nodA Sequences Research Articles

Genetic diversity, symbiotic efficiency, stress tolerance, and plant growth promotion traits of rhizobia nodulating Vachellia tortilis subsp. raddiana growing in dryland soils in southern Morocco

In the present study, we analyzed the genetic diversity, phylogenetic relationships, stress tolerance, phytobeneficial traits, and symbiotic characteristics of rhizobial strains isolated from root nodules of Vachellia tortilis subsp. raddiana grown in soils collected in the extreme Southwest of the Anti-Atlas Mountains in Morocco. Subsequent to Rep-PCR fingerprinting, 16S rDNA gene sequencing of 15 representative strains showed that all of them belong to the genus Ensifer. Phylogenetic analysis and concatenation of the housekeeping genes gyrB, rpoB, recA, and dnaK revealed that the entire collection (except strain LMR678) shared 99.08 % to 99.92% similarity with Ensifer sp. USDA 257 and 96.92% to 98.79% with Sinorhizobium BJ1. Phylogenetic analysis of nodC and nodA sequences showed that all strains but one (LMR678) formed a phylogenetic group with the type strain “E. aridi” LMR001T (similarity over 98%). Moreover, it was relevant that most strains belong to the symbiovar vachelliae. In vitro tests revealed that five strains produced IAA, four solubilized inorganic phosphate, and one produced siderophores. All strains showed tolerance to NaCl concentrations ranging from 2 to 12% and grew at up to 10% of PEG6000. A greenhouse plant inoculation test conducted during five months demonstrated that most rhizobial strains were infective and efficient. Strains LMR688, LMR692, and LMR687 exhibited high relative symbiotic efficiency values (respectively 231.6 %, 171.96 %, and 140.84 %). These strains could be considered as the most suitable candidates for inoculation of V. t. subsp. raddiana, to be used as a pioneer plant for restoring arid soils threatened with desertification.

Author's Correction: Stress Tolerance and Symbiotic and Phylogenic Features of Root Nodule Bacteria Associated with Medicago Species in Different Bioclimatic Regions of Tunisia.

Thirty two rhizobial isolates were obtained from different bioclimatic regions of Tunisia using as trap plants, Medicago sativa, Medicago ciliaris, Medicago polymorpha and Medicago minima. To study their diversity and characterize them in relation to Mediterranean conditions, abiotic stress resistance, symbiotic properties and genetic diversity in terms of 16S rRNA and nodA sequences were assessed. Five isolates from M. sativa, three from M. ciliaris and three from M. minima could grow at 45°C. Only two isolates from M. sativa grew at 4% NaCl. The most stress tolerant isolates were obtained from arid soils. A phylogenetic analysis of 16S rRNA genes revealed 29 isolates to be closely related to Ensifer including one (Pl.3-9) that showed a 16S rRNA sequence similar to that of Ensifer meliloti and nodA sequence similar to that of Ensifer medicae. However, three isolates were categorized into Agrobacterium containing the nodA of Ensifer. Furthermore, these isolates developed nodules on original hosts. The results for the four isolates suggest horizontal gene transfer between the species.

The Occurrence of Putative Nitric Oxide Dismutase (Nod) in an Alpine Wetland with a New Dominant Subcluster and the Potential Ability for a Methane Sink.

Recently, a new oxygenic pathway has been proposed based on the disproportionation of NO with putative NO dismutase (Nod). In addition to a new process in nitrogen cycling, this process provides ecological advantages for the degradation of substrates in anaerobic conditions, which is of great significance for wastewater treatment. However, the Nod distribution in aquatic environments is rarely investigated. In this study, we obtained the nod genes with an abundance of 2.38 ± 0.96 × 105 copies per gram of dry soil from the Zoige wetland and aligned the molecular characteristics in the corresponding Nod sequences. These Nod sequences were not only found existing in NC10 bacteria, but were also found forming some other clusters with Nod sequences from a WWTP reactor or contaminated aquifers. Moreover, a new subcluster in the aquifer-similar cluster was even dominant in the Zoige wetland and was named the Z-aquifer subcluster. Additionally, soils from the Zoige wetland showed a high potential rate (10.97 ± 1.42 nmol of CO2 per gram of dry soil per day) for nitrite-dependent anaerobic methane oxidation (N-DAMO) with low abundance of NC10 bacteria, which may suggest a potential activity of Nod in other clusters when considering the dominance of the Z-aquifer subcluster Nod. In conclusion, we verified the occurrence of Nod in an alpine wetland for the first time and found a new subcluster to be dominant in the Zoige wetland. Moreover, this new subcluster of Nod may even be active in the N-DAMO process in this alpine wetland, which needs further study to confirm.

