Coexistence of Burkholderia, Cupriavidus, and Rhizobium sp. Nodule Bacteria on two Mimosa spp. in Costa Rica

ABSTRACT rRNA gene sequencing and PCR assays indicated that 215 isolates of root nodule bacteria from two Mimosa species at three sites in Costa Rica belonged to the genera Burkholderia, Cupriavidus, and Rhizobium. This is the first report of Cupriavidus sp. nodule symbionts for Mimosa populations within their native geographic range in the neotropics. Burkholderia spp. predominated among samples from Mimosa pigra (86% of isolates), while there was a more even distribution of Cupriavidus, Burkholderia, and Rhizobium spp. on Mimosa pudica (38, 37, and 25% of isolates, respectively). All Cupriavidus and Burkholderia genotypes tested formed root nodules and fixed nitrogen on both M. pigra and M. pudica, and sequencing of rRNA genes in strains reisolated from nodules verified identity with inoculant strains. Inoculation tests further indicated that both Cupriavidus and Burkholderia spp. resulted in significantly higher plant growth and nodule nitrogenase activity (as measured by acetylene reduction assays) relative to plant performance with strains of Rhizobium. Given the prevalence of Burkholderia and Cupriavidus spp. on these Mimosa legumes and the widespread distribution of these plants both within and outside the neotropics, it is likely that both β-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.

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REP-PCR Analysis to Study Prokaryotic Biodiversity from Lake Meyghan

International Letters of Natural Sciences ◽

10.18052/www.scipress.com/ilns.61.69 ◽

2017 ◽

Vol 61 ◽

pp. 69-84 ◽

Cited By ~ 1

Author(s):

Ali Naghoni ◽

Giti Emtiazi ◽

Mohammad Ali Amoozegar ◽

Zahra Etemadifar ◽

Seyed Abolhassan Shahzadeh Fazeli

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequencing ◽

16S Rrna Gene Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Pcr Analysis ◽

Rrna Gene ◽

White Region ◽

Rrna Gene Sequencing

Repetitive extragenic palindromic elements-polymerase chain reaction (rep-PCR) with 16S ribosomal ribonucleic acid (16S rRNA) genes sequences successfully used for the analysis of microbial community. In this study, the prokaryotic community in Lake Meyghan described by using rep-PCR analysis along with 16S rRNA gene sequencing. The water samples were collected from Lake Meyghan in November 2013. All samples were diluted and cultured on three different media. To estimate the number of prokaryotes per milliliter of the lake we used quantitative real‑time PCR (qPCR). Rep-PCR combination with 16S rRNA gene sequencing was performed to investigate prokaryotes biodiversity in the lake. 305 strains were isolated in this work; 113 isolates for green region, 102 isolates for red region, and 90 isolates for white region. The dendrograms generated 10, 7, and 9 clusters for a 70 % similarity cut-off for green, red, and white regions, respectively. Based on rep-PCR and 16S rRNA gene sequencing, the recovered isolates were dominated by (77.5 %)Halobacteriacaeand many isolates were related to the generaHalorubrum,Haloarcula,Haloterrigena,Natrinema, andHalovivaxin the white region. In the red region more isolated strains (57.5 %) belonged toBacillaceaeand the remaining 42.5 % of isolates belonged to archaea domain,Halorubrum, andHaloarcula. In the green region members ofGammaproteobacteriawere recoverd, this region was dominant withPseudoalteromonas,Salinivibrio, andAliidiomarina.

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Natural Diversity of Frankia Strains in Actinorhizal Root Nodules from Promiscuous Hosts in the Family Myricaceae

Applied and Environmental Microbiology ◽

10.1128/aem.65.10.4521-4527.1999 ◽

1999 ◽

Vol 65 (10) ◽

pp. 4521-4527 ◽

Cited By ~ 38

Author(s):

Michael L. Clawson ◽

David R. Benson

Keyword(s):

Molecular Diversity ◽

Root Nodule ◽

Root Nodules ◽

Reservoir Host ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Myrica Gale ◽

