG 43111T). The original description of the genus Bosea included thiosulphate oxidation as a phenotypic feature, when the sole and type species of the genus, Bosea thiooxidans, was proposed. The three novel species described herein were not able to oxidize thiosulphate; thus, it is proposed that this characteristic be removed from the description of the genus and considered as specific for B. thiooxidans. The novel species of the genus Bosea proposed here form a well-separated cluster in the Bradyrhizobium group of the alpha-2 subclass of the Proteobacteria, on the basis of 16S rDNA gene sequence analysis. However, 16S rDNA gene sequence analysis was not sufficient to delineate the species; hence, DNA-DNA relatedness and phenotypic data were also required. All of the novel species described in this study are fastidious bacteria isolated from a hospital water supply, using co-cultivation with amoebae. This group of bacteria are hypothesized to be a potential cause of nosocomial infections. For treatment of infections caused by these novel bacteria, doxycycline appears to be the sole antibacterial compound with a consistently low MIC value.
Bacteria belonging to the family Rhizobiaceae may establish beneficial or harmful relationships with plants. The legume endosymbionts contain nod and nif genes responsible for nodule formation and nitrogen fixation, respectively, whereas the pathogenic strains carry vir genes responsible for the formation of tumors or hairy roots. The symbiotic and pathogenic strains currently belong to different species of the genus Rhizobium and, until now, no strains able to establish symbiosis with legumes and also to induce tumors or hairy roots in plants have been reported. Here, we report for the first time the occurrence of two rhizobial strains (163C and ATCC11325T) belonging to Rhizobium rhizogenes able to induce hairy roots or tumors in plants and also to nodulate Phaseolus vulgaris under natural environmental conditions. Symbiotic plasmids (pSym) containing nod and nif genes and pTi- or pRi-type plasmids containing vir genes were found in these strains. The nodD and nifH genes of the strains from this study are phylogenetically related to those of Sinorhizobium strains nodulating P. vulgaris. The virA and virB4 genes from strain 163C are phylogenetically related to those of R. tumefaciens C58, whereas the same genes from strain ATCC 11325T are related to those of hairy root-inducing strains. These findings may be of high relevance for the better understanding of plant-microbe interactions and knowledge of rhizobial phylogenetic history.
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