Molecular characterization of nitrogen fixing microsymbionts from root nodules of Vachellia (Acacia) jacquemontii, a native legume from the Thar Desert of India

To describe the structure of nodules of Vachellia (Acacia) jacquemontii, and to characterise the rhizobia that occupy them. Light and electron microscopy were used to analyse nodules. Rhizobia were characterised using their 16S rRNA, housekeeping and symbiosis-related gene sequences. Nodules of V. jacquemontii were typical of all other described mimosoid legumes. All 73 of the isolates were strains of Ensifer, and concatenated phylogenetic analysis of their housekeeping genes (rrs, recA, atpD, glnII and dnaK) suggested that they are novel, forming separate lineages close to E. saheli. The phylogenies of the symbiosis-essential genes nodA and nifH were inconsistent with the housekeeping phylogenies. The nodA sequences of most isolates were close to that of E. arboris HAMBI 1552T, but the nifH gene was found to be related to that of E. kostiensis HAMBI 1489T. All the tested Ensifer strains, except for AJ24, were found to be capable of nodulating other species of Vachellia as well as native Indian Mimosa and Prosopis spp. Stressful conditions caused by the alkaline soil of the Thar Desert have resulted in V. jacquemontii being nodulated by diverse and promiscuous Ensifer species that are capable of nodulating other native members of the tribe Mimoseae.

On complete convergence for Stout’s type weighted sums of NOD sequence

In this paper, the complete convergence for the weighted sums of independent and identically distributed random variables in Stout [9] is improved and extended under NOD setup. The more optimal moment condition is given. The main results also hold for END sequence.

Diversity of endophytic bacteria associated with nodules of two indigenous legumes at different altitudes of the Qilian Mountains in China

A total of 201 endophytic root nodule-associated bacteria collected from two legumes indigenous to different Qilian Mountain altitudes (Hexi Corridor) were characterized through 16S rDNA polymerase chain reaction (PCR)-restriction fragment length polymorphism, 16S rRNA gene sequence analysis, and enterobacterial repetitive intergenic consensus-PCR clustering. The isolates phylogenetically belonged to 35 species in the Phyllobacterium, Ensifer, Rhizobium, Microvirga, Sphingomonas, Paracoccus, Mycobacterium, Paenibacillus, Cohnella, Sporosarcina, Bacillus, Staphylococcus, Brevibacterium, Xenophilus, Erwinia, Leclercia, Acinetobacter, and Pseudomonas genera. Phylogenetic nodA sequence analysis showed higher similarity to Sinorhizobium meliloti with strains related to the Rhizobium, Sinorhizobium, and Acinetobacter genera. Sequence analysis of the nifH gene revealed that the strains belonging to Xenophilus, Acinetobacter, Phyllobacterium, and Rhizobium had genes similar to those of Mesorhizobium and Sinorhizobium. The results indicated that horizontal gene transfer could have occurred between rhizobia and non-rhizobial endophytes. Canonical correspondence analysis revealed that altitude and host plant species contributed more to the bacterial endosymbiont separation than other ecological factors. This study provided valuable information on the interactions between symbiotic bacteria, non-symbiotic bacteria and their habitats, and thus provided knowledge on their genetic diversity and ecology.

H�jek-R�nyi Type Inequalities and Strong Law of Large Numbers for NOD Sequences

In the paper, we get the precise results of H ´ ajek-R´ enyi type inequalities for the partial sums of negatively orthant depende nt sequences, which improve the results of Theorem 3.1 and Corollary 3.2 in Kim (2006). In addition, the Marcinkiewicz type strong law of large numbers is obtained. At last, the strong stability for weighted sums o f negatively orthant dependent sequences is discussed.

On asymptotic approximation of inverse moments for a class of nonnegative random variables

Sung [On inverse moments for a class of nonnegative random variables. J Inequal Appl. 2010;2010:1–13. Article ID 823767, doi:10.1155/2010/823767] obtained the asymptotic approximation of inverse moments for a class of nonnegative random variables with finite second moments and satisfying a Rosenthal-type inequality. In the paper, we further study the asymptotic approximation of inverse moments for a class of nonnegative random variables with finite first moments, which generalizes and improves the corresponding ones of Wu et al. [Asymptotic approximation of inverse moments of nonnegative random variables. Statist Probab Lett. 2009;79:1366–1371], Wang et al. [Exponential inequalities and inverse moment for NOD sequence. Statist Probab Lett. 2010;80:452–461; On complete convergence for weighted sums of ϕ mixing random variables. J Inequal Appl. 2010;2010:1–13, Article ID 372390, doi:10.1155/2010/372390], Sung (2010) and Hu et al. [A note on the inverse moment for the nonnegative random variables. Commun Statist Theory Methods. 2012. Article ID 673677, doi:10.1080/03610926.2012.673677].