The Family ◽

The Common ◽

Selection Of

ABSTRACT Actinorhizal plants invade nitrogen-poor soils because of their ability to form root nodule symbioses with N2-fixing actinomycetes known as Frankia. Frankia strains are difficult to isolate, so the diversity of strains inhabiting nodules in nature is not known. To address this problem, we have used the variability in bacterial 16S rRNA gene sequences amplified from root nodules as a means to estimate molecular diversity. Nodules were collected from 96 sites primarily in northeastern North America; each site contained one of three species of the family Myricaceae. Plants in this family are considered to be promiscuous hosts because several species are effectively nodulated by most isolated strains ofFrankia in the greenhouse. We found that strain evenness varies greatly between the plant species so that estimating total strain richness of Frankia within myricaceous nodules with the sample size used was problematical. Nevertheless, Myrica pensylvanica, the common bayberry, was found to have sufficient diversity to serve as a reservoir host for Frankia strains that infect plants from other actinorhizal families. Myrica gale, sweet gale, yielded a few dominant sequences, indicating either symbiont specialization or niche selection of particular ecotypes. Strains in Comptonia peregrina nodules had an intermediate level of diversity and were all from a single major group of Frankia.

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Relationships of Bradyrhizobia from the LegumesApios americana and Desmodium glutinosum

Applied and Environmental Microbiology ◽

10.1128/aem.65.11.4914-4920.1999 ◽

1999 ◽

Vol 65 (11) ◽

pp. 4914-4920 ◽

Cited By ~ 31

Author(s):

Matthew A. Parker

Keyword(s):

16S Rrna ◽

Root Nodule ◽

16S Rrna Genes ◽

Rrna Genes ◽

23S Rrna ◽

Enzyme Electrophoresis ◽

Nodule Bacteria ◽

Root Nodule Bacteria ◽

Rrna Sequences ◽

16S Rrna Sequences

ABSTRACT Multilocus enzyme electrophoresis, partial 23S rRNA sequences, and nearly full-length 16S rRNA sequences all indicated high genetic similarity among root-nodule bacteria associated with Apios americana, Desmodium glutinosum, andAmphicarpaea bracteata, three common herbaceous legumes whose native geographic ranges in eastern North America overlap extensively. A total of 19 distinct multilocus genotypes (electrophoretic types [ETs]) were found among the 35 A. americana and 33 D. glutinosum isolates analyzed. Twelve of these ETs (representing 78% of all isolates) were either identical to ETs previously observed in A. bracteatapopulations, or differed at only one locus. Within both 23S and 16S rRNA genes, several isolates from A. americana and D. glutinosum were either identical to A. bracteataisolates or showed only single nucleotide differences. Growth rates and nitrogenase activities of A. bracteata plants inoculated with isolates from D. glutinosum were equivalent to levels found with native A. bracteata bacterial isolates, but none of the three A. americana isolates tested had high symbiotic effectiveness on A. bracteata. Phylogenetic analysis of both 23S and 16S rRNA sequences indicated that bothA. americana and D. glutinosum harbored rare bacterial genotypes similar to Bradyrhizobium japonicumUSDA 110. However, the predominant root nodule bacteria on both legumes were closely related to Bradyrhizobium elkanii.

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Relative contributions to nitrogenase (acetylene reducing) activity of stem and root nodules in Sesbania rostrata

Canadian Journal of Microbiology ◽

10.1139/m92-095 ◽

1992 ◽

Vol 38 (6) ◽

pp. 577-583 ◽

Cited By ~ 5

Author(s):

J. K. Ladha ◽

Minviluz Garcia ◽

R. P. Pareek ◽

G. Rarivoson

Keyword(s):

