Isolation of Rhizobium Bacteria from Forage Legumes for the Development of Ruminant Feed

NASA Astrophysics Data System (ADS)

Fuskhah, E.; Purbajanti, E. D.; Anwar, S.

2018-02-01

The aimed of the study was to explore the presence of Rhizobium bacteria along the northern coast of Central Java, to develop a saline-resistant legumes. Rhizobium bacteria is a mutualistic bacterium capable of symbiosis with legumes so that legumes crop yields increase. The research begins with sampling of soil and root nodule of forage legumes along the Northern Coast of Central Java including Tegal, Pekalongan, Semarang, Demak, Pati. Soil samples were analysed for salinity, Total Dissolved Solids, and pH. Rhizobium bacteria were isolated from the acquired root nodule, then identified by biochemical test to ensure that the isolates obtained were Rhizobium bacteria. The results showed that the five districts/municipal sites sampled by the soil have very low salinity to very high levels. The highest level of soil salinity was found in Demak (Sayung) which has an electrical conductivity value (EC) of 17.77 mmhos/cm. The EC values of legumes overgrown soils showed a low salinity level while bare soils have high salinity levels. Feed crops legumes that could be found in the northern coast of Central Java were Centrosema pubescens, Calopogonium mucunoides, Leucaena leucocephala, and Sesbania grandiflora. The study obtained 6 kinds of isolates of rhizobium bacteria isolated from forage legumes, included 1) Centrosema pubescens isolated from Pekalongan, 2) Centrosema pubescens isolated from Tegal, 3) Calopogonium mucunoides isolated from Pekalongan, 4) Leucaenaleucocephala isolated from Tegal, 5) Leucaena leucocephala isolated from Semarang, 6) Sesbania grandiflora isolated from Tegal.

Burkholderia sp. induces functional nodules on the South African invasive legume Dipogon lignosus (Phaseoleae) in New Zealand soils.

PubMed

Liu, Wendy Y Y; Ridgway, Hayley J; James, Trevor K; James, Euan K; Chen, Wen-Ming; Sprent, Janet I; Young, J Peter W; Andrews, Mitchell

2014-10-01

The South African invasive legume Dipogon lignosus (Phaseoleae) produces nodules with both determinate and indeterminate characteristics in New Zealand (NZ) soils. Ten bacterial isolates produced functional nodules on D. lignosus. The 16S ribosomal RNA (rRNA) gene sequences identified one isolate as Bradyrhizobium sp., one isolate as Rhizobium sp. and eight isolates as Burkholderia sp. The Bradyrhizobium sp. and Rhizobium sp. 16S rRNA sequences were identical to those of strains previously isolated from crop plants and may have originated from inocula used on crops. Both 16S rRNA and DNA recombinase A (recA) gene sequences placed the eight Burkholderia isolates separate from previously described Burkholderia rhizobial species. However, the isolates showed a very close relationship to Burkholderia rhizobial strains isolated from South African plants with respect to their nitrogenase iron protein (nifH), N-acyltransferase nodulation protein A (nodA) and N-acetylglucosaminyl transferase nodulation protein C (nodC) gene sequences. Gene sequences and enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive element palindromic PCR (rep-PCR) banding patterns indicated that the eight Burkholderia isolates separated into five clones of one strain and three of another. One strain was tested and shown to produce functional nodules on a range of South African plants previously reported to be nodulated by Burkholderia tuberum STM678(T) which was isolated from the Cape Region. Thus, evidence is strong that the Burkholderia strains isolated here originated in South Africa and were somehow transported with the plants from their native habitat to NZ. It is possible that the strains are of a new species capable of nodulating legumes.

Methylotrophic Methylobacterium Bacteria Nodulate and Fix Nitrogen in Symbiosis with Legumes

PubMed Central

Sy, Abdoulaye; Giraud, Eric; Jourand, Philippe; Garcia, Nelly; Willems, Anne; de Lajudie, Philippe; Prin, Yves; Neyra, Marc; Gillis, Monique; Boivin-Masson, Catherine; Dreyfus, Bernard

2001-01-01

Rhizobia described so far belong to three distinct phylogenetic branches within the α-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, “Methylobacterium nodulans,” within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the α subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that “M. nodulans” is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that “M. nodulans” NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer. PMID:11114919

Chromium(VI) Toxicity in Legume Plants: Modulation Effects of Rhizobial Symbiosis

PubMed Central

Lushchak, Volodymyr I.

2018-01-01

Most legume species have the ability to establish a symbiotic relationship with soil nitrogen-fixing rhizobacteria that promote plant growth and productivity. There is an increasing evidence of reactive oxygen species (ROS) important role in formation of legume-rhizobium symbiosis and nodule functioning. Environmental pollutants such as chromium compounds can cause damage to rhizobia, legumes, and their symbiosis. In plants, toxic effects of chromium(VI) compounds are associated with the increased production of ROS and oxidative stress development as well as with inhibition of pigment synthesis and modification of virtually all cellular components. These metabolic changes result in inhibition of seed germination and seedling development as well as reduction of plant biomass and crop yield. However, if plants establish symbiosis with rhizobia, heavy metals are accumulated preferentially in nodules decreasing the toxicity of metals to the host plant. This review summarizes data on toxic effects of chromium on legume plants and legume-rhizobium symbiosis. In addition, we discussed the role of oxidative stress in both chromium toxicity and formation of rhizobial symbiosis and use of nodule bacteria for minimizing toxic effects of chromium on plants. PMID:29662899

The Symbiosome: Legume and Rhizobia Co-evolution toward a Nitrogen-Fixing Organelle?

PubMed Central

Coba de la Peña, Teodoro; Fedorova, Elena; Pueyo, José J.; Lucas, M. Mercedes

2018-01-01

In legume nodules, symbiosomes containing endosymbiotic rhizobial bacteria act as temporary plant organelles that are responsible for nitrogen fixation, these bacteria develop mutual metabolic dependence with the host legume. In most legumes, the rhizobia infect post-mitotic cells that have lost their ability to divide, although in some nodules cells do maintain their mitotic capacity after infection. Here, we review what is currently known about legume symbiosomes from an evolutionary and developmental perspective, and in the context of the different interactions between diazotroph bacteria and eukaryotes. As a result, it can be concluded that the symbiosome possesses organelle-like characteristics due to its metabolic behavior, the composite origin and differentiation of its membrane, the retargeting of host cell proteins, the control of microsymbiont proliferation and differentiation by the host legume, and the cytoskeletal dynamics and symbiosome segregation during the division of rhizobia-infected cells. Different degrees of symbiosome evolution can be defined, specifically in relation to rhizobial infection and to the different types of nodule. Thus, our current understanding of the symbiosome suggests that it might be considered a nitrogen-fixing link in organelle evolution and that the distinct types of legume symbiosomes could represent different evolutionary stages toward the generation of a nitrogen-fixing organelle. PMID:29403508

Bradyrhizobium sacchari sp. nov., a legume nodulating bacterium isolated from sugarcane roots.

PubMed

de Matos, Gustavo Feitosa; Zilli, Jerri Edson; de Araújo, Jean Luiz Simões; Parma, Marcia Maria; Melo, Itamar Soares; Radl, Viviane; Baldani, José Ivo; Rouws, Luc Felicianus Marie

2017-11-01

Members of the genus Bradyrhizobium are well-known as nitrogen-fixing microsymbionts of a wide variety of leguminous species, but they have also been found in different environments, notably as endophytes in non-legumes such as sugarcane. This study presents a detailed polyphasic characterization of four Bradyrhizobium strains (type strain BR 10280 T ), previously isolated from roots of sugarcane in Brazil. 16S rRNA sequence analysis, multilocus sequence analysis (MLSA) and analysis of the 16S-23S rRNA internal transcribed spacer showed that these strains form a novel clade close to, but different from B. huanghuaihaiense strain CCBAU 23303 T . Average nucleotide identity (ANI) analyses confirmed that BR 10280 T represents a novel species. Phylogenetic analysis based on nodC gene sequences also placed the strains close to CCBAU 23303 T , but different from this latter strain, the sugarcane strains did not nodulate soybean, although they effectively nodulated Vigna unguiculata, Cajanus cajan and Macroptilium atropurpureum. Physiological traits are in agreement with the placement of the strains in the genus Bradyrhizobium as a novel species for which the name Bradyrhizobium sacchari sp. nov. is proposed.

Specificity in Legume-Rhizobia Symbioses

PubMed Central

Andrews, Mitchell; Andrews, Morag E.

2017-01-01

Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N2) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium/Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae (Rhizobium), the genus level for Cytisus (Bradyrhizobium), Lupinus (Bradyrhizobium) and the New Zealand native Sophora spp. (Mesorhizobium) and species level for Cicer arietinum (Mesorhizobium), Listia bainesii (Methylobacterium) and Listia angolensis (Microvirga). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis (Neorhizobium galegeae sv. officinalis), Galega orientalis (Neorhizobium galegeae sv. orientalis), Hedysarum coronarium (Rhizobium sullae), Medicago laciniata (Ensifer meliloti sv. medicaginis), Medicago rigiduloides (Ensifer meliloti sv. rigiduloides) and Trifolium ambiguum (Rhizobium leguminosarum sv. trifolii). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia adapted to particular soils

Specificity in Legume-Rhizobia Symbioses.

PubMed

Andrews, Mitchell; Andrews, Morag E

2017-03-26

Most species in the Leguminosae (legume family) can fix atmospheric nitrogen (N₂) via symbiotic bacteria (rhizobia) in root nodules. Here, the literature on legume-rhizobia symbioses in field soils was reviewed and genotypically characterised rhizobia related to the taxonomy of the legumes from which they were isolated. The Leguminosae was divided into three sub-families, the Caesalpinioideae, Mimosoideae and Papilionoideae. Bradyrhizobium spp. were the exclusive rhizobial symbionts of species in the Caesalpinioideae, but data are limited. Generally, a range of rhizobia genera nodulated legume species across the two Mimosoideae tribes Ingeae and Mimoseae, but Mimosa spp. show specificity towards Burkholderia in central and southern Brazil, Rhizobium / Ensifer in central Mexico and Cupriavidus in southern Uruguay. These specific symbioses are likely to be at least in part related to the relative occurrence of the potential symbionts in soils of the different regions. Generally, Papilionoideae species were promiscuous in relation to rhizobial symbionts, but specificity for rhizobial genus appears to hold at the tribe level for the Fabeae ( Rhizobium ), the genus level for Cytisus ( Bradyrhizobium ), Lupinus ( Bradyrhizobium ) and the New Zealand native Sophora spp. ( Mesorhizobium ) and species level for Cicer arietinum ( Mesorhizobium ), Listia bainesii ( Methylobacterium ) and Listia angolensis ( Microvirga ). Specificity for rhizobial species/symbiovar appears to hold for Galega officinalis ( Neorhizobium galegeae sv. officinalis ) , Galega orientalis ( Neorhizobium galegeae sv. orientalis ), Hedysarum coronarium ( Rhizobium sullae ), Medicago laciniata ( Ensifer meliloti sv. medicaginis ), Medicago rigiduloides ( Ensifer meliloti sv. rigiduloide s) and Trifolium ambiguum ( Rhizobium leguminosarum sv. trifolii ). Lateral gene transfer of specific symbiosis genes within rhizobial genera is an important mechanism allowing legumes to form symbioses with rhizobia

Genetic diversity and symbiotic effectiveness of Bradyrhizobium strains nodulating selected annual grain legumes growing in Ethiopia.

PubMed

Degefu, Tulu; Wolde-Meskel, Endalkachew; Rasche, Frank

2018-01-01

Vigna unguiculata, Vigna radiata and Arachis hypogaea growing in Ethiopia are nodulated by a genetically diverse group of Bradyrhizobium strains. To determine the genetic identity and symbiotic effectiveness of these bacteria, a collection of 36 test strains originating from the root nodules of the three hosts was investigated using multilocus sequence analyses (MLSA) of core genes including 16S rRNA, recA, glnII, gyrB, atpD and dnaK. Sequence analysis of nodA and nifH genes along with tests for symbiotic effectiveness using δ 15 N analysis were also carried out. The phylogenetic trees derived from the MLSA grouped most test strains into four well-supported distinct positions designated as genospecies I-IV. The maximum likelihood (ML) tree that was constructed based on the nodA gene sequences separated the entire test strains into two lineages, where the majority of the test strains were clustered on one of a well-supported large branch that comprise Bradyrhizobium species from the tropics. This clearly suggested the monophyletic origin of the nodA genes within the bradyrhizobia of tropical origin. The δ 15 N-based symbiotic effectiveness test of seven selected strains revealed that strains GN100 (δ 15 N=0.73) and GN102 (δ 15 N=0.79) were highly effective nitrogen fixers when inoculated to cowpea, thus can be considered as inoculants in cowpea production. It was concluded that Ethiopian soils are a hotspot for rhizobial diversity. This calls for further research to unravel as yet unknown bradyrhizobia nodulating legume host species growing in the country. In this respect, prospective research should also address the mechanisms of symbiotic specificity that could lead to high nitrogen fixation in target legumes.

The carbon-nitrogen balance of the nodule and its regulation under elevated carbon dioxide concentration.

PubMed

Libault, Marc

2014-01-01

Legumes have developed a unique way to interact with bacteria: in addition to preventing infection from pathogenic bacteria like any other plant, legumes also developed a mutualistic symbiotic relationship with one gender of soil bacteria: rhizobium. This interaction leads to the development of a new root organ, the nodule, where the differentiated bacteria fix for the plant the atmospheric dinitrogen (atmN2). In exchange, the symbiont will benefit from a permanent source of carbon compounds, products of the photosynthesis. The substantial amounts of fixed carbon dioxide dedicated to the symbiont imposed to the plant a tight regulation of the nodulation process to balance carbon and nitrogen incomes and outcomes. Climate change including the increase of the concentration of the atmospheric carbon dioxide is going to modify the rates of plant photosynthesis, the balance between nitrogen and carbon, and, as a consequence, the regulatory mechanisms of the nodulation process. This review focuses on the regulatory mechanisms controlling carbon/nitrogen balances in the context of legume nodulation and discusses how the change in atmospheric carbon dioxide concentration could affect nodulation efficiency.

The Carbon-Nitrogen Balance of the Nodule and Its Regulation under Elevated Carbon Dioxide Concentration

PubMed Central

2014-01-01

Legumes have developed a unique way to interact with bacteria: in addition to preventing infection from pathogenic bacteria like any other plant, legumes also developed a mutualistic symbiotic relationship with one gender of soil bacteria: rhizobium. This interaction leads to the development of a new root organ, the nodule, where the differentiated bacteria fix for the plant the atmospheric dinitrogen (atmN2). In exchange, the symbiont will benefit from a permanent source of carbon compounds, products of the photosynthesis. The substantial amounts of fixed carbon dioxide dedicated to the symbiont imposed to the plant a tight regulation of the nodulation process to balance carbon and nitrogen incomes and outcomes. Climate change including the increase of the concentration of the atmospheric carbon dioxide is going to modify the rates of plant photosynthesis, the balance between nitrogen and carbon, and, as a consequence, the regulatory mechanisms of the nodulation process. This review focuses on the regulatory mechanisms controlling carbon/nitrogen balances in the context of legume nodulation and discusses how the change in atmospheric carbon dioxide concentration could affect nodulation efficiency. PMID:24987690

Blue light does not inhibit nodulation in Sesbania rostrata.

PubMed

Shimomura, Aya; Arima, Susumu; Hayashi, Makoto; Maymon, Maskit; Hirsch, Ann M; Suzuki, Akihiro

2017-01-02

Earlier, we reported that root nodulation was inhibited by blue light irradiation of Lotus japonicus. Because some legumes do not establish nodules exclusively on underground roots, we investigated whether nodule formation in Sesbania rostrata, which forms both root and "stem" nodules following inoculation with Azorhizobium caulinodans, is inhibited by blue light as are L. japonicus nodules. We found that neither S. rostrata nodulation nor nitrogen fixation was inhibited by blue light exposure. Moreover, although A. caulinodans proliferation was not affected by blue light irradiation, bacterial survival was decreased. Therefore, blue light appears to impose different responses depending on the legume-rhizobial symbiosis.

Redefining Nitric Oxide Production in Legume Nodules through Complementary Insights from Electron Paramagnetic Resonance Spectroscopy and Specific Fluorescent Probes.

PubMed

Calvo-Begueria, Laura; Rubio, Maria C; Martínez, Jesús I; Pérez-Rontomé, Carmen; Delgado, Maria J; Bedmar, Eulogio J; Becana, Manuel

2018-04-26

Nitric oxide (NO) is a signaling molecule with multiple functions in plants. Given its critical importance and reactivity as a gaseous free radical, we have examined NO production in legume nodules using electron paramagnetic resonance (EPR) spectroscopy and the specific fluorescent dye 4,5-diaminofluorescein diacetate. Also, in this context, we critically assess previous and current views of NO production and detection in nodules. EPR of intact nodules revealed that nitrosyl-leghemoglobin (Lb2+NO) was absent from bean or soybean nodules regardless of nitrate supply, but accumulated in soybean nodules treated with nitrate that were defective in nitrite or nitric oxide reductases or that were exposed to ambient temperature. Consequently, bacteroids are a major source of NO, denitrification enzymes are required for NO homeostasis, and Lb2+NO is not responsible for the inhibition of nitrogen fixation by nitrate. Further, we noted that Lb2+NO is artifactually generated in nodule extracts or in intact nodules not analyzed immediately after detachment. The fluorescent probe detected NO formation in bean and soybean nodule infected cells and in soybean nodule parenchyma. The NO signal was slightly decreased by inhibitors of nitrate reductase but not of nitric oxide synthase, which could indicate a minor contribution of plant nitrate reductase and supports the existence of nitrate- and arginine-independent pathways for NO production. Collectively, our data indicate that EPR and fluorometric methods are complementary to draw reliable conclusions about NO production in plants.

Competition Experiments for Legume Infection Identify Burkholderia phymatum as a Highly Competitive β-Rhizobium

PubMed Central

Lardi, Martina; de Campos, Samanta Bolzan; Purtschert, Gabriela; Eberl, Leo; Pessi, Gabriella

2017-01-01

Members of the genus Burkholderia (β-proteobacteria) have only recently been shown to be able to establish a nitrogen-fixing symbiosis with several legumes, which is why they are also referred to as β-rhizobia. Therefore, very little is known about the competitiveness of these species to nodulate different legume host plants. In this study, we tested the competitiveness of several Burkholderia type strains (B. diazotrophica, B. mimosarum, B. phymatum, B. sabiae, B. symbiotica and B. tuberum) to nodulate four legumes (Phaseolus vulgaris, Macroptilium atropurpureum, Vigna unguiculata and Mimosa pudica) under our closely defined growth conditions. The assessment of nodule occupancy of these species on different legume host plants revealed that B. phymatum was the most competitive strain in the three papilionoid legumes (bean, cowpea and siratro), while B. mimosarum outcompeted the other strains in mimosa. The analysis of phenotypes known to play a role in nodulation competitiveness (motility, exopolysaccharide production) and additional in vitro competition assays among β-rhizobial strains suggested that B. phymatum has the potential to be a very competitive legume symbiont. PMID:28861050

Mesorhizobium ciceri biovar biserrulae, a novel biovar nodulating the pasture legume Biserrula pelecinus L.

PubMed

Nandasena, Kemanthi G; O'Hara, Graham W; Tiwari, Ravi P; Willlems, Anne; Howieson, John G

2007-05-01

Biserrula pelecinus L. is a pasture legume species that forms a highly specific nitrogen-fixing symbiotic interaction with a group of bacteria that belong to Mesorhizobium. These mesorhizobia have >98.8 % sequence similarity to Mesorhizobium ciceri and Mesorhizobium loti for the 16S rRNA gene (1440 bp) and >99.3 % sequence similarity to M. ciceri for the dnaK gene (300 bp), and strain WSM1271 has 100 % sequence similarity to M. ciceri for GSII (600 bp). Strain WSM1271 had 85 % relatedness to M. ciceri LMG 14989(T) and 50 % relatedness to M. loti LMG 6125(T) when DNA-DNA hybridization was performed. WSM1271 also had a similar cellular fatty acid profile to M. ciceri. These results are strong evidence that the Biserrula mesorhizobia and M. ciceri belong to the same group of bacteria. Significant differences were revealed between the Biserrula mesorhizobia and M. ciceri in growth conditions, antibiotic resistance and carbon source utilization. The G+C content of the DNA of WSM1271 was 62.7 mol%, compared to 63-64 mol% for M. ciceri. The Biserrula mesorhizobia contained a plasmid ( approximately 500 bp), but the symbiotic genes were detected on a mobile symbiosis island and considerable variation was present in the symbiotic genes of Biserrula mesorhizobia and M. ciceri. There was <78.6 % sequence similarity for nodA and <66.9 % for nifH between Biserrula mesorhizobia and M. ciceri. Moreover, the Biserrula mesorhizobia did not nodulate the legume host of M. ciceri, Cicer arietinum, and M. ciceri did not nodulate B. pelecinus. These significant differences observed between Biserrula mesorhizobia and M. ciceri warrant the proposal of a novel biovar for Biserrula mesorhizobia within M. ciceri. The name Mesorhizobium ciceri biovar biserrulae is proposed, with strain WSM1271 (=LMG 23838=HAMBI 2942) as the reference strain.

Wide distribution range of rhizobial symbionts associated with pantropical sea-dispersed legumes.

PubMed

Bamba, Masaru; Nakata, Sayuri; Aoki, Seishiro; Takayama, Koji; Núñez-Farfán, Juan; Ito, Motomi; Miya, Masaki; Kajita, Tadashi

2016-12-01

To understand the geographic distributions of rhizobia that associated with widely distributed wild legumes, 66 nodules obtained from 41 individuals including three sea-dispersed legumes (Vigna marina, Vigna luteola, and Canavalia rosea) distributed across the tropical and subtropical coastal regions of the world were studied. Partial sequences of 16S rRNA and nodC genes extracted from the nodules showed that only Bradyrhizobium and Sinorhizobium were associated with the pantropical legumes, and some of the symbiont strains were widely distributed over the Pacific. Horizontal gene transfer of nodulation genes were observed within the Bradyrhizobium and Sinorhizobium lineages. BLAST searches in GenBank also identified records of these strains from various legumes across the world, including crop species. However, one of the rhizobial strains was not found in GenBank, which implies the strain may have adapted to the littoral environment. Our results suggested that some rhizobia, which associate with the widespread sea-dispersed legume, distribute across a broad geographic range. By establishing symbiotic relationships with widely distributed rhizobia, the pantropical legumes may also be able to extend their range much further than other legume species.

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

PubMed Central

Elliott, Geoffrey N.; Chen, Wen-Ming; Bontemps, Cyril; Chou, Jui-Hsing; Young, J. Peter W.; Sprent, Janet I.; James, Euan K.

2007-01-01

Background and Aims Species of the genus Burkholderia, from the Betaproteobacteria, have been isolated from legume nodules, but so far they have only been shown to form symbioses with species of Mimosa, sub-family Mimosoideae. This work investigates whether Burkholderia tuberum strains STM678 (isolated from Aspalathus carnosa) and DUS833 (from Aspalathus callosa) can nodulate species of the South African endemic papilionoid genera Cyclopia (tribe Podalyrieae) and Aspalathus (Crotalarieae) as well as the promiscuous legume Macroptilium atropurpureum (Phaseoleae). Method Bacterial strains and the phylogeny of their symbiosis-related (nod) genes were examined via 16S rRNA gene sequencing. Seedlings were grown in liquid culture and inoculated with one of the two strains of B. tuberum or with Sinorhizobium strain NGR 234 (from Lablab purpureus), Mesorhizobium strain DUS835 (from Aspalathus linearis) or Methylobacterium nodulans (from Crotalaria podocarpa). Some nodules, inoculated with green fluorescence protein (GFP)-tagged strains, were examined by light and electron microscopy coupled with immunogold labelling with a Burkholderia-specific antibody. The presence of active nitrogenase was checked by immunolabelling of nitrogenase and by the acetylene reduction assay. B. tuberum STM678 was also tested on a wide range of legumes from all three sub-families. Key Results Nodules were not formed on any of the Aspalathus spp. Only B. tuberum nodulated Cyclopia falcata, C. galioides, C. genistoides, C. intermedia and C. pubescens. It also effectively nodulated M. atropurpureum but no other species tested. GFP-expressing inoculant strains were located inside infected cells of C. genistoides, and bacteroids in both Cyclopia spp. and M. atropurpureum were immunogold-labelled with antibodies against Burkholderia and nitrogenase. Nitrogenase activity was also shown using the acetylene reduction assay. This is the first demonstration that a β-rhizobial strain can effectively

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

PubMed

Chen, Wen-Ming; de Faria, Sergio M; James, Euan K; Elliott, Geoffrey N; Lin, Kuan-Yin; Chou, Jui-Hsing; Sheu, Shih-Yi; Cnockaert, M; Sprent, Janet I; Vandamme, Peter

2007-05-01

Three strains, Br3437(T), Br3461 and Br3470, were isolated from nitrogen-fixing nodules on the roots of Mimosa scabrella (Br3437(T)) and Mimosa bimucronata (Br3461, Br3470), both of which are woody legumes native to Brazil. On the basis of 16S rRNA gene sequence similarities, all the strains were shown previously to belong to the genus Burkholderia. A polyphasic approach, including DNA-DNA hybridizations, PFGE of whole-genome DNA profiles, whole-cell protein analyses, fatty acid methyl ester analysis and extensive biochemical characterization, was used to clarify the taxonomic position of these strains further; the strains are here classified within a novel species, for which the name Burkholderia nodosa sp. nov. is proposed. The type strain, Br3437(T) (=LMG 23741(T)=BCRC 17575(T)), was isolated from nodules of M. scabrella.

The High-Affinity Phosphate Transporter GmPT5 Regulates Phosphate Transport to Nodules and Nodulation in Soybean1[W][OA

PubMed Central

Qin, Lu; Zhao, Jing; Tian, Jiang; Chen, Liyu; Sun, Zhaoan; Guo, Yongxiang; Lu, Xing; Gu, Mian; Xu, Guohua; Liao, Hong

2012-01-01

Legume biological nitrogen (N) fixation is the most important N source in agroecosystems, but it is also a process requiring a considerable amount of phosphorus (P). Therefore, developing legume varieties with effective N2 fixation under P-limited conditions could have profound significance for improving agricultural sustainability. We show here that inoculation with effective rhizobial strains enhanced soybean (Glycine max) N2 fixation and P nutrition in the field as well as in hydroponics. Furthermore, we identified and characterized a nodule high-affinity phosphate (Pi) transporter gene, GmPT5, whose expression was elevated in response to low P. Yeast heterologous expression verified that GmPT5 was indeed a high-affinity Pi transporter. Localization of GmPT5 expression based on β-glucuronidase staining in soybean composite plants with transgenic roots and nodules showed that GmPT5 expression occurred principally in the junction area between roots and young nodules and in the nodule vascular bundles for juvenile and mature nodules, implying that GmPT5 might function in transporting Pi from the root vascular system into nodules. Overexpression or knockdown of GmPT5 in transgenic composite soybean plants altered nodulation and plant growth performance, which was partially dependent on P supply. Through both in situ and in vitro 33P uptake assays using transgenic soybean roots and nodules, we demonstrated that GmPT5 mainly functions in transporting Pi from roots to nodules, especially under P-limited conditions. We conclude that the high-affinity Pi transporter, GmPT5, controls Pi entry from roots to nodules, is critical for maintaining Pi homeostasis in nodules, and subsequently regulates soybean nodulation and growth performance. PMID:22740613

Sulphadimethoxine inhibits Phaseolus vulgaris root growth and development of N-fixing nodules.

PubMed

Sartorius, Marilena; Riccio, Anna; Cermola, Michele; Casoria, Paolo; Patriarca, Eduardo J; Taté, Rosarita

2009-07-01

Sulphonamides contamination of cultivated lands occurs through the recurrent spreading of animal wastes from intensive farming. The aim of this study was to test the effect(s) of sulphadimethoxine on the beneficial N-fixing Rhizobium etli-Phaseolus vulgaris symbiosis under laboratory conditions. The consequence of increasing concentrations of sulphadimethoxine on the growth ability of free-living R. etli bacteria, as well as on seed germination, seedling development and growth of common bean plants was examined. We have established that sulphadimethoxine inhibited the growth of both symbiotic partners in a dose-dependent manner. Bacterial invasion occurring in developing root nodules was visualized by fluorescence microscopy generating EGFP-marked R. etli bacteria. Our results proved that the development of symbiotic N-fixing root nodules is hampered by sulphadimethoxine thus identifying sulphonamides as toxic compounds for the Rhizobium-legume symbiosis: a low-input sustainable agricultural practice.

Waterlogging tolerance, tissue nitrogen and oxygen transport in the forage legume Melilotus siculus: a comparison of nodulated and nitrate-fed plants.

PubMed

Konnerup, Dennis; Toro, Guillermo; Pedersen, Ole; Colmer, Timothy David

2018-03-14

Soil waterlogging adversely impacts most plants. Melilotus siculus is a waterlogging-tolerant annual forage legume, but data were lacking for the effects of root-zone hypoxia on nodulated plants reliant on N2 fixation. The aim was to compare the waterlogging tolerance and physiology of M. siculus reliant on N2 fixation or with access to NO3-. A factorial experiment imposed treatments of water level (drained or waterlogged), rhizobia (nil or inoculated) and mineral N supply (nil or 11 mm NO3-) for 21 d on plants in pots of vermiculite in a glasshouse. Nodulation, shoot and root growth and tissue N were determined. Porosity (gas volume per unit tissue volume) and respiration rates of root tissues and nodules, and O2 microelectrode profiling across nodules, were measured in a second experiment. Plants inoculated with the appropriate rhizobia, Ensifer (syn. Sinorhizobium) medicae, formed nodules. Nodulated plants grew as well as plants fed NO3-, both in drained and waterlogged conditions. The growth and total N content of nodulated plants (without any NO3- supplied) indicated N2 fixation. Respiration rates (mass basis) were highest in nodules and root tips and lowest in basal root tissues. Secondary aerenchyma (phellem) formed along basal root parts and a thin layer of this porous tissue also covered nodules, which together enhanced gas-phase diffusion of O2 to the nodules; O2 was below detection within the infected zone of the nodule interior. Melilotus siculus reliant on N2 fixation grew well both in drained and waterlogged conditions, and had similar tissue N concentrations. In waterlogged conditions the relatively high respiration rates of nodules must rely on O2 movement via the aerenchymatous phellem in hypocotyl, roots and the outer tissue layers of nodules.

[Modern bacterial taxonomy: techniques review--application to bacteria that nodulate leguminous plants (BNL)].

PubMed

Zakhia, Frédéric; de Lajudie, Philippe

2006-03-01

Taxonomy is the science that studies the relationships between organisms. It comprises classification, nomenclature, and identification. Modern bacterial taxonomy is polyphasic. This means that it is based on several molecular techniques, each one retrieving the information at different cellular levels (proteins, fatty acids, DNA...). The obtained results are combined and analysed to reach a "consensus taxonomy" of a microorganism. Until 1970, a small number of classification techniques were available for microbiologists (mainly phenotypic characterization was performed: a legume species nodulation ability for a Rhizobium, for example). With the development of techniques based on polymerase chain reaction for characterization, the bacterial taxonomy has undergone great changes. In particular, the classification of the legume nodulating bacteria has been repeatedly modified over the last 20 years. We present here a review of the currently used molecular techniques in bacterial characterization, with examples of application of these techniques for the study of the legume nodulating bacteria.

Competition by Bradyrhizobium Strains for Nodulation of the Nonlegume Parasponia andersonii

PubMed Central

Trinick, M. J.; Hadobas, P. A.

1989-01-01

Bradyrhizobium strains isolated from the nonlegume Parasponia spp. formed a group of strains that were highly competitive for nodulation of P. andersonii when paired with strains isolated from legumes. Strains from legumes, including those of similar effectiveness to NGR231 and CP283, were not able to form nodules as single occupants on P. andersonii in the presence of Parasponia strains. However, NGR86, an isolate from Macroptilium lathyroides, jointly occupied one-third of the nodules formed with each of the three strains isolated from Parasponia spp. Time taken for nodules to appear may have influenced the outcome of competition, since CP283 and all isolates from legumes were slow to nodulate P. andersonii. Among the Parasponia strains, competitiveness for nodulation of P. andersonii was not associated with effectiveness of nitrogen fixation. The highly effective strain CP299 was a poor competitor when paired with the least effective strain NGR231. CP283 was the least competitive of the Parasponia strains but was still able to dominate nodules when paired with legume isolates. Dual occupancy was high, up to 67% when the inoculum contained CP299 and CP273. Both the Muc+ and Muc- types of CP283 form a symbiosis of similar effectiveness and were similarly competitive at high inoculation densities, but the Muc- form was more competitive at low inoculum densities. Both forms frequently occupied the same nodule. Bradyrhizobium strains isolated from Parasponia spp. may have specific genetic information that favor their ability to competitively and effectively infect plants in the genus Parasponia (Ulmaceae) outside the Leguminosae. PMID:16347913

CYTOKININ OXIDASE/DEHYDROGENASE3 Maintains Cytokinin Homeostasis during Root and Nodule Development in Lotus japonicus1[OPEN

PubMed Central

Heckmann, Anne B.; Kelly, Simon

2016-01-01

Cytokinins are required for symbiotic nodule development in legumes, and cytokinin signaling responses occur locally in nodule primordia and in developing nodules. Here, we show that the Lotus japonicus Ckx3 cytokinin oxidase/dehydrogenase gene is induced by Nod factor during the early phase of nodule initiation. At the cellular level, pCkx3::YFP reporter-gene studies revealed that the Ckx3 promoter is active during the first cortical cell divisions of the nodule primordium and in growing nodules. Cytokinin measurements in ckx3 mutants confirmed that CKX3 activity negatively regulates root cytokinin levels. Particularly, tZ and DHZ type cytokinins in both inoculated and uninoculated roots were elevated in ckx3 mutants, suggesting that these are targets for degradation by the CKX3 cytokinin oxidase/dehydrogenase. The effect of CKX3 on the positive and negative roles of cytokinin in nodule development, infection and regulation was further clarified using ckx3 insertion mutants. Phenotypic analysis indicated that ckx3 mutants have reduced nodulation, infection thread formation and root growth. We also identify a role for cytokinin in regulating nodulation and nitrogen fixation in response to nitrate as ckx3 phenotypes are exaggerated at increased nitrate levels. Together, these findings show that cytokinin accumulation is tightly regulated during nodulation in order to balance the requirement for cell divisions with negative regulatory effects of cytokinin on infection events and root development. PMID:26644503

Nodulation outer proteins: double-edged swords of symbiotic rhizobia

USDA-ARS?s Scientific Manuscript database

Rhizobia are nitrogen-fixing bacteria that establish a nodule symbiosis with legumes. Nodule formation is the result of a complex bacterial infection process, which depends on signals and surface determinants produced by both symbiotic partners. Among them, rhizobial nodulation outer proteins (Nops)...

How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground

PubMed Central

Kouchi, Hiroshi; Imaizumi-Anraku, Haruko; Hayashi, Makoto; Hakoyama, Tsuneo; Nakagawa, Tomomi; Umehara, Yosuke; Suganuma, Norio; Kawaguchi, Masayoshi

2010-01-01

The nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria is the most prominent plant–microbe endosymbiotic system and, together with mycorrhizal fungi, has critical importance in agriculture. The introduction of two model legume species, Lotus japonicus and Medicago truncatula, has enabled us to identify a number of host legume genes required for symbiosis. A total of 26 genes have so far been cloned from various symbiotic mutants of these model legumes, which are involved in recognition of rhizobial nodulation signals, early symbiotic signaling cascades, infection and nodulation processes, and regulation of nitrogen fixation. These accomplishments during the past decade provide important clues to understanding not only the molecular mechanisms underlying plant–microbe endosymbiotic associations but also the evolutionary aspects of nitrogen-fixing symbiosis between legume plants and Rhizobium bacteria. In this review we survey recent progress in molecular genetic studies using these model legumes. PMID:20660226

Long-term non-invasive and continuous measurements of legume nodule activity.

PubMed

Cabeza, Ricardo A; Liese, Rebecca; Fischinger, Stephanie A; Sulieman, Saad; Avenhaus, Ulrike; Lingner, Annika; Hein, Hans; Koester, Beke; Baumgarten, Vanessa; Dittert, Klaus; Schulze, Joachim

2015-02-01

Symbiotic nitrogen fixation is a process of considerable economic, ecological and scientific interest. The central enzyme nitrogenase reduces H(+) alongside N2 , and the evolving H2 allows a continuous and non-invasive in vivo measurement of nitrogenase activity. The objective of this study was to show that an elaborated set-up providing such measurements for periods as long as several weeks will produce specific insight into the nodule activity's dependence on environmental conditions and genotype features. A system was developed that allows the air-proof separation of a root/nodule and a shoot compartment. H2 evolution in the root/nodule compartment can be monitored continuously. Nutrient solution composition, temperature, CO2 concentration and humidity around the shoots can concomitantly be maintained and manipulated. Medicago truncatula plants showed vigorous growth in the system when relying on nitrogen fixation. The set-up was able to provide specific insights into nitrogen fixation. For example, nodule activity depended on the temperature in their surroundings, but not on temperature or light around shoots. Increased temperature around the nodules was able to induce higher nodule activity in darkness versus light around shoots for a period of as long as 8 h. Conditions that affected the N demand of the shoots (ammonium application, Mg or P depletion, super numeric nodules) induced consistent and complex daily rhythms in nodule activity. It was shown that long-term continuous measurements of nodule activity could be useful for revealing special features in mutants and could be of importance when synchronizing nodule harvests for complex analysis of their metabolic status. © 2014 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Cytokinins in Symbiotic Nodulation: When, Where, What For?