An invasive Mimosa in India does not adopt the symbionts of its native relatives.

The large monophyletic genus Mimosa comprises approx. 500 species, most of which are native to the New World, with Central Brazil being the main centre of radiation. All Brazilian Mimosa spp. so far examined are nodulated by rhizobia in the betaproteobacterial genus Burkholderia. Approximately 10 Mya, transoceanic dispersal resulted in the Indian subcontinent hosting up to six endemic Mimosa spp. The nodulation ability and rhizobial symbionts of two of these, M. hamata and M. himalayana, both from north-west India, are here examined, and compared with those of M. pudica, an invasive species. Nodules were collected from several locations, and examined by light and electron microscopy. Rhizobia isolated from them were characterized in terms of their abilities to nodulate the three Mimosa hosts. The molecular phylogenetic relationships of the rhizobia were determined by analysis of 16S rRNA, nifH and nodA gene sequences. Both native Indian Mimosa spp. nodulated effectively in their respective rhizosphere soils. Based on 16S rRNA, nifH and nodA sequences, their symbionts were identified as belonging to the alphaproteobacterial genus Ensifer, and were closest to the 'Old World' Ensifer saheli, E. kostiensis and E. arboris. In contrast, the invasive M. pudica was predominantly nodulated by Betaproteobacteria in the genera Cupriavidus and Burkholderia. All rhizobial strains tested effectively nodulated their original hosts, but the symbionts of the native species could not nodulate M. pudica. The native Mimosa spp. in India are not nodulated by the Burkholderia symbionts of their South American relatives, but by a unique group of alpha-rhizobial microsymbionts that are closely related to the 'local' Old World Ensifer symbionts of other mimosoid legumes in north-west India. They appear not to share symbionts with the invasive M. pudica, symbionts of which are mostly beta-rhizobial.

Establishment and survival of the South African legume Lessertia spp. and rhizobia in Western Australian agricultural systems

Background and aims The South African herbaceous legume species Lessertia capitata, L. diffusa, L. excisa L. incana and L. herbacea were introduced to Australia to assess plant establishment and survival, as well as the saprophytic ability of their root nodule bacteria (RNB). Methods Five Lessertia spp., were inoculated with selected RNB strains and were sown in five different agroclimatic areas of the Western Australian wheatbelt during 2007 and 2008. Plant population and summer survival were evaluated in situ. Soil samples and nodules from host plants were also taken from each site. The re-isolated rhizobia were RPO1-PCR fingerprinted and their partial dnaK and nodA genes were sequenced to confirm their identity. Results Plants achieved only poor establishment followed by weak summer survival. More than 83 % of the rhizobia re-isolated from Lessertia did not correlate with the original inoculants’ fingerprints, and were identified as Rhizobium leguminosarum. The nodA sequences of the naturalised strains were also

A Novel Strain D5 Isolated from Acacia confusa

We isolated a novel strain D5 from nodules of Acacia confusa. Under strict sterile conditions the strain could successfully nodulate Acacia confusa, A. crassicarpa and A. mangium, with nitrogenase activity ranging from 18.90 to 19.86 nmol·g−1·min−1. In the phylogenetic tree based on a complete 16S rRNA gene sequence, the sequence of strain D5 shared 99% homology with that of four species of genus Pseudomonas. The 685 bp nodA fragment amplified from strain D5 shared 95% homology with the nodA sequence of 9 species of genus Bradyrhizobium, with a genetic distance of 0.01682. The 740 bp nifH gene fragment was amplified from strain D5. This strain D5 nifH gene and Bradyrhizobium spp. formed a branch, showing 98% homology and a genetic distance of 0. The homology between this branch and the Bradyrhizobium spp. DG in another branch was 99%, with a genetic distance of 0.007906. These results indicate that this strain D5 is a new type of nitrogen-fixing bacterium.