Acetylene Reduction ◽

Root Nodule ◽

Nitrogenase Activity ◽

Root Nodules ◽

Dry Weight ◽

Acetylene Reduction Activity ◽

Sesbania Rostrata ◽

Reduction Activity ◽

Acetylene Reducing Activity ◽

Aerial Stem

Six experiments, two each in the phytotron, greenhouse, and field, were conducted to assess the contribution of nitrogenase activity (acetylene reduction) by stem nodules in the presence and absence of root nodules of Sesbania rostrata (Brem & Oberm). In a greenhouse experiment, the effect of detaching already formed aerial stem nodules on the restoration of root nodules and nitrogenase activity was studied. The field experiment compared nodulation and acetylene-reduction activity by dual-nodulating S. rostrata and root-nodulating Sesbania cannabina. Acetylene-reduction activity expressed per gram of nodule dry weight was higher for stem nodules than for root nodules. Root nodule dry weight and acetylene-reduction activity failed to increase after stem inoculation, but root nodule dry weight and acetylene-reduction activity increased several fold within 15 days of detachment of aerial stem nodules. Stem nodulation, which occurred without inoculation under lowland field condition, suppressed root nodulation, thus accounting for more than 75% of total nitrogenase activity. Sesbania rostrata showed higher acetylene-reduction activity than S. cannabina. In dual-nodulating plants, root and stem nodules appeared to strike a balance in competition for energy, which may be controlled by stem nodulation. Key words: Sesbania rostrata, Azorhizobium caulinodans, stem nodule, root nodule, acetylene-reducing activity.

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Methylobacterium nodulans sp. nov., for a group of aerobic, facultatively methylotrophic, legume root-nodule-forming and nitrogen-fixing bacteria

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02902-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 2269-2273 ◽

Cited By ~ 138

Author(s):

Philippe Jourand ◽

Eric Giraud ◽

Gilles Béna ◽

Abdoulaye Sy ◽

Anne Willems ◽

...

Keyword(s):

Carbon Source ◽

16S Rrna ◽

Root Nodule ◽

Root Nodules ◽

Phenotypic Characterization ◽

Rrna Gene ◽

Nitrogen Fixing ◽

Bacterial Strains ◽

Protein Patterns ◽

Gene Encoding

Data on 72 non-pigmented bacterial strains that specifically induce nitrogen-fixing root nodules on the legume species Crotalaria glaucoides, Crotalaria perrottetii and Crotalaria podocarpa are reviewed. By SDS-PAGE analysis of total protein patterns and by 16S rRNA PCR-RFLP, these strains form a homogeneous group that is separate from other legume root-nodule-forming bacteria. The 16S rRNA gene-based phylogeny indicates that these bacteria belong to the genus Methylobacterium. They can grow on C1 compounds such as methanol, formate and formaldehyde but not methylamine as sole carbon source, and carry an mxaF gene, encoding methanol dehydrogenase, which supports their methylotrophic metabolism. Presence of a nodA nodulation gene, and ability to nodulate plants of Crotalaria species and to fix nitrogen are features that separate the strains currently included in this group from other members of the genus Methylobacterium. The present study includes additional genotypic and phenotypic characterization of this novel Methylobacterium species, i.e. nifH gene sequence, morphology, physiology, enzymic and carbon source assimilation tests and antibiotic resistance. The name Methylobacterium nodulans sp. nov. (type strain, ORS 2060T=CNCM I 2342T=LMG 21967T) is proposed for this group of root-nodule-forming bacteria.

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Characterization of Rhizobial Bacteria Nodulating Astragalus corrugatus and Hippocrepis areolata in Tunisian Arid Soils

Polish Journal of Microbiology ◽

10.5604/17331331.1215612 ◽

2016 ◽

Vol 65 (3) ◽

pp. 331-339 ◽

Cited By ~ 4

Author(s):

Mosbah Mahdhi ◽

Nadia Houidheg ◽

Neji Mahmoudi ◽

Abdelhakim Msaadek ◽

Mokhtar Rejili ◽

...

Keyword(s):

Host Plants ◽

Root Nodules ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Carbon And Nitrogen ◽

16S Rdna Pcr ◽

Pcr Rflp ◽

Phenotypic Features ◽

Rrna Gene Sequencing

Fifty seven bacterial isolates from root nodules of two spontaneous legumes (Astragalus corrugatus and Hippocrepis areolata) growing in the arid areas of Tunisia were characterized by phenotypic features, 16S rDNA PCR-RFLP and 16S rRNA gene sequencing. Phenotypically, our results indicate that A. corrugatus and H. areolata isolates showed heterogenic responses to the different phenotypic features. All isolates were acid producers, fast growers and all of them used different compounds as sole carbon and nitrogen source. The majority of isolate grew at pHs between 6 and 9, at temperatures up to 40°C and tolerated 3% NaCl concentrations. Phylogenetically, the new isolates were affiliated to four genera Sinorhizobium, Rhizobium, Mesorhizobium and Agrobacterium. About 73% of the isolates were species within the genera Sinorhizobium and Rhizobium. The isolates which failed to nodulate their host plants of origin were associated to Agrobacterium genus (three isolates).