PubMed

Gamas, Pascal; Brault, Mathias; Jardinaud, Marie-Françoise; Frugier, Florian

2017-09-01

Substantial progress has been made in the understanding of early stages of the symbiotic interaction between legume plants and rhizobium bacteria. Those include the specific recognition of symbiotic partners, the initiation of bacterial infection in root hair cells, and the inception of a specific organ in the root cortex, the nodule. Increasingly complex regulatory networks have been uncovered in which cytokinin (CK) phytohormones play essential roles in different aspects of early symbiotic stages. Intriguingly, these roles can be either positive or negative, cell autonomous or non-cell autonomous, and vary, depending on time, root tissues, and possibly legume species. Recent developments on CK symbiotic functions and interconnections with other signaling pathways during nodule initiation are the focus of this review. Copyright © 2017 Elsevier Ltd. All rights reserved.

Proof that Burkholderia Strains Form Effective Symbioses with Legumes: a Study of Novel Mimosa-Nodulating Strains from South America

PubMed Central

Chen, Wen-Ming; de Faria, Sergio M.; Straliotto, Rosângela; Pitard, Rosa M.; Simões-Araùjo, Jean L.; Chou, Jui-Hsing; Chou, Yi-Ju; Barrios, Edmundo; Prescott, Alan R.; Elliott, Geoffrey N.; Sprent, Janet I.; Young, J. Peter W.; James, Euan K.

2005-01-01

Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other β-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known β-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes. PMID:16269788

Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America.

PubMed

Chen, Wen-Ming; de Faria, Sergio M; Straliotto, Rosângela; Pitard, Rosa M; Simões-Araùjo, Jean L; Chou, Jui-Hsing; Chou, Yi-Ju; Barrios, Edmundo; Prescott, Alan R; Elliott, Geoffrey N; Sprent, Janet I; Young, J Peter W; James, Euan K

2005-11-01

Twenty Mimosa-nodulating bacterial strains from Brazil and Venezuela, together with eight reference Mimosa-nodulating rhizobial strains and two other beta-rhizobial strains, were examined by amplified rRNA gene restriction analysis. They fell into 16 patterns and formed a single cluster together with the known beta-rhizobia, Burkholderia caribensis, Burkholderia phymatum, and Burkholderia tuberum. The 16S rRNA gene sequences of 15 of the 20 strains were determined, and all were shown to belong to the genus Burkholderia; four distinct clusters could be discerned, with strains isolated from the same host species usually clustering very closely. Five of the strains (MAP3-5, Br3407, Br3454, Br3461, and Br3469) were selected for further studies of the symbiosis-related genes nodA, the NodD-dependent regulatory consensus sequences (nod box), and nifH. The nodA and nifH sequences were very close to each other and to those of B. phymatum STM815, B. caribensis TJ182, and Cupriavidus taiwanensis LMG19424 but were relatively distant from those of B. tuberum STM678. In addition to nodulating their original hosts, all five strains could also nodulate other Mimosa spp., and all produced nodules on Mimosa pudica that had nitrogenase (acetylene reduction) activities and structures typical of effective N2-fixing symbioses. Finally, both wild-type and green fluorescent protein-expressing transconjugant strains of Br3461 and MAP3-5 produced N2-fixing nodules on their original hosts, Mimosa bimucronata (Br3461) and Mimosa pigra (MAP3-5), and hence this confirms strongly that Burkholderia strains can form effective symbioses with legumes.

Strigolactones in the Rhizobium-legume symbiosis: Stimulatory effect on bacterial surface motility and down-regulation of their levels in nodulated plants.

PubMed

Peláez-Vico, María A; Bernabéu-Roda, Lydia; Kohlen, Wouter; Soto, María J; López-Ráez, Juan A

2016-04-01

Strigolactones (SLs) are multifunctional molecules acting as modulators of plant responses under nutrient deficient conditions. One of the roles of SLs is to promote beneficial association with arbuscular mycorrhizal (AM) fungi belowground under such stress conditions, mainly phosphorus shortage. Recently, a role of SLs in the Rhizobium-legume symbiosis has been also described. While SLs' function in AM symbiosis is well established, their role in the Rhizobium-legume interaction is still emerging. Recently, SLs have been suggested to stimulate surface motility of rhizobia, opening the possibility that they could also act as molecular cues. The possible effect of SLs in the motility in the alfalfa symbiont Sinorhizobium meliloti was investigated, showing that the synthetic SL analogue GR24 stimulates swarming motility in S. meliloti in a dose-dependent manner. On the other hand, it is known that SL production is regulated by nutrient deficient conditions and by AM symbiosis. Using the model alfalfa-S. meliloti, the impact of phosphorus and nitrogen deficiency, as well as of nodulation on SL production was also assessed. The results showed that phosphorus starvation promoted SL biosynthesis, which was abolished by nitrogen deficiency. In addition, a negative effect of nodulation on SL levels was detected, suggesting a conserved mechanism of SL regulation upon symbiosis establishment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

PubMed Central

Limpens, Erik; Moling, Sjef; Hooiveld, Guido; Pereira, Patrícia A.; Bisseling, Ton; Becker, Jörg D.; Küster, Helge

2013-01-01

Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital “in situ”. This digital “in situ” offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies. PMID:23734198

Taxonomically Different Co-Microsymbionts of a Relict Legume, Oxytropis popoviana, Have Complementary Sets of Symbiotic Genes and Together Increase the Efficiency of Plant Nodulation.

PubMed

Safronova, Vera I; Belimov, Andrey A; Sazanova, Anna L; Chirak, Elizaveta R; Verkhozina, Alla V; Kuznetsova, Irina G; Andronov, Evgeny E; Puhalsky, Jan V; Tikhonovich, Igor A

2018-06-20

Ten rhizobial strains were isolated from root nodules of a relict legume Oxytropis popoviana Peschkova. For identification of the isolates, sequencing of rrs, the 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 a Bradyrhizobium sp. Two strains, M. japonicum Opo-242 and Bradyrhizobium sp. strain 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 plant nodulation and nitrogen fixation were present in the isolate Opo-242. Strain Opo-243 did not contain the principal nod, nif, and fix genes; however, five genes (nodP, nodQ, nifL, nolK, and noeL) affecting the specificity of plant-rhizobia interactions but absent in isolate Opo-242 were detected. Strain Opo-243 could not induce nodules but significantly accelerated the root nodule formation after coinoculation with 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.

Insights into the history of the legume-betaproteobacterial symbiosis.

PubMed

Angus, Annette A; Hirsch, Ann M

2010-01-01

The interaction between legumes and rhizobia has been well studied in the context of a mutualistic, nitrogen-fixing symbiosis. The fitness of legumes, including important agricultural crops, is enhanced by the plants' ability to develop symbiotic associations with certain soil bacteria that fix atmospheric nitrogen into a utilizable form, namely, ammonia, via a chemical reaction that only bacteria and archaea can perform. Of the bacteria, members of the alpha subclass of the protebacteria are the best-known nitrogen-fixing symbionts of legumes. Recently, members of the beta subclass of the proteobacteria that induce nitrogen-fixing nodules on legume roots in a species-specific manner have been identified. In this issue, Bontemps et al. reveal that not only are these newly identified rhizobia novel in shifting the paradigm of our understanding of legume symbiosis, but also, based on symbiotic gene phylogenies, have a history that is both ancient and stable. Expanding our understanding of novel plant growth promoting rhizobia will be a valuable resource for incorporating alternative strategies of nitrogen fixation for enhancing plant growth.

The Class II Trehalose 6-phosphate Synthase Gene PvTPS9 Modulates Trehalose Metabolism in Phaseolus vulgaris Nodules

PubMed Central

Barraza, Aarón; Contreras-Cubas, Cecilia; Estrada-Navarrete, Georgina; Reyes, José L.; Juárez-Verdayes, Marco A.; Avonce, Nelson; Quinto, Carmen; Díaz-Camino, Claudia; Sanchez, Federico

2016-01-01

Legumes form symbioses with rhizobia, producing nitrogen-fixing nodules on the roots of the plant host. The network of plant signaling pathways affecting carbon metabolism may determine the final number of nodules. The trehalose biosynthetic pathway regulates carbon metabolism and plays a fundamental role in plant growth and development, as well as in plant-microbe interactions. The expression of genes for trehalose synthesis during nodule development suggests that this metabolite may play a role in legume-rhizobia symbiosis. In this work, PvTPS9, which encodes a Class II trehalose-6-phosphate synthase (TPS) of common bean (Phaseolus vulgaris), was silenced by RNA interference in transgenic nodules. The silencing of PvTPS9 in root nodules resulted in a reduction of 85% (± 1%) of its transcript, which correlated with a 30% decrease in trehalose contents of transgenic nodules and in untransformed leaves. Composite transgenic plants with PvTPS9 silenced in the roots showed no changes in nodule number and nitrogen fixation, but a severe reduction in plant biomass and altered transcript profiles of all Class II TPS genes. Our data suggest that PvTPS9 plays a key role in modulating trehalose metabolism in the symbiotic nodule and, therefore, in the whole plant. PMID:27847509

Nitrogen modulation of legume root architecture signaling pathways involves phytohormones and small regulatory molecules.

PubMed

Mohd-Radzman, Nadiatul A; Djordjevic, Michael A; Imin, Nijat

2013-10-01

Nitrogen, particularly nitrate is an important yield determinant for crops. However, current agricultural practice with excessive fertilizer usage has detrimental effects on the environment. Therefore, legumes have been suggested as a sustainable alternative for replenishing soil nitrogen. Legumes can uniquely form nitrogen-fixing nodules through symbiotic interaction with specialized soil bacteria. Legumes possess a highly plastic root system which modulates its architecture according to the nitrogen availability in the soil. Understanding how legumes regulate root development in response to nitrogen availability is an important step to improving root architecture. The nitrogen-mediated root development pathway starts with sensing soil nitrogen level followed by subsequent signal transduction pathways involving phytohormones, microRNAs and regulatory peptides that collectively modulate the growth and shape of the root system. This review focuses on the current understanding of nitrogen-mediated legume root architecture including local and systemic regulations by different N-sources and the modulations by phytohormones and small regulatory molecules.

NrcR, a New Transcriptional Regulator of Rhizobium tropici CIAT 899 Involved in the Legume Root-Nodule Symbiosis

PubMed Central

del Cerro, Pablo; Rolla-Santos, Amanda A. P.; Valderrama-Fernández, Rocío; Gil-Serrano, Antonio; Bellogín, Ramón A.; Gomes, Douglas Fabiano; Pérez-Montaño, Francisco; Megías, Manuel; Hungría, Mariangela; Ollero, Francisco Javier

2016-01-01

The establishment of nitrogen-fixing rhizobium-legume symbioses requires a highly complex cascade of events. In this molecular dialogue the bacterial NodD transcriptional regulators in conjunction with plant inducers, mostly flavonoids, are responsible for the biosynthesis and secretion of Nod factors which are key molecules for successful nodulation. Other transcriptional regulators related to the symbiotic process have been identified in rhizobial genomes, including negative regulators such as NolR. Rhizobium tropici CIAT 899 is an important symbiont of common bean (Phaseolus vulgaris L.), and its genome encompasses intriguing features such as five copies of nodD genes, as well as other possible transcriptional regulators including the NolR protein. Here we describe and characterize a new regulatory gene located in the non-symbiotic plasmid pRtrCIAT899c, that shows homology (46% identity) with the nolR gene located in the chromosome of CIAT 899. The mutation of this gene, named nrcR (nolR-like plasmid c Regulator), enhanced motility and exopolysaccharide production in comparison to the wild-type strain. Interestingly, the number and decoration of Nod Factors produced by this mutant were higher than those detected in the wild-type strain, especially under salinity stress. The nrcR mutant showed delayed nodulation and reduced competitiveness with P. vulgaris, and reduction in nodule number and shoot dry weight in both P. vulgaris and Leucaena leucocephala. Moreover, the mutant exhibited reduced capacity to induce the nodC gene in comparison to the wild-type CIAT 899. The finding of a new nod-gene regulator located in a non-symbiotic plasmid may reveal the existence of even more complex mechanisms of regulation of nodulation genes in R. tropici CIAT 899 that may be applicable to other rhizobial species. PMID:27096734

Symbiotic N2-Fixer Community Composition, but Not Diversity, Shifts in Nodules of a Single Host Legume Across a 2-Million-Year Dune Chronosequence.

PubMed

Birnbaum, Christina; Bissett, Andrew; Teste, Francois P; Laliberté, Etienne

2018-04-16

Long-term soil age gradients are useful model systems to study how changes in nutrient limitation shape communities of plant root mutualists because they represent strong natural gradients of nutrient availability, particularly of nitrogen (N) and phosphorus (P). Here, we investigated changes in the dinitrogen (N 2 )-fixing bacterial community composition and diversity in nodules of a single host legume (Acacia rostellifera) across the Jurien Bay chronosequence, a retrogressive 2 million-year-old sequence of coastal dunes representing an exceptionally strong natural soil fertility gradient. We collected nodules from plants grown in soils from five chronosequence stages ranging from very young (10s of years; associated with strong N limitation for plant growth) to very old (> 2,000,000 years; associated with strong P limitation), and sequenced the nifH gene in root nodules to determine the composition and diversity of N 2 -fixing bacterial symbionts. A total of 335 unique nifH gene operational taxonomic units (OTUs) were identified. Community composition of N 2 -fixing bacteria within nodules, but not diversity, changed with increasing soil age. These changes were attributed to pedogenesis-driven shifts in edaphic conditions, specifically pH, exchangeable manganese, resin-extractable phosphate, nitrate and nitrification rate. A large number of common N 2 -fixing bacteria genera (e.g. Bradyrhizobium, Ensifer, Mesorhizobium and Rhizobium) belonging to the Rhizobiaceae family (α-proteobacteria) comprised 70% of all raw sequences and were present in all nodules. However, the oldest soils, which show some of the lowest soil P availability ever recorded, harboured the largest proportion of unclassified OTUs, suggesting a unique set of N 2 -fixing bacteria adapted to extreme P limitation. Our results show that N 2 -fixing bacterial composition varies strongly during long-term ecosystem development, even within the same host, and therefore rhizobia show strong edaphic

NopP, a phosphorylated effector of Rhizobium sp. strain NGR234, is a major determinant of nodulation of the tropical legumes Flemingia congesta and Tephrosia vogelii.

PubMed

Skorpil, Peter; Saad, Maged M; Boukli, Nawal M; Kobayashi, Hajime; Ares-Orpel, Florencia; Broughton, William J; Deakin, William J

2005-09-01

Rhizobium sp. NGR234 nodulates many plants, some of which react to proteins secreted via a type three secretion system (T3SS) in a positive- (Flemingia congesta, Tephrosia vogelii) or negative- (Crotalaria juncea, Pachyrhizus tuberosus) manner. T3SSs are devices that Gram-negative bacteria use to inject effector proteins into the cytoplasm of eukaryotic cells. The only two rhizobial T3SS effector proteins characterized to date are NopL and NopP of NGR234. NopL can be phosphorylated by plant kinases and we show this to be true for NopP as well. Mutation of nopP leads to a dramatic reduction in nodule numbers on F. congesta and T. vogelii. Concomitant mutation of nopL and nopP further diminishes nodulation capacity to levels that, on T. vogelii, are lower than those produced by the T3SS null mutant NGR(Omega)rhcN. We also show that the T3SS of NGR234 secretes at least one additional effector, which remains to be identified. In other words, NGR234 secretes a cocktail of effectors, some of which have positive effects on nodulation of certain plants while others are perceived negatively and block nodulation. NopL and NopP are two components of this mix that extend the ability of NGR234 to nodulate certain legumes.

Growth and foliar nitrogen concentrations of interplanted native woody legumes and pecan

Treesearch

J.W. Van Sambeek; Nadia E. Navarrete-Tindall; Kenneth L. Hunt

2008-01-01

The interplanting and underplanting of nodulated nitrogen-fixing plants in tree plantings can increase early growth and foliage nitrogen content of hardwoods, especially black walnut and pecan. Recent studies have demonstrated that some non-nodulated woody legumes may be capable of fixing significant levels of atmospheric nitrogen. The following nine nurse crop...

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE PAGES

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha; ...

2016-06-23

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

High-quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen-fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gehlot, Hukam Singh; Ardley, Julie; Tak, Nisha

Ensifer sp. PC2 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a nitrogen-fixing nodule of the tree legume P. cineraria (L.) Druce (Khejri), which is a keystone species that grows in arid and semi-arid regions of the Indian Thar desert. Strain PC2 exists as a dominant saprophyte in alkaline soils of Western Rajasthan. It is fast growing, well-adapted to arid conditions and is able to form an effective symbiosis with several annual crop legumes as well as species of mimosoid trees and shrubs. Here we describe the features of Ensifer sp. PC2, together with genome sequence informationmore » and its annotation. The 8,458,965 bp high-quality permanent draft genome is arranged into 171 scaffolds of 171 contigs containing 8,344 protein-coding genes and 139 RNA-only encoding genes, and is one of the rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project proposal.« less

The lipopolysaccharide lipid-a long chain fatty acid is important for rhizobium leguminosarum growth and stress adaptation in free-living and nodule environments

USDA-ARS?s Scientific Manuscript database

Rhizobium bacteria live in soil and plant environments, are capable of inducing symbiotic nodules on legumes, invade these nodules, and develop into bacteroids that fix atmospheric nitrogen into ammonium. Lipopolysaccharide (LPS) is anchored in the bacterial outer membrane through a specialized lipi...

Effect of co-inoculation with mycorrhiza and rhizobia on the nodule trehalose content of different bean genotypes.

PubMed

Ballesteros-Almanza, L; Altamirano-Hernandez, J; Peña-Cabriales, J J; Santoyo, G; Sanchez-Yañez, J M; Valencia-Cantero, E; Macias-Rodriguez, L; Lopez-Bucio, J; Cardenas-Navarro, R; Farias-Rodriguez, R

2010-08-17

Studies on Rhizobium-legume symbiosis show that trehalose content in nodules under drought stress correlates positively with an increase in plant tolerance to this stress. Fewer reports describe trehalose accumulation in mycorrhiza where, in contrast with rhizobia, there is no flux of carbohydrates from the microsymbiont to the plant. However, the trehalose dynamics in the Mycorrhiza-Rhizobium-Legume tripartite symbiosis is unknown. The present study explores the role of this tripartite symbiosis in the trehalose content of nodules grown under contrasting moisture conditions. Three wild genotypes (P. filiformis, P. acutifolis and P. vulgaris) and two commercial genotypes of Phaseolus vulgaris (Pinto villa and Flor de Mayo) were used. Co-inoculation treatments were conducted with Glomus intraradices and a mixture of seven native rhizobial strains, and trehalose content was determined by GC/MS. The results showed a negative effect of mycorrhizal inoculation on nodule development, as mycorrhized plants showed fewer nodules and lower nodule dry weight compared to plants inoculated only with Rhizobium. Mycorrhizal colonization was also higher in plants inoculated only with Glomus as compared to plants co-inoculated with both microsymbionts. In regard to trehalose, co-inoculation negatively affects its accumulation in the nodules of each genotype tested. However, the correlation analysis showed a significantly positive correlation between mycorrhizal colonization and nodule trehalose content.

Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes

USDA-ARS?s Scientific Manuscript database

Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD af...

Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.)

PubMed Central

Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

2016-01-01

A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. PMID:27348121

Phenetic, genetic diversity and symbiotic compatibility of rhizobial strains nodulating pigeon pea in Northern India.

PubMed

Arora, Naveen Kumar; Khare, Ekta; Singh, Sachin; Tewari, Sakshi

2018-01-01

Pigeon pea ( Cajanus cajan ) is one of the most important legumes grown in the northern province of Uttar Pradesh, India. However, its productively in Uttar Pradesh is lower than the average yield of adjoining states. During the course of the present study, a survey of pigeon pea growing agricultural fields was carried out and it was found that 80% of plants were inadequately nodulated. The study was aimed to evaluate the pigeon pea symbiotic compatibility and nodulation efficiency of root nodulating bacteria isolated from various legumes, and to explore the phenetic and genetic diversity of rhizobial population nodulating pigeon pea growing in fields of Uttar Pradesh. Amongst all the 96 isolates, 40 isolates showed nodulation in pigeon pea. These 40 isolates were further characterized by phenotypic, biochemical and physiological tests. Intrinsic antibiotic resistance pattern was taken to generate similarity matrix revealing 10 phenons. The study shows that most of the isolates nodulating pigeon pea in this region were rapid growers. The dendrogram generated using the NTSYSpc software grouped RAPD patterns into 19 clusters. The high degree of phenetic and genetic diversity encountered is probably because of a history of mixed cropping of legumes. The assessment of diversity is a very important tool and can be used to improve the nodulation and quality of pigeon pea crop. It is also concluded that difference between phenetic and RAPD clustering pattern is an indication that rhizobial diversity of pigeon pea is not as yet completely understood and settled.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities.

PubMed

Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

2016-12-06

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance.

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

PubMed Central

Zgadzaj, Rafal; Garrido-Oter, Ruben; Jensen, Dorthe Bodker; Koprivova, Anna; Schulze-Lefert, Paul; Radutoiu, Simona

2016-01-01

Lotus japonicus has been used for decades as a model legume to study the establishment of binary symbiotic relationships with nitrogen-fixing rhizobia that trigger root nodule organogenesis for bacterial accommodation. Using community profiling of 16S rRNA gene amplicons, we reveal that in Lotus, distinctive nodule- and root-inhabiting communities are established by parallel, rather than consecutive, selection of bacteria from the rhizosphere and root compartments. Comparative analyses of wild-type (WT) and symbiotic mutants in Nod factor receptor5 (nfr5), Nodule inception (nin) and Lotus histidine kinase1 (lhk1) genes identified a previously unsuspected role of the nodulation pathway in the establishment of different bacterial assemblages in the root and rhizosphere. We found that the loss of nitrogen-fixing symbiosis dramatically alters community structure in the latter two compartments, affecting at least 14 bacterial orders. The differential plant growth phenotypes seen between WT and the symbiotic mutants in nonsupplemented soil were retained under nitrogen-supplemented conditions that blocked the formation of functional nodules in WT, whereas the symbiosis-impaired mutants maintain an altered community structure in the nitrogen-supplemented soil. This finding provides strong evidence that the root-associated community shift in the symbiotic mutants is a direct consequence of the disabled symbiosis pathway rather than an indirect effect resulting from abolished symbiotic nitrogen fixation. Our findings imply a role of the legume host in selecting a broad taxonomic range of root-associated bacteria that, in addition to rhizobia, likely contribute to plant growth and ecological performance. PMID:27864511

The deubiquitinating enzyme AMSH1 is required for rhizobial infection and nodule organogenesis in Lotus japonicus.

PubMed

Małolepszy, Anna; Urbański, Dorian Fabian; James, Euan K; Sandal, Niels; Isono, Erika; Stougaard, Jens; Andersen, Stig Uggerhøj

2015-08-01

Legume-rhizobium symbiosis contributes large quantities of fixed nitrogen to both agricultural and natural ecosystems. This global impact and the selective interaction between rhizobia and legumes culminating in development of functional root nodules have prompted detailed studies of the underlying mechanisms. We performed a screen for aberrant nodulation phenotypes using the Lotus japonicus LORE1 insertion mutant collection. Here, we describe the identification of amsh1 mutants that only develop small nodule primordia and display stunted shoot growth, and show that the aberrant nodulation phenotype caused by LORE1 insertions in the Amsh1 gene may be separated from the shoot phenotype. In amsh1 mutants, rhizobia initially became entrapped in infection threads with thickened cells walls. Some rhizobia were released into plant cells much later than observed for the wild-type; however, no typical symbiosome structures were formed. Furthermore, cytokinin treatment only very weakly induced nodule organogenesis in amsh1 mutants, suggesting that AMSH1 function is required downstream of cytokinin signaling. Biochemical analysis showed that AMSH1 is an active deubiquitinating enzyme, and that AMSH1 specifically cleaves K63-linked ubiquitin chains. Post-translational ubiquitination and deubiquitination processes involving the AMSH1 deubiquitinating enzyme are thus involved in both infection and organogenesis in Lotus japonicus. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Importance of rhizobia in Agriculture: potential of the commercial inoculants and native strains for improving legume yields in different land-use systems

NASA Astrophysics Data System (ADS)

Lesueur, D.; Atieno, M.; Mathu, S.; Herrmann, L.

2012-04-01

Legumes play an important role in the traditional diets of many regions throughout the world because they provide a multitude of benefits to both the soil and other crops grown in combination with them or following them in several cropping systems. The ability of legumes to fix atmospheric nitrogen in association with rhizobia gives them the capacity to grow in very degraded soils. But do we have to systematically inoculate legumes? For example our results suggested that the systematic inoculation of both cowpea and green gram in Kenya with commercial inoculants to improve yields is not really justified, native strains performing better than inoculated strains. But when native rhizobia nodulating legumes are not naturally present, application of rhizobial inoculants is very commonly used. Our results showed that the utilization of effective good-quality rhizobial inoculants by farmers have a real potential to improve legume yields in unfertile soils requesting high applications of mineral fertilizers. For example an effective soybean commercial inoculants was tested in different locations in Kenya (in about 150 farms in 3 mandate areas presenting different soil characteristics and environmental conditions). Application of the rhizobial inoculant significantly increased the soybean yields in all mandate areas (about 75% of the farms). Nodule occupancy analysis showed that a high number of nodules occupied by the inoculated strain did not obviously lead to an increase of soybean production. Soil factors (pH, P, C, N…) seemed to affect the inoculant efficiency whether the strain is occupying the nodules or not. Our statistic analysis showed that soil pH significantly affected nodulation and yield, though the effect was variable depending on the region. We concluded that the competitiveness of rhizobial strains might not be the main factor explaining the effect (or lack of) of legumes inoculation in the field. Another study was aiming to assess if several factors

nip, a Symbiotic Medicago truncatula Mutant That Forms Root Nodules with Aberrant Infection Threads and Plant Defense-Like Response1

PubMed Central

Veereshlingam, Harita; Haynes, Janine G.; Penmetsa, R. Varma; Cook, Douglas R.; Sherrier, D. Janine; Dickstein, Rebecca

2004-01-01

To investigate the legume-Rhizobium symbiosis, we isolated and studied a novel symbiotic mutant of the model legume Medicago truncatula, designated nip (numerous infections and polyphenolics). When grown on nitrogen-free media in the presence of the compatible bacterium Sinorhizobium meliloti, the nip mutant showed nitrogen deficiency symptoms. The mutant failed to form pink nitrogen-fixing nodules that occur in the wild-type symbiosis, but instead developed small bump-like nodules on its roots that were blocked at an early stage of development. Examination of the nip nodules by light microscopy after staining with X-Gal for S. meliloti expressing a constitutive GUS gene, by confocal microscopy following staining with SYTO-13, and by electron microscopy revealed that nip initiated symbiotic interactions and formed nodule primordia and infection threads. The infection threads in nip proliferated abnormally and very rarely deposited rhizobia into plant host cells; rhizobia failed to differentiate further in these cases. nip nodules contained autofluorescent cells and accumulated a brown pigment. Histochemical staining of nip nodules revealed this pigment to be polyphenolic accumulation. RNA blot analyses demonstrated that nip nodules expressed only a subset of genes associated with nodule organogenesis, as well as elevated expression of a host defense-associated phenylalanine ammonia lyase gene. nip plants were observed to have abnormal lateral roots. nip plant root growth and nodulation responded normally to ethylene inhibitors and precursors. Allelism tests showed that nip complements 14 other M. truncatula nodulation mutants but not latd, a mutant with a more severe nodulation phenotype as well as primary and lateral root defects. Thus, the nip mutant defines a new locus, NIP, required for appropriate infection thread development during invasion of the nascent nodule by rhizobia, normal lateral root elongation, and normal regulation of host defense-like responses

The Ribosomal RNA is a Useful Marker to Visualize Rhizobia Interacting with Legume Plants

ERIC Educational Resources Information Center

Rinaudi, Luciana; Isola, Maria C.; Giordano, Walter

2004-01-01

Symbiosis between rhizobia and leguminous plants leads to the formation of nitrogen-fixing root nodules. In the present article, we recommend the use of the ribosomal RNA (rRNA) isolated from legume nodules in an experimental class with the purpose of introducing students to the structure of eukaryotic and prokaryotic ribosomes and of…

Genome-Wide Identification of Medicago Peptides Involved in Macronutrient Responses and Nodulation1[OPEN

PubMed Central

Dai, Xinbin; Zhuang, Zhaohong; Torres-Jerez, Ivone; Nogales, Joaquina

2017-01-01

Growing evidence indicates that small, secreted peptides (SSPs) play critical roles in legume growth and development, yet the annotation of SSP-coding genes is far from complete. Systematic reannotation of the Medicago truncatula genome identified 1,970 homologs of established SSP gene families and an additional 2,455 genes that are potentially novel SSPs, previously unreported in the literature. The expression patterns of known and putative SSP genes based on 144 RNA sequencing data sets covering various stages of macronutrient deficiencies and symbiotic interactions with rhizobia and mycorrhiza were investigated. Focusing on those known or suspected to act via receptor-mediated signaling, 240 nutrient-responsive and 365 nodulation-responsive Signaling-SSPs were identified, greatly expanding the number of SSP gene families potentially involved in acclimation to nutrient deficiencies and nodulation. Synthetic peptide applications were shown to alter root growth and nodulation phenotypes, revealing additional regulators of legume nutrient acquisition. Our results constitute a powerful resource enabling further investigations of specific SSP functions via peptide treatment and reverse genetics. PMID:29030416

Rhizobium cellulase CelC2 is essential for primary symbiotic infection of legume host roots

PubMed Central

Robledo, M.; Jiménez-Zurdo, J. I.; Velázquez, E.; Trujillo, M. E.; Zurdo-Piñeiro, J. L.; Ramírez-Bahena, M. H.; Ramos, B.; Díaz-Mínguez, J. M.; Dazzo, F.; Martínez-Molina, E.; Mateos, P. F.

2008-01-01

The rhizobia–legume, root-nodule symbiosis provides the most efficient source of biologically fixed ammonia fertilizer for agricultural crops. Its development involves pathways of specificity, infectivity, and effectivity resulting from expressed traits of the bacterium and host plant. A key event of the infection process required for development of this root-nodule symbiosis is a highly localized, complete erosion of the plant cell wall through which the bacterial symbiont penetrates to establish a nitrogen-fixing, intracellular endosymbiotic state within the host. This process of wall degradation must be delicately balanced to avoid lysis and destruction of the host cell. Here, we describe the purification, biochemical characterization, molecular genetic analysis, biological activity, and symbiotic function of a cell-bound bacterial cellulase (CelC2) enzyme from Rhizobium leguminosarum bv. trifolii, the clover-nodulating endosymbiont. The purified enzyme can erode the noncrystalline tip of the white clover host root hair wall, making a localized hole of sufficient size to allow wild-type microsymbiont penetration. This CelC2 enzyme is not active on root hairs of the nonhost legume alfalfa. Microscopy analysis of the symbiotic phenotypes of the ANU843 wild type and CelC2 knockout mutant derivative revealed that this enzyme fulfils an essential role in the primary infection process required for development of the canonical nitrogen-fixing R. leguminosarum bv. trifolii-white clover symbiosis. PMID:18458328

Localization of superoxide dismutases and hydrogen peroxide in legume root nodules.

PubMed

Rubio, Maria C; James, Euan K; Clemente, Maria R; Bucciarelli, Bruna; Fedorova, Maria; Vance, Carroll P; Becana, Manuel

2004-12-01

Superoxide dismutases (SODs) catalyze the dismutation of superoxide radicals to O2 and H2O2 and thus represent a primary line of antioxidant defense in all aerobic organisms. H2O2 is a signal molecule involved in the plant's response to pathogen attack and other stress conditions as well as in nodulation. In this work, we have tested the hypothesis that SODs are a source of H2O2 in indeterminate alfalfa (Medicago sativa) and pea (Pisum sativum) nodules. The transcripts and proteins of the major SODs of nodules were localized by in situ RNA hybridization and immunogold electron microscopy, respectively, whereas H2O2 was localized cytochemically by electron microscopy of cerium-perfused nodule tissue. The transcript and protein of cytosolic CuZnSOD are most abundant in the meristem (I) and invasion (II) zones, interzone II-III, and distal part of the N2-fixing zone (III), and those of MnSOD in zone III, especially in the infected cells. At the subcellular level, CuZnSOD was found in the infection threads, cytosol adjacent to cell walls, and apoplast, whereas MnSOD was in the bacteroids, bacteria within infection threads, and mitochondria. The distinct expression pattern of CuZnSOD and MnSOD suggests specific roles of the enzymes in nodules. Large amounts of H2O2 were found at the same three nodule sites as CuZnSOD but not in association with MnSOD. This colocalization led us to postulate that cytosolic CuZnSOD is a source of H2O2 in nodules. Furthermore, the absence or large reduction of H2O2 in nodule tissue preincubated with enzyme inhibitors (cyanide, azide, diphenyleneiodonium, diethyldithiocarbamate) provides strong support to the hypothesis that at least some of the H2O2 originates by the sequential operation of an NADPH oxidase-like enzyme and CuZnSOD. Results also show that there is abundant H2O2 associated with degrading bacteroids in the senescent zone (IV), which reflects the oxidative stress ensued during nodule senescence.

Mutualism and Adaptive Divergence: Co-Invasion of a Heterogeneous Grassland by an Exotic Legume-Rhizobium Symbiosis

PubMed Central

Porter, Stephanie S.; Stanton, Maureen L.; Rice, Kevin J.

2011-01-01

Species interactions play a critical role in biological invasions. For example, exotic plant and microbe mutualists can facilitate each other's spread as they co-invade novel ranges. Environmental context may influence the effect of mutualisms on invasions in heterogeneous environments, however these effects are poorly understood. We examined the mutualism between the legume, Medicago polymorpha, and the rhizobium, Ensifer medicae, which have both invaded California grasslands. Many of these invaded grasslands are composed of a patchwork of harsh serpentine and relatively benign non-serpentine soils. We grew legume genotypes collected from serpentine or non-serpentine soil in both types of soil in combination with rhizobium genotypes from serpentine or non-serpentine soils and in the absence of rhizobia. Legumes invested more strongly in the mutualism in the home soil type and trends in fitness suggested that this ecotypic divergence was adaptive. Serpentine legumes had greater allocation to symbiotic root nodules in serpentine soil than did non-serpentine legumes and non-serpentine legumes had greater allocation to nodules in non-serpentine soil than did serpentine legumes. Therefore, this invasive legume has undergone the rapid evolution of divergence for soil-specific investment in the mutualism. Contrary to theoretical expectations, the mutualism was less beneficial for legumes grown on the stressful serpentine soil than on the non-serpentine soil, possibly due to the inhibitory effects of serpentine on the benefits derived from the interaction. The soil-specific ability to allocate to a robust microbial mutualism may be a critical, and previously overlooked, adaptation for plants adapting to heterogeneous environments during invasion. PMID:22174755

Genetic and Molecular Mechanisms Underlying Symbiotic Specificity in Legume-Rhizobium Interactions.

PubMed

Wang, Qi; Liu, Jinge; Zhu, Hongyan

2018-01-01

Legumes are able to form a symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia. The result of this symbiosis is to form nodules on the plant root, within which the bacteria can convert atmospheric nitrogen into ammonia that can be used by the plant. Establishment of a successful symbiosis requires the two symbiotic partners to be compatible with each other throughout the process of symbiotic development. However, incompatibility frequently occurs, such that a bacterial strain is unable to nodulate a particular host plant or forms nodules that are incapable of fixing nitrogen. Genetic and molecular mechanisms that regulate symbiotic specificity are diverse, involving a wide range of host and bacterial genes/signals with various modes of action. In this review, we will provide an update on our current knowledge of how the recognition specificity has evolved in the context of symbiosis signaling and plant immunity.

The Sulfate Transporter SST1 Is Crucial for Symbiotic Nitrogen Fixation in Lotus japonicus Root Nodules

PubMed Central

Krusell, Lene; Krause, Katja; Ott, Thomas; Desbrosses, Guilhem; Krämer, Ute; Sato, Shusei; Nakamura, Yasukazu; Tabata, Satoshi; James, Euan K.; Sandal, Niels; Stougaard, Jens; Kawaguchi, Masayoshi; Miyamoto, Ai; Suganuma, Norio; Udvardi, Michael K.