Rhizobia with 16S rRNA and nifH Similar to Mesorhizobium huakuii but Novel recA, glnII, nodA and nodC Genes Are Symbionts of New Zealand Carmichaelinae

New Zealand became geographically isolated about 80 million years ago and this separation gave rise to a unique native flora including four genera of legume, Carmichaelia, Clianthus and Montigena in the Carmichaelinae clade, tribe Galegeae, and Sophora, tribe Sophoreae, sub-family Papilionoideae. Ten bacterial strains isolated from NZ Carmichaelinae growing in natural ecosystems grouped close to the Mesorhizobium huakuii type strain in relation to their 16S rRNA and nifH gene sequences. However, the ten strains separated into four groups on the basis of their recA and glnII sequences: all groups were clearly distinct from all Mesorhizobium type strains. The ten strains separated into two groups on the basis of their nodA sequences but grouped closely together in relation to nodC sequences; all nodA and nodC sequences were novel. Seven strains selected and the M. huakuii type strain (isolated from Astragalus sinicus) produced functional nodules on Carmichaelia spp., Clianthus puniceus and A. sinicus but did not nodulate two Sophora species. We conclude that rhizobia closely related to M. huakuii on the basis of 16S rRNA and nifH gene sequences, but with variable recA and glnII genes and novel nodA and nodC genes, are common symbionts of NZ Carmichaelinae.

Molecular and phenotypic characterization of strains nodulating Anthyllis vulneraria in mine tailings, and proposal of Aminobacter anthyllidis sp. nov., the first definition of Aminobacter as legume-nodulating bacteria

Bacterial strains from Zn–Pb mine tailings were isolated by trapping with Anthyllis vulneraria, a legume-host suitable for mine substratum phytostabilisation. Sequence analysis of the 16S rRNA gene and three housekeeping genes (atpD, dnaK and recA) showed that they were related to those of the genus Aminobacter. DNA–DNA relatedness of representative isolates supported the placement of novel strains in Aminobacter as a new species. Phenotypic data emphasize their differentiation from the other related species of Aminobacter and Mesorhizobium. Aminobacter isolates exhibited nodA sequences tightly related with M. loti as the closest nodA relative. By contrast, their nodA sequences were highly divergent from those of M. metallidurans, another species associated with A. vulneraria that carries two complete copies of nodA. Therefore, the novel bacterial strains efficient on A. vulneraria represented the first occurrence of legume symbionts in the genus Aminobacter. They represent a new species for which the name Aminobacter anthyllidis sp. nov. is proposed (type strain STM4645T=LMG26462T=CFBP7437T).

Microvirga lupini sp. nov., Microvirga lotononidis sp. nov. and Microvirga zambiensis sp. nov. are alphaproteobacterial root-nodule bacteria that specifically nodulate and fix nitrogen with geographically and taxonomically separate legume hosts

Strains of Gram-negative, rod-shaped, non-spore-forming bacteria were isolated from nitrogen-fixing nodules of the native legumes Listia angolensis (from Zambia) and Lupinus texensis (from Texas, USA). Phylogenetic analysis of the 16S rRNA gene showed that the novel strains belong to the genus Microvirga, with ≥ 96.1% sequence similarity with type strains of this genus. The closest relative of the representative strains Lut6(T) and WSM3557(T) was Microvirga flocculans TFB(T), with 97.6-98.0% similarity, while WSM3693(T) was most closely related to Microvirga aerilata 5420S-16(T), with 98.8% similarity. Analysis of the concatenated sequences of four housekeeping gene loci (dnaK, gyrB, recA and rpoB) and cellular fatty acid profiles confirmed the placement of Lut6(T), WSM3557(T) and WSM3693(T) within the genus Microvirga. DNA-DNA relatedness values, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of Lut6(T), WSM3557(T) and WSM3693(T) from each other and from other Microvirga species with validly published names. The nodA sequence of Lut6(T) was placed in a clade that contained strains of Rhizobium, Mesorhizobium and Sinorhizobium, while the 100% identical nodA sequences of WSM3557(T) and WSM3693(T) clustered with Bradyrhizobium, Burkholderia and Methylobacterium strains. Concatenated sequences for nifD and nifH show that the sequences of Lut6(T), WSM3557(T) and WSM3693(T) were most closely related to that of Rhizobium etli CFN42(T) nifDH. On the basis of genotypic, phenotypic and DNA relatedness data, three novel species of Microvirga are proposed: Microvirga lupini sp. nov. (type strain Lut6(T) =LMG 26460(T) =HAMBI 3236(T)), Microvirga lotononidis sp. nov. (type strain WSM3557(T) =LMG 26455(T) =HAMBI 3237(T)) and Microvirga zambiensis sp. nov. (type strain WSM3693(T) =LMG 26454(T) =HAMBI 3238(T)).