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Root nodule bacteria fromClitoria ternateaL. are putative invasive nonrhizobial endophytes

Canadian Journal of Microbiology ◽

10.1139/cjm-2014-0483 ◽

2015 ◽

Vol 61 (2) ◽

pp. 131-142 ◽

Cited By ~ 12

Author(s):

Abhinav Aeron ◽

Puneet Singh Chauhan ◽

Ramesh Chand Dubey ◽

Dinesh Kumar Maheshwari ◽

Vivek K. Bajpai

Keyword(s):

Root Nodule ◽

Root Nodules ◽

Nifh Gene ◽

Nodule Bacteria ◽

Root Nodule Bacteria ◽

The Common ◽

Leguminous Crops ◽

Free Media ◽

Diversity Studies ◽

Phenotypic Clustering

In this study, bacteria (8 species and 5 genera) belonging to the classes Betaproteobacteria, Gammaproteobacteria, and Sphingobacteria were isolated from root nodules of the multipurpose legume Clitoria ternatea L. and identified on the basis of partial 16S rRNA sequencing. The root nodule bacteria were subjected to phenotypic clustering and diversity studies using biochemical kits, including Hi-Media Carbokit™, Enterobacteriaceae™ identification kit, ERIC–PCR, and 16S ARDRA. All the strains showed growth on Ashby’s N-free media over 7 generations, indicative of presumptive nitrogen fixation and further confirmed by amplification of the nifH gene. None of the strains showed the capability to renodulate the host plant, neither alone nor in combination with standard rhizobial strains, which was further confirmed by the absence of nodC bands in PCR assay. The results clearly indicate the common existence of nonrhizobial microflora inside the root nodules of legumes, which were thought to be colonized only by rhizobia and were responsible for N2fixation in leguminous crops. However, with the recent discovery of nodule endophytes from a variety of legumes, as also observed here, it can be assumed that symbiotic rhizobia are not all alone and that these invasive endophytes belonging to various bacterial genera are more than just opportunistic colonizers of specialized nodule niche.

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Вплив глюкозовмісних моноцукрів на симбіотичнi властивостi бульбочкових бактерій сої та формування урожаю рослинами

Ukrainian Journal of Ecology ◽

10.15421/2018_236 ◽

2018 ◽

Vol 8 (1) ◽

pp. 460-465 ◽

Cited By ~ 1

Author(s):

O.V. Kyrychenko ◽

Yu.O. Khomenko ◽

S.Ya. Kots

Keyword(s):