2005-01-01

Symbiotic nitrogen fixation (SNF) by intracellular rhizobia within legume root nodules requires the exchange of nutrients between host plant cells and their resident bacteria. Little is known at the molecular level about plant transporters that mediate such exchanges. Several mutants of the model legume Lotus japonicus have been identified that develop nodules with metabolic defects that cannot fix nitrogen efficiently and exhibit retarded growth under symbiotic conditions. Map-based cloning of defective genes in two such mutants, sst1-1 and sst1-2 (for symbiotic sulfate transporter), revealed two alleles of the same gene. The gene is expressed in a nodule-specific manner and encodes a protein homologous with eukaryotic sulfate transporters. Full-length cDNA of the gene complemented a yeast mutant defective in sulfate transport. Hence, the gene was named Sst1. The sst1-1 and sst1-2 mutants exhibited normal growth and development under nonsymbiotic growth conditions, a result consistent with the nodule-specific expression of Sst1. Data from a previous proteomic study indicate that SST1 is located on the symbiosome membrane in Lotus nodules. Together, these results suggest that SST1 transports sulfate from the plant cell cytoplasm to the intracellular rhizobia, where the nutrient is essential for protein and cofactor synthesis, including nitrogenase biosynthesis. This work shows the importance of plant sulfate transport in SNF and the specialization of a eukaryotic transporter gene for this purpose. PMID:15805486

A Phylogenetic Strategy Based on a Legume-Specific Whole Genome Duplication Yields Symbiotic Cytokinin Type-A Response Regulators1[C][W][OA

PubMed Central

Op den Camp, Rik H.M.; De Mita, Stéphane; Lillo, Alessandra; Cao, Qingqin; Limpens, Erik; Bisseling, Ton; Geurts, René

2011-01-01

Legumes host their Rhizobium spp. symbiont in novel root organs called nodules. Nodules originate from differentiated root cortical cells that dedifferentiate and subsequently form nodule primordia, a process controlled by cytokinin. A whole-genome duplication has occurred at the root of the legume Papilionoideae subfamily. We hypothesize that gene pairs originating from this duplication event and are conserved in distinct Papilionoideae lineages have evolved symbiotic functions. A phylogenetic strategy was applied to search for such gene pairs to identify novel regulators of nodulation, using the cytokinin phosphorelay pathway as a test case. In this way, two paralogous type-A cytokinin response regulators were identified that are involved in root nodule symbiosis. Response Regulator9 (MtRR9) and MtRR11 in medicago (Medicago truncatula) and an ortholog in lotus (Lotus japonicus) are rapidly induced upon Rhizobium spp. Nod factor signaling. Constitutive expression of MtRR9 results in arrested primordia that have emerged from cortical, endodermal, and pericycle cells. In legumes, lateral root primordia are not exclusively formed from pericycle cells but also require the involvement of the root cortical cell layer. Therefore, the MtRR9-induced foci of cell divisions show a strong resemblance to lateral root primordia, suggesting an ancestral function of MtRR9 in this process. Together, these findings provide a proof of principle for the applied phylogenetic strategy to identify genes with a symbiotic function in legumes. PMID:22034625

Comparative transcriptome analysis of nodules of two Mesorhizobium-chickpea associations with differential symbiotic efficiency under phosphate deficiency.

PubMed

Nasr Esfahani, Maryam; Inoue, Komaki; Chu, Ha Duc; Nguyen, Kien Huu; Van Ha, Chien; Watanabe, Yasuko; Burritt, David J; Herrera-Estrella, Luis; Mochida, Keiichi; Tran, Lam-Son Phan

2017-09-01

Phosphate (Pi) deficiency is known to be a major limitation for symbiotic nitrogen fixation (SNF), and hence legume crop productivity globally. However, very little information is available on the adaptive mechanisms, particularly in the important legume crop chickpea (Cicer arietinum L.), which enable nodules to respond to low-Pi availability. Thus, to elucidate these mechanisms in chickpea nodules at molecular level, we used an RNA sequencing approach to investigate transcriptomes of the nodules in Mesorhizobium mediterraneum SWRI9-(MmSWRI9)-chickpea and M. ciceri CP-31-(McCP-31)-chickpea associations under Pi-sufficient and Pi-deficient conditions, of which the McCP-31-chickpea association has a better SNF capacity than the MmSWRI9-chickpea association during Pi starvation. Our investigation revealed that more genes showed altered expression patterns in MmSWRI9-induced nodules than in McCP-31-induced nodules (540 vs. 225) under Pi deficiency, suggesting that the Pi-starvation-more-sensitive MmSWRI9-induced nodules required expression change in a larger number of genes to cope with low-Pi stress than the Pi-starvation-less-sensitive McCP-31-induced nodules. The functional classification of differentially expressed genes (DEGs) was examined to gain an understanding of how chickpea nodules respond to Pi starvation, caused by soil Pi deficiency. As a result, more DEGs involved in nodulation, detoxification, nutrient/ion transport, transcriptional factors, key metabolic pathways, Pi remobilization and signalling were found in Pi-starved MmSWRI9-induced nodules than in Pi-starved McCP-31-induced nodules. Our findings have enabled the identification of molecular processes that play important roles in the acclimation of nodules to Pi deficiency, ultimately leading to the development of Pi-efficient chickpea symbiotic associations suitable for Pi-deficient soils. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

A NIN-LIKE PROTEIN mediates nitrate-induced control of root nodule symbiosis in Lotus japonicus.

PubMed

Nishida, Hanna; Tanaka, Sachiko; Handa, Yoshihiro; Ito, Momoyo; Sakamoto, Yuki; Matsunaga, Sachihiro; Betsuyaku, Shigeyuki; Miura, Kenji; Soyano, Takashi; Kawaguchi, Masayoshi; Suzaki, Takuya

2018-02-05

Legumes and rhizobia establish symbiosis in root nodules. To balance the gains and costs associated with the symbiosis, plants have developed two strategies for adapting to nitrogen availability in the soil: plants can regulate nodule number and/or stop the development or function of nodules. Although the former is accounted for by autoregulation of nodulation, a form of systemic long-range signaling, the latter strategy remains largely enigmatic. Here, we show that the Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) gene encoding a NIN-LIKE PROTEIN transcription factor acts as a key regulator in the nitrate-induced pleiotropic control of root nodule symbiosis. NRSYM1 accumulates in the nucleus in response to nitrate and directly regulates the production of CLE-RS2, a root-derived mobile peptide that acts as a negative regulator of nodule number. Our data provide the genetic basis for how plants respond to the nitrogen environment and control symbiosis to achieve proper plant growth.

LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species.

PubMed

Moolhuijzen, P; Cakir, M; Hunter, A; Schibeci, D; Macgregor, A; Smith, C; Francki, M; Jones, M G K; Appels, R; Bellgard, M

2006-06-01

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume

Genome Sequence of Micromonospora lupini Lupac 08, Isolated from Root Nodules of Lupinus angustifolius

PubMed Central

Alonso-Vega, Pablo; Normand, Philippe; Bacigalupe, Rodrigo; Pujic, Petar; Lajus, Aurelie; Vallenet, David; Carro, Lorena; Coll, Pedro

2012-01-01

Micromonospora strains have been isolated from diverse niches, including soil, water, and marine sediments and root nodules of diverse symbiotic plants. In this work, we report the genome sequence of Micromonospora lupini Lupac 08 isolated from root nodules of the wild legume Lupinus angustifolious. PMID:22815450

Conservation of nodulation genes between Rhizobium meliloti and a slow-growing Rhizobium strain that nodulates a nonlegume host

PubMed Central

Marvel, Deborah J.; Kuldau, Gretchen; Hirsch, Ann; Richards, Eric; Torrey, John G.; Ausubel, Frederick M.

1985-01-01

Parasponia, a woody member of the elm family, is the only nonlegume genus whose members are known to form an effective nitrogen-fixing symbiosis with a Rhizobium species. The bacterial strain RP501 is a slow-growing strain of Rhizobium isolated from Parasponia nodules. Strain RP501 also nodulates the legumes siratro (Macroptilium atropurpureum) and cowpea (Vigna unguiculata). Using a cosmid clone bank of RP501 DNA, we isolated a 13.4-kilobase (kb) EcoRI fragment that complemented insertion and point mutations in three contiguous nodulation genes (nodABC) of Rhizobium meliloti, the endosymbiont of alfalfa (Medicago sativa). The complemented R. meliloti nod mutants induced effective nitrogen-fixing nodules on alfalfa seedlings but not on siratro, cowpeas, or Parasponia. The cloned RP501 nodulation locus hybridized to DNA fragments carrying the R. meliloti nodABC genes. A 3-kb cluster of Tn5 insertion mutations on the RP501 13.4-kb EcoRI fragment prevented complementation of R. meliloti nodABC mutations. Images PMID:16593600

Thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones.

PubMed

Clemente, Maria R; Bustos-Sanmamed, Pilar; Loscos, Jorge; James, Euan K; Pérez-Rontomé, Carmen; Navascués, Joaquín; Gay, Marina; Becana, Manuel

2012-06-01

In plants and other organisms, glutathione (GSH) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γECS) and glutathione synthetase (GSHS). In legumes, homoglutathione (hGSH) can replace GSH and is synthesized by γECS and a specific homoglutathione synthetase (hGSHS). The subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in Lotus japonicus plants treated for 1-48 h with 50 μM of hormones. Immunogold localization studies revealed that γECS is confined to chloroplasts and plastids, whereas hGSHS is also in the cytosol. Addition of hormones caused differential expression of thiol synthetases in roots. After 24-48 h, abscisic and salicylic acids downregulated GSHS whereas jasmonic acid upregulated it. Cytokinins and polyamines activated GSHS but not γECS or hGSHS. Jasmonic acid elicited a coordinated response of the three genes and auxin induced both hGSHS expression and activity. Results show that the thiol biosynthetic pathway is compartmentalized in legumes. Moreover, the similar response profiles of the GSH and hGSH contents in roots of non-nodulated and nodulated plants to the various hormonal treatments indicate that thiol homeostasis is independent of the nitrogen source of the plants. The differential regulation of the three mRNA levels, hGSHS activity, and thiol contents by hormones indicates a fine control of thiol biosynthesis at multiple levels and strongly suggests that GSH and hGSH play distinct roles in plant development and stress responses.

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis

PubMed Central

Reyero-Saavedra, María del Rocio; Qiao, Zhenzhen; Sánchez-Correa, María del Socorro; Díaz-Pineda, M. Enrique; Covarrubias, Alejandra A.; Libault, Marc; Valdés-López, Oswaldo

2017-01-01

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B (NF-YB), Nodule Inception (NIN) and Flotillin2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia. PMID:29182547

Gene Silencing of Argonaute5 Negatively Affects the Establishment of the Legume-Rhizobia Symbiosis.

PubMed

Reyero-Saavedra, María Del Rocio; Qiao, Zhenzhen; Sánchez-Correa, María Del Socorro; Díaz-Pineda, M Enrique; Reyes, Jose L; Covarrubias, Alejandra A; Libault, Marc; Valdés-López, Oswaldo

2017-11-28

The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, can bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean ( Glycine max ) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean ( Phaseolus vulgaris ) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 h of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: Nuclear Factor Y-B ( NF-YB ), Nodule Inception ( NIN ) and Flotillin2 ( FLOT2 ). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia.

A Novel Family in Medicago truncatula Consisting of More Than 300 Nodule-Specific Genes Coding for Small, Secreted Polypeptides with Conserved Cysteine Motifs1[w

PubMed Central

Mergaert, Peter; Nikovics, Krisztina; Kelemen, Zsolt; Maunoury, Nicolas; Vaubert, Danièle; Kondorosi, Adam; Kondorosi, Eva

2003-01-01

Transcriptome analysis of Medicago truncatula nodules has led to the discovery of a gene family named NCR (nodule-specific cysteine rich) with more than 300 members. The encoded polypeptides were short (60–90 amino acids), carried a conserved signal peptide, and, except for a conserved cysteine motif, displayed otherwise extensive sequence divergence. Family members were found in pea (Pisum sativum), broad bean (Vicia faba), white clover (Trifolium repens), and Galega orientalis but not in other plants, including other legumes, suggesting that the family might be specific for galegoid legumes forming indeterminate nodules. Gene expression of all family members was restricted to nodules except for two, also expressed in mycorrhizal roots. NCR genes exhibited distinct temporal and spatial expression patterns in nodules and, thus, were coupled to different stages of development. The signal peptide targeted the polypeptides in the secretory pathway, as shown by green fluorescent protein fusions expressed in onion (Allium cepa) epidermal cells. Coregulation of certain NCR genes with genes coding for a potentially secreted calmodulin-like protein and for a signal peptide peptidase suggests a concerted action in nodule development. Potential functions of the NCR polypeptides in cell-to-cell signaling and creation of a defense system are discussed. PMID:12746522

Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement

PubMed Central

Ramalingam, Abirami; Kudapa, Himabindu; Pazhamala, Lekha T.; Weckwerth, Wolfram; Varshney, Rajeev K.

2015-01-01

The crop legumes such as chickpea, common bean, cowpea, peanut, pigeonpea, soybean, etc. are important sources of nutrition and contribute to a significant amount of biological nitrogen fixation (>20 million tons of fixed nitrogen) in agriculture. However, the production of legumes is constrained due to abiotic and biotic stresses. It is therefore imperative to understand the molecular mechanisms of plant response to different stresses and identify key candidate genes regulating tolerance which can be deployed in breeding programs. The information obtained from transcriptomics has facilitated the identification of candidate genes for the given trait of interest and utilizing them in crop breeding programs to improve stress tolerance. However, the mechanisms of stress tolerance are complex due to the influence of multi-genes and post-transcriptional regulations. Furthermore, stress conditions greatly affect gene expression which in turn causes modifications in the composition of plant proteomes and metabolomes. Therefore, functional genomics involving various proteomics and metabolomics approaches have been obligatory for understanding plant stress tolerance. These approaches have also been found useful to unravel different pathways related to plant and seed development as well as symbiosis. Proteome and metabolome profiling using high-throughput based systems have been extensively applied in the model legume species, Medicago truncatula and Lotus japonicus, as well as in the model crop legume, soybean, to examine stress signaling pathways, cellular and developmental processes and nodule symbiosis. Moreover, the availability of protein reference maps as well as proteomics and metabolomics databases greatly support research and understanding of various biological processes in legumes. Protein-protein interaction techniques, particularly the yeast two-hybrid system have been advantageous for studying symbiosis and stress signaling in legumes. In this review, several

Type 3 Secretion System (T3SS) of Bradyrhizobium sp. DOA9 and Its Roles in Legume Symbiosis and Rice Endophytic Association.

PubMed

Songwattana, Pongpan; Noisangiam, Rujirek; Teamtisong, Kamonluck; Prakamhang, Janpen; Teulet, Albin; Tittabutr, Panlada; Piromyou, Pongdet; Boonkerd, Nantakorn; Giraud, Eric; Teaumroong, Neung

2017-01-01

The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod , nif , and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod -box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (Ω rhcN ) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four ( Arachis hypogea , Vigna radiata , Crotalaria juncea , and Macroptilium atropurpureum ) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one ( Stylosanthes hamata ) responded negatively (fewer nodules and less nitrogen fixation) and four species ( Aeschynomene americana , Aeschynomene afraspera , Indigofera tinctoria , and Desmodium tortuosum ) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice.

Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration

PubMed Central

Avenhaus, Ulrike; Cabeza, Ricardo A.; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

2016-01-01

Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be

Short-Term Molecular Acclimation Processes of Legume Nodules to Increased External Oxygen Concentration.

PubMed

Avenhaus, Ulrike; Cabeza, Ricardo A; Liese, Rebecca; Lingner, Annika; Dittert, Klaus; Salinas-Riester, Gabriela; Pommerenke, Claudia; Schulze, Joachim

2015-01-01

Nitrogenase is an oxygen labile enzyme. Microaerobic conditions within the infected zone of nodules are maintained primarily by an oxygen diffusion barrier (ODB) located in the nodule cortex. Flexibility of the ODB is important for the acclimation processes of nodules in response to changes in external oxygen concentration. The hypothesis of the present study was that there are additional molecular mechanisms involved. Nodule activity of Medicago truncatula plants were continuously monitored during a change from 21 to 25 or 30% oxygen around root nodules by measuring nodule H2 evolution. Within about 2 min of the increase in oxygen concentration, a steep decline in nitrogenase activity occurred. A quick recovery commenced about 8 min later. A qPCR-based analysis of the expression of genes for nitrogenase components showed a tendency toward upregulation during the recovery. The recovery resulted in a new constant activity after about 30 min, corresponding to approximately 90% of the pre-treatment level. An RNAseq-based comparative transcriptome profiling of nodules at that point in time revealed that genes for nodule-specific cysteine-rich (NCR) peptides, defensins, leghaemoglobin and chalcone and stilbene synthase were significantly upregulated when considered as a gene family. A gene for a nicotianamine synthase-like protein (Medtr1g084050) showed a strong increase in count number. The gene appears to be of importance for nodule functioning, as evidenced by its consistently high expression in nodules and a strong reaction to various environmental cues that influence nodule activity. A Tnt1-mutant that carries an insert in the coding sequence (cds) of that gene showed reduced nitrogen fixation and less efficient acclimation to an increased external oxygen concentration. It was concluded that sudden increases in oxygen concentration around nodules destroy nitrogenase, which is quickly counteracted by an increased neoformation of the enzyme. This reaction might be

N-fixation in legumes--An assessment of the potential threat posed by ozone pollution.

PubMed

Hewitt, D K L; Mills, G; Hayes, F; Norris, D; Coyle, M; Wilkinson, S; Davies, W

2016-01-01

The growth, development and functioning of legumes are often significantly affected by exposure to tropospheric ozone (O3) pollution. However, surprisingly little is known about how leguminous Nitrogen (N) fixation responds to ozone, with a scarcity of studies addressing this question in detail. In the last decade, ozone impacts on N-fixation in soybean, cowpea, mung bean, peanut and clover have been shown for concentrations which are now commonly recorded in ambient air or are likely to occur in the near future. We provide a synthesis of the existing literature addressing this issue, and also explore the effects that may occur on an agroecosystem scale by predicting reductions in Trifolium (clovers) root nodule biomass in United Kingdom (UK) pasture based on ozone concentration data for a "high" (2006) and "average" ozone year (2008). Median 8% and 5% reductions in clover root nodule biomass in pasture across the UK were predicted for 2006 and 2008 respectively. Seasonal exposure to elevated ozone, or short-term acute concentrations >100 ppb, are sufficient to reduce N-fixation and/or impact nodulation, in a range of globally-important legumes. However, an increasing global burden of CO2, the use of artificial fertiliser, and reactive N-pollution may partially mitigate impacts of ozone on N-fixation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.

PubMed

Hernandez-Lucas, I; Segovia, L; Martinez-Romero, E; Pueppke, S G

1995-07-01

We determined the nucleotide sequences of 16S rRNA gene segments from five Rhizobium strains that have been isolated from tropical legume species. All share the capacity to nodulate Phaseolus vulgaris L., the common bean. Phylogenetic analysis confirmed that these strains are of two different chromosomal lineages. We defined the host ranges of two strains of Rhizobium etli and three strains of R. tropici, comparing them with those of the two most divergently related new strains. Twenty-two of the 43 tested legume species were nodulated by three or more of these strains. All seven strains have broad host ranges that include woody species such as Albizia lebbeck, Gliricidia maculata, and Leucaena leucocephala.

Phylogenetic relationships and host range of Rhizobium spp. that nodulate Phaseolus vulgaris L.

PubMed Central

Hernandez-Lucas, I; Segovia, L; Martinez-Romero, E; Pueppke, S G

1995-01-01

We determined the nucleotide sequences of 16S rRNA gene segments from five Rhizobium strains that have been isolated from tropical legume species. All share the capacity to nodulate Phaseolus vulgaris L., the common bean. Phylogenetic analysis confirmed that these strains are of two different chromosomal lineages. We defined the host ranges of two strains of Rhizobium etli and three strains of R. tropici, comparing them with those of the two most divergently related new strains. Twenty-two of the 43 tested legume species were nodulated by three or more of these strains. All seven strains have broad host ranges that include woody species such as Albizia lebbeck, Gliricidia maculata, and Leucaena leucocephala. PMID:7618891

The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene.

PubMed

Chaintreuil, Clémence; Gully, Djamel; Hervouet, Catherine; Tittabutr, Panlada; Randriambanona, Herizo; Brown, Spencer C; Lewis, Gwilym P; Bourge, Mickaël; Cartieaux, Fabienne; Boursot, Marc; Ramanankierana, Heriniaina; D'Hont, Angélique; Teaumroong, Neung; Giraud, Eric; Arrighi, Jean-François

2016-08-01

The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

A Legume TOR Protein Kinase Regulates Rhizobium Symbiosis and Is Essential for Infection and Nodule Development1[OPEN

PubMed Central

Blanco, Lourdes; Quinto, Carmen

2016-01-01

The target of rapamycin (TOR) protein kinase regulates metabolism, growth, and life span in yeast, animals, and plants in coordination with nutrient status and environmental conditions. The nutrient-dependent nature of TOR functionality makes this kinase a putative regulator of symbiotic associations involving nutrient acquisition. However, TOR’s role in these processes remains to be understood. Here, we uncovered the role of TOR during the bean (Phaseolus vulgaris)-Rhizobium tropici (Rhizobium) symbiotic interaction. TOR was expressed in all tested bean tissues, with higher transcript levels in the root meristems and senesced nodules. We showed TOR promoter expression along the progressing infection thread and in the infected cells of mature nodules. Posttranscriptional gene silencing of TOR using RNA interference (RNAi) showed that this gene is involved in lateral root elongation and root cell organization and also alters the density, size, and number of root hairs. The suppression of TOR transcripts also affected infection thread progression and associated cortical cell divisions, resulting in a drastic reduction of nodule numbers. TOR-RNAi resulted in reduced reactive oxygen species accumulation and altered CyclinD1 and CyclinD3 expression, which are crucial factors for infection thread progression and nodule organogenesis. Enhanced expression of TOR-regulated ATG genes in TOR-RNAi roots suggested that TOR plays a role in the recognition of Rhizobium as a symbiont. Together, these data suggest that TOR plays a vital role in the establishment of root nodule symbiosis in the common bean. PMID:27698253

Rhizobium meliloti lipooligosaccharide nodulation factors: different structural requirements for bacterial entry into target root hair cells and induction of plant symbiotic developmental responses.

PubMed

Ardourel, M; Demont, N; Debellé, F; Maillet, F; de Billy, F; Promé, J C; Dénarié, J; Truchet, G

1994-10-01

Rhizobium meliloti produces lipochitooligosaccharide nodulation NodRm factors that are required for nodulation of legume hosts. NodRm factors are O-acetylated and N-acylated by specific C16-unsaturated fatty acids. nodL mutants produce non-O-acetylated factors, and nodFE mutants produce factors with modified acyl substituents. Both mutants exhibited a significantly reduced capacity to elicit infection thread (IT) formation in alfalfa. However, once initiated, ITs developed and allowed the formation of nitrogen-fixing nodules. In contrast, double nodF/nodL mutants were unable to penetrate into legume hosts and to form ITs. Nevertheless, these mutants induced widespread cell wall tip growth in trichoblasts and other epidermal cells and were also able to elicit cortical cell activation at a distance. NodRm factor structural requirements are thus clearly more stringent for bacterial entry than for the elicitation of developmental plant responses.

A Dicarboxylate Transporter, LjALMT4, Mainly Expressed in Nodules of Lotus japonicus.

PubMed

Takanashi, Kojiro; Sasaki, Takayuki; Kan, Tomohiro; Saida, Yuka; Sugiyama, Akifumi; Yamamoto, Yoko; Yazaki, Kazufumi

2016-07-01

Legume plants can establish symbiosis with soil bacteria called rhizobia to obtain nitrogen as a nutrient directly from atmospheric N2 via symbiotic nitrogen fixation. Legumes and rhizobia form nodules, symbiotic organs in which fixed-nitrogen and photosynthetic products are exchanged between rhizobia and plant cells. The photosynthetic products supplied to rhizobia are thought to be dicarboxylates but little is known about the movement of dicarboxylates in the nodules. In terms of dicarboxylate transporters, an aluminum-activated malate transporter (ALMT) family is a strong candidate responsible for the membrane transport of carboxylates in nodules. Among the seven ALMT genes in the Lotus japonicus genome, only one, LjALMT4, shows a high expression in the nodules. LjALMT4 showed transport activity in a Xenopus oocyte system, with LjALMT4 mediating the efflux of dicarboxylates including malate, succinate, and fumarate, but not tricarboxylates such as citrate. LjALMT4 also mediated the influx of several inorganic anions. Organ-specific gene expression analysis showed LjALMT4 mRNA mainly in the parenchyma cells of nodule vascular bundles. These results suggest that LjALMT4 may not be involved in the direct supply of dicarboxylates to rhizobia in infected cells but is responsible for supplying malate as well as several anions necessary for symbiotic nitrogen fixation, via nodule vasculatures.

Phenotypic and genotypic characterization of rhizobia from diverse geographical origin that nodulate Pachyrhizus species.

PubMed

Rodríguez-Navarro, Dulce N; Camacho, María; Leidi, Eduardo O; Rivas, Raúl; Velázquez, Encarna

2004-11-01

Legumes from the genus Pachyrhizus, commonly known as yam bean, are cultivated in several countries from the American continent and constitute an alternative source for sustainable starch, oil and protein production. The endosymbionts of these legumes have been poorly studied although it is known that this legume is nodulated by fast and slow growing rhizobia. In this study we have analyzed a collection of strains isolated in several countries using different phenotypic and molecular methods. The results obtained by SDS-PAGE analysis, LPS profiling and TP-RAPD fingerprinting showed the high diversity of the strains analyzed, although all of them presented slow growth in yeast mannitol agar (YMA) medium. These results were confirmed using 16S-23S internal transcribed spacer (ITS) region and complete sequencing of the 16S rRNA gene, showing that most strains analyzed belong to different species of genus Bradyrhizobium. Three strains were closely related to B. elkanii and the rest of the strains were related to the phylogenetic group constituted by B. japonicum, B. liaoningense, B. yuanmingense and B. betae. These results support that the study of rhizobia nodulating unexplored legumes in different geographical locations will allow the discovery of new species able to establish legume symbioses.

Thiol synthetases of legumes: immunogold localization and differential gene regulation by phytohormones

PubMed Central

Clemente, Maria R.; Bustos-Sanmamed, Pilar; Loscos, Jorge; James, Euan K.; Pérez-Rontomé, Carmen; Navascués, Joaquín; Gay, Marina; Becana, Manuel

2012-01-01

In plants and other organisms, glutathione (GSH) biosynthesis is catalysed sequentially by γ-glutamylcysteine synthetase (γECS) and glutathione synthetase (GSHS). In legumes, homoglutathione (hGSH) can replace GSH and is synthesized by γECS and a specific homoglutathione synthetase (hGSHS). The subcellular localization of the enzymes was examined by electron microscopy in several legumes and gene expression was analysed in Lotus japonicus plants treated for 1–48 h with 50 μM of hormones. Immunogold localization studies revealed that γECS is confined to chloroplasts and plastids, whereas hGSHS is also in the cytosol. Addition of hormones caused differential expression of thiol synthetases in roots. After 24–48 h, abscisic and salicylic acids downregulated GSHS whereas jasmonic acid upregulated it. Cytokinins and polyamines activated GSHS but not γECS or hGSHS. Jasmonic acid elicited a coordinated response of the three genes and auxin induced both hGSHS expression and activity. Results show that the thiol biosynthetic pathway is compartmentalized in legumes. Moreover, the similar response profiles of the GSH and hGSH contents in roots of non-nodulated and nodulated plants to the various hormonal treatments indicate that thiol homeostasis is independent of the nitrogen source of the plants. The differential regulation of the three mRNA levels, hGSHS activity, and thiol contents by hormones indicates a fine control of thiol biosynthesis at multiple levels and strongly suggests that GSH and hGSH play distinct roles in plant development and stress responses. PMID:22442424

Type 3 Secretion System (T3SS) of Bradyrhizobium sp. DOA9 and Its Roles in Legume Symbiosis and Rice Endophytic Association

PubMed Central

Songwattana, Pongpan; Noisangiam, Rujirek; Teamtisong, Kamonluck; Prakamhang, Janpen; Teulet, Albin; Tittabutr, Panlada; Piromyou, Pongdet; Boonkerd, Nantakorn; Giraud, Eric; Teaumroong, Neung

2017-01-01

The Bradyrhizobium sp. DOA9 strain isolated from a paddy field has the ability to nodulate a wide spectrum of legumes. Unlike other bradyrhizobia, this strain has a symbiotic plasmid harboring nod, nif, and type 3 secretion system (T3SS) genes. This T3SS cluster contains all the genes necessary for the formation of the secretory apparatus and the transcriptional activator (TtsI), which is preceded by a nod-box motif. An in silico search predicted 14 effectors putatively translocated by this T3SS machinery. In this study, we explored the role of the T3SS in the symbiotic performance of DOA9 by evaluating the ability of a T3SS mutant (ΩrhcN) to nodulate legumes belonging to Dalbergioid, Millettioid, and Genistoid tribes. Among the nine species tested, four (Arachis hypogea, Vigna radiata, Crotalaria juncea, and Macroptilium atropurpureum) responded positively to the rhcN mutation (ranging from suppression of plant defense reactions, an increase in the number of nodules and a dramatic improvement in nodule development and infection), one (Stylosanthes hamata) responded negatively (fewer nodules and less nitrogen fixation) and four species (Aeschynomene americana, Aeschynomene afraspera, Indigofera tinctoria, and Desmodium tortuosum) displayed no phenotype. We also tested the role of the T3SS in the ability of the DOA9 strain to endophytically colonize rice roots, but detected no effect of the T3SS mutation, in contrast to what was previously reported in the Bradyrhizobium SUTN9-2 strain. Taken together, these data indicate that DOA9 contains a functional T3SS that interferes with the ability of the strain to interact symbiotically with legumes but not with rice. PMID:28979252

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

PubMed Central

Hedin, Lars O.; Leake, Jonathan R.

2017-01-01

Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58–42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N2) and higher leaf N compared with non-legumes (35–65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO2). Here we hypothesize that the increasing abundance of N2-fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N2-fixation and nodule formation. PMID:28814651

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

PubMed

Epihov, Dimitar Z; Batterman, Sarah A; Hedin, Lars O; Leake, Jonathan R; Smith, Lisa M; Beerling, David J

2017-08-16

Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58-42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N 2 ) and higher leaf N compared with non-legumes (35-65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO 2 ). Here we hypothesize that the increasing abundance of N 2 -fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO 2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N 2 -fixation and nodule formation. © 2017 The Author(s).

Disentangling the complexities of how legumes and their symbionts regulate plant nitrogen access and storage

USGS Publications Warehouse

Reed, Sasha C.

2017-01-01

Nitrogen (N) availability strongly influences the structure and function of ecosystems (e.g. Vitousek & Howarth, 1991), but only a relatively small number of microbial groups have the ability to convert the N2 in our atmosphere into biologically available forms.This process, N2 fixation, is the dominant source of new N to the biosphere outside of anthropogenic inputs (Vitousek et al., 2013).Some N2-fixing microorganisms live independently on plant leaves, on decomposing organic material, and in soil (Reed et al.,2011), while others have co-evolved with a few higher plant taxa to form symbioses that fix N2 in root nodules (e.g. Sprent & Raven,1985). The relationship between these legumes and their root nodule symbionts (rhizobia) is one of the most well studied plant –microbe symbioses. Yet, many important questions about the controls, interactions, and implications of legume N2 fixation remain unanswered. In this issue of New Phytologist (pp. 690–699),Wolf, Funk, & Menge elegantly address a fundamental set of questions about N2 fixation in their examination of how herbaceous legumes, their symbionts, and external N availability interact to govern legume access and storage of N.

Genome-Wide Identification of TCP Family Transcription Factors in Medicago truncatula Reveals Significant Roles of miR319-Targeted TCPs in Nodule Development

PubMed Central

Wang, Hongfeng; Wang, Hongwei; Liu, Rong; Xu, Yiteng; Lu, Zhichao; Zhou, Chuanen

2018-01-01

TCP proteins, the plant-specific transcription factors, are involved in the regulation of multiple aspects of plant development among different species, such as leaf development, branching, and flower symmetry. However, thus far, the roles of TCPs in legume, especially in nodulation are still not clear. In this study, a genome-wide analysis of TCP genes was carried out to discover their evolution and function in Medicago truncatula. In total, 21 MtTCPs were identified and classified into class I and class II, and the class II MtTCPs were further divided into two subclasses, CIN and CYC/TB1. The expression profiles of MtTCPs are dramatically different. The universal expression of class I MtTCPs was detected in all organs. However, the MtTCPs in CIN subclass were highly expressed in leaf and most of the members in CYC/TB1 subclass were highly expressed in flower. Such organ-specific expression patterns of MtTCPs suggest their different roles in plant development. In addition, most MtTCPs were down-regulated during the nodule development, except for the putative MtmiR319 targets, MtTCP3, MtTCP4, and MtTCP10A. Overexpression of MtmiR319A significantly reduced the expression level of MtTCP3/4/10A/10B and resulted in the decreased nodule number, indicating the important roles of MtmiR319-targeted MtTCPs in nodulation. Taken together, this study systematically analyzes the MtTCP gene family at a genome-wide level and their possible functions in nodulation, which lay the basis for further explorations of MtmiR319/MtTCPs module in association with nodule development in M. truncatula.

Cluster Bean—A Ureide- or Amide-Producing Legume? 1

PubMed Central

Sheoran, Inder S.; Luthra, Yash P.; Kuhad, Mohinder S.; Singh, Randhir

1982-01-01

Xylem sap of cluster bean (Cyamopsis tetragonoloba L. cv FS-277) and pigeonpea (Cajanus cajan cv UPAS-120) were analyzed for total nitrogen, amide nitrogen, and ureide nitrogen at flowering stage. Nitrogenase, uricase, and allantoinase were compared in nodules of cluster bean and pigeonpea. Xylem sap of cluster bean exhibited higher amounts of amides as compared to ureides, and the activities of uricase and allantoinase (ureide-producing enzymes) in nodules were also low, whereas the reverse was the case for pigeonpea. Based on these investigations, it has been concluded that cluster bean is an amide-producing legume rather than ureide-producing as had been reported earlier. PMID:16662600

Economy of Photosynthate Use in Nitrogen-fixing Legume Nodules: Observations on Two Contrasting Symbioses.

PubMed

Layzell, D B; Rainbird, R M; Atkins, C A; Pate, J S

1979-11-01

The economy of C use by root nodules was examined in two symbioses, Vigna unguiculata (L.) Walp. (cv. Caloona):Rhizobium CB756 and Lupinus albus L. (cv. Ultra):Rhizobium WU425 over a 2-week period in early vegetative growth. Plants were grown in minus N water culture with cuvettes attached to the nodulated zone of their primary roots for collection of evolved CO(2) and H(2). Increments in total plant N and in C and N of nodules, and C:N weight ratios of xylem and phloem exudates were studied by periodic sampling from the plant populations. Itemized budgets were constructed for the partitioning and utilization of C in the two species. For each milligram N fixed and assimilated by the cowpea association, 1.54 +/- 0.26 (standard error) milligrams C as CO(2) and negligible H(2) were evolved and 3.11 milligrams of translocated C utilized by the nodules. Comparable values for nodules of the lupin association were 3.64 +/- 0.28 milligrams C as CO(2), 0.22 +/- 0.05 milligrams H(2), and 6.58 milligrams C. More efficient use of C by cowpea nodules was due to a lesser requirement of C for synthesis of exported N compounds, a smaller allocation of C to nodule dry matter, and a lower evolution of CO(2). The activity of phosphoenolpyruvate carboxylase in nodule extracts and the rate of (14)CO(2) fixation by detached nodules were greater for the cowpea symbiosis (0.56 +/- 0.06 and 0.22 milligrams C as CO(2) fixed per gram fresh weight per hour, respectively) than for the lupin 0.06 +/- 0.02 and 0.01 milligrams C as CO(2) fixed per gram fresh weight per hour. The significance of the data was discussed in relation to current information on theoretical costs of nitrogenase functioning and associated nodule processes.

Nod factor supply under water stress conditions modulates cytokinin biosynthesis and enhances nodule formation and N nutrition in soybean.

PubMed

Prudent, Marion; Salon, Christophe; Smith, Donald L; Emery, R J Neil

2016-09-01

Nod factors (NF) are molecules produced by rhizobia which are involved in the N 2 -fixing symbiosis with legume plants, enabling the formation of specific organs called nodules. Under drought conditions, nitrogen acquisition by N 2 -fixation is depressed, resulting in low legume productivity. In this study, we evaluated the effects of NF supply on nitrogen acquisition and on cytokinin biosynthesis of soybean plants grown under drought. NF supply to water stressed soybeans increased the CK content of all organs. The profile of CK metabolites also shifted from t-Z to cis-Z and an accumulation of nucleotide and glucoside conjugates. The changes in CK coincided with enhanced nodule formation with sustained nodule specific activity, which ultimately increased the total nitrogen fixed by the plant.

Nodulation outer proteins: double-edged swords of symbiotic rhizobia.