Genetic diversity of root nodule bacteria nodulating Lotus corniculatus and Anthyllis vulneraria in Sweden

Very little is known about the genetic diversity and phylogeny of rhizobia nodulating Lotus species in northern temperate regions. We have therefore studied the genetic diversity among a total of 61 root nodule bacteria isolated from Lotus corniculatus and Anthyllis vulneraria from different geographic sites and habitats in Sweden by restriction fragment length polymorphism (RFLP) of the internal transcribed spacer between their 16S rRNA and 23S rRNA (IGS) region. A high diversity consisting of 26 IGS types from 54 L. corniculatus isolates and five IGS types from seven A. vulneraria isolates was found. The 16S rRNA sequences and phylogeny of representatives of the different IGS types showed four interesting exceptions from the majority of the isolates belonging to the genus Mesorhizobium: Two isolates were both found to be closely related to Rhodococcus spp., and two other isolates showed close relationship with Geobacillus spp. and Paenibacillus spp., respectively. The nodA sequences and phylogeny showed that all the isolates, including those not belonging to the traditional rhizobia genera, harbored nodA sequences which were typical of Mesorhizobium loti. Generally, the 16S rRNA and nodA phylogenetic trees were not congruent in that isolates with similar 16S rRNA sequences were associated with isolates harboring different nodA sequences. All the isolates were confirmed to nodulate L. corniculatus in an inoculation test. This is the first report of members of these non-rhizobia genera being able to nodulate legumes, and we suggest that they may have acquired their nodulating properties through lateral gene transfer.

The Bahadur representation for sample quantile under NOD sequence

In this paper, we investigate the Bahadur representation of sample quantile based on negatively orthant dependent sequence, which is weaker than negatively associated sequence. Our results extend and improve the results of Ling [(2008), ‘The Bahadur Representation for Sample Quantiles Under Negatively Associated Sequence’, Statistics & Probability Letters, 78, 2660–2663].

Stress Tolerance and Symbiotic and Phylogenic Features of Root Nodule Bacteria Associated with Medicago Species in Different Bioclimatic Regions of Tunisia

Thirty two rhizobial isolates were obtained from different bioclimatic regions of Tunisia using as trap plants, Medicago sativa, Medicago ciliaris, Medicago polymorpha and Medicago minima. To study their diversity and characterize them in relation to Mediterranean conditions, abiotic stress resistance, symbiotic properties and genetic diversity in terms of 16S rRNA and nodA sequences were assessed. Five isolates from M. sativa, three from M. ciliaris and three from M. minima could grow at 45°C. Only two isolates from M. sativa grew at 4% NaCl. The most stress tolerant isolates were obtained from arid soils. A phylogenetic analysis of 16S rRNA genes revealed 29 isolates to be closely related to Ensifer including one (Pl.3-9) that showed a 16S rRNA sequence similar to that of Ensifer meliloti and nodA sequence similar to that of Ensifer medicae. However, three isolates were categorized into Agrobacterium containing the nodA of Ensifer. Furthermore, these isolates developed nodules on original hosts. The results for the four isolates suggest horizontal gene transfer between the species.

Exponential inequalities and inverse moment for NOD sequence

Some exponential inequalities for a negatively orthant dependent sequence are obtained. By using the exponential inequalities, we study the asymptotic approximation of inverse moment for negatively orthant dependent random variables, which generalizes and improves the corresponding results of Kaluszka and Okolewski [Kaluszka, M., Okolewski, A., 2004. On Fatou-type lemma for monotone moments of weakly convergent random variables. Statist. Probab. Lett. 66, 45–50], Hu et al. [Hu, S.H., Chen, G.J., Wang, X.J., Chen, E.B., 2007. On inverse moments of nonnegative weakly convergent random variables. Acta Math. Appl. Sin. 30, 361–367(in Chinese)] and Wu et al. [Wu, T.J., Shi, X.P., Miao, B.Q., 2009. Asymptotic approximation of inverse moments of nonnegative random variables. Statist. Probab. Lett. 79, 1366–1371].

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

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

Mesorhizobium septentrionale sp. nov. and Mesorhizobium temperatum sp. nov., isolated from Astragalus adsurgens growing in the northern regions of China

Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA-DNA relatedness was between 11.3 and 47.1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4.3 and 25.2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014(T)=CCBAU 11014(T)=HAMBI 2582(T)) and Mesorhizobium temperatum sp. nov. (type strain, SDW018(T)=CCBAU 11018(T)=HAMBI 2583(T)), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.