High Efficiency ◽

Nitrogenase Activity ◽

Root Nodules ◽

Control Level ◽

Soybean Seeds ◽

Nodule Bacteria ◽

Natural Agents ◽

Soybean Nodule ◽

Productive Potential ◽

Symbiotic Properties

The symbiotic properties of soybean nodule bacteria, root nodules forming (nodulation ability), nitrogen-fixing activity and efficiency under the influence of monosaccharides (0.01 M glucose and N-acetyl-D-glucosamine) on rhizobium culture were investigated in greenhouse with sandy soils. Nodulation activity and efficiency was estimated by the number and weight of the nodules formed on the roots of plants; by the formation of vegetative mass and by the yield of soybean seeds. Nitrogenase activity was determined by acetylene-reductase method. The control variant was inoculated by monoculture of soybean rhizobium. A significant increase in the degree of realization of the nodulation ability of rhizobium has been established under the influence of glucose-containing monosaccharides on the culture of microorganisms. Adding glucose to bacteria led to increase the average number of nodules per plant by 1.6, 2.2, and 1.7 times respectively in the phase of development of two true leaves, flowering and active bean formation in soybean. At the same time the weight of the root nodules was increased by 1.4, 2.3, and 1.4 times respectively as compared to control. The number of root nodules was increased by 2.2, 2.3, and 1.4 times as compared to the control while of glucosamine was used; while the weight of these nodules were 2.1 and 1.9 times higher than control in the phase of development of two true leaves and flowering, while in the phase of active beans formation it did not differ from control.The functional activityof the soybean symbiotic system that was formed by rhizobial culture and modified by glucose, had the highest positive effect, since the nitrogen-fixing activity remained stable and was 2.1 and 1.7 times higher than control.Rhizobia, to suspension of which we added glucosamine, formed a symbiosis with activity that was 1.7 times higher than monoculture in the flowering phase, but later it was at the control level. We registered that inoculants on the basis of bacteria and glucose-containing monosaccharides activated seeds germination. The first true leaf of plants (up to 3.5 times higher than control), their above green mass (25-27% higher) and root system (10-16% higher) were actively formed while we used inoculant with rhizobia and glucose. Plants in the variant with the pre-sowing inoculation of seeds by bacteria and glucosamine almost did not differ from the control.The yield of soybean seeds significantly exceeded (up to 14%) the crop, produced by plants with inoculation by monoculture of rhizobia under the influence of glucose-containing monosaccharides. We indicated high efficiency of soybean-rhizobium symbiosis formed by nodule bacteria modified of glucose-containing monosaccharides. Thus, the use of glucose-containing monosaccherides as additional “green” and safe natural agents in complex inoculants with nodule soybean bacteria promotes a more complete implementation of the symbiotic and productive potential of soybean-rhizobial symbiosis compared with the use for seeds pre-sowing treatment only of rhizobia monoculture in greenhouse with sandy culture.

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Nitrogen fixation in legume root nodules: biochemical studies with soybean

Proceedings of the Royal Society of London Series B Biological Sciences ◽

10.1098/rspb.1969.0029 ◽

1969 ◽

Vol 172 (1029) ◽

pp. 401-416 ◽

Cited By ~ 26

Keyword(s):

Nitrogen Fixation ◽

Root Nodule ◽

Root Nodules ◽

Reducing Power ◽

Nitrogen Fixing ◽

Nodule Bacteria ◽

Stages Of Growth ◽

Host Cytoplasm ◽

Photosynthetic Product ◽

Power And Energy

It is now clear from studies with soybean root nodules that the nitrogen fixing activity resides in the bacteroids which are the symbiotic form of the root nodule bacteria. These develop as a result of a complex series of changes in metabolism and structure which occur in the bacteria during the final stages of growth within membrane-enclosed vesicles in the host cytoplasm. Nitrogenase appears when these changes are complete. The primary product of nitrogen fixation is NH 3 , which in intact nodules, is rapidly transformed into α -amino compounds which are used by the host plant. In suspensions of bacteroids and in cell-free extracts prepared from them, the reaction terminates in NH 3 , which is released into the medium. Free O 2 , which is required for the production of energy for nitrogen fixation by nodules and by bacteroid suspensions, also causes inactivation of the nitrogen fixing system and exerts important kinetic influences upon the reaction. Reducing power and energy for the reduction of N 2 to NH 3 is provided by a photosynthetic product from the host in nodules; in bacteroid suspensions, a substrate such as succinate is required. In cell-free extracts, requirements for energy and reductant are met by ATP and dithionite. The natural reductant has not yet been identified. A schematic representation of various factors which affect nitrogen fixation in nodules, bacteroid suspensions and cell-free extracts is presented.

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Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.021014-0 ◽

2011 ◽

Vol 61 (2) ◽

pp. 299-309 ◽

Cited By ~ 79

Author(s):

Mohammad S. Hoque ◽

Linda M. Broadhurst ◽

Peter H. Thrall

Keyword(s):

Root Nodule ◽

Root Nodules ◽

Disease Suppression ◽

Rrna Gene ◽

Bacterial Strains ◽

Symbiotic Relationships ◽

South Eastern ◽

Eastern Australia ◽

Microbe Interactions ◽

Ecological Importance

Symbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant–microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.

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