PubMed

Staehelin, Christian; Krishnan, Hari B

2015-09-15

Rhizobia are nitrogen-fixing bacteria that establish a nodule symbiosis with legumes. Nodule formation depends on signals and surface determinants produced by both symbiotic partners. Among them, rhizobial Nops (nodulation outer proteins) play a crucial symbiotic role in many strain-host combinations. Nops are defined as proteins secreted via a rhizobial T3SS (type III secretion system). Functional T3SSs have been characterized in many rhizobial strains. Nops have been identified using various genetic, biochemical, proteomic, genomic and experimental approaches. Certain Nops represent extracellular components of the T3SS, which are visible in electron micrographs as bacterial surface appendages called T3 (type III) pili. Other Nops are T3 effector proteins that can be translocated into plant cells. Rhizobial T3 effectors manipulate cellular processes in host cells to suppress plant defence responses against rhizobia and to promote symbiosis-related processes. Accordingly, mutant strains deficient in synthesis or secretion of T3 effectors show reduced symbiotic properties on certain host plants. On the other hand, direct or indirect recognition of T3 effectors by plant cells expressing specific R (resistance) proteins can result in effector triggered defence responses that negatively affect rhizobial infection. Hence Nops are double-edged swords that may promote establishment of symbiosis with one legume (symbiotic factors) and impair symbiotic processes when bacteria are inoculated on another legume species (asymbiotic factors). In the present review, we provide an overview of our current understanding of Nops. We summarize their symbiotic effects, their biochemical properties and their possible modes of action. Finally, we discuss future perspectives in the field of T3 effector research. © 2015 Authors; published by Portland Press Limited.

Integrated roles of BclA and DD-carboxypeptidase 1 in Bradyrhizobium differentiation within NCR-producing and NCR-lacking root nodules.

PubMed

Barrière, Quentin; Guefrachi, Ibtissem; Gully, Djamel; Lamouche, Florian; Pierre, Olivier; Fardoux, Joël; Chaintreuil, Clémence; Alunni, Benoît; Timchenko, Tatiana; Giraud, Eric; Mergaert, Peter

2017-08-22

Legumes harbor in their symbiotic nodule organs nitrogen fixing rhizobium bacteria called bacteroids. Some legumes produce Nodule-specific Cysteine-Rich (NCR) peptides in the nodule cells to control the intracellular bacterial population. NCR peptides have antimicrobial activity and drive bacteroids toward terminal differentiation. Other legumes do not produce NCR peptides and their bacteroids are not differentiated. Bradyrhizobia, infecting NCR-producing Aeschynomene plants, require the peptide uptake transporter BclA to cope with the NCR peptides as well as a specific peptidoglycan-modifying DD-carboxypeptidase, DD-CPase1. We show that Bradyrhizobium diazoefficiens strain USDA110 forms undifferentiated bacteroids in NCR-lacking soybean nodules. Unexpectedly, in Aeschynomene afraspera nodules the nitrogen fixing USDA110 bacteroids are hardly differentiated despite the fact that this host produces NCR peptides, suggesting that USDA110 is insensitive to the host peptide effectors and that nitrogen fixation can be uncoupled from differentiation. In agreement with the absence of bacteroid differentiation, USDA110 does not require its bclA gene for nitrogen fixing symbiosis with these two host plants. Furthermore, we show that the BclA and DD-CPase1 act independently in the NCR-induced morphological differentiation of bacteroids. Our results suggest that BclA is required to protect the rhizobia against the NCR stress but not to induce the terminal differentiation pathway.

Leghemoglobin is nitrated in functional legume nodules in a tyrosine residue within the heme cavity by a nitrite/peroxide-dependent mechanism

PubMed Central

Sainz, Martha; Calvo-Begueria, Laura; Pérez-Rontomé, Carmen; Wienkoop, Stefanie; Abián, Joaquín; Staudinger, Christiana; Bartesaghi, Silvina; Radi, Rafael; Becana, Manuel

2015-01-01

SUMMARY Protein Tyr nitration is a post-translational modification yielding 3-nitrotyrosine (NO2-Tyr). Formation of NO2-Tyr is generally considered as a marker of nitroxidative stress and is involved in some human pathophysiological disorders, but it has been poorly studied in plants. Leghemoglobin (Lb) is an abundant hemeprotein of legume nodules that plays an essential role as O2 transporter. Liquid chromatography coupled to tandem mass spectrometry was used for a targeted search and quantification of NO2-Tyr in Lbs. For all Lbs examined, Tyr30, located in the distal heme pocket, is the major target of nitration. Lower amounts were found for NO2-Tyr25 and NO2-Tyr133. Nitrated Lb and other as yet unidentified nitrated proteins were also detected in nodules of plants not receiving NO3− and were found to decrease during senescence. This demonstrates formation of nitric oxide (•NO) and NO2− by alternative means to nitrate reductase, probably via a NO synthase-like enzyme, and strongly suggests that nitrated proteins perform biological functions and are not merely metabolic byproducts. In vitro assays with purified Lbs revealed that Tyr nitration requires NO2− + H2O2 and that peroxynitrite is not an efficient inducer of nitration, possibly by isomerizing it to NO3−. Nitrated Lb is formed via oxoferryl Lb, which generates nitrogen dioxide and tyrosyl radicals. This mechanism is distinctly different from that involved in heme nitration. Formation of NO2-Tyr in Lbs is a consequence of active metabolism in functional nodules, where Lbs may act as a sink of toxic peroxynitrite and may play a protective role in the symbiosis. PMID:25603991

Leghemoglobin is nitrated in functional legume nodules in a tyrosine residue within the heme cavity by a nitrite/peroxide-dependent mechanism.

PubMed

Sainz, Martha; Calvo-Begueria, Laura; Pérez-Rontomé, Carmen; Wienkoop, Stefanie; Abián, Joaquín; Staudinger, Christiana; Bartesaghi, Silvina; Radi, Rafael; Becana, Manuel

2015-03-01

Protein tyrosine (Tyr) nitration is a post-translational modification yielding 3-nitrotyrosine (NO2 -Tyr). Formation of NO2 -Tyr is generally considered as a marker of nitro-oxidative stress and is involved in some human pathophysiological disorders, but has been poorly studied in plants. Leghemoglobin (Lb) is an abundant hemeprotein of legume nodules that plays an essential role as an O2 transporter. Liquid chromatography coupled to tandem mass spectrometry was used for a targeted search and quantification of NO2 -Tyr in Lb. For all Lbs examined, Tyr30, located in the distal heme pocket, is the major target of nitration. Lower amounts were found for NO2 -Tyr25 and NO2 -Tyr133. Nitrated Lb and other as yet unidentified nitrated proteins were also detected in nodules of plants not receiving NO3- and were found to decrease during senescence. This demonstrates formation of nitric oxide (˙NO) and NO2- by alternative means to nitrate reductase, probably via a ˙NO synthase-like enzyme, and strongly suggests that nitrated proteins perform biological functions and are not merely metabolic byproducts. In vitro assays with purified Lb revealed that Tyr nitration requires NO2- + H2 O2 and that peroxynitrite is not an efficient inducer of nitration, probably because Lb isomerizes it to NO3-. Nitrated Lb is formed via oxoferryl Lb, which generates nitrogen dioxide and tyrosyl radicals. This mechanism is distinctly different from that involved in heme nitration. Formation of NO2 -Tyr in Lb is a consequence of active metabolism in functional nodules, where Lb may act as a sink of toxic peroxynitrite and may play a protective role in the symbiosis. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Functional Implication of β-Carotene Hydroxylases in Soybean Nodulation1[C][W][OA

PubMed Central

Kim, Yun-Kyoung; Kim, Sunghan; Um, Ji-Hyun; Kim, Kyunga; Choi, Sun-Kang; Um, Byung-Hun; Kang, Suk-Woo; Kim, Jee-Woong; Takaichi, Shinichi; Song, Seok-Bo; Lee, Choon-Hwan; Kim, Ho-Seung; Kim, Ki Woo; Nam, Kyoung Hee; Lee, Suk-Ha; Kim, Yul-Ho; Park, Hyang-Mi; Ha, Sun-Hwa; Verma, Desh Pal S.; Cheon, Choong-Ill

2013-01-01

Legume-Rhizobium spp. symbiosis requires signaling between the symbiotic partners and differential expression of plant genes during nodule development. Previously, we cloned a gene encoding a putative β-carotene hydroxylase (GmBCH1) from soybean (Glycine max) whose expression increased during nodulation with Bradyrhizobium japonicum. In this work, we extended our study to three GmBCHs to examine their possible role(s) in nodule development, as they were additionally identified as nodule specific, along with the completion of the soybean genome. In situ hybridization revealed the expression of three GmBCHs (GmBCH1, GmBCH2, and GmBCH3) in the infected cells of root nodules, and their enzymatic activities were confirmed by functional assays in Escherichia coli. Localization of GmBCHs by transfecting Arabidopsis (Arabidopsis thaliana) protoplasts with green fluorescent protein fusions and by electron microscopic immunogold detection in soybean nodules indicated that GmBCH2 and GmBCH3 were present in plastids, while GmBCH1 appeared to be cytosolic. RNA interference of the GmBCHs severely impaired nitrogen fixation as well as nodule development. Surprisingly, we failed to detect zeaxanthin, a product of GmBCH, or any other carotenoids in nodules. Therefore, we examined the possibility that most of the carotenoids in nodules are converted or cleaved to other compounds. We detected the expression of some carotenoid cleavage dioxygenases (GmCCDs) in wild-type nodules and also a reduced amount of zeaxanthin in GmCCD8-expressing E. coli, suggesting cleavage of the carotenoid. In view of these findings, we propose that carotenoids such as zeaxanthin synthesized in root nodules are cleaved by GmCCDs, and we discuss the possible roles of the carotenoid cleavage products in nodulation. PMID:23700351

Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures

PubMed Central

Lardi, Martina; Murset, Valérie; Fischer, Hans-Martin; Mesa, Socorro; Ahrens, Christian H.; Zamboni, Nicola; Pessi, Gabriella

2016-01-01

Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection–time-of-flight mass spectrometry analysis the metabolome of (i) nodules and roots from four different B. diazoefficiens host plants; (ii) soybean nodules harvested at different time points during nodule development; and (iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by independent transcriptomics data. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions. PMID:27240350

Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome.

PubMed

Lemaire, Benny; Van Cauwenberghe, Jannick; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Muasya, A Muthama

2015-11-01

The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Impact of the energy crop Jatropha curcas L. on the composition of rhizobial populations nodulating cowpea (Vigna unguiculata L.) and acacia (Acacia seyal L.).

PubMed

Dieng, Amadou; Duponnois, Robin; Floury, Antoine; Laguerre, Gisèle; Ndoye, Ibrahima; Baudoin, Ezékiel

2015-03-01

Jatropha curcas, a Euphorbiaceae species that produces many toxicants, is increasingly planted as an agrofuel plant in Senegal. The purpose of this study was to determine whether soil priming induced by J. curcas monoculture could alter the rhizobial populations that nodulate cowpea and acacia, two locally widespread legumes. Soil samples were transferred into a greenhouse from three fields previously cultivated with Jatropha for 1, 2, and 15 years, and the two trap legumes were grown in them. Control soil samples were also taken from adjacent Jatropha-fallow plots. Both legumes tended to develop fewer but larger nodules when grown in Jatropha soils. Nearly all the nifH sequences amplified from nodule DNA were affiliated to the Bradyrhizobium genus. Only sequences from Acacia seyal nodules grown in the most recent Jatropha plantation were related to the Mesorhizobium genus, which was much a more conventional finding on A. seyal than the unexpected Bradyrhizobium genus. Apart from this particular case, only minor differences were found in the respective compositions of Jatropha soil versus control soil rhizobial populations. Lastly, the structure of these rhizobial populations was systematically imbalanced owing to the overwhelming dominance of a very small number of nifH genotypes, some of which were identical across soil types or even sites. Despite these weak and sparse effects on rhizobial diversity, future investigations should focus on the characterization of the nitrogen-fixing abilities of the predominant rhizobial strains. Copyright © 2014 Elsevier GmbH. All rights reserved.

Burkholderia species associated with legumes of Chiapas, Mexico, exhibit stress tolerance and growth in aromatic compounds.

PubMed

de León-Martínez, José A; Yañez-Ocampo, Gustavo; Wong-Villarreal, Arnoldo

Leguminous plants have received special interest for the diversity of β-proteobacteria in their nodules and are promising candidates for biotechnological applications. In this study, 15 bacterial strains were isolated from the nodules of the following legumes: Indigofera thibaudiana, Mimosa diplotricha, Mimosa albida, Mimosa pigra, and Mimosa pudica, collected in 9 areas of Chiapas, Mexico. The strains were grouped into four profiles of genomic fingerprints through BOX-PCR and identified based on their morphology, API 20NE biochemical tests, sequencing of the 16S rRNA, nifH and nodC genes as bacteria of the Burkholderia genus, genetically related to Burkholderia phenoliruptrix, Burkholderia phymatum, Burkholderia sabiae, and Burkholderia tuberum. The Burkholderia strains were grown under stress conditions with 4% NaCl, 45°C, and benzene presence at 0.1% as the sole carbon source. This is the first report on the isolation of these nodulating species of the Burkholderia genus in legumes in Mexico. Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype.

PubMed

Leite, Jakson; Fischer, Doreen; Rouws, Luc F M; Fernandes-Júnior, Paulo I; Hofmann, Andreas; Kublik, Susanne; Schloter, Michael; Xavier, Gustavo R; Radl, Viviane

2016-01-01

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea ( Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium , and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.

Legume receptors perceive the rhizobial lipochitin oligosaccharide signal molecules by direct binding

PubMed Central

Broghammer, Angelique; Krusell, Lene; Blaise, Mickaël; Sauer, Jørgen; Sullivan, John T.; Maolanon, Nicolai; Vinther, Maria; Lorentzen, Andrea; Madsen, Esben B.; Jensen, Knud J.; Roepstorff, Peter; Thirup, Søren; Ronson, Clive W.; Thygesen, Mikkel B.; Stougaard, Jens

2012-01-01

Lipochitin oligosaccharides called Nod factors function as primary rhizobial signal molecules triggering legumes to develop new plant organs: root nodules that host the bacteria as nitrogen-fixing bacteroids. Here, we show that the Lotus japonicus Nod factor receptor 5 (NFR5) and Nod factor receptor 1 (NFR1) bind Nod factor directly at high-affinity binding sites. Both receptor proteins were posttranslationally processed when expressed as fusion proteins and extracted from purified membrane fractions of Nicotiana benthamiana or Arabidopsis thaliana. The N-terminal signal peptides were cleaved, and NFR1 protein retained its in vitro kinase activity. Processing of NFR5 protein was characterized by determining the N-glycosylation patterns of the ectodomain. Two different glycan structures with identical composition, Man3XylFucGlcNAc4, were identified by mass spectrometry and located at amino acid positions N68 and N198. Receptor–ligand interaction was measured by using ligands that were labeled or immobilized by application of chemoselective chemistry at the anomeric center. High-affinity ligand binding was demonstrated with both solid-phase and free solution techniques. The Kd values obtained for Nod factor binding were in the nanomolar range and comparable to the concentration range sufficient for biological activity. Structure-dependent ligand specificity was shown by using chitin oligosaccharides. Taken together, our results suggest that ligand recognition through direct ligand binding is a key step in the receptor-mediated activation mechanism leading to root nodule development in legumes. PMID:22859506

Legume small GTPases and their role in the establishment of symbiotic associations with Rhizobium spp

PubMed Central

Memon, Abdul R

2009-01-01

Small GTP-binding genes act as molecular switches regulating myriad of cellular processes including vesicle-mediated intracellular trafficking, signal transduction, cytoskeletal reorganization and cell division in plants and animals. Even though these genes are well conserved both functionally and sequentially across whole Eukaryotae, occasional lineage-specific diversification in some plant species in terms of both functional and expressional characteristics have been reported. Hence, comparative phyletic and correlative functional analyses of legume small GTPases homologs with the genes from other Metazoa and Embryophyta species would be very beneficial for gleaning out the small GTPases that could have specialized in legume-specific processes; e.g., nodulation. The completion of genome sequences of two model legumes, Medicago truncatula and Lotus japonicus will significantly improve our knowledge about mechanism of biological processes taking place in legume-rhizobia symbiotic associations. Besides, the need for molecular switches coordinating busy cargo-trafficking between symbiosis partners would suggest a possible subfunctionalization of small GTPases in Fabaceae for these functions. Therefore, more detailed investigation into the functional characteristics of legume small GTPases would be helpful for the illumination of the events initialized with the perception of bacteria by host, followed by the formation of infection thread and the engulfment of rhizobial bacteria, and end with the senescence of nitrogen-fixing organelles, nodules. In summary, a more thorough functional and evolutionary characterization of small GTPases across the main lineages of Embryophyta is significant for better comprehension of evolutionary history of Plantae, that is because, these genes are associated with multitude of vital biological processes including organogenesis. PMID:19794839

Visualization of symbiotic tissue in intact root nodules of Vicia tetrasperma using GFP-marked Rhizobium leguminosarum bv. viciae.

PubMed

Chovanec, P; Hovorka, O; Novák, K

2008-01-01

In rhizobial symbiosis with legume plant hosts, the symbiotic tissue in the root nodules of indeterminate type is localized to the basal part of the nodule where the symbiotic zones contain infected cells (IC) interspersed with uninfected cells (UC) that are devoid of rhizobia. Although IC are easily distinguished in nodule sections using standard histochemical techniques, their observation in intact nodules is hampered by nodule tissue characteristics. Tagging of Rhizobium leguminosarum bv. viciae strain 128C30 with a constitutively expressed gene for green fluorescent protein (nonshifted mutant form cycle3) in combination with the advantages of the tiny nodules formed by Vicia tetrasperma (L.) SCHREB . allowed for vital observation of symbiotic tissue using fluorescence microscopy. Separation of a red-shifted background channel and digital image stacking along z-axis enabled us to construct a nodule image in a classical fluorescence microscopy of nodules exceeding 1 mm in diameter. In parallel, visualization of nodule bacteria inside the symbiotic tissue by confocal microscopy at the excitation wavelength 488 nm clearly distinguished IC/UC pattern in the nodule virtual sections and revealed red-shifted fluorescence of nonrhizobial origin. This signal was located on the periphery of IC and increased with their degradation, thus suggesting accumulation of secondary metabolites, presumably flavonoids. The simultaneous detection of bacteria and secondary metabolites can be used for monitoring changes to intact nodule physiology in the model legumes. The advantage of V. tetrasperma as a suggested laboratory model for pea cross-inoculation group has been demonstrated.

Growth, photosynthetic acclimation and yield quality in legumes under climate change simulations: an updated survey.

PubMed

Irigoyen, J J; Goicoechea, N; Antolín, M C; Pascual, I; Sánchez-Díaz, M; Aguirreolea, J; Morales, F

2014-09-01

Continued emissions of CO2, derived from human activities, increase atmospheric CO2 concentration. The CO2 rise stimulates plant growth and affects yield quality. Effects of elevated CO2 on legume quality depend on interactions with N2-fixing bacteria and mycorrhizal fungi. Growth at elevated CO2 increases photosynthesis under short-term exposures in C3 species. Under long-term exposures, however, plants generally acclimate to elevated CO2 decreasing their photosynthetic capacity. An updated survey of the literature indicates that a key factor, perhaps the most important, that characteristically influences this phenomenon, its occurrence and extent, is the plant source-sink balance. In legumes, the ability of exchanging C for N at nodule level with the N2-fixing symbionts creates an extra C sink that avoids the occurrence of photosynthetic acclimation. Arbuscular mycorrhizal fungi colonizing roots may also result in increased C sink, preventing photosynthetic acclimation. Defoliation (Anthyllis vulneraria, simulated grazing) or shoot cutting (alfalfa, usual management as forage) largely increases root/shoot ratio. During re-growth at elevated CO2, new shoots growth and nodule respiration function as strong C sinks that counteracts photosynthetic acclimation. In the presence of some limiting factor, the legumes response to elevated CO2 is weakened showing photosynthetic acclimation. This survey has identified limiting factors that include an insufficient N supply from bacterial strains, nutrient-poor soils, low P supply, excess temperature affecting photosynthesis and/or nodule activity, a genetically determined low nodulation capacity, an inability of species or varieties to increase growth (and therefore C sink) at elevated CO2 and a plant phenological state or season when plant growth is stopped. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Partial Purification of a Legume Nodulation Factor Present in Coconut Water 1

PubMed Central

Schaffer, A. G.; Alexander, M.

1967-01-01

The nodulation of adventitious roots growing from segments of bean hypocotyl tissue was used as a bioassay for the material present in coconut water which stimulated nodulation. The active material in coconut water is acidic, but it was not possible to extract it from an acid solution with organic solvents. A purification of approximately 70-fold (on a dry wt basis) was obtained using activated charcoal, but at least 10 different compounds were present in the active fractions. A purified fraction of coconut water, which is stimulatory to the growth of carrot root explants, was active in the nodulation assay at a concentration of 2 μg/ml. This represents a 4000-fold purification of the diffusible fraction of coconut water. The charcoal fractionation procedure can be applied to the active material present in extracts of bean leaves. PMID:16656538

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia.

PubMed

Lardi, Martina; Pessi, Gabriella

2018-05-18

Biological nitrogen fixation gives legumes a pronounced growth advantage in nitrogen-deprived soils and is of considerable ecological and economic interest. In exchange for reduced atmospheric nitrogen, typically given to the plant in the form of amides or ureides, the legume provides nitrogen-fixing rhizobia with nutrients and highly specialised root structures called nodules. To elucidate the molecular basis underlying physiological adaptations on a genome-wide scale, functional genomics approaches, such as transcriptomics, proteomics, and metabolomics, have been used. This review presents an overview of the different functional genomics approaches that have been performed on rhizobial symbiosis, with a focus on studies investigating the molecular mechanisms used by the bacterial partner to interact with the legume. While rhizobia belonging to the alpha-proteobacterial group (alpha-rhizobia) have been well studied, few studies to date have investigated this process in beta-proteobacteria (beta-rhizobia).

Detection of S-Nitrosothiol and Nitrosylated Proteins in Arachis hypogaea Functional Nodule: Response of the Nitrogen Fixing Symbiont

PubMed Central

Maiti, Debasis; Sarkar, Tuhin Subhra; Ghosh, Sanjay

2012-01-01

To detect the presence of NO, ROS and RNS in nodules of crack entry legumes, we used Arachis hypogaea functional nodule. The response of two cognate partner rhizobia was compared towards NO and GSNO using S. meliloti and Bradyrhizobium sp NC921001. ROS, NO, nitrosothiol and bacteroids were detected by fluorescence microscopy. Redox enzymes and thiol pools were detected biochemically. Nitrosothiols were found to be present but ROS and NO were absent in A. hypogaea nodule. A number of S-nitrosylated proteins were also detected. The total thiol pool and most of the redox enzymes were low in nodule cytosolic extract but these were found to be high in the partner microorganisms indicating partner rhizobia could protect the nodule environment against the nitrosothiols. Both S. meliloti and Bradyrhizobium sp NC921001 were found to contain GSNO reductase. Interestingly, there was a marked difference in growth pattern between S. meliloti and Bradyrhizobium sp in presence of sodium nitroprusside (SNP) and S-nitrosoglutathione (GSNO). Bradyrhizobium sp was found to be much more tolerant to NO donor compounds than the S. meliloti. In contrast, S. meliloti showed resistance to GSNO but was sensitive to SNP. Together our data indicate that nodule environment of crack entry legumes is different than the nodules of infection mode entry in terms of NO, ROS and RNS. Based on our biochemical characterization, we propose that exchange of redox molecules and reactive chemical species is possible between the bacteroid and nodule compartment. PMID:23029073

Negotiation of mutualism: rhizobia and legumes

PubMed Central

Akçay, Erol; Roughgarden, Joan

2006-01-01

The evolution and persistence of biological cooperation have been an important puzzle in evolutionary theory. Here, we suggest a new approach based on bargaining theory to tackle the question. We present a mechanistic model for negotiation of benefits between a nitrogen-fixing nodule and a legume plant. To that end, we first derive growth rates for the nodule and plant from metabolic models of each as a function of material fluxes between them. We use these growth rates as pay-off functions in the negotiation process, which is analogous to collective bargaining between a firm and a workers' union. Our model predicts that negotiations lead to the Nash bargaining solution, maximizing the product of players' pay-offs. This work introduces elements of cooperative game theory into the field of mutualistic interactions. In the discussion of the paper, we argue for the benefits of such an approach in studying the question of biological cooperation. PMID:17015340

Nodulation in Dimorphandra wilsonii Rizz. (Caesalpinioideae), a Threatened Species Native to the Brazilian Cerrado

PubMed Central

Fonseca, Márcia Bacelar; Peix, Alvaro; de Faria, Sergio Miana; Mateos, Pedro F.; Rivera, Lina P.; Simões-Araujo, Jean L.; França, Marcel Giovanni Costa; dos Santos Isaias, Rosy Mary; Cruz, Cristina; Velázquez, Encarna; Scotti, Maria Rita; Sprent, Janet I.; James, Euan K.

2012-01-01

The threatened caesalpinioid legume Dimorphandra wilsonii, which is native to the Cerrado biome in Brazil, was examined for its nodulation and N2-fixing ability, and was compared with another, less-threatened species, D. jorgei. Nodulation and potential N2 fixation was shown on seedlings that had been inoculated singly with five bradyrhizobial isolates from mature D. wilsonii nodules. The infection of D. wilsonii by two of these strains (Dw10.1, Dw12.5) was followed in detail using light and transmission electron microscopy, and was compared with that of D. jorgei by Bradyrhizobium strain SEMIA6099. The roots of D. wilsonii were infected via small transient root hairs at 42 d after inoculation (dai), and nodules were sufficiently mature at 63 dai to express nitrogenase protein. Similar infection and nodule developmental processes were observed in D. jorgei. The bacteroids in mature Dimorphandra nodules were enclosed in plant cell wall material containing a homogalacturonan (pectic) epitope that was recognized by the monoclonal antibody JIM5. Analysis of sequences of their rrs (16S rRNA) genes and their ITS regions showed that the five D. wilsonii strains, although related to SEMIA6099, may constitute five undescribed species of genus Bradyrhizobium, whilst their nodD and nifH gene sequences showed that they formed clearly separated branches from other rhizobial strains. This is the first study to describe in full the N2-fixing symbiotic interaction between defined rhizobial strains and legumes in the sub-family Caesalpinioideae. This information will hopefully assist in the conservation of the threatened species D. wilsonii. PMID:23185349

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype

PubMed Central

Leite, Jakson; Fischer, Doreen; Rouws, Luc F. M.; Fernandes-Júnior, Paulo I.; Hofmann, Andreas; Kublik, Susanne; Schloter, Michael; Xavier, Gustavo R.; Radl, Viviane

2017-01-01

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions. PMID:28163711

Lignin Modification Leads to Increased Nodule Numbers in Alfalfa1[C][W][OPEN

PubMed Central

Gallego-Giraldo, Lina; Bhattarai, Kishor; Pislariu, Catalina I.; Nakashima, Jin; Jikumaru, Yusuke; Kamiya, Yuji; Udvardi, Michael K.; Monteros, Maria J.; Dixon, Richard A.

2014-01-01

Reduction of lignin levels in the forage legume alfalfa (Medicago sativa) by down-regulation of the monolignol biosynthetic enzyme hydroxycinnamoyl coenzyme A:shikimate hydroxycinnamoyl transferase (HCT) results in strongly increased digestibility and processing ability of lignocellulose. However, these modifications are often also associated with dwarfing and other changes in plant growth. Given the importance of nitrogen fixation for legume growth, we evaluated the impact of constitutively targeted lignin modification on the belowground organs (roots and nodules) of alfalfa plants. HCT down-regulated alfalfa plants exhibit a striking reduction in root growth accompanied by an unexpected increase in nodule numbers when grown in the greenhouse or in the field. This phenotype is associated with increased levels of gibberellins and certain flavonoid compounds in roots. Although HCT down-regulation reduced biomass yields in both the greenhouse and field experiments, the impact on the allocation of nitrogen to shoots or roots was minimal. It is unlikely, therefore, that the altered growth phenotype of reduced-lignin alfalfa is a direct result of changes in nodulation or nitrogen fixation efficiency. Furthermore, HCT down-regulation has no measurable effect on carbon allocation to roots in either greenhouse or 3-year field trials. PMID:24406794

Truncated hemoglobins in actinorhizal nodules of Datisca glomerata.

PubMed

Pawlowski, K; Jacobsen, K R; Alloisio, N; Ford Denison, R; Klein, M; Tjepkema, J D; Winzer, T; Sirrenberg, A; Guan, C; Berry, A M

2007-11-01

Three types of hemoglobins exist in higher plants, symbiotic, non-symbiotic, and truncated hemoglobins. Symbiotic (class II) hemoglobins play a role in oxygen supply to intracellular nitrogen-fixing symbionts in legume root nodules, and in one case ( Parasponia Sp.), a non-symbiotic (class I) hemoglobin has been recruited for this function. Here we report the induction of a host gene, dgtrHB1, encoding a truncated hemoglobin in Frankia-induced nodules of the actinorhizal plant Datisca glomerata. Induction takes place specifically in cells infected by the microsymbiont, prior to the onset of bacterial nitrogen fixation. A bacterial gene (Frankia trHBO) encoding a truncated hemoglobin with O (2)-binding kinetics suitable for the facilitation of O (2) diffusion ( ) is also expressed in symbiosis. Nodule oximetry confirms the presence of a molecule that binds oxygen reversibly in D. glomerata nodules, but indicates a low overall hemoglobin concentration suggesting a local function. Frankia trHbO is likely to be responsible for this activity. The function of the D. glomerata truncated hemoglobin is unknown; a possible role in nitric oxide detoxification is suggested.

RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N2 fixation before emerging P deficiency reaches the nodules

PubMed Central

Cabeza, Ricardo A.; Liese, Rebecca; Lingner, Annika; von Stieglitz, Ilsabe; Neumann, Janice; Salinas-Riester, Gabriela; Pommerenke, Claudia; Dittert, Klaus; Schulze, Joachim

2014-01-01

Legume nodules are plant tissues with an exceptionally high concentration of phosphorus (P), which, when there is scarcity of P, is preferentially maintained there rather than being allocated to other plant organs. The hypothesis of this study was that nodules are affected before the P concentration in the organ declines during whole-plant P depletion. Nitrogen (N2) fixation and P concentration in various organs were monitored during a whole-plant P-depletion process in Medicago truncatula. Nodule gene expression was profiled through RNA-seq at day 5 of P depletion. Until that point in time P concentration in leaves reached a lower threshold but was maintained in nodules. N2-fixation activity per plant diverged from that of fully nourished plants beginning at day 5 of the P-depletion process, primarily because fewer nodules were being formed, while the activity of the existing nodules was maintained for as long as two weeks into P depletion. RNA-seq revealed nodule acclimation on a molecular level with a total of 1140 differentially expressed genes. Numerous genes for P remobilization from organic structures were increasingly expressed. Various genes involved in nodule malate formation were upregulated, while genes involved in fermentation were downregulated. The fact that nodule formation was strongly repressed with the onset of P deficiency is reflected in the differential expression of various genes involved in nodulation. It is concluded that plants follow a strategy to maintain N2 fixation and viable leaf tissue as long as possible during whole-plant P depletion to maintain their ability to react to emerging new P sources (e.g. through active P acquisition by roots). PMID:25151618

Development and Evaluation of LEGUME ID: A ToolBook Multimedia Module.

ERIC Educational Resources Information Center

Hannaway, David B.; And Others

1992-01-01

Describes the development and advantages of LEGUME ID, a multimedia module for agricultural education. LEGUME ID is an example of how teachers, given the opportunity through accessible computer software programs, can create powerful teaching tools. Summarized is a student response to the use of this teacher-produced software program. (MCO)

Selection and characterization of coal mine autochthonous rhizobia for the inoculation of herbaceous legumes.

PubMed

Hernández, Anabel González; de Moura, Ginaini Doin; Binati, Renato Leal; Nascimento, Francisco Xavier Inês; Londoño, Diana Morales; Mamede, Ana Carolina Peixoto; da Silva, Emanuela Pille; de Armas, Rafael Dutra; Giachini, Admir José; Rossi, Márcio José; Soares, Cláudio Roberto Fonsêca Sousa

2017-09-01

Coal open pit mining in the South of Santa Catarina state (Brazil) was inappropriately developed, affecting approximately 6.700 ha. Re-vegetation is an alternative for the recovery of these areas. Furthermore, the use of herbaceous legumes inoculated with nitrogen fixing bacteria is motivated due to the difficulty implementing a vegetation cover in these areas, mainly due to low nutrient availability. Therefore, the aim of this work was to evaluate, among 16 autochthonous rhizobia isolated from the coal mining areas, those with the greatest potential to increase growth of the herbaceous legumes Vicia sativa and Calopogonium mucunoides. Tests were conducted in greenhouse containing 17 inoculation treatments (16 autochthonous rhizobia + Brazilian recommended strain for each plant species), plus two treatments without inoculation (with and without mineral nitrogen). After 60 days, nodulation, growth, N uptake, and symbiotic efficiency were evaluated. Isolates characterization was assessed by the production of indole acetic acid, ACC deaminase, siderophores, and inorganic phosphate solubilization. The classification of the isolates was performed by 16 S rDNA gene sequencing. Only isolates UFSC-M4 and UFSC-M8 were able to nodulate C. mucunoides. Among rhizobia capable of nodulating V. sativa, only UFSC-M8 was considered efficient. It was found the presence of more than one growth-promoting attributes in the same organism, and isolate UFSC-M8 presented all of them. Isolates were classified as belonging to Rhizobium, Burkholderia and Curtobacterium. The results suggest the inoculation of Vicia sativa with strain UFSC-M8, classified as Rhizobium sp., as a promising alternative for the revegetation of coal mining degraded areas.

A Sinorhizobium meliloti-specific N-acyl homoserine lactone quorum-sensing signal increases nodule numbers in Medicago truncatula independent of autoregulation.

PubMed

Veliz-Vallejos, Debora F; van Noorden, Giel E; Yuan, Mengqi; Mathesius, Ulrike

2014-01-01

N-acyl homoserine lactones (AHLs) act as quorum sensing signals that regulate cell-density dependent behaviors in many gram-negative bacteria, in particular those important for plant-microbe interactions. AHLs can also be recognized by plants, and this may influence their interactions with bacteria. Here we tested whether the exposure to AHLs affects the nodule-forming symbiosis between legume hosts and rhizobia. We treated roots of the model legume, Medicago truncatula, with a range of AHLs either from its specific symbiont, Sinorhizobium meliloti, or from the potential pathogens, Pseudomonas aeruginosa and Agrobacterium vitis. We found increased numbers of nodules formed on root systems treated with the S. meliloti-specific AHL, 3-oxo-C14-homoserine lactone, at a concentration of 1 μM, while the other AHLs did not result in significant changes to nodule numbers. We did not find any evidence for altered nodule invasion by the rhizobia. Quantification of flavonoids that could act as nod gene inducers in S. meliloti did not show any correlation with increased nodule numbers. The effects of AHLs were specific for an increase in nodule numbers, but not lateral root numbers or root length. Increased nodule numbers following 3-oxo-C14-homoserine lactone treatment were under control of autoregulation of nodulation and were still observed in the autoregulation mutant, sunn4 (super numeric nodules4). However, increases in nodule numbers by 3-oxo-C14-homoserine lactone were not found in the ethylene-insensitive sickle mutant. A comparison between M. truncatula with M. sativa (alfalfa) and Trifolium repens (white clover) showed that the observed effects of AHLs on nodule numbers were specific to M. truncatula, despite M. sativa nodulating with the same symbiont. We conclude that plant perception of the S. meliloti-specific 3-oxo-C14-homoserine lactone influences nodule numbers in M. truncatula via an ethylene-dependent, but autoregulation-independent mechanism.

Evolutionary signals of symbiotic persistence in the legume-rhizobia mutualism.

PubMed

Werner, Gijsbert D A; Cornwell, William K; Cornelissen, Johannes H C; Kiers, E Toby

2015-08-18

Understanding the origins and evolutionary trajectories of symbiotic partnerships remains a major challenge. Why are some symbioses lost over evolutionary time whereas others become crucial for survival? Here, we use a quantitative trait reconstruction method to characterize different evolutionary stages in the ancient symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria, asking how labile is symbiosis across different host clades. We find that more than half of the 1,195 extant nodulating legumes analyzed have a high likelihood (>95%) of being in a state of high symbiotic persistence, meaning that they show a continued capacity to form the symbiosis over evolutionary time, even though the partnership has remained facultative and is not obligate. To explore patterns associated with the likelihood of loss and retention of the N2-fixing symbiosis, we tested for correlations between symbiotic persistence and legume distribution, climate, soil and trait data. We found a strong latitudinal effect and demonstrated that low mean annual temperatures are associated with high symbiotic persistence in legumes. Although no significant correlations between soil variables and symbiotic persistence were found, nitrogen and phosphorus leaf contents were positively correlated with legumes in a state of high symbiotic persistence. This pattern suggests that highly demanding nutrient lifestyles are associated with more stable partnerships, potentially because they "lock" the hosts into symbiotic dependency. Quantitative reconstruction methods are emerging as a powerful comparative tool to study broad patterns of symbiont loss and retention across diverse partnerships.

Characterization of the papilionoid-Burkholderia interaction in the Fynbos biome: The diversity and distribution of beta-rhizobia nodulating Podalyria calyptrata (Fabaceae, Podalyrieae).

PubMed

Lemaire, Benny; Van Cauwenberghe, Jannick; Verstraete, Brecht; Chimphango, Samson; Stirton, Charles; Honnay, Olivier; Smets, Erik; Sprent, Janet; James, Euan K; Muasya, A Muthama

2016-02-01

The South African Fynbos soils are renowned for nitrogen-fixing Burkholderia associated with diverse papilionoid legumes of the tribes Crotalarieae, Hypocalypteae, Indigofereae, Phaseoleae and Podalyrieae. However, despite numerous rhizobial studies in the region, the symbiotic diversity of Burkholderia has not been investigated in relation to a specific host legume and its geographical provenance. This study analyzed the diversity of nodulating strains of Burkholderia from the legume species Podalyria calyptrata. Diverse lineages were detected that proved to be closely related to Burkholderia taxa, originating from hosts in other legume tribes. By analyzing the genetic variation of chromosomal (recA) and nodulation (nodA) sequence data in relation to the sampling sites we assessed the geographical distribution patterns of the P. calyptrata symbionts. Although we found a degree of genetically differentiated rhizobial populations, a correlation between genetic (recA and nodA) and geographic distances among populations was not observed, suggesting high rates of dispersal and rhizobial colonization within Fynbos soils. Copyright © 2015 Elsevier GmbH. All rights reserved.

Nodulation of Lupinus albus by Strains of Ochrobactrum lupini sp. nov.

PubMed Central

Trujillo, Martha E.; Willems, Anne; Abril, Adriana; Planchuelo, Ana-María; Rivas, Raúl; Ludeña, Dolores; Mateos, Pedro F.; Martínez-Molina, Eustoquio; Velázquez, Encarna

2005-01-01

The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the α-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to α and β subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21T (LMG 20667T) is the type strain. PMID:15746334

High diversity of Bradyrhizobium strains isolated from several legume species and land uses in Brazilian tropical ecosystems.

PubMed

Azarias Guimarães, Amanda; Florentino, Ligiane Aparecida; Alves Almeida, Kize; Lebbe, Liesbeth; Barroso Silva, Karina; Willems, Anne; de Souza Moreira, Fatima Maria

2015-09-01

The genus Bradyrhizobium stands out among nitrogen-fixing legume-nodulating bacteria because it predominates among the efficient microsymbionts of forest, forage, and green manure legume species, as well as important species of grain legumes, such as soybean, cowpea, and peanut. Therefore, the diversity of Bradyrhizobium strains is a relevant resource from environmental and economic perspectives, and strains isolated from diverse legume species and land uses in Brazilian tropical ecosystems were assessed in this study. To accomplish this, sequences of four housekeeping genes (atpD, dnaK, gyrB, and recA) were individually analysed, with the first three also being considered using multilocus sequence analysis (MLSA). The sensitivity of the strains to different antibiotics, their tolerance to different levels of salinity, and their ability to nodulate soybean plants were also measured. The phylogenetic trees based on each individual gene, and on the concatenated housekeeping genes, revealed several strain clusters separated from any currently described species. The Bradyrhizobium strains studied were generally resistant to antibiotics. All strains were able to grow at salinity levels of up to 0.5% NaCl, whereas only strains UFLA03-142, UFLA03-143, UFLA03-145, and UFLA03-146 grew in the presence of 1% NaCl. Together, the results indicated that some of the strains studied were potential novel species, indicating that the various soils and ecosystems in Brazil may harbour an as yet unknown diversity of rhizobia. Copyright © 2015 Elsevier GmbH. All rights reserved.

Rhizobium–legume symbiosis shares an exocytotic pathway required for arbuscule formation

PubMed Central

Ivanov, Sergey; Fedorova, Elena E.; Limpens, Erik; De Mita, Stephane; Genre, Andrea; Bonfante, Paola; Bisseling, Ton

2012-01-01

Endosymbiotic interactions are characterized by the formation of specialized membrane compartments, by the host in which the microbes are hosted, in an intracellular manner. Two well-studied examples, which are of major agricultural and ecological importance, are the widespread arbuscular mycorrhizal symbiosis and the Rhizobium–legume symbiosis. In both symbioses, the specialized host membrane that surrounds the microbes forms a symbiotic interface, which facilitates the exchange of, for example, nutrients in a controlled manner and, therefore, forms the heart of endosymbiosis. Despite their key importance, the molecular and cellular mechanisms underlying the formation of these membrane interfaces are largely unknown. Recent studies strongly suggest that the Rhizobium–legume symbiosis coopted a signaling pathway, including receptor, from the more ancient arbuscular mycorrhizal symbiosis to form a symbiotic interface. Here, we show that two highly homologous exocytotic vesicle-associated membrane proteins (VAMPs) are required for formation of the symbiotic membrane interface in both interactions. Silencing of these Medicago VAMP72 genes has a minor effect on nonsymbiotic plant development and nodule formation. However, it blocks symbiosome as well as arbuscule formation, whereas root colonization by the microbes is not affected. Identification of these VAMP72s as common symbiotic regulators in exocytotic vesicle trafficking suggests that the ancient exocytotic pathway forming the periarbuscular membrane compartment has also been coopted in the Rhizobium–legume symbiosis. PMID:22566631

The Independent Acquisition of Plant Root Nitrogen-Fixing Symbiosis in Fabids Recruited the Same Genetic Pathway for Nodule Organogenesis

PubMed Central

Svistoonoff, Sergio; Benabdoun, Faiza Meriem; Nambiar-Veetil, Mathish; Imanishi, Leandro; Vaissayre, Virginie; Cesari, Stella; Diagne, Nathalie; Hocher, Valérie; de Billy, Françoise; Bonneau, Jocelyne; Wall, Luis; Ykhlef, Nadia; Rosenberg, Charles; Bogusz, Didier; Franche, Claudine; Gherbi, Hassen

2013-01-01

Only species belonging to the Fabid clade, limited to four classes and ten families of Angiosperms, are able to form nitrogen-fixing root nodule symbioses (RNS) with soil bacteria. This concerns plants of the legume family (Fabaceae) and Parasponia (Cannabaceae) associated with the Gram-negative proteobacteria collectively called rhizobia and actinorhizal plants associated with the Gram-positive actinomycetes of the genus Frankia. Calcium and calmodulin-dependent protein kinase (CCaMK) is a key component of the common signaling pathway leading to both rhizobial and arbuscular mycorrhizal symbioses (AM) and plays a central role in cross-signaling between root nodule organogenesis and infection processes. Here, we show that CCaMK is also needed for successful actinorhiza formation and interaction with AM fungi in the actinorhizal tree Casuarina glauca and is also able to restore both nodulation and AM symbioses in a Medicago truncatula ccamk mutant. Besides, we expressed auto-active CgCCaMK lacking the auto-inhibitory/CaM domain in two actinorhizal species: C. glauca (Casuarinaceae), which develops an intracellular infection pathway, and Discaria trinervis (Rhamnaceae) which is characterized by an ancestral intercellular infection mechanism. In both species, we found induction of nodulation independent of Frankia similar to response to the activation of CCaMK in the rhizobia-legume symbiosis and conclude that the regulation of actinorhiza organogenesis is conserved regardless of the infection mode. It has been suggested that rhizobial and actinorhizal symbioses originated from a common ancestor with several independent evolutionary origins. Our findings are consistent with the recruitment of a similar genetic pathway governing rhizobial and Frankia nodule organogenesis. PMID:23741336

[Development and technological transfer of functional pastas extended with legumes].

PubMed

Granito, Marisela; Ascanio, Vanesa

2009-03-01

Development and technological transfer of functional pastas extended with legumes. Semolina pasta is a highly consumed foodstuff, the biological value of which is low because its protein is deficient in lysine. However, if the semolina is extended with legumes rich in this essential aminoacid, not only and aminoacid supplementation is produced, but also the dietary fibre and minerals are increased. In this work, pastas extended in 10% with a white variety of Phaseolus vulgaris and with Cajanus cajan were produced on a pilot plant scale, and this technology was transferred to a cooperative producing artisanal pastas. The cooking qualities and the physical, chemical, and nutritional characteristics of the pastas were evaluated, as well as the sensorial acceptability in institutionalized elderly people. The extension of the pastas with legume flours increased the optimum cooking time (15 to 20%), the weight (20% and 25%), and the loss of solids by cooking. Similarly, the functional value of the pastas increased by increasing the contents of minerals and dietary fibre. The protein content, as well as the protein digestibility in vitro also increased; however, the parameters of colour L, a and b, and the total starch content of the pastas decreased. At consumer level, the pastas extended with legumes had a good acceptability, for what it was concluded that the extension of the semolina with legume flours in the manufacture of pastas is technologically feasible.

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria.

PubMed Central

Martínez-Hidalgo, Pilar; Galindo-Villardón, Purificación; Igual, José M.; Martínez-Molina, Eustoquio

2014-01-01

Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed. PMID:25227415

Micromonospora from nitrogen fixing nodules of alfalfa (Medicago sativa L.). A new promising Plant Probiotic Bacteria.

PubMed

Martínez-Hidalgo, Pilar; Galindo-Villardón, Purificación; Trujillo, Martha E; Igual, José M; Martínez-Molina, Eustoquio

2014-09-17

Biotic interactions can improve agricultural productivity without costly and environmentally challenging inputs. Micromonospora strains have recently been reported as natural endophytes of legume nodules but their significance for plant development and productivity has not yet been established. The aim of this study was to determine the diversity and function of Micromonospora isolated from Medicago sativa root nodules. Micromonospora-like strains from field alfalfa nodules were characterized by BOX-PCR fingerprinting and 16S rRNA gene sequencing. The ecological role of the interaction of the 15 selected representative Micromonospora strains was tested in M. sativa. Nodulation, plant growth and nutrition parameters were analyzed. Alfalfa nodules naturally contain abundant and highly diverse populations of Micromonospora, both at the intra- and at interspecific level. Selected Micromonospora isolates significantly increase the nodulation of alfalfa by Ensifer meliloti 1021 and also the efficiency of the plant for nitrogen nutrition. Moreover, they promote aerial growth, the shoot-to-root ratio, and raise the level of essential nutrients. Our results indicate that Micromonospora acts as a Rhizobia Helper Bacteria (RHB) agent and has probiotic effects, promoting plant growth and increasing nutrition efficiency. Its ecological role, biotechnological potential and advantages as a plant probiotic bacterium (PPB) are also discussed.

Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis.

PubMed

Carro, Lorena; Spröer, Cathrin; Alonso, Pilar; Trujillo, Martha E

2012-03-01

It was recently reported that Micromonospora inhabits the intracellular tissues of nitrogen fixing nodules of the wild legume Lupinus angustifolius. To determine if Micromonospora populations are also present in nitrogen fixing nodules of cultivated legumes such as Pisum sativum, we carried out the isolation of this actinobacterium from P. sativum plants collected in two man-managed fields in the region of Castilla and León (Spain). In this work, we describe the isolation of 93 Micromonospora strains recovered from nitrogen fixing nodules and the rhizosphere of P. sativum. The genomic diversity of the strains was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). Forty-six isolates and 34 reference strains were further analyzed using a multilocus sequence analysis scheme developed to address the phylogeny of the genus Micromonospora and to evaluate the species distribution in the two studied habitats. The MLSA results were evaluated by DNA-DNA hybridization to determine their usefulness for the delineation of Micromonospora at the species level. In most cases, DDH values below 70% were obtained with strains that shared a sequence similarity of 98.5% or less. Thus, MLSA studies clearly supported the established taxonomy of the genus Micromonospora and indicated that genomic species could be delineated as groups of strains that share > 98.5% sequence similarity based on the 5 genes selected. The species diversity of the strains isolated from both the rhizosphere and nodules was very high and in many cases the new strains could not be related to any of the currently described species. Copyright © 2011 Elsevier GmbH. All rights reserved.

The importance of nodule CO2 fixation for the efficiency of symbiotic nitrogen fixation in pea at vegetative growth and during pod formation.

PubMed

Fischinger, Stephanie Anastasia; Schulze, Joachim

2010-05-01

Nodule CO2 fixation is of pivotal importance for N2 fixation. The process provides malate for bacteroids and oxaloacetate for nitrogen assimilation. The hypothesis of the present paper was that grain legume nodules would adapt to higher plant N demand and more restricted carbon availability at pod formation through increased nodule CO2 fixation and a more efficient N2 fixation. Growth, N2 fixation, and nodule composition during vegetative growth and at pod formation were studied in pea plants (Pisum sativum L.). In parallel experiments, 15N2 and 13CO2 uptake, as well as nodule hydrogen and CO2 release, was measured. Plants at pod formation showed higher growth rates and N2 fixation per plant when compared with vegetative growth. The specific activity of active nodules was about 25% higher at pod formation. The higher nodule activity was accompanied by higher amino acid concentration in nodules and xylem sap with a higher share of asparagine. Nodule 13CO2 fixation was increased at pod formation, both per plant and per 15N2 fixed unit. However, malate concentration in nodules was only 40% of that during vegetative growth and succinate was no longer detectable. The data indicate that increased N2 fixation at pod formation is connected with strongly increased nodule CO2 fixation. While the sugar concentration in nodules at pod formation was not altered, the concentration of organic acids, namely malate and succinate, was significantly lower. It is concluded that strategies to improve the capability of nodules to fix CO2 and form organic acids might prolong intensive N2 fixation into the later stages of pod formation and pod filling in grain legumes.

Molybdate in Rhizobial Seed-Coat Formulations Improves the Production and Nodulation of Alfalfa

PubMed Central

Zhou, Jiqiong; Deng, Bo; Zhang, Yingjun; Cobb, Adam B.; Zhang, Zhao

2017-01-01

Rhizobia-legume symbiosis is the most well researched biological nitrogen fixation system. Coating legume seeds with rhizobia is now a recognized practical measure for improving the production of legume corp. However, the efficacy of some commercial rhizobia inoculants cannot be guaranteed in China due to the low rate of live rhizobia in these products. A greenhouse experiment was conducted to assess the effects of different rhizobial inoculant formulations on alfalfa productivity and nitrogen fixation. Two rhizobia strains, (ACCC17631 and ACCC17676), that are effective partners with alfalfa variety Zhongmu No. 1 were assessed with different concentrations of ammonium molybdate in seed-coat formulations with two different coating adhesives. Our study showed that the growth, nodulation, and nitrogen fixation ability of the plants inoculated with the ACCC17631 rhizobial strain were greatest when the ammonium molybdate application was0.2% of the formulation. An ammonium molybdate concentration of 0.1% was most beneficial to the growth of the plants inoculated with the ACCC17676 rhizobial strain. The sodium carboxymethyl cellulose and sodium alginate, used as coating adhesives, did not have a significant effect on alfalfa biomass and nitrogen fixation. However, the addition of skimmed milk to the adhesive improved nitrogenase activity. These results demonstrate that a new rhizobial seed-coat formulation benefitted alfalfa nodulation and yield. PMID:28099471

Molybdate in Rhizobial Seed-Coat Formulations Improves the Production and Nodulation of Alfalfa.

PubMed

Zhou, Jiqiong; Deng, Bo; Zhang, Yingjun; Cobb, Adam B; Zhang, Zhao

2017-01-01

Rhizobia-legume symbiosis is the most well researched biological nitrogen fixation system. Coating legume seeds with rhizobia is now a recognized practical measure for improving the production of legume corp. However, the efficacy of some commercial rhizobia inoculants cannot be guaranteed in China due to the low rate of live rhizobia in these products. A greenhouse experiment was conducted to assess the effects of different rhizobial inoculant formulations on alfalfa productivity and nitrogen fixation. Two rhizobia strains, (ACCC17631 and ACCC17676), that are effective partners with alfalfa variety Zhongmu No. 1 were assessed with different concentrations of ammonium molybdate in seed-coat formulations with two different coating adhesives. Our study showed that the growth, nodulation, and nitrogen fixation ability of the plants inoculated with the ACCC17631 rhizobial strain were greatest when the ammonium molybdate application was0.2% of the formulation. An ammonium molybdate concentration of 0.1% was most beneficial to the growth of the plants inoculated with the ACCC17676 rhizobial strain. The sodium carboxymethyl cellulose and sodium alginate, used as coating adhesives, did not have a significant effect on alfalfa biomass and nitrogen fixation. However, the addition of skimmed milk to the adhesive improved nitrogenase activity. These results demonstrate that a new rhizobial seed-coat formulation benefitted alfalfa nodulation and yield.

Endophytic occupation of root nodules and roots of Melilotus dentatus by Agrobacterium tumefaciens.

PubMed

Wang, Ling Ling; Wang, En Tao; Liu, Jie; Li, Ying; Chen, Wen Xin

2006-10-01

Agrobacterium strains have been frequently isolated from the root nodules of different legumes. Various possible mechanisms have been proposed to explain the existence of these bacteria in nodules, but there is no sufficient experimental evidence to support the estimations. In this work, we proved that the Agrobacterium strain CCBAU 81181, which was originally isolated from the root nodules of Onobrychis viciaefolia, and a symbiotic strain of Sinorhizobium meliloti CCBAU 10062 could coinhabit the root nodules of Melilotus dentatus. Analyses were performed by using a fluorescence marker, reisolation of bacteria from nodules, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of whole cellular proteins, and polymerase chain reaction amplification of symbiotic genes. The inoculation of A. tumefaciens CCBAU 81181 did not affect the growth and nodulation of plants. CCBAU 81181 and 24 other Agrobacterium strains isolated from nodules were incapable of nodulating on their original or alternative host and 22 strains of these strains were endophytes in the roots and stems of their hosts. Also, the tumor-inducing A. tumefaciens strains IAM 13129(T) and C58 were found capable of entering the roots of Glycyrrhiza pallidiflora, but did not cause pathogenic symptoms. With these results, we conclude that A. tumefaciens strains could be endophytic bacteria in the roots, stems, and root nodules. This finding partially explains why Agrobacterium strains were frequently isolated from the surface-sterilized nodules.

The glutathione peroxidase gene family of Lotus japonicus: characterization of genomic clones, expression analyses and immunolocalization in legumes.

PubMed

Ramos, Javier; Matamoros, Manuel A; Naya, Loreto; James, Euan K; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

2009-01-01

Despite the multiple roles played by antioxidants in rhizobia-legume symbioses, little is known about glutathione peroxidases (GPXs) in legumes. Here the characterization of six GPX genes of Lotus japonicus is reported. Expression of GPX genes was analysed by quantitative reverse transcription-polymerase chain reaction in L. japonicus and Lotus corniculatus plants exposed to various treatments known to generate reactive oxygen and/or nitrogen species. LjGPX1 and LjGPX3 were the most abundantly expressed genes in leaves, roots and nodules. Compared with roots, LjGPX1 and LjGPX6 were highly expressed in leaves and LjGPX3 and LjGPX6 in nodules. In roots, salinity decreased GPX4 expression, aluminium decreased expression of the six genes, and cadmium caused up-regulation of GPX3, GPX4 and GPX5 after 1 h and down-regulation of GPX1, GPX2, GPX4 and GPX6 after 3-24 h. Exposure of roots to sodium nitroprusside (a nitric oxide donor) for 1 h increased the mRNA levels of GPX4 and GPX6 by 3.3- and 30-fold, respectively. Thereafter, the GPX6 mRNA level remained consistently higher than that of the control. Immunogold labelling revealed the presence of GPX proteins in root and nodule amyloplasts and in leaf chloroplasts of L. japonicus and other legumes. Labelling was associated with starch grains. These results underscore the differential regulation of GPX expression in response to cadmium, aluminium and nitric oxide, and strongly support a role for GPX6 and possibly other GPX genes in stress and/or metabolic signalling.

Legume-rhizobium symbiotic promiscuity and effectiveness do not affect plant invasiveness.

PubMed

Keet, Jan-Hendrik; Ellis, Allan G; Hui, Cang; Le Roux, Johannes J

2017-06-01

The ability to fix atmospheric nitrogen is thought to play an important role in the invasion success of legumes. Interactions between legumes and nitrogen-fixing bacteria (rhizobia) span a continuum of specialization, and promiscuous legumes are thought to have higher chances of forming effective symbioses in novel ranges. Using Australian Acacia species in South Africa, it was hypothesized that widespread and highly invasive species will be more generalist in their rhizobial symbiotic requirements and more effective in fixing atmospheric nitrogen compared with localized and less invasive species. To test these hypotheses, eight localized and 11 widespread acacias were examined using next-generation sequencing data for the nodulation gene, nodC , to compare the identity, species richness, diversity and compositional similarity of rhizobia associated with these acacias. Stable isotope analysis was also used to determine levels of nitrogen obtained from the atmosphere via symbiotic nitrogen fixation. No differences were found in richness, diversity and community composition between localized and widespread acacias. Similarly, widespread and localized acacias did not differ in their ability to fix atmospheric nitrogen. However, for some species by site comparisons, significant differences in δ15N isotopic signatures were found, indicating differential symbiotic effectiveness between these species at specific localities. Overall, the results support recent findings that root nodule rhizobial diversity and community composition do not differ between acacias that vary in their invasiveness. Differential invasiveness of acacias in South Africa is probably linked to attributes such as differences in propagule pressure, reasons for (e.g. forestry vs. ornamental) and extent of, plantings in the country. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement.

PubMed

Zhou, Chuanen; Han, Lu; Pislariu, Catalina; Nakashima, Jin; Fu, Chunxiang; Jiang, Qingzhen; Quan, Li; Blancaflor, Elison B; Tang, Yuhong; Bouton, Joseph H; Udvardi, Michael; Xia, Guangmin; Wang, Zeng-Yu

2011-11-01

Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop.

Nodulation and nitrogen fixation by Mimosa spp. in the Cerrado and Caatinga biomes of Brazil.

PubMed

dos Reis, Fábio Bueno; Simon, Marcelo F; Gross, Eduardo; Boddey, Robert M; Elliott, Geoffrey N; Neto, Nicolau E; Loureiro, M de Fatima; de Queiroz, Luciano P; Scotti, Maria Rita; Chen, Wen-Ming; Norén, Agneta; Rubio, Maria C; de Faria, Sergio M; Bontemps, Cyril; Goi, Silvia R; Young, J Peter W; Sprent, Janet I; James, Euan K

2010-06-01

*An extensive survey of nodulation in the legume genus Mimosa was undertaken in two major biomes in Brazil, the Cerrado and the Caatinga, in both of which there are high degrees of endemicity of the genus. *Nodules were collected from 67 of the 70 Mimosa spp. found. Thirteen of the species were newly reported as nodulating. Nodules were examined by light and electron microscopy, and all except for M. gatesiae had a structure typical of effective Mimosa nodules. The endosymbiotic bacteria in nodules from all of the Mimosa spp. were identified as Burkholderia via immunolabelling with an antibody against Burkholderia phymatum STM815. *Twenty of the 23 Mimosa nodules tested were shown to contain nitrogenase by immunolabelling with an antibody to the nitrogenase Fe- (nifH) protein, and using the delta(15)N ((15)N natural abundance) technique, contributions by biological N(2) fixation of up to 60% of total plant N were calculated for Caatinga Mimosa spp. *It is concluded that nodulation in Mimosa is a generic character, and that the preferred symbionts of Brazilian species are Burkholderia. This is the first study to demonstrate N(2) fixation by beta-rhizobial symbioses in the field.

Nodule-enhanced expression of a sucrose phosphate synthase gene member (MsSPSA) has a role in carbon and nitrogen metabolism in the nodules of alfalfa (Medicago sativa L.)

PubMed Central

Aleman, Lorenzo; Ortega, Jose Luis; Martinez-Grimes, Martha; Seger, Mark; Holguin, Francisco Omar; Uribe, Diana J.; Garcia-Ibilcieta, David

2013-01-01

Sucrose phosphate synthase (SPS) catalyzes the first step in the synthesis of sucrose in photosynthetic tissues. We characterized the expression of three different isoforms of SPS belonging to two different SPS gene families in alfalfa (Medicago sativa L.), a previously identified SPS (MsSPSA) and two novel isoforms belonging to class B (MsSPSB and MsSPSB3). While MsSPSA showed nodule-enhanced expression, both MsSPSB genes exhibited leaf-enhanced expression. Alfalfa leaf and nodule SPS enzymes showed differences in chromatographic and electrophoretic migration and differences in Vmax and allosteric regulation. The root nodules in legume plants are a strong sink for photosynthates with its need for ATP, reducing power and carbon skeletons for dinitrogen fixation and ammonia assimilation. The expression of genes encoding SPS and other key enzymes in sucrose metabolism, sucrose phosphate phosphatase and sucrose synthase, was analyzed in the leaves and nodules of plants inoculated with Sinorhizobium meliloti. Based on the expression pattern of these genes, the properties of the SPS isoforms and the concentration of starch and soluble sugars in nodules induced by a wild type and a nitrogen fixation deficient strain, we propose that SPS has an important role in the control of carbon flux into different metabolic pathways in the symbiotic nodules. PMID:19898977

Diverse bacteria isolated from root nodules of Trifolium, Crotalaria and Mimosa grown in the subtropical regions of China.

PubMed

Liu, Xiao Yun; Wang, En Tao; Li, Ying; Chen, Wen Xin

2007-07-01

To analyze the diversity and relationships of rhizobia in the subtropical and tropical zones of China, we characterized 67 bacterial strains isolated from root nodules of five legume species in the genera Trifolium, Crotalaria and Mimosa . PCR-amplified 16S rDNA RFLP, numerical taxonomy, SDS-PAGE of whole cell proteins, sequencing of 16S rDNA and DNA-DNA hybridization grouped the isolates into 17 lineages belonging to Bradyrhizobium, Mesorhizobium, Rhizobium, Sinorhizobium and Burkholderia, as well as a non-symbiotic group of Agrobacterium. The Rhizobium group contained twenty strains isolated from Mimosa pudica, Crotalaria pallida and two species of Trifolium. Fifteen of them were R. leguminosarum. Twenty-one strains isolated from four species of Trifolium, Crotalaria and Mimosa were classified into five groups of Bradyrhizobium, including B. japonicum. Agrobacterium group composed of 20 isolates from Mimosa pudica, C. pallida and Trifolium fragiferum. In addition, several strains of Sinorhizobium and Mesorhizobium associated with Trifolium and Burkholderia associated with Mimosa pudica were also identified. The predominance of Bradyrhizobium in the nodules of Trifolium was a novel finding and it demonstrated that the nodule microsymbionts might be selected by both the geographic factors and the legume hosts.

The nodulation factor hydrolase of Medicago truncatula: characterization of an enzyme specifically cleaving rhizobial nodulation signals.

PubMed

Tian, Ye; Liu, Wei; Cai, Jie; Zhang, Lan-Yue; Wong, Kam-Bo; Feddermann, Nadja; Boller, Thomas; Xie, Zhi-Ping; Staehelin, Christian

2013-11-01

Nodule formation induced by nitrogen-fixing rhizobia depends on bacterial nodulation factors (NFs), modified chitin oligosaccharides with a fatty acid moiety. Certain NFs can be cleaved and inactivated by plant chitinases. However, the most abundant NF of Sinorhizobium meliloti, an O-acetylated and sulfated tetramer, is resistant to hydrolysis by all plant chitinases tested so far. Nevertheless, this NF is rapidly degraded in the host rhizosphere. Here, we identify and characterize MtNFH1 (for Medicago truncatula Nod factor hydrolase 1), a legume enzyme structurally related to defense-related class V chitinases (glycoside hydrolase family 18). MtNFH1 lacks chitinase activity but efficiently hydrolyzes all tested NFs of S. meliloti. The enzyme shows a high cleavage preference, releasing exclusively lipodisaccharides from NFs. Substrate specificity and kinetic properties of MtNFH1 were compared with those of class V chitinases from Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum), which cannot hydrolyze tetrameric NFs of S. meliloti. The Michaelis-Menten constants of MtNFH1 for NFs are in the micromolar concentration range, whereas nonmodified chitin oligosaccharides represent neither substrates nor inhibitors for MtNFH1. The three-dimensional structure of MtNFH1 was modeled on the basis of the known structure of class V chitinases. Docking simulation of NFs to MtNFH1 predicted a distinct binding cleft for the fatty acid moiety, which is absent in the class V chitinases. Point mutation analysis confirmed the modeled NF-MtNFH1 interaction. Silencing of MtNFH1 by RNA interference resulted in reduced NF degradation in the rhizosphere of M. truncatula. In conclusion, we have found a novel legume hydrolase that specifically inactivates NFs.

Rheumatoid Nodules.

PubMed

Tilstra, Jeremy S; Lienesch, Douglas W

2015-07-01

Rheumatoid nodules are a common manifestation of rheumatoid arthritis. These lesions are often easily identified based on typical diagnostic features and characteristic locations. When biopsied, nodules have a characteristic histologic appearance. Uncommonly, rheumatoid nodules can occur in systemic locations. There is no evidence that systemic therapy treats underlying rheumatoid nodules. Paradoxically, methotrexate and possibly tumor necrosis factor inhibitors can increase nodule development. Treatment of rheumatoid nodules is often not necessary, unless patients are experiencing pain or there is interference of mechanical function. This review outlines the available data on and associations of rheumatoid nodules. Copyright © 2015 Elsevier Inc. All rights reserved.

Functional analysis of duplicated Symbiosis Receptor Kinase (SymRK) genes during nodulation and mycorrhizal infection in soybean (Glycine max).

PubMed

Indrasumunar, Arief; Wilde, Julia; Hayashi, Satomi; Li, Dongxue; Gresshoff, Peter M

2015-03-15

Association between legumes and rhizobia results in the formation of root nodules, where symbiotic nitrogen fixation occurs. The early stages of this association involve a complex of signalling events between the host and microsymbiont. Several genes dealing with early signal transduction have been cloned, and one of them encodes the leucine-rich repeat (LRR) receptor kinase (SymRK; also termed NORK). The Symbiosis Receptor Kinase gene is required by legumes to establish a root endosymbiosis with Rhizobium bacteria as well as mycorrhizal fungi. Using degenerate primer and BAC sequencing, we cloned duplicated SymRK homeologues in soybean called GmSymRKα and GmSymRKβ. These duplicated genes have high similarity of nucleotide (96%) and amino acid sequence (95%). Sequence analysis predicted a malectin-like domain within the extracellular domain of both genes. Several putative cis-acting elements were found in promoter regions of GmSymRKα and GmSymRKβ, suggesting a participation in lateral root development, cell division and peribacteroid membrane formation. The mutant of SymRK genes is not available in soybean; therefore, to know the functions of these genes, RNA interference (RNAi) of these duplicated genes was performed. For this purpose, RNAi construct of each gene was generated and introduced into the soybean genome by Agrobacterium rhizogenes-mediated hairy root transformation. RNAi of GmSymRKβ gene resulted in an increased reduction of nodulation and mycorrhizal infection than RNAi of GmSymRKα, suggesting it has the major activity of the duplicated gene pair. The results from the important crop legume soybean confirm the joint phenotypic action of GmSymRK genes in both mycorrhizal and rhizobial infection seen in model legumes. Copyright © 2015 Elsevier GmbH. All rights reserved.

Rhizobia from Lanzarote, the Canary Islands, that nodulate Phaseolus vulgaris have characteristics in common with LMW RNA group II Sinorhizobium meliloti of Medicago, Melilotus and Trigonella from soils of mainland Spain

USDA-ARS?s Scientific Manuscript database

Several isolates from nodules of Phaseolus vulgaris grown in soil of Lanzarote, an island of the Canaries, had electrophoretic LMW RNA patterns identical with a less common pattern within S. meliloti (assigned as group II) obtained from nodules of alfalfa and alfalfa-related legumes grown in northe...

Construction of a Lotus japonicus late nodulin expressed sequence tag library and identification of novel nodule-specific genes.

PubMed Central

Szczyglowski, K; Hamburger, D; Kapranov, P; de Bruijn, F J

1997-01-01

A range of novel expressed sequence tags (ESTs) associated with late developmental events during nodule organogenesis in the legume Lotus japonicus were identified using mRNA differential display; 110 differentially displayed polymerase chain reaction products were cloned and analyzed. Of 88 unique cDNAs obtained, 22 shared significant homology to DNA/protein sequences in the respective databases. This group comprises, among others, a nodule-specific homolog of protein phosphatase 2C, a peptide transporter protein, and a nodule-specific form of cytochrome P450. RNA gel-blot analysis of 16 differentially displayed ESTs confirmed their nodule-specific expression pattern. The kinetics of mRNA accumulation of the majority of the ESTs analyzed were found to resemble the expression pattern observed for the L. japonicus leghemoglobin gene. These results indicate that the newly isolated molecular markers correspond to genes induced during late developmental stages of L. japonicus nodule organogenesis and provide important, novel tools for the study of nodulation. PMID:9276951

Legume Shrubs Are More Nitrogen-Homeostatic than Non-legume Shrubs

PubMed Central

Guo, Yanpei; Yang, Xian; Schöb, Christian; Jiang, Youxu; Tang, Zhiyao

2017-01-01

Legumes are characterized as keeping stable nutrient supply under nutrient-limited conditions. However, few studies examined the legumes' stoichiometric advantages over other plants across various taxa in natural ecosystems. We explored differences in nitrogen (N) and phosphorus (P) stoichiometry of different tissue types (leaf, stem, and root) between N2-fixing legume shrubs and non-N2-fixing shrubs from 299 broadleaved deciduous shrubland sites in northern China. After excluding effects of taxonomy and environmental variables, these two functional groups differed considerably in nutrient regulation. N concentrations and N:P ratios were higher in legume shrubs than in non-N2-fixing shrubs. N concentrations were positively correlated between the plants and soil for non-N2-fixing shrubs, but not for legume shrubs, indicating a stronger stoichiometric homeostasis in legume shrubs than in non-N2-fixing shrubs. N concentrations were positively correlated among three tissue types for non-N2-fixing shrubs, but not between leaves and non-leaf tissues for legume shrubs, demonstrating that N concentrations were more dependent among tissues for non-N2-fixing shrubs than for legume shrubs. N and P concentrations were correlated within all tissues for both functional groups, but the regression slopes were flatter for legume shrubs than non-N2-fixing shrubs, implying that legume shrubs were more P limited than non-N2-fixing shrubs. These results address significant differences in stoichiometry between legume shrubs and non-N2-fixing shrubs, and indicate the influence of symbiotic nitrogen fixation (SNF) on plant stoichiometry. Overall, N2-fixing legume shrubs are higher and more stoichiometrically homeostatic in N concentrations. However, due to excess uptake of N, legumes may suffer from potential P limitation. With their N advantage, legume shrubs could be good nurse plants in restoration sites with degraded soil, but their P supply should be taken care of during management

Legume Shrubs Are More Nitrogen-Homeostatic than Non-legume Shrubs.

PubMed

Guo, Yanpei; Yang, Xian; Schöb, Christian; Jiang, Youxu; Tang, Zhiyao

2017-01-01

Legumes are characterized as keeping stable nutrient supply under nutrient-limited conditions. However, few studies examined the legumes' stoichiometric advantages over other plants across various taxa in natural ecosystems. We explored differences in nitrogen (N) and phosphorus (P) stoichiometry of different tissue types (leaf, stem, and root) between N 2 -fixing legume shrubs and non-N 2 -fixing shrubs from 299 broadleaved deciduous shrubland sites in northern China. After excluding effects of taxonomy and environmental variables, these two functional groups differed considerably in nutrient regulation. N concentrations and N:P ratios were higher in legume shrubs than in non-N 2 -fixing shrubs. N concentrations were positively correlated between the plants and soil for non-N 2 -fixing shrubs, but not for legume shrubs, indicating a stronger stoichiometric homeostasis in legume shrubs than in non-N 2 -fixing shrubs. N concentrations were positively correlated among three tissue types for non-N 2 -fixing shrubs, but not between leaves and non-leaf tissues for legume shrubs, demonstrating that N concentrations were more dependent among tissues for non-N 2 -fixing shrubs than for legume shrubs. N and P concentrations were correlated within all tissues for both functional groups, but the regression slopes were flatter for legume shrubs than non-N 2 -fixing shrubs, implying that legume shrubs were more P limited than non-N 2 -fixing shrubs. These results address significant differences in stoichiometry between legume shrubs and non-N 2 -fixing shrubs, and indicate the influence of symbiotic nitrogen fixation (SNF) on plant stoichiometry. Overall, N 2 -fixing legume shrubs are higher and more stoichiometrically homeostatic in N concentrations. However, due to excess uptake of N, legumes may suffer from potential P limitation. With their N advantage, legume shrubs could be good nurse plants in restoration sites with degraded soil, but their P supply should be taken care

MtSWEET11, a Nodule-Specific Sucrose Transporter of Medicago truncatula

DOE PAGES

Kryvoruchko, Igor S.; Sinharoy, Senjuti; Torres-Jerez, Ivone; ...

2016-03-28

Optimization of nitrogen fixation by rhizobia in legumes is a key area of research for sustainable agriculture. Symbiotic nitrogen fixation (SNF) occurs in specialized organs called nodules and depends on a steady supply of carbon to both plant and bacterial cells. Here we report the functional characterization of a nodule-specific Suc transporter, MtSWEET11 from Medicago truncatula. MtSWEET11 belongs to a clade of plant SWEET proteins that are capable of transporting Suc and play critical roles in pathogen susceptibility. When expressed in mammalian cells, MtSWEET11 transported sucrose (Suc) but not glucose (Glc). The MtSWEET11 gene was found to be expressed inmore » infected root hair cells, and in the meristem, invasion zone, and vasculature of nodules. Expression of an MtSWEET11-GFP fusion protein in nodules resulted in green fluorescence associated with the plasma membrane of uninfected cells and infection thread and symbiosome membranes of infected cells. Two independent Tnt1-insertion sweet11 mutants were uncompromised in SNF. Furthermore, although MtSWEET11 appears to be involved in Suc distribution within nodules, it is not crucial for SNF, probably because other Suc transporters can fulfill its role(s).« less

From Model to Crop: Functional Analysis of a STAY-GREEN Gene in the Model Legume Medicago truncatula and Effective Use of the Gene for Alfalfa Improvement1[W][OA

PubMed Central

Zhou, Chuanen; Han, Lu; Pislariu, Catalina; Nakashima, Jin; Fu, Chunxiang; Jiang, Qingzhen; Quan, Li; Blancaflor, Elison B.; Tang, Yuhong; Bouton, Joseph H.; Udvardi, Michael; Xia, Guangmin; Wang, Zeng-Yu

2011-01-01

Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop. PMID:21957014

Split-root systems applied to the study of the legume-rhizobial symbiosis: what have we learned?

PubMed

Larrainzar, Estíbaliz; Gil-Quintana, Erena; Arrese-Igor, Cesar; González, Esther M; Marino, Daniel

2014-12-01

Split-root system (SRS) approaches allow the differential treatment of separate and independent root systems, while sharing a common aerial part. As such, SRS is a useful tool for the discrimination of systemic (shoot origin) versus local (root/nodule origin) regulation mechanisms. This type of approach is particularly useful when studying the complex regulatory mechanisms governing the symbiosis established between legumes and Rhizobium bacteria. The current work provides an overview of the main insights gained from the application of SRS approaches to understand how nodule number (nodulation autoregulation) and nitrogen fixation are controlled both under non-stressful conditions and in response to a variety of stresses. Nodule number appears to be mainly controlled at the systemic level through a signal which is produced by nodule/root tissue, translocated to the shoot, and transmitted back to the root system, involving shoot Leu-rich repeat receptor-like kinases. In contrast, both local and systemic mechanisms have been shown to operate for the regulation of nitrogenase activity in nodules. Under drought and heavy metal stress, the regulation is mostly local, whereas the application of exogenous nitrogen seems to exert a regulation of nitrogen fixation both at the local and systemic levels. © 2014 Institute of Botany, Chinese Academy of Sciences.

Transcription factors network in root endosymbiosis establishment and development.

PubMed

Diédhiou, Issa; Diouf, Diaga

2018-02-15

Root endosymbioses are mutualistic interactions between plants and the soil microorganisms (Fungus, Frankia or Rhizobium) that lead to the formation of nitrogen-fixing root nodules and/or arbuscular mycorrhiza. These interactions enable many species to survive in different marginal lands to overcome the nitrogen-and/or phosphorus deficient environment and can potentially reduce the chemical fertilizers used in agriculture which gives them an economic, social and environmental importance. The formation and the development of these structures require the mediation of specific gene products among which the transcription factors play a key role. Three of these transcription factors, viz., CYCLOPS, NSP1 and NSP2 are well conserved between actinorhizal, legume, non-legume and mycorrhizal symbioses. They interact with DELLA proteins to induce the expression of NIN in nitrogen fixing symbiosis or RAM1 in mycorrhizal symbiosis. Recently, the small non coding RNA including micro RNAs (miRNAs) have emerged as major regulators of root endosymbioses. Among them, miRNA171 targets NSP2, a TF conserved in actinorhizal, legume, non-legume and mycorrhizal symbioses. This review will also focus on the recent advances carried out on the biological function of others transcription factors during the root pre-infection/pre-contact, infection or colonization. Their role in nodule formation and AM development will also be described.

NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner

PubMed Central

Domonkos, Ágota; Kovács, Szilárd; Gombár, Anikó; Kiss, Ernő; Horváth, Beatrix; Kováts, Gyöngyi Z.; Farkas, Attila; Tóth, Mónika T.; Ayaydin, Ferhan; Bóka, Károly; Fodor, Lili; Endre, Gabriella; Kaló, Péter

2017-01-01

Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatula DNF2 (defective in nitrogen fixation 2) and NAD1 (nodules with activated defense 1) genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence. The previously identified nodule-specific NAD1 gene encodes a protein of unknown function. Herein, we present the analysis of novel NAD1 mutant alleles to better understand the function of NAD1 in the repression of immune responses in symbiotic nodules. By exploiting the advantage of plant double and rhizobial mutants defective in establishing nitrogen-fixing symbiotic interaction, we show that NAD1 functions following the release of rhizobia from the infection threads and colonization of nodule cells. The suppression of plant defense is self-dependent of the differentiation status of the rhizobia. The corresponding phenotype of nad1 and dnf2 mutants and the similarity in the induction of defense-associated genes in both mutants suggest that NAD1 and DNF2 operate close together in the same pathway controlling defense responses in symbiotic nodules. PMID:29240711

NAD1 Controls Defense-Like Responses in Medicago truncatula Symbiotic Nitrogen Fixing Nodules Following Rhizobial Colonization in a BacA-Independent Manner.

PubMed

Domonkos, Ágota; Kovács, Szilárd; Gombár, Anikó; Kiss, Ernő; Horváth, Beatrix; Kováts, Gyöngyi Z; Farkas, Attila; Tóth, Mónika T; Ayaydin, Ferhan; Bóka, Károly; Fodor, Lili; Ratet, Pascal; Kereszt, Attila; Endre, Gabriella; Kaló, Péter

2017-12-14

Legumes form endosymbiotic interaction with host compatible rhizobia, resulting in the development of nitrogen-fixing root nodules. Within symbiotic nodules, rhizobia are intracellularly accommodated in plant-derived membrane compartments, termed symbiosomes. In mature nodule, the massively colonized cells tolerate the existence of rhizobia without manifestation of visible defense responses, indicating the suppression of plant immunity in the nodule in the favur of the symbiotic partner. Medicago truncatula DNF2 (defective in nitrogen fixation 2) and NAD1 (nodules with activated defense 1) genes are essential for the control of plant defense during the colonization of the nitrogen-fixing nodule and are required for bacteroid persistence. The previously identified nodule-specific NAD1 gene encodes a protein of unknown function. Herein, we present the analysis of novel NAD1 mutant alleles to better understand the function of NAD1 in the repression of immune responses in symbiotic nodules. By exploiting the advantage of plant double and rhizobial mutants defective in establishing nitrogen-fixing symbiotic interaction, we show that NAD1 functions following the release of rhizobia from the infection threads and colonization of nodule cells. The suppression of plant defense is self-dependent of the differentiation status of the rhizobia. The corresponding phenotype of nad1 and dnf2 mutants and the similarity in the induction of defense-associated genes in both mutants suggest that NAD1 and DNF2 operate close together in the same pathway controlling defense responses in symbiotic nodules.

Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family.

PubMed

Dash, Sudhansu; Campbell, Jacqueline D; Cannon, Ethalinda K S; Cleary, Alan M; Huang, Wei; Kalberer, Scott R; Karingula, Vijay; Rice, Alex G; Singh, Jugpreet; Umale, Pooja E; Weeks, Nathan T; Wilkey, Andrew P; Farmer, Andrew D; Cannon, Steven B

2016-01-04

Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working on particular species, and also numerous GDPs for these species. LIS has been redesigned in the last three years both to better integrate data sets across the crop and model legumes, and to better accommodate specialized GDPs that serve particular legume species. To integrate data sets, LIS provides genome and map viewers, holds synteny mappings among all sequenced legume species and provides a set of gene families to allow traversal among orthologous and paralogous sequences across the legumes. To better accommodate other specialized GDPs, LIS uses open-source GMOD components where possible, and advocates use of common data templates, formats, schemas and interfaces so that data collected by one legume research community are accessible across all legume GDPs, through similar interfaces and using common APIs. This federated model for the legumes is managed as part of the 'Legume Federation' project (accessible via http://legumefederation.org), which can be thought of as an umbrella project encompassing LIS and other legume GDPs. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Molecular Signals Controlling the Inhibition of Nodulation by Nitrate in Medicago truncatula

PubMed Central

van Noorden, Giel E.; Verbeek, Rob; Dinh, Quy Dung; Jin, Jian; Green, Alexandra; Ng, Jason Liang Pin; Mathesius, Ulrike

2016-01-01

The presence of nitrogen inhibits legume nodule formation, but the mechanism of this inhibition is poorly understood. We found that 2.5 mM nitrate and above significantly inhibited nodule initiation but not root hair curling in Medicago trunatula. We analyzed protein abundance in M. truncatula roots after treatment with either 0 or 2.5 mM nitrate in the presence or absence of its symbiont Sinorhizobium meliloti after 1, 2 and 5 days following inoculation. Two-dimensional gel electrophoresis combined with mass spectrometry was used to identify 106 differentially accumulated proteins responding to nitrate addition, inoculation or time point. While flavonoid-related proteins were less abundant in the presence of nitrate, addition of Nod gene-inducing flavonoids to the Sinorhizobium culture did not rescue nodulation. Accumulation of auxin in response to rhizobia, which is also controlled by flavonoids, still occurred in the presence of nitrate, but did not localize to a nodule initiation site. Several of the changes included defense- and redox-related proteins, and visualization of reactive oxygen species indicated that their induction in root hairs following Sinorhizobium inoculation was inhibited by nitrate. In summary, the presence of nitrate appears to inhibit nodulation via multiple pathways, including changes to flavonoid metabolism, defense responses and redox changes. PMID:27384556

Rhizobia from Lanzarote, the Canary Islands, That Nodulate Phaseolus vulgaris Have Characteristics in Common with Sinorhizobium meliloti Isolates from Mainland Spain▿

PubMed Central

Zurdo-Piñeiro, José Luis; García-Fraile, Paula; Rivas, Raúl; Peix, Alvaro; León-Barrios, Milagros; Willems, Anne; Mateos, Pedro Francisco; Martínez-Molina, Eustoquio; Velázquez, Encarna; van Berkum, Peter

2009-01-01

The stable, low-molecular-weight (LMW) RNA fractions of several rhizobial isolates of Phaseolus vulgaris grown in the soil of Lanzarote, an island of the Canary Islands, were identical to a less-common pattern found within Sinorhizobium meliloti (assigned to group II) obtained from nodules of alfalfa and alfalfa-related legumes grown in northern Spain. The P. vulgaris isolates and the group II LMW RNA S. meliloti isolates also were distinguishable in that both had two conserved inserts of 20 and 46 bp in the 16S-23S internal transcribed spacer region that were not present in other strains of S. meliloti. The isolates from P. vulgaris nodulated bean but not Medicago sativa, while those recovered from Medicago, Melilotus, and Trigonella spp. nodulated both host legumes. The bean isolates also were distinguished from those of Medicago, Melilotus, and Trigonella spp. by nodC sequence analysis. The nodC sequences of the bean isolates were most similar to those reported for S. meliloti bv. mediterranense and Sinorhizobium fredii bv. mediterranense (GenBank accession numbers DQ333891 and AF217267, respectively). None of the evidence placed the bean isolates from Lanzarote in the genus Rhizobium, which perhaps is inconsistent with seed-borne transmission of Rhizobium etli from the Americas to the Canaries as an explanation for the presence of bean-nodulating rhizobia in soils of Lanzarote. PMID:19218416

Rhizobia from Lanzarote, the Canary Islands, that nodulate Phaseolus vulgaris have characteristics in common with Sinorhizobium meliloti isolates from mainland Spain.

PubMed

Zurdo-Piñeiro, José Luis; García-Fraile, Paula; Rivas, Raúl; Peix, Alvaro; León-Barrios, Milagros; Willems, Anne; Mateos, Pedro Francisco; Martínez-Molina, Eustoquio; Velázquez, Encarna; van Berkum, Peter

2009-04-01

The stable, low-molecular-weight (LMW) RNA fractions of several rhizobial isolates of Phaseolus vulgaris grown in the soil of Lanzarote, an island of the Canary Islands, were identical to a less-common pattern found within Sinorhizobium meliloti (assigned to group II) obtained from nodules of alfalfa and alfalfa-related legumes grown in northern Spain. The P. vulgaris isolates and the group II LMW RNA S. meliloti isolates also were distinguishable in that both had two conserved inserts of 20 and 46 bp in the 16S-23S internal transcribed spacer region that were not present in other strains of S. meliloti. The isolates from P. vulgaris nodulated bean but not Medicago sativa, while those recovered from Medicago, Melilotus, and Trigonella spp. nodulated both host legumes. The bean isolates also were distinguished from those of Medicago, Melilotus, and Trigonella spp. by nodC sequence analysis. The nodC sequences of the bean isolates were most similar to those reported for S. meliloti bv. mediterranense and Sinorhizobium fredii bv. mediterranense (GenBank accession numbers DQ333891 and AF217267, respectively). None of the evidence placed the bean isolates from Lanzarote in the genus Rhizobium, which perhaps is inconsistent with seed-borne transmission of Rhizobium etli from the Americas to the Canaries as an explanation for the presence of bean-nodulating rhizobia in soils of Lanzarote.

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia

PubMed Central

Msaddak, Abdelhakim; Durán, David; Rejili, Mokhtar; Mars, Mohamed; Ruiz-Argüeso, Tomás; Imperial, Juan; Palacios, José

2017-01-01

ABSTRACT The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, and the other five clusters were close to different recently defined Bradyrhizobium species. Isolates close to Microvirga were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes (rrs, recA, glnII, gyrB, and dnaK) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene nodC identified four groups, three formed by Bradyrhizobium isolates and one by the Microvirga and Phyllobacterium isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of L. micranthus root nodule symbionts in northern Tunisia, including strains from the Bradyrhizobiaceae, Methylobacteriaceae, and Phyllobacteriaceae families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including L. micranthus from other Mediterranean areas, which are nodulated mostly by Bradyrhizobium strains. IMPORTANCE Lupinus micranthus is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia

Diverse Bacteria Affiliated with the Genera Microvirga, Phyllobacterium, and Bradyrhizobium Nodulate Lupinus micranthus Growing in Soils of Northern Tunisia.

PubMed

Msaddak, Abdelhakim; Durán, David; Rejili, Mokhtar; Mars, Mohamed; Ruiz-Argüeso, Tomás; Imperial, Juan; Palacios, José; Rey, Luis

2017-03-15

The genetic diversity of bacterial populations nodulating Lupinus micranthus in five geographical sites from northern Tunisia was examined. Phylogenetic analyses of 50 isolates based on partial sequences of recA and gyrB grouped strains into seven clusters, five of which belong to the genus Bradyrhizobium (28 isolates), one to Phyllobacterium (2 isolates), and one, remarkably, to Microvirga (20 isolates). The largest Bradyrhizobium cluster (17 isolates) grouped with the B. lupini species, and the other five clusters were close to different recently defined Bradyrhizobium species. Isolates close to Microvirga were obtained from nodules of plants from four of the five sites sampled. We carried out an in-depth phylogenetic study with representatives of the seven clusters using sequences from housekeeping genes ( rrs , recA , glnII , gyrB , and dnaK ) and obtained consistent results. A phylogeny based on the sequence of the symbiotic gene nodC identified four groups, three formed by Bradyrhizobium isolates and one by the Microvirga and Phyllobacterium isolates. Symbiotic behaviors of the representative strains were tested, and some congruence between symbiovars and symbiotic performance was observed. These data indicate a remarkable diversity of L. micranthus root nodule symbionts in northern Tunisia, including strains from the Bradyrhizobiaceae , Methylobacteriaceae , and Phyllobacteriaceae families, in contrast with those of the rhizobial populations nodulating lupines in the Old World, including L. micranthus from other Mediterranean areas, which are nodulated mostly by Bradyrhizobium strains. IMPORTANCE Lupinus micranthus is a legume broadly distributed in the Mediterranean region and plays an important role in soil fertility and vegetation coverage by fixing nitrogen and solubilizing phosphate in semiarid areas. Direct sowing to extend the distribution of this indigenous legume can contribute to the prevention of soil erosion in pre-Saharan lands of Tunisia

Cereal grains, legumes and diabetes.

PubMed

Venn, B J; Mann, J I

2004-11-01

This review examines the evidence for the role of whole grain foods and legumes in the aetiology and management of diabetes. MedLine and SilverPlatter ('Nutrition' and 'Food Science FSTA') databases were searched to identify epidemiological and experimental studies relating to the effects of whole grain foods and legumes on indicators of carbohydrate metabolism. Epidemiological studies strongly support the suggestion that high intakes of whole grain foods protect against the development of type II diabetes mellitus (T2DM). People who consume approximately 3 servings per day of whole grain foods are less likely to develop T2DM than low consumers (<3 servings per week) with a risk reduction in the order of 20-30%. The role of legumes in the prevention of diabetes is less clear, possibly because of the relatively low intake of leguminous foods in the populations studied. However, legumes share several qualities with whole grains of potential benefit to glycaemic control including slow release carbohydrate and a high fibre content. A substantial increase in dietary intake of legumes as replacement food for more rapidly digested carbohydrate might therefore be expected to improve glycaemic control and thus reduce incident diabetes. This is consistent with the results of dietary intervention studies that have found improvements in glycaemic control after increasing the dietary intake of whole grain foods, legumes, vegetables and fruit. The benefit has been attributed to an increase in soluble fibre intake. However, prospective studies have found that soluble fibre intake is not associated with a lower incidence of T2DM. On the contrary, it is cereal fibre that is largely insoluble that is associated with a reduced risk of developing T2DM. Despite this, the addition of wheat bran to the diets of diabetic people has not improved indicators of glycaemic control. These apparently contradictory findings might be explained by metabolic studies that have indicated improvement

The Nodulation Factor Hydrolase of Medicago truncatula: Characterization of an Enzyme Specifically Cleaving Rhizobial Nodulation Signals1[W][OPEN

PubMed Central

Tian, Ye; Liu, Wei; Cai, Jie; Zhang, Lan-Yue; Wong, Kam-Bo; Feddermann, Nadja; Boller, Thomas; Xie, Zhi-Ping; Staehelin, Christian

2013-01-01

Nodule formation induced by nitrogen-fixing rhizobia depends on bacterial nodulation factors (NFs), modified chitin oligosaccharides with a fatty acid moiety. Certain NFs can be cleaved and inactivated by plant chitinases. However, the most abundant NF of Sinorhizobium meliloti, an O-acetylated and sulfated tetramer, is resistant to hydrolysis by all plant chitinases tested so far. Nevertheless, this NF is rapidly degraded in the host rhizosphere. Here, we identify and characterize MtNFH1 (for Medicago truncatula Nod factor hydrolase 1), a legume enzyme structurally related to defense-related class V chitinases (glycoside hydrolase family 18). MtNFH1 lacks chitinase activity but efficiently hydrolyzes all tested NFs of S. meliloti. The enzyme shows a high cleavage preference, releasing exclusively lipodisaccharides from NFs. Substrate specificity and kinetic properties of MtNFH1 were compared with those of class V chitinases from Arabidopsis (Arabidopsis thaliana) and tobacco (Nicotiana tabacum), which cannot hydrolyze tetrameric NFs of S. meliloti. The Michaelis-Menten constants of MtNFH1 for NFs are in the micromolar concentration range, whereas nonmodified chitin oligosaccharides represent neither substrates nor inhibitors for MtNFH1. The three-dimensional structure of MtNFH1 was modeled on the basis of the known structure of class V chitinases. Docking simulation of NFs to MtNFH1 predicted a distinct binding cleft for the fatty acid moiety, which is absent in the class V chitinases. Point mutation analysis confirmed the modeled NF-MtNFH1 interaction. Silencing of MtNFH1 by RNA interference resulted in reduced NF degradation in the rhizosphere of M. truncatula. In conclusion, we have found a novel legume hydrolase that specifically inactivates NFs. PMID:24082029

Influence of cadmium stress and arbuscular mycorrhizal fungi on nodule senescence in Cajanus cajan (L.) Millsp.

PubMed

Garg, Neera; Bhandari, Purnima

2012-01-01

Cadmium (Cd) causes oxidative damage and affects nodulation and nitrogen fixation process of legumes. Arbuscular mycorrhizal (AM) fungi have been demonstrated to alleviate heavy metal stress of plants. The present study was conducted to assess role of AM in alleviating negative effects of Cd on nodule senescence in Cajanus cajan genotypes differing in their metal tolerance. Fifteen day-old plants were subjected to Cd treatments--25 mg and 50 mg Cd per kg dry soil and were grown with and without Glomus mosseae. Cd treatments led to a decline in mycorrhizal infection (MI), nodule number and dry weights which was accompanied by reductions in leghemoglobin content, nitrogenase activity, organic acid contents. Cd supply caused a marked decrease in nitrogen (N), phosphorus (P), and iron (Fe) contents. Conversely, Cd increased membrane permeability, thiobarbituric acid reactive substances (TBARS), hydrogen peroxide (H2O2), and Cd contents in nodules. AM inoculations were beneficial in reducing the above mentioned harmful effects of Cd and significantly improved nodule functioning. Activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) increased markedly in nodules of mycorrhizal-stressed plants. The negative effects of Cd were genotype and concentration dependent.

Differentiation of Symbiotic Cells and Endosymbionts in Medicago truncatula Nodulation Are Coupled to Two Transcriptome-Switches

PubMed Central

Maunoury, Nicolas; Redondo-Nieto, Miguel; Bourcy, Marie; Van de Velde, Willem; Alunni, Benoit; Laporte, Philippe; Durand, Patricia; Agier, Nicolas; Marisa, Laetitia; Vaubert, Danièle; Delacroix, Hervé; Duc, Gérard; Ratet, Pascal; Aggerbeck, Lawrence; Kondorosi, Eva; Mergaert, Peter

2010-01-01

The legume plant Medicago truncatula establishes a symbiosis with the nitrogen-fixing bacterium Sinorhizobium meliloti which takes place in root nodules. The formation of nodules employs a complex developmental program involving organogenesis, specific cellular differentiation of the host cells and the endosymbiotic bacteria, called bacteroids, as well as the specific activation of a large number of plant genes. By using a collection of plant and bacterial mutants inducing non-functional, Fix− nodules, we studied the differentiation processes of the symbiotic partners together with the nodule transcriptome, with the aim of unravelling links between cell differentiation and transcriptome activation. Two waves of transcriptional reprogramming involving the repression and the massive induction of hundreds of genes were observed during wild-type nodule formation. The dominant features of this “nodule-specific transcriptome” were the repression of plant defense-related genes, the transient activation of cell cycle and protein synthesis genes at the early stage of nodule development and the activation of the secretory pathway along with a large number of transmembrane and secretory proteins or peptides throughout organogenesis. The fifteen plant and bacterial mutants that were analyzed fell into four major categories. Members of the first category of mutants formed non-functional nodules although they had differentiated nodule cells and bacteroids. This group passed the two transcriptome switch-points similarly to the wild type. The second category, which formed nodules in which the plant cells were differentiated and infected but the bacteroids did not differentiate, passed the first transcriptome switch but not the second one. Nodules in the third category contained infection threads but were devoid of differentiated symbiotic cells and displayed a root-like transcriptome. Nodules in the fourth category were free of bacteria, devoid of differentiated symbiotic

Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family

USDA-ARS?s Scientific Manuscript database

The Legume Information System (LIS), at http://legumeinfo.org, is a genomic data portal (GDP) for the legume family. LIS provides access to genetic and genomic information for major crop and model legumes. With more than two-dozen domesticated legume species, there are numerous specialists working o...

Organogenic nodule formation in hop: a tool to study morphogenesis in plants with biotechnological and medicinal applications.

PubMed

Fortes, Ana M; Santos, Filipa; Pais, Maria S

2010-01-01

The usage of Humulus lupulus for brewing increased the demand for high-quality plant material. Simultaneously, hop has been used in traditional medicine and recently recognized with anticancer and anti-infective properties. Tissue culture techniques have been reported for a wide range of species, and open the prospect for propagation of disease-free, genetically uniform and massive amounts of plants in vitro. Moreover, the development of large-scale culture methods using bioreactors enables the industrial production of secondary metabolites. Reliable and efficient tissue culture protocol for shoot regeneration through organogenic nodule formation was established for hop. The present review describes the histological, and biochemical changes occurring during this morphogenic process, together with an analysis of transcriptional and metabolic profiles. We also discuss the existence of common molecular factors among three different morphogenic processes: organogenic nodules and somatic embryogenesis, which strictly speaking depend exclusively on intrinsic developmental reprogramming, and legume nitrogen-fixing root nodules, which arises in response to symbiosis. The review of the key factors that participate in hop nodule organogenesis and the comparison with other morphogenic processes may have merit as a study presenting recent advances in complex molecular networks occurring during morphogenesis and together, these provide a rich framework for biotechnology applications.

Nodule morphology, symbiotic specificity and association with unusual rhizobia are distinguishing features of the genus Listia within the southern African crotalarioid clade Lotononis s.l.

PubMed Central

Ardley, Julie K.; Reeve, Wayne G.; O'Hara, Graham W.; Yates, Ron J.; Dilworth, Michael J.; Howieson, John G.

2013-01-01

Background and Aims The legume clade Lotononis sensu lato (s.l.; tribe Crotalarieae) comprises three genera: Listia, Leobordea and Lotononis sensu stricto (s.s.). Listia species are symbiotically specific and form lupinoid nodules with rhizobial species of Methylobacterium and Microvirga. This work investigated whether these symbiotic traits were confined to Listia by determining the ability of rhizobial strains isolated from species of Lotononis s.l. to nodulate Listia, Leobordea and Lotononis s.s. hosts and by examining the morphology and structure of the resulting nodules. Methods Rhizobia were characterized by sequencing their 16S rRNA and nodA genes. Nodulation and N2 fixation on eight taxonomically diverse Lotononis s.l. species were determined in glasshouse trials. Nodules of all hosts, and the process of infection and nodule initiation in Listia angolensis and Listia bainesii, were examined by light microscopy. Key Results Rhizobia associated with Lotononis s.l. were phylogenetically diverse. Leobordea and Lotononis s.s. isolates were most closely related to Bradyrhizobium spp., Ensifer meliloti, Mesorhizobium tianshanense and Methylobacterium nodulans. Listia angolensis formed effective nodules only with species of Microvirga. Listia bainesii nodulated only with pigmented Methylobacterium. Five lineages of nodA were found. Listia angolensis and L. bainesii formed lupinoid nodules, whereas nodules of Leobordea and Lotononis s.s. species were indeterminate. All effective nodules contained uniformly infected central tissue. Listia angolensis and L. bainesii nodule initials occurred on the border of the hypocotyl and along the tap root, and nodule primordia developed in the outer cortical layer. Neither root hair curling nor infection threads were seen. Conclusions Two specificity groups occur within Lotononis s.l.: Listia species are symbiotically specific, while species of Leobordea and Lotononis s.s. are generally promiscuous and interact with rhizobia of

Medicago truncatula Zinc-Iron Permease6 provides zinc to rhizobia-infected nodule cells.

PubMed

Abreu, Isidro; Saéz, Ángela; Castro-Rodríguez, Rosario; Escudero, Viviana; Rodríguez-Haas, Benjamín; Senovilla, Marta; Larue, Camille; Grolimund, Daniel; Tejada-Jiménez, Manuel; Imperial, Juan; González-Guerrero, Manuel

2017-11-01

Zinc is a micronutrient required for symbiotic nitrogen fixation. It has been proposed that in model legume Medicago truncatula, zinc is delivered by the root vasculature into the nodule and released in the infection/differentiation zone. There, transporters must introduce this element into rhizobia-infected cells to metallate the apoproteins that use zinc as a cofactor. MtZIP6 (Medtr4g083570) is an M. truncatula Zinc-Iron Permease (ZIP) that is expressed only in roots and nodules, with the highest expression levels in the infection/differentiation zone. Immunolocalization studies indicate that it is located in the plasma membrane of nodule rhizobia-infected cells. Down-regulating MtZIP6 expression levels with RNAi does not result in any strong phenotype when plants are fed mineral nitrogen. However, these plants displayed severe growth defects when they depended on nitrogen fixed by their nodules, losing of 80% of their nitrogenase activity. The reduction of this activity was likely an indirect effect of zinc being retained in the infection/differentiation zone and not reaching the cytosol of rhizobia-infected cells. These data are consistent with a model in which MtZIP6 would be responsible for zinc uptake by rhizobia-infected nodule cells in the infection/differentiation zone. © 2017 John Wiley & Sons Ltd.

Exo-Oligosaccharides of Rhizobium sp. Strain NGR234 Are Required for Symbiosis with Various Legumes

PubMed Central

Staehelin, Christian; Forsberg, Lennart S.; D'Haeze, Wim; Gao, Mu-Yun; Carlson, Russell W.; Xie, Zhi-Ping; Pellock, Brett J.; Jones, Kathryn M.; Walker, Graham C.; Streit, Wolfgang R.; Broughton, William J.

2006-01-01

Rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. Nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, K-antigens, and exopolysaccharides (EPS). An acidic EPS from Rhizobium sp. strain NGR234 consists of glucosyl (Glc), galactosyl (Gal), glucuronosyl (GlcA), and 4,6-pyruvylated galactosyl (PvGal) residues with β-1,3, β-1,4, β-1,6, α-1,3, and α-1,4 glycoside linkages. Here we examined the role of NGR234 genes in the synthesis of EPS. Deletions within the exoF, exoL, exoP, exoQ, and exoY genes suppressed accumulation of EPS in bacterial supernatants, a finding that was confirmed by chemical analyses. The data suggest that the repeating subunits of EPS are assembled by an ExoQ/ExoP/ExoF-dependent mechanism, which is related to the Wzy polymerization system of group 1 capsular polysaccharides in Escherichia coli. Mutation of exoK (NGRΩexoK), which encodes a putative glycanase, resulted in the absence of low-molecular-weight forms of EPS. Analysis of the extracellular carbohydrates revealed that NGRΩexoK is unable to accumulate exo-oligosaccharides (EOSs), which are O-acetylated nonasaccharide subunits of EPS having the formula Gal(Glc)5(GlcA)2PvGal. When used as inoculants, both the exo-deficient mutants and NGRΩexoK were unable to form nitrogen-fixing nodules on some hosts (e.g., Albizia lebbeck and Leucaena leucocephala), but they were able to form nitrogen-fixing nodules on other hosts (e.g., Vigna unguiculata). EOSs of the parent strain were biologically active at very low levels (yield in culture supernatants, ∼50 μg per liter). Thus, NGR234 produces symbiotically active EOSs by enzymatic degradation of EPS, using the extracellular endo-β-1,4-glycanase encoded by exoK (glycoside hydrolase family 16). We propose that the derived EOSs (and not EPS) are bacterial components that play a crucial role in nodule formation in various legumes. PMID:16923883

Exo-oligosaccharides of Rhizobium sp. strain NGR234 are required for symbiosis with various legumes.

PubMed

Staehelin, Christian; Forsberg, Lennart S; D'Haeze, Wim; Gao, Mu-Yun; Carlson, Russell W; Xie, Zhi-Ping; Pellock, Brett J; Jones, Kathryn M; Walker, Graham C; Streit, Wolfgang R; Broughton, William J

2006-09-01

Rhizobia are nitrogen-fixing bacteria that establish endosymbiotic associations with legumes. Nodule formation depends on various bacterial carbohydrates, including lipopolysaccharides, K-antigens, and exopolysaccharides (EPS). An acidic EPS from Rhizobium sp. strain NGR234 consists of glucosyl (Glc), galactosyl (Gal), glucuronosyl (GlcA), and 4,6-pyruvylated galactosyl (PvGal) residues with beta-1,3, beta-1,4, beta-1,6, alpha-1,3, and alpha-1,4 glycoside linkages. Here we examined the role of NGR234 genes in the synthesis of EPS. Deletions within the exoF, exoL, exoP, exoQ, and exoY genes suppressed accumulation of EPS in bacterial supernatants, a finding that was confirmed by chemical analyses. The data suggest that the repeating subunits of EPS are assembled by an ExoQ/ExoP/ExoF-dependent mechanism, which is related to the Wzy polymerization system of group 1 capsular polysaccharides in Escherichia coli. Mutation of exoK (NGROmegaexoK), which encodes a putative glycanase, resulted in the absence of low-molecular-weight forms of EPS. Analysis of the extracellular carbohydrates revealed that NGROmegaexoK is unable to accumulate exo-oligosaccharides (EOSs), which are O-acetylated nonasaccharide subunits of EPS having the formula Gal(Glc)5(GlcA)2PvGal. When used as inoculants, both the exo-deficient mutants and NGROmegaexoK were unable to form nitrogen-fixing nodules on some hosts (e.g., Albizia lebbeck and Leucaena leucocephala), but they were able to form nitrogen-fixing nodules on other hosts (e.g., Vigna unguiculata). EOSs of the parent strain were biologically active at very low levels (yield in culture supernatants, approximately 50 microg per liter). Thus, NGR234 produces symbiotically active EOSs by enzymatic degradation of EPS, using the extracellular endo-beta-1,4-glycanase encoded by exoK (glycoside hydrolase family 16). We propose that the derived EOSs (and not EPS) are bacterial components that play a crucial role in nodule formation in various legumes.

Effector-Triggered Immunity Determines Host Genotype-Specific Incompatibility in Legume-Rhizobium Symbiosis.

PubMed

Yasuda, Michiko; Miwa, Hiroki; Masuda, Sachiko; Takebayashi, Yumiko; Sakakibara, Hitoshi; Okazaki, Shin

2016-08-01

Symbiosis between legumes and rhizobia leads to the formation of N2-fixing root nodules. In soybean, several host genes, referred to as Rj genes, control nodulation. Soybean cultivars carrying the Rj4 gene restrict nodulation by specific rhizobia such as Bradyrhizobium elkanii We previously reported that the restriction of nodulation was caused by B. elkanii possessing a functional type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria. In the present study, we investigated the molecular basis for the T3SS-dependent nodulation restriction in Rj4 soybean. Inoculation tests revealed that soybean cultivar BARC-2 (Rj4/Rj4) restricted nodulation by B. elkanii USDA61, whereas its nearly isogenic line BARC-3 (rj4/rj4) formed nitrogen-fixing nodules with the same strain. Root-hair curling and infection threads were not observed in the roots of BARC-2 inoculated with USDA61, indicating that Rj4 blocked B. elkanii infection in the early stages. Accumulation of H2O2 and salicylic acid (SA) was observed in the roots of BARC-2 inoculated with USDA61. Transcriptome analyses revealed that inoculation of USDA61, but not its T3SS mutant in BARC-2, induced defense-related genes, including those coding for hypersensitive-induced responsive protein, which act in effector-triggered immunity (ETI) in Arabidopsis. These findings suggest that B. elkanii T3SS triggers the SA-mediated ETI-type response in Rj4 soybean, which consequently blocks symbiotic interactions. This study revealed a common molecular mechanism underlying both plant-pathogen and plant-symbiont interactions, and suggests that establishment of a root nodule symbiosis requires the evasion or suppression of plant immune responses triggered by rhizobial effectors. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Leghemoglobin green derivatives with nitrated hemes evidence production of highly reactive nitrogen species during aging of legume nodules.

PubMed

Navascués, Joaquín; Pérez-Rontomé, Carmen; Gay, Marina; Marcos, Manuel; Yang, Fei; Walker, F Ann; Desbois, Alain; Abián, Joaquín; Becana, Manuel

2012-02-14

Globins constitute a superfamily of proteins widespread in all kingdoms of life, where they fulfill multiple functions, such as efficient O(2) transport and modulation of nitric oxide bioactivity. In plants, the most abundant Hbs are the symbiotic leghemoglobins (Lbs) that scavenge O(2) and facilitate its diffusion to the N(2)-fixing bacteroids in nodules. The biosynthesis of Lbs during nodule formation has been studied in detail, whereas little is known about the green derivatives of Lbs generated during nodule senescence. Here we characterize modified forms of Lbs, termed Lba(m), Lbc(m), and Lbd(m), of soybean nodules. These green Lbs have identical globins to the parent red Lbs but their hemes are nitrated. By combining UV-visible, MS, NMR, and resonance Raman spectroscopies with reconstitution experiments of the apoprotein with protoheme or mesoheme, we show that the nitro group is on the 4-vinyl. In vitro nitration of Lba with excess nitrite produced several isomers of nitrated heme, one of which is identical to those found in vivo. The use of antioxidants, metal chelators, and heme ligands reveals that nitration is contingent upon the binding of nitrite to heme Fe, and that the reactive nitrogen species involved derives from nitrous acid and is most probably the nitronium cation. The identification of these green Lbs provides conclusive evidence that highly oxidizing and nitrating species are produced in nodules leading to nitrosative stress. These findings are consistent with a previous report showing that the modified Lbs are more abundant in senescing nodules and have aberrant O(2) binding.

Iron-induced nitric oxide leads to an increase in the expression of ferritin during the senescence of Lotus japonicus nodules.

PubMed

Chungopast, Sirinapa; Duangkhet, Mallika; Tajima, Shigeyuki; Ma, Jian Feng; Nomura, Mika

2017-01-01

Iron is an essential nutrient for legume-rhizobium symbiosis and accumulates abundantly in the nodules. However, the concentration of free iron in the cells is strictly controlled to avoid toxicity. It is known that ferritin accumulates in the cells as an iron storage protein. During nodule senescence, the expression of the ferritin gene, Ljfer1, was induced in Lotus japonicus. We investigated a signal transduction pathway leading to the increase of Ljfer1 in the nodule. The Ljfer1 promoter of L. japonicus contains a conserved Iron-Dependent Regulatory Sequence (IDRS). The expression of Ljfer1 was induced by the application of iron or sodium nitroprusside, which is a nitric oxide (NO) donor. The application of iron to the nodule increased the level of NO. These data strongly suggest that iron-induced NO leads to increased expression of Ljfer1 during the senescence of L. japonicus nodules. Copyright © 2016 Elsevier GmbH. All rights reserved.

Immunolocalization of antioxidant enzymes in high-pressure frozen root and stem nodules of Sesbania rostrata.

PubMed

Rubio, Maria C; Becana, Manuel; Kanematsu, Sumio; Ushimaru, Takashi; James, Euan K

2009-01-01

The activities and localizations of superoxide dismutases (SODs) were compared in root and stem nodules of the semi-aquatic legume Sesbania rostrata using gel-activity assays and immunogold labelling, respectively. Nodules were fixed by high-pressure freezing and dehydrated by freeze substitution. Stem nodules showed more total and specific SOD activities than root nodules because of the presence of chloroplastic CuZnSOD. Most of the total SOD activity of stem and root nodules resulted from 'cytosolic' CuZnSOD, localized in the cytoplasm and chromatin, and from MnSOD in the bacteroids and in the mitochondria of vascular tissue. FeSOD was present in nodule plastids and in leaf chloroplasts, and was found to be associated with chromatin. Superoxide production was detected histochemically in the vascular bundles and in the infected tissue of stem and root nodules, whereas peroxide accumulation was observed in the cortical cell walls and intercellular spaces, as well as within the infection threads of both nodule types. These data suggest a role of CuZnSOD and FeSOD in protecting nuclear DNA from reactive oxygen species and/or in modulating gene activity. The enhanced levels of CuZnSOD, MnSOD and superoxide production in vascular bundle cells are consistent with a role of CuZnSOD and superoxide in the lignification of xylem vessels, but also suggest additional functions in coping with superoxide production by the high respiratory activity of parenchyma cells.

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

PubMed

Barrett, Craig F; Parker, Matthew A

2006-02-01

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 beta-proteobacterial genera are more ubiquitous as root nodule symbionts than previously believed.

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

PubMed Central

Barrett, Craig F.; Parker, Matthew A.

2006-01-01

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. PMID:16461667

[Thyroid nodule].

PubMed

Clerc, Jérôme

2005-01-31

The thyroid nodule is a frequent, most often benign, chronic, multifocal and slowly progressive disease. The first line strategy is to diagnose cancerous nodules (<5%) and relies upon fine needle aspiration (FNA), a specialised technique which in trained hands has a false negative rate of below 5%. The interest to explore small thyroid nodules is controversial since the prognosis of thyroid cancer is excellent for lesions measuring less than 20 mm. Though imaging accuracy is quite limited in assessing the diagnosis of thyroid cancer, both ultrasounds (US) and thyroid scan are helpful to enhance nodular identification (>30%), to sort the nodules relevant for cytological sampling and to optimize the follow-up, the major source of health costs. Suspicious and non contributive FNAs must have a control FNA within 6 months. Nodules with a non suspicious FNA (>85%) require long term follow-up. This follow-up is mainly morphological. New or evolutive nodules, as assessed by palpation or US, will require iterative FNAs or should be considered for surgery. In patients with hyperfunctioning nodules on the scan (10 to 20%), a yearly evaluation of the TSH level is sufficient. These nodules account either for autonomously functioning ones, which slowly develop towards thyrotoxicosis, or for hyperplastic nodules frequently disclosing a lymphocytic thyroiditis. Morbidity due to thyroid autonomy is still underestimated especially in aging patients with TSH levels < or =0.60 mU/L. An algorithmic approach to the diagnostic and follow-up evaluation of thyroid nodule is suggested.

Genetic control of inflorescence architecture in legumes

PubMed Central

Benlloch, Reyes; Berbel, Ana; Ali, Latifeh; Gohari, Gholamreza; Millán, Teresa; Madueño, Francisco

2015-01-01

The architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. Inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. Elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to being able to breed key architectural traits in crop species. Inflorescence architecture depends on the identity and activity of the meristems in the inflorescence apex, which determines when flowers are formed, how many are produced and their relative position in the inflorescence axis. Arabidopsis thaliana, where the genetic control of inflorescence development is best known, has a simple inflorescence, where the primary inflorescence meristem directly produces the flowers, which are thus borne in the main inflorescence axis. In contrast, legumes represent a more complex inflorescence type, the compound inflorescence, where flowers are not directly borne in the main inflorescence axis but, instead, they are formed by secondary or higher order inflorescence meristems. Studies in model legumes such as pea (Pisum sativum) or Medicago truncatula have led to a rather good knowledge of the genetic control of the development of the legume compound inflorescence. In addition, the increasing availability of genetic and genomic tools for legumes is allowing to rapidly extending this knowledge to other grain legume crops. This review aims to describe the current knowledge of the genetic network controlling inflorescence development in legumes. It also discusses how the combination of this knowledge with the use of emerging genomic tools and resources may allow rapid advances in the breeding of grain legume crops. PMID:26257753

Peroxiredoxins and NADPH-dependent thioredoxin systems in the model legume Lotus japonicus.

PubMed

Tovar-Méndez, Alejandro; Matamoros, Manuel A; Bustos-Sanmamed, Pilar; Dietz, Karl-Josef; Cejudo, Francisco Javier; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

2011-07-01

Peroxiredoxins (Prxs), thioredoxins (Trxs), and NADPH-thioredoxin reductases (NTRs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. This study provides a comprehensive survey of this network in the model legume Lotus japonicus. The aims were to identify and characterize these gene families and to assess whether the NTR-Trx systems are operative in nodules. Quantitative reverse transcription-polymerase chain reaction and immunological and proteomic approaches were used for expression profiling. We identified seven Prx, 14 Trx, and three NTR functional genes. The PrxQ1 gene was found to be transcribed in two alternative spliced variants and to be expressed at high levels in leaves, stems, petals, pods, and seeds and at low levels in roots and nodules. The 1CPrx gene showed very high expression in the seed embryos and low expression in vegetative tissues and was induced by nitric oxide and cytokinins. In sharp contrast, cytokinins down-regulated all other Prx genes, except PrxQ1, in roots and nodules, but only 2CPrxA and PrxQ1 in leaves. Gene-specific changes in Prx expression were also observed in response to ethylene, abscisic acid, and auxins. Nodules contain significant mRNA and protein amounts of cytosolic PrxIIB, Trxh1, and NTRA and of plastidic NTRC. Likewise, they express cytosolic Trxh3, Trxh4, Trxh8, and Trxh9, mitochondrial PrxIIF and Trxo, and plastidic Trxm2, Trxm4, and ferredoxin-Trx reductase. These findings reveal a complex regulation of Prxs that is dependent on the isoform, tissue, and signaling molecule and support that redox NTR-Trx systems are functional in the cytosol, mitochondria, and plastids of nodules.

Metabolic changes of iron uptake in N(2)-fixing common bean nodules during iron deficiency.

PubMed

Slatni, Tarek; Vigani, Gianpiero; Salah, Imen Ben; Kouas, Saber; Dell'Orto, Marta; Gouia, Houda; Zocchi, Graziano; Abdelly, Chedly

2011-08-01

Iron is an important nutrient in N(2)-fixing legume nodules. The demand for this micronutrient increases during the symbiosis establishment, where the metal is utilized for the synthesis of various iron-containing proteins in both the plant and the bacteroid. Unfortunately, in spite of its importance, iron is poorly available to plant uptake since its solubility is very low when in its oxidized form Fe(III). In the present study, the effect of iron deficiency on the activity of some proteins involved in Strategy I response, such as Fe-chelate reductase (FC-R), H(+)-ATPase, and phosphoenolpyruvate carboxylase (PEPC) and the protein level of iron regulated transporter (IRT1) and H(+)-ATPase proteins has been investigated in both roots and nodules of a tolerant (Flamingo) and a susceptible (Coco blanc) cultivar of common bean plants. The main results of this study show that the symbiotic tolerance of Flamingo can be ascribed to a greater increase in the FC-R and H(+)-ATPase activities in both roots and nodules, leading to a more efficient Fe supply to nodulating tissues. The strong increase in PEPC activity and organic acid content, in the Flamingo root nodules, suggests that under iron deficiency nodules can modify their metabolism in order to sustain those activities necessary to acquire Fe directly from the soil solution. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Deletion of the SACPD-C locus alters the symbiotic relationship between Bradyrhizobium japonicum USDA110 and soybean, resulting in elicitation of plant defense response and nodulation defects

USDA-ARS?s Scientific Manuscript database

Legumes form symbiotic association with soil-dwelling bacteria collectively called rhizobia. This association results in the formation of nodules, unique plant-derived organs, within which the rhizobia are housed. Rhizobia encoded-nitrogenase facilitates the conversation of atmospheric nitrogen int...

The abundance and diversity of legume-nodulating rhizobia in 28-year-old plantations of tropical, subtropical, and exotic tree species: a case study from the Forest Reserve of Bandia, Senegal.

PubMed

Sene, Godar; Thiao, Mansour; Samba-Mbaye, Ramatoulaye; Khasa, Damase; Kane, Aboubacry; Mbaye, Mame Samba; Beaulieu, Marie-Ève; Manga, Anicet; Sylla, Samba Ndao

2013-01-01

Several fast-growing and multipurpose tree species have been widely used in West Africa to both reverse the tendency of land degradation and restore soil productivity. Although beneficial effects have been reported on soil stabilization, there still remains a lack of information about their impact on soil microorganisms. Our investigation has been carried out in exotic and native tree plantations of 28 years and aimed to survey and compare the abundance and genetic diversity of natural legume-nodulating rhizobia (LNR). The study of LNR is supported by the phylogenetic analysis which clustered the isolates into three genera: Bradyrhizobium, Mesorhizobium, and Sinorhizobium. The results showed close positive correlations between the sizes of LNR populations estimated both in the dry and rainy seasons and the presence of legume tree hosts. There were significant increases in Rhizobium spp. population densities in response to planting with Acacia spp., and high genetic diversities and richness of genotypes were fittest in these tree plantations. This suggests that enrichment of soil Rhizobium spp. populations is host specific. The results indicated also that species of genera Mesorhizobium and Sinorhizobium were lacking in plantations of non-host species. By contrast, there was a widespread distribution of Bradyrhizobium spp. strains across the tree plantations, with no evident specialization in regard to plantation type. Finally, the study provides information about the LNR communities associated with a range of old tree plantations and some aspects of their relationships to soil factors, which may facilitate the management of man-made forest systems that target ecosystem rehabilitation and preservation of soil biota.

Development and comparison of projection and image space 3D nodule insertion techniques

NASA Astrophysics Data System (ADS)

Robins, Marthony; Solomon, Justin; Sahbaee, Pooyan; Samei, Ehsan

2016-04-01

This study aimed to develop and compare two methods of inserting computerized virtual lesions into CT datasets. 24 physical (synthetic) nodules of three sizes and four morphologies were inserted into an anthropomorphic chest phantom (LUNGMAN, KYOTO KAGAKU). The phantom was scanned (Somatom Definition Flash, Siemens Healthcare) with and without nodules present, and images were reconstructed with filtered back projection and iterative reconstruction (SAFIRE) at 0.6 mm slice thickness using a standard thoracic CT protocol at multiple dose settings. Virtual 3D CAD models based on the physical nodules were virtually inserted (accounting for the system MTF) into the nodule-free CT data using two techniques. These techniques include projection-based and image-based insertion. Nodule volumes were estimated using a commercial segmentation tool (iNtuition, TeraRecon, Inc.). Differences were tested using paired t-tests and R2 goodness of fit between the virtually and physically inserted nodules. Both insertion techniques resulted in nodule volumes very similar to the real nodules (<3% difference) and in most cases the differences were not statistically significant. Also, R2 values were all <0.97 for both insertion techniques. These data imply that these techniques can confidently be used as a means of inserting virtual nodules in CT datasets. These techniques can be instrumental in building hybrid CT datasets composed of patient images with virtually inserted nodules.

Deciphering composition and function of the root microbiome of a legume plant.

PubMed

Hartman, Kyle; van der Heijden, Marcel Ga; Roussely-Provent, Valexia; Walser, Jean-Claude; Schlaeppi, Klaus

2017-01-17

Diverse assemblages of microbes colonize plant roots and collectively function as a microbiome. Earlier work has characterized the root microbiomes of numerous plant species, but little information is available for legumes despite their key role in numerous ecosystems including agricultural systems. Legumes form a root nodule symbiosis with nitrogen-fixing Rhizobia bacteria and thereby account for large, natural nitrogen inputs into soils. Here, we describe the root bacteria microbiome of the legume Trifolium pratense combining culture-dependent and independent methods. For a functional understanding of individual microbiome members and their impact on plant growth, we began to inoculate root microbiome members alone or in combination to Trifolium roots. At a whole-root scale, Rhizobia bacteria accounted for ~70% of the root microbiome. Other enriched members included bacteria from the genera Pantoea, Sphingomonas, Novosphingobium, and Pelomonas. We built a reference stock of 200 bacteria isolates, and we found that they corresponded to ~20% of the abundant root microbiome members. We developed a microcosm system to conduct simplified microbiota inoculation experiments with plants. We observed that while an abundant root microbiome member reduced plant growth when inoculated alone, this negative effect was alleviated if this Flavobacterium was co-inoculated with other root microbiome members. The Trifolium root microbiome was dominated by nutrient-providing Rhizobia bacteria and enriched for bacteria from genera that may provide disease protection. First microbiota inoculation experiments indicated that individual community members can have plant growth compromising activities without being apparently pathogenic, and a more diverse root community can alleviate plant growth compromising activities of its individual members. A trait-based characterization of the reference stock bacteria will permit future microbiota manipulation experiments to decipher overall

Development of a clinical decision model for thyroid nodules.

PubMed

Stojadinovic, Alexander; Peoples, George E; Libutti, Steven K; Henry, Leonard R; Eberhardt, John; Howard, Robin S; Gur, David; Elster, Eric A; Nissan, Aviram

2009-08-10

Thyroid nodules represent a common problem brought to medical attention. Four to seven percent of the United States adult population (10-18 million people) has a palpable thyroid nodule, however the majority (>95%) of thyroid nodules are benign. While, fine needle aspiration remains the most cost effective and accurate diagnostic tool for thyroid nodules in current practice, over 20% of patients undergoing FNA of a thyroid nodule have indeterminate cytology (follicular neoplasm) with associated malignancy risk prevalence of 20-30%. These patients require thyroid lobectomy/isthmusectomy purely for the purpose of attaining a definitive diagnosis. Given that the majority (70-80%) of these patients have benign surgical pathology, thyroidectomy in these patients is conducted principally with diagnostic intent. Clinical models predictive of malignancy risk are needed to support treatment decisions in patients with thyroid nodules in order to reduce morbidity associated with unnecessary diagnostic surgery. Data were analyzed from a completed prospective cohort trial conducted over a 4-year period involving 216 patients with thyroid nodules undergoing ultrasound (US), electrical impedance scanning (EIS) and fine needle aspiration cytology (FNA) prior to thyroidectomy. A Bayesian model was designed to predict malignancy in thyroid nodules based on multivariate dependence relationships between independent covariates. Ten-fold cross-validation was performed to estimate classifier error wherein the data set was randomized into ten separate and unique train and test sets consisting of a training set (90% of records) and a test set (10% of records). A receiver-operating-characteristics (ROC) curve of these predictions and area under the curve (AUC) were calculated to determine model robustness for predicting malignancy in thyroid nodules. Thyroid nodule size, FNA cytology, US and EIS characteristics were highly predictive of malignancy. Cross validation of the model created with

Novel organization of the common nodulation genes in Rhizobium leguminosarum bv. phaseoli strains.

PubMed Central

Vázquez, M; Dávalos, A; de las Peñas, A; Sánchez, F; Quinto, C

1991-01-01

Nodulation by Rhizobium, Bradyrhizobium, and Azorhizobium species in the roots of legumes and nonlegumes requires the proper expression of plant genes and of both common and specific bacterial nodulation genes. The common nodABC genes form an operon or are physically mapped together in all species studied thus far. Rhizobium leguminosarum bv. phaseoli strains are classified in two groups. The type I group has reiterated nifHDK genes and a narrow host range of nodulation. The type II group has a single copy of the nifHDK genes and a wide host range of nodulation. We have found by genetic and nucleotide sequence analysis that in type I strain CE-3, the functional common nodA gene is separated from the nodBC genes by 20 kb and thus is transcriptionally separated from the latter genes. This novel organization could be the result of a complex rearrangement, as we found zones of identity between the two separated nodA and nodBC regions. Moreover, this novel organization of the common nodABC genes seems to be a general characteristic of R. leguminosarum bv. phaseoli type I strains. Despite the separation, the coordination of the expression of these genes seems not to be altered. PMID:1991718

Effects of co-inoculation with arbuscular mycorrhizal fungi and rhizobia on fungal occupancy in chickpea root and nodule determined by real-time PCR.

PubMed

Tavasolee, Alireza; Aliasgharzad, Naser; Salehi, Gholam Reza; Mardi, Mohsen; Asgharzadeh, Ahmad; Akbarivala, Sepide

2011-08-01

Legume roots in nature are usually colonized with rhizobia and different arbuscular mycorrhizal fungi (AMF) species. Light microscopy that visualizes the presence of AMF in roots is not able to differentiate the ratio of each AMF species in the root and nodule tissues in mixed fungal inoculation. The purpose of this study was to characterize the dominant species of mycorrhiza in roots and nodules of plants co-inoculated with mycorrhizal fungi and rhizobial strains. Glomus intraradices (GI), Glomus mosseae (GM), their mix (GI + GM), and six Mesorhizobium ciceri strains were used to inoculate chickpea. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to assess occupancy of these fungal species in roots and nodules. Results showed that GI molecular ratio and relative density were higher than GM in both roots and nodules. These differences in molecular ratio and density between GI and GM in nodules were three folds higher than roots. The results suggested that M. ciceri strains have different effects on nodulation and mycorrhizal colonization pattern. Plants with bacterial S3 and S1 strains produced the highest root nodulation and higher fungal density in both the roots and nodules.

Unlocking the potential of orphan legumes.

PubMed

Cullis, Christopher; Kunert, Karl J

2017-04-01

Orphan, or underutilized, legumes are domesticated legumes with useful properties, but with less importance than major world crops due to use and supply constraints. However, they play a significant role in many developing countries, providing food security and nutrition to consumers, as well as income to resource-poor farmers. They have been largely neglected by both researchers and industry due to their limited economic importance in the global market. Orphan legumes are better adapted than the major legume crops to extreme soil and climatic conditions, with high tolerance to abiotic environmental stresses such as drought. As a stress response they can also produce compounds with pharmaceutical value. Orphan legumes are therefore a likely source of important traits for introduction into major crops to aid in combating the stresses associated with global climate change. Modern large-scale genomics techniques are now being applied to many of these previously understudied crops, with the first successes reported in the genomics area. However, greater investment of resources and manpower are necessary if the potential of orphan legumes is to be unlocked and applied in the future. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

The Activity of Nodules of the Supernodulating Mutant Mtsunn Is not Limited by Photosynthesis under Optimal Growth Conditions

PubMed Central

Cabeza, Ricardo A.; Lingner, Annika; Liese, Rebecca; Sulieman, Saad; Senbayram, Mehmet; Tränkner, Merle; Dittert, Klaus; Schulze, Joachim

2014-01-01

Legumes match the nodule number to the N demand of the plant. When a mutation in the regulatory mechanism deprives the plant of that ability, an excessive number of nodules are formed. These mutants show low productivity in the fields, mainly due to the high carbon burden caused through the necessity to supply numerous nodules. The objective of this study was to clarify whether through optimal conditions for growth and CO2 assimilation a higher nodule activity of a supernodulating mutant of Medicago truncatula (M. truncatula) can be induced. Several experimental approaches reveal that under the conditions of our experiments, the nitrogen fixation of the supernodulating mutant, designated as sunn (super numeric nodules), was not limited by photosynthesis. Higher specific nitrogen fixation activity could not be induced through short- or long-term increases in CO2 assimilation around shoots. Furthermore, a whole plant P depletion induced a decline in nitrogen fixation, however this decline did not occur significantly earlier in sunn plants, nor was it more intense compared to the wild-type. However, a distinctly different pattern of nitrogen fixation during the day/night cycles of the experiment indicates that the control of N2 fixing activity of the large number of nodules is an additional problem for the productivity of supernodulating mutants. PMID:24727372

Development of a clinical decision model for thyroid nodules

PubMed Central

Stojadinovic, Alexander; Peoples, George E; Libutti, Steven K; Henry, Leonard R; Eberhardt, John; Howard, Robin S; Gur, David; Elster, Eric A; Nissan, Aviram

2009-01-01

Background Thyroid nodules represent a common problem brought to medical attention. Four to seven percent of the United States adult population (10–18 million people) has a palpable thyroid nodule, however the majority (>95%) of thyroid nodules are benign. While, fine needle aspiration remains the most cost effective and accurate diagnostic tool for thyroid nodules in current practice, over 20% of patients undergoing FNA of a thyroid nodule have indeterminate cytology (follicular neoplasm) with associated malignancy risk prevalence of 20–30%. These patients require thyroid lobectomy/isthmusectomy purely for the purpose of attaining a definitive diagnosis. Given that the majority (70–80%) of these patients have benign surgical pathology, thyroidectomy in these patients is conducted principally with diagnostic intent. Clinical models predictive of malignancy risk are needed to support treatment decisions in patients with thyroid nodules in order to reduce morbidity associated with unnecessary diagnostic surgery. Methods Data were analyzed from a completed prospective cohort trial conducted over a 4-year period involving 216 patients with thyroid nodules undergoing ultrasound (US), electrical impedance scanning (EIS) and fine needle aspiration cytology (FNA) prior to thyroidectomy. A Bayesian model was designed to predict malignancy in thyroid nodules based on multivariate dependence relationships between independent covariates. Ten-fold cross-validation was performed to estimate classifier error wherein the data set was randomized into ten separate and unique train and test sets consisting of a training set (90% of records) and a test set (10% of records). A receiver-operating-characteristics (ROC) curve of these predictions and area under the curve (AUC) were calculated to determine model robustness for predicting malignancy in thyroid nodules. Results Thyroid nodule size, FNA cytology, US and EIS characteristics were highly predictive of malignancy. Cross

Global Synthesis of Drought Effects on Food Legume Production

PubMed Central

Daryanto, Stefani; Wang, Lixin; Jacinthe, Pierre-André

2015-01-01

Food legume crops play important roles in conservation farming systems and contribute to food security in the developing world. However, in many regions of the world, their production has been adversely affected by drought. Although water scarcity is a severe abiotic constraint of legume crops productivity, it remains unclear how the effects of drought co-vary with legume species, soil texture, agroclimatic region, and drought timing. To address these uncertainties, we collected literature data between 1980 and 2014 that reported monoculture legume yield responses to drought under field conditions, and analyzed this data set using meta-analysis techniques. Our results showed that the amount of water reduction was positively related with yield reduction, but the extent of the impact varied with legume species and the phenological state during which drought occurred. Overall, lentil (Lens culinaris), groundnut (Arachis hypogaea), and pigeon pea (Cajanus cajan) were found to experience lower drought-induced yield reduction compared to legumes such as cowpea (Vigna unguiculata) and green gram (Vigna radiate). Yield reduction was generally greater when legumes experienced drought during their reproductive stage compared to during their vegetative stage. Legumes grown in soil with medium texture also exhibited greater yield reduction compared to those planted on soil of either coarse or fine texture. In contrast, regions and their associated climatic factors did not significantly affect legume yield reduction. In the face of changing climate, our study provides useful information for agricultural planning and research directions for development of drought-resistant legume species to improve adaptation and resilience of agricultural systems in the drought-prone regions of the world. PMID:26061704

Does plant immunity play a critical role during initiation of the legume-rhizobium symbiosis?

PubMed

Tóth, Katalin; Stacey, Gary

2015-01-01

Plants are exposed to many different microbes in their habitats. These microbes may be benign or pathogenic, but in some cases they are beneficial for the host. The rhizosphere provides an especially rich palette for colonization by beneficial (associative and symbiotic) microorganisms, which raises the question as to how roots can distinguish such 'friends' from possible 'foes' (i.e., pathogens). Plants possess an innate immune system that can recognize pathogens, through an arsenal of protein receptors, including receptor-like kinases (RLKs) and receptor-like proteins (RLPs) located at the plasma membrane. In addition, the plant host has intracellular receptors (so called NBS-LRR proteins or R proteins) that directly or indirectly recognize molecules released by microbes into the plant cell. A successful cooperation between legume plants and rhizobia leads to beneficial symbiotic interaction. The key rhizobial, symbiotic signaling molecules [lipo-chitooligosaccharide Nod factors (NF)] are perceived by the host legume plant using lysin motif-domain containing RLKs. Perception of the symbiotic NFs trigger signaling cascades leading to bacterial infection and accommodation of the symbiont in a newly formed root organ, the nodule, resulting in a nitrogen-fixing root nodule symbiosis. The net result of this symbiosis is the intracellular colonization of the plant with thousands of bacteria; a process that seems to occur in spite of the immune ability of plants to prevent pathogen infection. In this review, we discuss the potential of the invading rhizobial symbiont to actively avoid this innate immune response, as well as specific examples of where the plant immune response may modulate rhizobial infection and host range.

The development of Fe-nodules surrounding biological material mediated by microorganisms

NASA Astrophysics Data System (ADS)

Yoshida, Hidekazu; Yamamoto, Koshi; Murakami, Yuki; Katsuta, Nagayoshi; Hayashi, Toru; Naganuma, Takeshi

2008-09-01

Takashikozo is a phenomenon of Quaternary sediments in Japan. They are cylindrical Fe-oxyhydroxide nodules that form as plaques round plant roots, where Fe is preferentially concentrated to develop a solid wall. Structural features suggest that after the roots have decayed, the central space where the roots were situated acts as a flow path for oxidized water. Analysis of microbial 16S rDNA extracted from the nodules identified iron-oxidizing bacteria encrusted round the roots where they are the likely initiators of nodule formation. Direct microscopic observation revealed an accumulation of Fe-oxyhydroxides that fill the pore spaces and is also likely to be linked with the encrusting microbial colonies. Geological history and nanofossil evidence suggest that these Fe-nodules may have been buried at a depth of up to several tens of meters for at least 105 years in reducing Quaternary sediments. Thus Fe-oxyhydroxide nodules that have formed in a geological environment at the interfaces between water and rock by microbial mediation can persist under reducing conditions. If this is the case, the phenomenon is significant as an analogue of post-closure conditions in radioactive waste repositories, since it could influence nuclide migration.

Flavonoids and Auxin Transport Inhibitors Rescue Symbiotic Nodulation in the Medicago truncatula Cytokinin Perception Mutant cre1

PubMed Central

Ng, Jason Liang Pin; Hassan, Samira; Truong, Thy T.; Hocart, Charles H.; Laffont, Carole; Frugier, Florian; Mathesius, Ulrike

2015-01-01

Initiation of symbiotic nodules in legumes requires cytokinin signaling, but its mechanism of action is largely unknown. Here, we tested whether the failure to initiate nodules in the Medicago truncatula cytokinin perception mutant cre1 (cytokinin response1) is due to its altered ability to regulate auxin transport, auxin accumulation, and induction of flavonoids. We found that in the cre1 mutant, symbiotic rhizobia cannot locally alter acro- and basipetal auxin transport during nodule initiation and that these mutants show reduced auxin (indole-3-acetic acid) accumulation and auxin responses compared with the wild type. Quantification of flavonoids, which can act as endogenous auxin transport inhibitors, showed a deficiency in the induction of free naringenin, isoliquiritigenin, quercetin, and hesperetin in cre1 roots compared with wild-type roots 24 h after inoculation with rhizobia. Coinoculation of roots with rhizobia and the flavonoids naringenin, isoliquiritigenin, and kaempferol, or with the synthetic auxin transport inhibitor 2,3,5,-triiodobenzoic acid, rescued nodulation efficiency in cre1 mutants and allowed auxin transport control in response to rhizobia. Our results suggest that CRE1-dependent cytokinin signaling leads to nodule initiation through the regulation of flavonoid accumulation required for local alteration of polar auxin transport and subsequent auxin accumulation in cortical cells during the early stages of nodulation. PMID:26253705

Risk factors for pulmonary nodules in north China: A prospective cohort study.

PubMed

He, Yu-Tong; Zhang, Ya-Chen; Shi, Gao-Feng; Wang, Qi; Xu, Qian; Liang, Di; Du, Yu; Li, Dao-Juan; Jin, Jing; Shan, Bao-En

2018-06-01

Pulmonary nodules have become common incidental findings with the widespread use of computed tomography (CT) technology. Such nodules have the potential to become early lung cancer lesions, so understanding more about factors that may be associated with them is important. The present work was based on a large prospective cohort comprising 32,438 participants in Hebei Province (China) between January 2014 and March 2016. Participants aged 40-75 years completed a questionnaire, underwent low-dose CT (LDCT), and were followed up to March 2017. Grouped by the results of LDCT, normal participants and those with pulmonary nodules were included in the data analysis. In total 7752 subjects were included in this study, of whom 2040 (26.32%) were pulmonary nodule patients. Older age, current smoking status (hazard ratio (HR) = 1.43, 95% confidence interval (95%CI): 1.21, 1.68), exposure to second-hand smoke (SHS) at work (HR = 1.17, 95%CI: 1.01, 1.35), dust exposure (HR = 1.49, 95%CI: 1.06, 2.11), history of lung disease (HR = 1.44, 95%CI: 1.16, 1.77), and family history of cancer (HR = 1.28, 95%CI: 1.12, 1.48) were associated with pulmonary nodules. However, consumption of vegetables (HR = 0.82, 95%CI: 0.68, 0.99), tea (HR = 0.88, 95%CI: 0.78, 0.99) and legumes reduced the risk. Approximately 10.09% and 8.58% of pulmonary nodule incidences were attributed to tobacco smoking and low fruit intake, respectively. An estimated 6.36% and 3.88% of patients with pulmonary nodules attributable to family history of cancer and history of lung disease were detected. The results of this study suggest that age, smoking, SHS, dietary factors, occupational exposures, history of disease and family history of cancer may affect the incidence of pulmonary nodules. Copyright © 2018 Elsevier B.V. All rights reserved.

The Proteome of Seed Development in the Model Legume Lotus japonicus1[C][W

PubMed Central

Dam, Svend; Laursen, Brian S.; Ørnfelt, Jane H.; Jochimsen, Bjarne; Stærfeldt, Hans Henrik; Friis, Carsten; Nielsen, Kasper; Goffard, Nicolas; Besenbacher, Søren; Krusell, Lene; Sato, Shusei; Tabata, Satoshi; Thøgersen, Ida B.; Enghild, Jan J.; Stougaard, Jens

2009-01-01

We have characterized the development of seeds in the model legume Lotus japonicus. Like soybean (Glycine max) and pea (Pisum sativum), Lotus develops straight seed pods and each pod contains approximately 20 seeds that reach maturity within 40 days. Histological sections show the characteristic three developmental phases of legume seeds and the presence of embryo, endosperm, and seed coat in desiccated seeds. Furthermore, protein, oil, starch, phytic acid, and ash contents were determined, and this indicates that the composition of mature Lotus seed is more similar to soybean than to pea. In a first attempt to determine the seed proteome, both a two-dimensional polyacrylamide gel electrophoresis approach and a gel-based liquid chromatography-mass spectrometry approach were used. Globulins were analyzed by two-dimensional polyacrylamide gel electrophoresis, and five legumins, LLP1 to LLP5, and two convicilins, LCP1 and LCP2, were identified by matrix-assisted laser desorption ionization quadrupole/time-of-flight mass spectrometry. For two distinct developmental phases, seed filling and desiccation, a gel-based liquid chromatography-mass spectrometry approach was used, and 665 and 181 unique proteins corresponding to gene accession numbers were identified for the two phases, respectively. All of the proteome data, including the experimental data and mass spectrometry spectra peaks, were collected in a database that is available to the scientific community via a Web interface (http://www.cbs.dtu.dk/cgi-bin/lotus/db.cgi). This database establishes the basis for relating physiology, biochemistry, and regulation of seed development in Lotus. Together with a new Web interface (http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress4legumes/) collecting all protein identifications for Lotus, Medicago, and soybean seed proteomes, this database is a valuable resource for comparative seed proteomics and pathway analysis within and beyond the legume family. PMID:19129418

Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.

PubMed

Terpolilli, Jason; Hill, Yvette; Tian, Rui; Howieson, John; Bräu, Lambert; Goodwin, Lynne; Han, James; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

2013-12-20

Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022 is highly effective at fixing nitrogen with M. truncatula and other annual species such as M. tornata and M. littoralis and is also highly effective with the perennial M. sativa (alfalfa or lucerne). In common with other characterized E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha and M. sphaerocarpos and does not nodulate M. murex. Here we describe the features of E. meliloti WSM1022, together with genome sequence information and its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121 scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

The Lipopolysaccharide Lipid A Long-Chain Fatty Acid Is Important for Rhizobium leguminosarum Growth and Stress Adaptation in Free-Living and Nodule Environments.

PubMed

Bourassa, Dianna V; Kannenberg, Elmar L; Sherrier, D Janine; Buhr, R Jeffrey; Carlson, Russell W

2017-02-01

Rhizobium bacteria live in soil and plant environments, are capable of inducing symbiotic nodules on legumes, invade these nodules, and develop into bacteroids that fix atmospheric nitrogen into ammonia. Rhizobial lipopolysaccharide (LPS) is anchored in the bacterial outer membrane through a specialized lipid A containing a very long-chain fatty acid (VLCFA). VLCFA function for rhizobial growth in soil and plant environments is not well understood. Two genes, acpXL and lpxXL, encoding acyl carrier protein and acyltransferase, are among the six genes required for biosynthesis and transfer of VLCFA to lipid A. Rhizobium leguminosarum mutant strains acpXL, acpXL - /lpxXL - , and lpxXL - were examined for LPS structure, viability, and symbiosis. Mutations in acpXL and lpxXL abolished VLCFA attachment to lipid A. The acpXL mutant transferred a shorter acyl chain instead of VLCFA. Strains without lpxXL neither added VLCFA nor a shorter acyl chain. In all strains isolated from nodule bacteria, lipid A had longer acyl chains compared with laboratory-cultured bacteria, whereas mutant strains displayed altered membrane properties, modified cationic peptide sensitivity, and diminished levels of cyclic β-glucans. In pea nodules, mutant bacteroids were atypically formed and nitrogen fixation and senescence were affected. The role of VLCFA for rhizobial environmental fitness is discussed.

Diverse Mesorhizobium bacteria nodulate native Astragalus and Oxytropis in arctic and subarctic areas in Eurasia.

PubMed

Ampomah, Osei Yaw; Mousavi, Seyed Abdollah; Lindström, Kristina; Huss-Danell, Kerstin

2017-01-01

Rhizobia nodulating native Astragalus and Oxytropis spp. in Northern Europe are not well-studied. In this study, we isolated bacteria from nodules of four Astragalus spp. and two Oxytropis spp. from the arctic and subarctic regions of Sweden and Russia. The phylogenetic analyses were performed by using sequences of three housekeeping genes (16S rRNA, rpoB and recA) and two accessory genes (nodC and nifH). The results of our multilocus sequence analysis (MLSA) of the three housekeeping genes tree showed that all the 13 isolates belonged to the genus Mesorhizobium and were positioned in six clades. Our concatenated housekeeping gene tree also suggested that the isolates nodulating Astragalus inopinatus, Astragalus frigidus, Astragalus alpinus ssp. alpinus and Oxytropis revoluta might be designated as four new Mesorhizobium species. The 13 isolates were grouped in three clades in the nodC and nifH trees. 15 N analysis suggested that the legumes in association with these isolates were actively fixing nitrogen. Copyright © 2016 Elsevier GmbH. All rights reserved.

Integrated analysis of zone-specific protein and metabolite profiles within nitrogen-fixing Medicago truncatula-Sinorhizobium medicae nodules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ogden, Aaron J.; Gargouri, Mahmoud; Park, JeongJin

Symbiotic nitrogen fixation (SNF) between rhizobia and legumes requires metabolic coordination within specialized root organs called nodules. Nodules formed in the symbiosis between S. medicae and barrel medic (M. truncatula) are indeterminate, cylindrical, and contain spatially distinct developmental zones. Bacteria in the infection zone II (ZII), interzone II-III (IZ), and nitrogen fixation zone III (ZIII) represent different stages in the metabolic progression from free-living bacteria into nitrogen fixing bacteroids. To better understand the coordination of plant and bacterial metabolism within the nodule, we used liquid and gas chromatography coupled to tandem mass spectrometry (MS) to observe protein and metabolite profilesmore » representative of ZII, IZ, ZIII, whole-nodule, and primary root. Our MS-based approach confidently identified 361 S. medicae proteins and 888 M. truncatula proteins, as well as 160 metabolites from each tissue. The data are consistent with several organ- and zone-specific protein and metabolite localization patterns characterized previously. Here, we used our comprehensive dataset to demonstrate how multiple branches of primary metabolism are coordinated between symbionts and zones, including central carbon, fatty acid, and amino acid metabolism. For example, M. truncatula glycolysis enzymes accumulate from zone I to zone III within the nodule, while equivalent S. medicae enzymes decrease in abundance. We also show the localization of S. medicae's transition to dicarboxylic acid-dependent carbon metabolism within the IZ. The spatial abundance patterns of S. medicae fatty acid (FA) biosynthesis enzymes indicate an increased demand for FA production in the IZ and ZIII as compared to ZI. Our observations provide a resource for those seeking to understand coordinated physiological changes during the development of SNF.« less

Integrated analysis of zone-specific protein and metabolite profiles within nitrogen-fixing Medicago truncatula-Sinorhizobium medicae nodules

DOE PAGES

Ogden, Aaron J.; Gargouri, Mahmoud; Park, JeongJin; ...

2017-07-10

Symbiotic nitrogen fixation (SNF) between rhizobia and legumes requires metabolic coordination within specialized root organs called nodules. Nodules formed in the symbiosis between S. medicae and barrel medic (M. truncatula) are indeterminate, cylindrical, and contain spatially distinct developmental zones. Bacteria in the infection zone II (ZII), interzone II-III (IZ), and nitrogen fixation zone III (ZIII) represent different stages in the metabolic progression from free-living bacteria into nitrogen fixing bacteroids. To better understand the coordination of plant and bacterial metabolism within the nodule, we used liquid and gas chromatography coupled to tandem mass spectrometry (MS) to observe protein and metabolite profilesmore » representative of ZII, IZ, ZIII, whole-nodule, and primary root. Our MS-based approach confidently identified 361 S. medicae proteins and 888 M. truncatula proteins, as well as 160 metabolites from each tissue. The data are consistent with several organ- and zone-specific protein and metabolite localization patterns characterized previously. Here, we used our comprehensive dataset to demonstrate how multiple branches of primary metabolism are coordinated between symbionts and zones, including central carbon, fatty acid, and amino acid metabolism. For example, M. truncatula glycolysis enzymes accumulate from zone I to zone III within the nodule, while equivalent S. medicae enzymes decrease in abundance. We also show the localization of S. medicae's transition to dicarboxylic acid-dependent carbon metabolism within the IZ. The spatial abundance patterns of S. medicae fatty acid (FA) biosynthesis enzymes indicate an increased demand for FA production in the IZ and ZIII as compared to ZI. Our observations provide a resource for those seeking to understand coordinated physiological changes during the development of SNF.« less

A conserved α-proteobacterial small RNA contributes to osmoadaptation and symbiotic efficiency of rhizobia on legume roots.

PubMed

Robledo, Marta; Peregrina, Alexandra; Millán, Vicenta; García-Tomsig, Natalia I; Torres-Quesada, Omar; Mateos, Pedro F; Becker, Anke; Jiménez-Zurdo, José I

2017-07-01

Small non-coding RNAs (sRNAs) are expected to have pivotal roles in the adaptive responses underlying symbiosis of nitrogen-fixing rhizobia with legumes. Here, we provide primary insights into the function and activity mechanism of the Sinorhizobium meliloti trans-sRNA NfeR1 (Nodule Formation Efficiency RNA). Northern blot probing and transcription tracking with fluorescent promoter-reporter fusions unveiled high nfeR1 expression in response to salt stress and throughout the symbiotic interaction. The strength and differential regulation of nfeR1 transcription are conferred by a motif, which is conserved in nfeR1 promoter regions in α-proteobacteria. NfeR1 loss-of-function compromised osmoadaptation of free-living bacteria, whilst causing misregulation of salt-responsive genes related to stress adaptation, osmolytes catabolism and membrane trafficking. Nodulation tests revealed that lack of NfeR1 affected competitiveness, infectivity, nodule development and symbiotic efficiency of S. meliloti on alfalfa roots. Comparative computer predictions and a genetic reporter assay evidenced a redundant role of three identical NfeR1 unpaired anti Shine-Dalgarno motifs for targeting and downregulation of translation of multiple mRNAs from transporter genes. Our data provide genetic evidence of the hyperosmotic conditions of the endosymbiotic compartments. NfeR1-mediated gene regulation in response to this cue could contribute to coordinate nutrient uptake with the metabolic reprogramming concomitant to symbiotic transitions. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

micro RNA 172 (miR172) signals epidermal infection and is expressed in cells primed for bacterial invasion in Lotus japonicus roots and nodules.

PubMed

Holt, Dennis B; Gupta, Vikas; Meyer, Dörte; Abel, Nikolaj B; Andersen, Stig U; Stougaard, Jens; Markmann, Katharina

2015-10-01

Legumes interact with rhizobial bacteria to form nitrogen-fixing root nodules. Host signalling following mutual recognition ensures a specific response, but is only partially understood. Focusing on the stage of epidermal infection with Mesorhizobium loti, we analysed endogenous small RNAs (sRNAs) of the model legume Lotus japonicus to investigate their involvement in host response regulation. We used Illumina sequencing to annotate the L. japonicus sRNA-ome and isolate infection-responsive sRNAs, followed by candidate-based functional characterization. Sequences from four libraries revealed 219 novel L. japonicus micro RNAs (miRNAs) from 114 newly assigned families, and 76 infection-responsive sRNAs. Unlike infection-associated coding genes such as NODULE INCEPTION (NIN), a micro RNA 172 (miR172) isoform showed strong accumulation in dependency of both Nodulation (Nod) factor and compatible rhizobia. The genetics of miR172 induction support the existence of distinct epidermal and cortical signalling events. MIR172a promoter activity followed a previously unseen pattern preceding infection thread progression in epidermal and cortical cells. Nodule-associated miR172a expression was infection-independent, representing the second of two genetically separable activity waves. The combined data provide a valuable resource for further study, and identify miR172 as an sRNA marking successful epidermal infection. We show that miR172 acts upstream of several APETALA2-type (AP2) transcription factors, and suggest that it has a role in fine-tuning AP2 levels during bacterial symbiosis. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Estimating variability in grain legume yields across Europe and the Americas

NASA Astrophysics Data System (ADS)

Cernay, Charles; Ben-Ari, Tamara; Pelzer, Elise; Meynard, Jean-Marc; Makowski, David

2015-06-01

Grain legume production in Europe has recently come under scrutiny. Although legume crops are often promoted to provide environmental services, European farmers tend to turn to non-legume crops. It is assumed that high variability in legume yields explains this aversion, but so far this hypothesis has not been tested. Here, we estimate the variability of major grain legume and non-legume yields in Europe and the Americas from yield time series over 1961-2013. Results show that grain legume yields are significantly more variable than non-legume yields in Europe. These differences are smaller in the Americas. Our results are robust at the level of the statistical methods. In all regions, crops with high yield variability are allocated to less than 1% of cultivated areas. Although the expansion of grain legumes in Europe may be hindered by high yield variability, some species display risk levels compatible with the development of specialized supply chains.

A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution.

PubMed

Hane, James K; Ming, Yao; Kamphuis, Lars G; Nelson, Matthew N; Garg, Gagan; Atkins, Craig A; Bayer, Philipp E; Bravo, Armando; Bringans, Scott; Cannon, Steven; Edwards, David; Foley, Rhonda; Gao, Ling-Ling; Harrison, Maria J; Huang, Wei; Hurgobin, Bhavna; Li, Sean; Liu, Cheng-Wu; McGrath, Annette; Morahan, Grant; Murray, Jeremy; Weller, James; Jian, Jianbo; Singh, Karam B

2017-03-01

Lupins are important grain legume crops that form a critical part of sustainable farming systems, reducing fertilizer use and providing disease breaks. It has a basal phylogenetic position relative to other crop and model legumes and a high speciation rate. Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is gaining popularity as a health food, which is high in protein and dietary fibre but low in starch and gluten-free. We report the draft genome assembly (609 Mb) of NLL cultivar Tanjil, which has captured >98% of the gene content, sequences of additional lines and a dense genetic map. Lupins are unique among legumes and differ from most other land plants in that they do not form mycorrhizal associations. Remarkably, we find that NLL has lost all mycorrhiza-specific genes, but has retained genes commonly required for mycorrhization and nodulation. In addition, the genome also provided candidate genes for key disease resistance and domestication traits. We also find evidence of a whole-genome triplication at around 25 million years ago in the genistoid lineage leading to Lupinus. Our results will support detailed studies of legume evolution and accelerate lupin breeding programmes. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Isoenzymes of superoxide dismutase in nodules of Phaseolus vulgaris L. , Pisum sativum L. , and Vigna unguiculata (L. ) Walp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Becana, M.; Paris, F.J.; Sandalio, L.M.

1989-08-01

The activity and isozymic composition of superoxide dismutase were determined in nodules of Phaseolus vulgaris L., Pisum sativum L., and Vigna unguiculata (L.) Walp. A Mn-SOD was present in Rhizobium and two in Bradyrhizobium and bacteroids. Nodule mitochondria from all three legume species had a single Mn-SOD with similar relative mobility, whereas the cytosol contained several CuZn-SODs: two in Phaseolus and Pisum, and four in Vigna. In the cytoplasm of V. unguiculata nodules, a Fe-containing SOD was also present, with an electrophoretic mobility between those of CuZn- and Mn-SODs, and an estimated molecular weight of 57,000. Total SOD activity ofmore » the soluble fraction of host cells, expressed on a nodule fresh weight basis, exceeded markedly that of bacteroids. Likewise, specific SOD activities of free-living bacteria were superior or equal to those of their symbiotic forms. Soluble extracts of bacteria and bacteroids did not show peroxidase activity, but the nodule cell cytoplasm contained diverse peroxidase isozymes which were readily distinguishable from leghemoglobin components by electrophoresis. Data indicated that peroxidases and leghemoglobins did not significantly interfere with SOD localization on gels. Treatment with chloroform-ethanol scarcely affected the isozymic pattern of SODs and peroxidases, and had limited success in the removal of leghemoglobin.« less

Development and evaluation of a computer-aided diagnostic scheme for lung nodule detection in chest radiographs by means of two-stage nodule enhancement with support vector classification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen Sheng; Suzuki, Kenji; MacMahon, Heber

2011-04-15

Purpose: To develop a computer-aided detection (CADe) scheme for nodules in chest radiographs (CXRs) with a high sensitivity and a low false-positive (FP) rate. Methods: The authors developed a CADe scheme consisting of five major steps, which were developed for improving the overall performance of CADe schemes. First, to segment the lung fields accurately, the authors developed a multisegment active shape model. Then, a two-stage nodule-enhancement technique was developed for improving the conspicuity of nodules. Initial nodule candidates were detected and segmented by using the clustering watershed algorithm. Thirty-one shape-, gray-level-, surface-, and gradient-based features were extracted from each segmentedmore » candidate for determining the feature space, including one of the new features based on the Canny edge detector to eliminate a major FP source caused by rib crossings. Finally, a nonlinear support vector machine (SVM) with a Gaussian kernel was employed for classification of the nodule candidates. Results: To evaluate and compare the scheme to other published CADe schemes, the authors used a publicly available database containing 140 nodules in 140 CXRs and 93 normal CXRs. The CADe scheme based on the SVM classifier achieved sensitivities of 78.6% (110/140) and 71.4% (100/140) with averages of 5.0 (1165/233) FPs/image and 2.0 (466/233) FPs/image, respectively, in a leave-one-out cross-validation test, whereas the CADe scheme based on a linear discriminant analysis classifier had a sensitivity of 60.7% (85/140) at an FP rate of 5.0 FPs/image. For nodules classified as ''very subtle'' and ''extremely subtle,'' a sensitivity of 57.1% (24/42) was achieved at an FP rate of 5.0 FPs/image. When the authors used a database developed at the University of Chicago, the sensitivities was 83.3% (40/48) and 77.1% (37/48) at an FP rate of 5.0 (240/48) FPs/image and 2.0 (96/48) FPs /image, respectively. Conclusions: These results compare favorably to those

Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique

PubMed Central

Chidebe, Ifeoma N.

2017-01-01

ABSTRACT Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLASTn sequence analysis of 16S rRNA and four housekeeping genes (glnII, gyrB, recA, and rpoB) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi, Bradyrhizobium arachidis, Bradyrhizobium yuanmingense, and a novel Bradyrhizobium sp., as well as Rhizobium tropici, Rhizobium pusense, and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes. IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea

Distribution and Phylogeny of Microsymbionts Associated with Cowpea (Vigna unguiculata) Nodulation in Three Agroecological Regions of Mozambique.

PubMed

Chidebe, Ifeoma N; Jaiswal, Sanjay K; Dakora, Felix D

2018-01-15

Cowpea derives most of its N nutrition from biological nitrogen fixation (BNF) via symbiotic bacteroids in root nodules. In Sub-Saharan Africa, the diversity and biogeographic distribution of bacterial microsymbionts nodulating cowpea and other indigenous legumes are not well understood, though needed for increased legume production. The aim of this study was to describe the distribution and phylogenies of rhizobia at different agroecological regions of Mozambique using PCR of the BOX element (BOX-PCR), restriction fragment length polymorphism of the internal transcribed spacer (ITS-RFLP), and sequence analysis of ribosomal, symbiotic, and housekeeping genes. A total of 122 microsymbionts isolated from two cowpea varieties (IT-1263 and IT-18) grouped into 17 clades within the BOX-PCR dendrogram. The PCR-ITS analysis yielded 17 ITS types for the bacterial isolates, while ITS-RFLP analysis placed all test isolates in six distinct clusters (I to VI). BLAST n sequence analysis of 16S rRNA and four housekeeping genes ( glnII , gyrB , recA , and rpoB ) showed their alignment with Rhizobium and Bradyrhizobium species. The results revealed a group of highly diverse and adapted cowpea-nodulating microsymbionts which included Bradyrhizobium pachyrhizi , Bradyrhizobium arachidis , Bradyrhizobium yuanmingense , and a novel Bradyrhizobium sp., as well as Rhizobium tropici , Rhizobium pusense , and Neorhizobium galegae in Mozambican soils. Discordances observed in single-gene phylogenies could be attributed to horizontal gene transfer and/or subsequent recombinations of the genes. Natural deletion of 60 bp of the gyrB region was observed in isolate TUTVU7; however, this deletion effect on DNA gyrase function still needs to be confirmed. The inconsistency of nifH with core gene phylogenies suggested differences in the evolutionary history of both chromosomal and symbiotic genes. IMPORTANCE A diverse group of both Bradyrhizobium and Rhizobium species responsible for cowpea

[Baked product development based fermented legumes and cereals for schoolchildren snack].

PubMed

Granito, Marisela; Valero, Yolmar; Zambrano, Rosaura

2010-03-01

The objective of this work was to develop three foodstuffs based on mixes of wheat and fermented and non-fermented legumes, for the purpose of contributing with a healthy alternative for school snacks. To this aim, refined wheat flour was partially substituted with whole legume flours for the preparation of cakes, brownies and cookies, foodstuffs traditionally consumed by school age children. Cakes were formulated substituting 20% of wheat flour with Phaseolus vulgaris flour, brownies with 30% of Cajanus cajan flour and cookies with 30% of Vigna sinensis flour, using fermented and non-fermented legumes in the three products. When these products were subjected to sensorial evaluation through a test of degree of acceptability and using a hedonic scale of 7 points, values higher than 5 in the attributes taste, color and overall appraisal were found for all the products. In addition, the preference was measured with a group of 90 school children, corroborating the results obtained at laboratory level. Chemical characterization showed protein contents between 12 and 13% for the cake, 10 and 11% for the brownies and 10% for the cookies and protein digestibilities in vitro of 91%, 87% and 93%, respectively. The calorie supply, calculated per portion was of 199 kcal, 246 kcal and 237 kcal, for cakes, brownies and cookies, respectively. It was concluded that it is technically possible to incorporate fermented and non-fermented Phaseolus vulgaris, Vigna sinensis and Cajanus cajan, to highly consumed products such as cakes, brownies and cookies with a higher nutritional content and well-accepted by school-age children.

Engineered ACC deaminase-expressing free-living cells of Mesorhizobium loti show increased nodulation efficiency and competitiveness on Lotus spp.

PubMed

Conforte, Valeria P; Echeverria, Mariela; Sánchez, Cintia; Ugalde, Rodolfo A; Menéndez, Ana B; Lepek, Viviana C

2010-08-01

Ethylene inhibits the establishment of symbiosis between rhizobia and legumes. Several rhizobia species express the enzyme ACC deaminase, which degrades the ethylene precursor 1-cyclopropane-1-carboxilate (ACC), leading to reductions in the amount of ethylene evolved by the plant. M. loti has a gene encoding ACC deaminase, but this gene is under the activity of the NifA-RpoN-dependent promoter; thus, it is only expressed inside the nodule. The M. loti structural gene ACC deaminase (acdS) was integrated into the M. loti chromosome under a constitutive promoter activity. The resulting strain induced the formation of a higher number of nodules and was more competitive than the wild-type strain on Lotus japonicus and L. tenuis. These results suggest that the introduction of the ACC deaminase activity within M. loti in a constitutive way could be a novel strategy to increase nodulation competitiveness of the bacteria, which could be useful for the forage inoculants industry.

Isolation and Characterization of Alfalfa-Nodulating Rhizobia Present in Acidic Soils of Central Argentina and Uruguay

PubMed Central

del Papa, María F.; Balagué, Laura J.; Sowinski, Susana Castro; Wegener, Caren; Segundo, Eduardo; Abarca, Francisco Martínez; Toro, Nicolás; Niehaus, Karsten; Pühler, Alfred; Aguilar, O. Mario; Martínez-Drets, Gloria; Lagares, Antonio

1999-01-01

We describe the isolation and characterization of alfalfa-nodulating rhizobia from acid soils of different locations in Central Argentina and Uruguay. A collection of 465 isolates was assembled, and the rhizobia were characterized for acid tolerance. Growth tests revealed the existence of 15 acid-tolerant (AT) isolates which were able to grow at pH 5.0 and formed nodules in alfalfa with a low rate of nitrogen fixation. Analysis of those isolates, including partial sequencing of the genes encoding 16S rRNA and genomic PCR-fingerprinting with MBOREP1 and BOXC1 primers, demonstrated that the new isolates share a genetic background closely related to that of the previously reported Rhizobium sp. Or191 recovered from an acid soil in Oregon (B. D. Eardly, J. P. Young, and R. K. Selander, Appl. Environ. Microbiol. 58:1809–1815, 1992). Growth curves, melanin production, temperature tolerance, and megaplasmid profiles of the AT isolates were all coincident with these characteristics in strain Or191. In addition to the ability of all of these strains to nodulate alfalfa (Medicago sativa) inefficiently, the AT isolates also nodulated the common bean and Leucaena leucocephala, showing an extended host range for nodulation of legumes. In alfalfa, the time course of nodule formation by the AT isolate LPU 83 showed a continued nodulation restricted to the emerging secondary roots, which was probably related to the low rate of nitrogen fixation by the largely ineffective nodules. Results demonstrate the complexity of the rhizobial populations present in the acidic soils represented by a main group of N2-fixing rhizobia and a second group of ineffective and less-predominant isolates related to the AT strain Or191. PMID:10103231

Priority regions for research on dryland cereals and legumes

PubMed Central

Hyman, Glenn; Barona, Elizabeth; Biradar, Chandrashekhar; Guevara, Edward; Dixon, John; Beebe, Steve; Castano, Silvia Elena; Alabi, Tunrayo; Gumma, Murali Krishna; Sivasankar, Shoba; Rivera, Ovidio; Espinosa, Herlin; Cardona, Jorge

2016-01-01

Dryland cereals and legumes  are important crops in farming systems across the world.  Yet they are frequently neglected among the priorities for international agricultural research and development, often due to lack of information on their magnitude and extent. Given what we know about the global distribution of dryland cereals and legumes, what regions should be high priority for research and development to improve livelihoods and food security? This research evaluated the geographic dimensions of these crops and the farming systems where they are found worldwide. The study employed geographic information science and data to assess the key farming systems and regions for these crops. Dryland cereal and legume crops should be given high priority in 18 farming systems worldwide, where their cultivated area comprises more than 160 million ha. These regions include the dryer areas of South Asia, West and East Africa, the Middle East and North Africa, Central America and other parts of Asia. These regions are prone to drought and heat stress, have limiting soil constraints, make up half of the global population and account for 60 percent of the global poor and malnourished. The dryland cereal and legume crops and farming systems merit more research and development attention to improve productivity and address development problems. This project developed an open access dataset and information resource that provides the basis for future analysis of the geographic dimensions of dryland cereals and legumes. PMID:27303632

Pleiotropic effect of fluoranthene on anthocyanin synthesis and nodulation of Medicago sativa is reversed by the plant flavone luteolin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wetzel, A.; Parniske, M.; Werner, D.

1995-05-01

The symbiosis between leguminous plants and soil bacteria of the genus Rhizobium is of considerable agronominal importance. Recently it has been found, that polycyclic aromatic hydrocarbons (PAHs; e.g. anthracene, phenanthrene, fluoranthene), occurring as ubiquitous environmental contaminants can inhibit nodulation of Medicago sativa. Fluoranthene is one of the dominant PAHs found in urban particulate matter, sewage sludge or beside motorways. Several organisms have been shown to be able to metabolize and mineralize fluoranthene but the uptake of fluoranthene is limited due to low solubility of fluoranthene in water and strong adsorption to humic substances in soil. Rhizobium meliloti cannot degrade fluoranthene.more » Toxic effects of fluoranthene on bacterial growth have never been observed. In contrast to their rhizobial symbiotic partners, alfalfa plants grown on a solidified fluoranthene-containing medium, exhibited symptoms of toxicity. They showed a dose-responsive decrease in shoot length and, if inoculated with R. meliloti, inhibition of nodule formation. Growth retardation is accompanied by a decrease in anthocyanin pigmentation of shoots, and an atypical accumulation of anthocyanins in roots. Plant flavonoids are known to play a central role in the signal exchange of the Legume-Rhizobium symbiosis. Phenylpropane derived compounds and flavonoids have been implicated in nodule development. Since fluoranthene impairs nodulation and induces the production of anthocyanins, it is possible that these events are causally linked via phenylpropanoid metabolism. These experiments attempt to overcome the inhibitory effects of fluoranthene by exogeneous application of the flavonoid luteolin. This paper demonstrates that luteolin antagonizes the fluoranthene mediated inhibition of nodule formation and prevents the accumulation of anthocyanins in roots. 29 refs., 4 figs., 1 tab.« less

Orphan legume crops enter the genomics era!

PubMed

Varshney, Rajeev K; Close, Timothy J; Singh, Nagendra K; Hoisington, David A; Cook, Douglas R

2009-04-01

Many of the world's most important food legumes are grown in arid and semi-arid regions of Africa and Asia, where crop productivity is hampered by biotic and abiotic stresses. Until recently, these crops have also suffered from a dearth of genomic and molecular-genetic resources and thus were 'orphans' of the genome revolution. However, the community of legume researchers has begun a concerted effort to change this situation. The driving force is a series of international collaborations that benefit from recent advances in genome sequencing and genotyping technologies. The focus of these activities is the development of genome-scale data sets that can be used in high-throughput approaches to facilitate genomics-assisted breeding in these legumes.

MtMOT1.2 is responsible for molybdate supply to Medicago truncatula nodules.

PubMed

Gil-Díez, Patricia; Tejada-Jiménez, Manuel; León-Mediavilla, Javier; Wen, Jiangqi; Mysore, Kirankumar S; Imperial, Juan; González-Guerrero, Manuel

2018-06-25

Symbiotic nitrogen fixation in legume root nodules requires a steady supply of molybdenum for synthesis of the iron-molybdenum cofactor of nitrogenase. This nutrient has to be provided by the host plant from the soil, crossing several symplastically disconnected compartments through molybdate transporters, including members of the MOT1 family. MtMOT1.2 is a Medicago truncatula MOT1 family member located in the endodermal cells in roots and nodules. Immunolocalization of a tagged MtMOT1.2 indicates that it is associated to the plasma membrane and to intracellular membrane systems, where it would be transporting molybdate towards the cytosol, as indicated in yeast transport assays. Loss-of-function mot1.2-1 mutant showed reduced growth compared to wild-type plants when nitrogen fixation was required, but not when nitrogen was provided as nitrate. While no effect on molybdenum-dependent nitrate reductase activity was observed, nitrogenase activity was severely affected, explaining the observed difference of growth depending on nitrogen source. This phenotype was the result of molybdate not reaching the nitrogen-fixing nodules, since genetic complementation with a wild-type MtMOT1.2 gene or molybdate-fortification of the nutrient solution, both restored wild-type levels of growth and nitrogenase activity. These results support a model in which MtMOT1.2 would mediate molybdate delivery by the vasculature into the nodules. This article is protected by copyright. All rights reserved.

Phylogeny of nodulation genes and symbiotic diversity of Acacia senegal (L.) Willd. and A. seyal (Del.) Mesorhizobium strains from different regions of Senegal.

PubMed

Bakhoum, Niokhor; Galiana, Antoine; Le Roux, Christine; Kane, Aboubacry; Duponnois, Robin; Ndoye, Fatou; Fall, Dioumacor; Noba, Kandioura; Sylla, Samba Ndao; Diouf, Diégane

2015-04-01

Acacia senegal and Acacia seyal are small, deciduous legume trees, most highly valued for nitrogen fixation and for the production of gum arabic, a commodity of international trade since ancient times. Symbiotic nitrogen fixation by legumes represents the main natural input of atmospheric N2 into ecosystems which may ultimately benefit all organisms. We analyzed the nod and nif symbiotic genes and symbiotic properties of root-nodulating bacteria isolated from A. senegal and A. seyal in Senegal. The symbiotic genes of rhizobial strains from the two Acacia species were closed to those of Mesorhizobium plurifarium and grouped separately in the phylogenetic trees. Phylogeny of rhizobial nitrogen fixation gene nifH was similar to those of nodulation genes (nodA and nodC). All A. senegal rhizobial strains showed identical nodA, nodC, and nifH gene sequences. By contrast, A. seyal rhizobial strains exhibited different symbiotic gene sequences. Efficiency tests demonstrated that inoculation of both Acacia species significantly affected nodulation, total dry weight, acetylene reduction activity (ARA), and specific acetylene reduction activity (SARA) of plants. However, these cross-inoculation tests did not show any specificity of Mesorhizobium strains toward a given Acacia host species in terms of infectivity and efficiency as stated by principal component analysis (PCA). This study demonstrates that large-scale inoculation of A. senegal and A. seyal in the framework of reafforestation programs requires a preliminary step of rhizobial strain selection for both Acacia species.

A phosphoenol pyruvate phosphatase transcript is induced in the root nodule cortex of Phaseolus vulgaris under conditions of phosphorus deficiency

PubMed Central

Bargaz, A.; Drevon, J.J.

2012-01-01

Although previous studies on N2-fixing legumes have demonstrated the contribution of acid phosphatases to their phosphorus (P) use efficiency under P-deficient growth conditions, localization of these enzymes in bean nodules has not been demonstrated. In this study, phosphoenol pyruvate phosphatase (PEPase) gene transcripts were localized within the nodule tissues of two recombinant inbred lines, RIL115 (P-deficiency tolerant) and RIL147 (P-deficiency sensitive), of Phaseolus vulgaris. Nodules were induced by Rhizobium tropici CIAT899 under hydroaeroponic conditions with a sufficient versus a deficient P supply. The results indicated that PEPase transcripts were particularly abundant in the nodule infected zone and cortex of both RILs. Analysis of fluorescence intensity indicated that nodule PEPase was induced under conditions of P deficiency to a significantly higher extent in RIL147 than in RIL115, and more in the inner cortex (91%) than in the outer cortex (71%) or the infected zone (79%). In addition, a significant increase (39%) in PEPase enzyme activity in the P-deficient RIL147 correlated with an increase (58%) in the efficiency of use in rhizobial symbiosis. It was concluded that nodule PEPase is upregulated under conditions of P deficiency in the P-deficiency-sensitive RIL147, and that this gene may contribute to adaptation of rhizobial symbiosis to low-P environments. PMID:22771853

Bioavailability of minerals in legumes.

PubMed

Sandberg, Ann-Sofie

2002-12-01

The mineral content of legumes is generally high, but the bioavailability is poor due to the presence of phytate, which is a main inhibitor of Fe and Zn absorption. Some legumes also contain considerable amounts of Fe-binding polyphenols inhibiting Fe absorption. Furthermore, soya protein per se has an inhibiting effect on Fe absorption. Efficient removal of phytate, and probably also polyphenols, can be obtained by enzymatic degradation during food processing, either by increasing the activity of the naturally occurring plant phytases and polyphenol degrading enzymes, or by addition of enzyme preparations. Biological food processing techniques that increase the activity of the native enzymes are soaking, germination, hydrothermal treatment and fermentation. Food processing can be optimized towards highest phytate degradation provided that the optimal conditions for phytase activity in the plant is known. In contrast to cereals, some legumes have highest phytate degradation at neutral or alkaline pH. Addition of microbial enzyme preparations seems to be the most efficient for complete degradation during processing. Fe and Zn absorption have been shown to be low from legume-based diets. It has also been demonstrated that nutritional Fe deficiency reaches its greatest prevalence in populations subsisting on cereal- and legume-based diets. However, in a balanced diet containing animal protein a high intake of legumes is not considered a risk in terms of mineral supply. Furthermore, once phytate, and in certain legumes polyphenols, is degraded, legumes would become good sources of Fe and Zn as the content of these minerals is high.

Development and validation of a prediction model for measurement variability of lung nodule volumetry in patients with pulmonary metastases.

PubMed

Hwang, Eui Jin; Goo, Jin Mo; Kim, Jihye; Park, Sang Joon; Ahn, Soyeon; Park, Chang Min; Shin, Yeong-Gil

2017-08-01

To develop a prediction model for the variability range of lung nodule volumetry and validate the model in detecting nodule growth. For model development, 50 patients with metastatic nodules were prospectively included. Two consecutive CT scans were performed to assess volumetry for 1,586 nodules. Nodule volume, surface voxel proportion (SVP), attachment proportion (AP) and absolute percentage error (APE) were calculated for each nodule and quantile regression analyses were performed to model the 95% percentile of APE. For validation, 41 patients who underwent metastasectomy were included. After volumetry of resected nodules, sensitivity and specificity for diagnosis of metastatic nodules were compared between two different thresholds of nodule growth determination: uniform 25% volume change threshold and individualized threshold calculated from the model (estimated 95% percentile APE). SVP and AP were included in the final model: Estimated 95% percentile APE = 37.82 · SVP + 48.60 · AP-10.87. In the validation session, the individualized threshold showed significantly higher sensitivity for diagnosis of metastatic nodules than the uniform 25% threshold (75.0% vs. 66.0%, P = 0.004) CONCLUSION: Estimated 95% percentile APE as an individualized threshold of nodule growth showed greater sensitivity in diagnosing metastatic nodules than a global 25% threshold. • The 95 % percentile APE of a particular nodule can be predicted. • Estimated 95 % percentile APE can be utilized as an individualized threshold. • More sensitive diagnosis of metastasis can be made with an individualized threshold. • Tailored nodule management can be provided during nodule growth follow-up.

Morphological and Genetic Diversity of Rhizobia Nodulating Cowpea (Vigna unguiculata L.) from Agricultural Soils of Lower Eastern Kenya.

PubMed

Ondieki, Damaris K; Nyaboga, Evans N; Wagacha, John M; Mwaura, Francis B

2017-01-01

Limited nitrogen (N) content in the soil is a major challenge to sustainable and high crop production in many developing countries. The nitrogen fixing symbiosis of legumes with rhizobia plays an important role in supplying sufficient N for legumes and subsequent nonleguminous crops. To identify rhizobia strains which are suitable for bioinoculant production, characterization of rhizobia is a prerequisite. The objective of this study was to assess the morphological and genetic diversity of rhizobia that nodulates cowpea in agricultural soils of lower eastern Kenya. Twenty-eight rhizobia isolates were recovered from soil samples collected from farmers' fields in Machakos, Makueni, and Kitui counties in lower eastern Kenya and characterized based on morphological characteristics. Thirteen representative isolates were selected and characterized using BOX repetitive element PCR fingerprinting. Based on the dendrogram generated from morphological characteristics, the test isolates were distributed into two major clusters at a similarity of 75%. Phylogenetic tree, based on BOX repetitive element PCR, grouped the isolates into two clusters at 90% similarity level. The clustering of the isolates did not show a relationship to the origin of soil samples, although the isolates were genetically diverse. This study is a prerequisite to the selection of suitable cowpea rhizobia to develop bioinoculants for sustainable crop production in Kenya.

Lenticular fibroxanthomatous nodule.

PubMed

Lee, Seok J; Ling, Jun X; Aaberg, Thomas M; Grossniklaus, Hans E

2003-02-01

To describe two patients with unique lenticular nodular proliferations. Observational case reports. The clinical histories and pathologic findings of two patients with lenticular nodular proliferations were reviewed. One patient with persistent hyperplastic primary vitreous and another patient with trauma developed lenticular nodular proliferations. The nodules were vascularized collections of foamy histiocytes, multinucleated cells, lens capsule, and lens epithelium that had undergone fibrous metaplasia. The lesions were classified as lenticular fibroxanthomatous nodules. A lenticular fibroxanthomatous nodule is a unique clinicopathologic entity that should be differentiated from Soemmerring ring, Elschnig pearl, and other simulating entities such as juvenile xanthogranuloma.

Peroxiredoxins and NADPH-Dependent Thioredoxin Systems in the Model Legume Lotus japonicus1[W][OA

PubMed Central

Tovar-Méndez, Alejandro; Matamoros, Manuel A.; Bustos-Sanmamed, Pilar; Dietz, Karl-Josef; Cejudo, Francisco Javier; Rouhier, Nicolas; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

2011-01-01

Peroxiredoxins (Prxs), thioredoxins (Trxs), and NADPH-thioredoxin reductases (NTRs) constitute central elements of the thiol-disulfide redox regulatory network of plant cells. This study provides a comprehensive survey of this network in the model legume Lotus japonicus. The aims were to identify and characterize these gene families and to assess whether the NTR-Trx systems are operative in nodules. Quantitative reverse transcription-polymerase chain reaction and immunological and proteomic approaches were used for expression profiling. We identified seven Prx, 14 Trx, and three NTR functional genes. The PrxQ1 gene was found to be transcribed in two alternative spliced variants and to be expressed at high levels in leaves, stems, petals, pods, and seeds and at low levels in roots and nodules. The 1CPrx gene showed very high expression in the seed embryos and low expression in vegetative tissues and was induced by nitric oxide and cytokinins. In sharp contrast, cytokinins down-regulated all other Prx genes, except PrxQ1, in roots and nodules, but only 2CPrxA and PrxQ1 in leaves. Gene-specific changes in Prx expression were also observed in response to ethylene, abscisic acid, and auxins. Nodules contain significant mRNA and protein amounts of cytosolic PrxIIB, Trxh1, and NTRA and of plastidic NTRC. Likewise, they express cytosolic Trxh3, Trxh4, Trxh8, and Trxh9, mitochondrial PrxIIF and Trxo, and plastidic Trxm2, Trxm4, and ferredoxin-Trx reductase. These findings reveal a complex regulation of Prxs that is dependent on the isoform, tissue, and signaling molecule and support that redox NTR-Trx systems are functional in the cytosol, mitochondria, and plastids of nodules. PMID:21562331

Trade-Offs between Economic and Environmental Impacts of Introducing Legumes into Cropping Systems

PubMed Central

Reckling, Moritz; Bergkvist, Göran; Watson, Christine A.; Stoddard, Frederick L.; Zander, Peter M.; Walker, Robin L.; Pristeri, Aurelio; Toncea, Ion; Bachinger, Johann

2016-01-01

Europe's agriculture is highly specialized, dependent on external inputs and responsible for negative environmental impacts. Legume crops are grown on less than 2% of the arable land and more than 70% of the demand for protein feed supplement is imported from overseas. The integration of legumes into cropping systems has the potential to contribute to the transition to a more resource-efficient agriculture and reduce the current protein deficit. Legume crops influence the production of other crops in the rotation making it difficult to evaluate the overall agronomic effects of legumes in cropping systems. A novel assessment framework was developed and applied in five case study regions across Europe with the objective of evaluating trade-offs between economic and environmental effects of integrating legumes into cropping systems. Legumes resulted in positive and negative impacts when integrated into various cropping systems across the case studies. On average, cropping systems with legumes reduced nitrous oxide emissions by 18 and 33% and N fertilizer use by 24 and 38% in arable and forage systems, respectively, compared to systems without legumes. Nitrate leaching was similar with and without legumes in arable systems and reduced by 22% in forage systems. However, grain legumes reduced gross margins in 3 of 5 regions. Forage legumes increased gross margins in 3 of 3 regions. Among the cropping systems with legumes, systems could be identified that had both relatively high economic returns and positive environmental impacts. Thus, increasing the cultivation of legumes could lead to economic competitive cropping systems and positive environmental impacts, but achieving this aim requires the development of novel management strategies informed by the involvement of advisors and farmers. PMID:27242870

Trade-Offs between Economic and Environmental Impacts of Introducing Legumes into Cropping Systems.

PubMed

Reckling, Moritz; Bergkvist, Göran; Watson, Christine A; Stoddard, Frederick L; Zander, Peter M; Walker, Robin L; Pristeri, Aurelio; Toncea, Ion; Bachinger, Johann

2016-01-01

Europe's agriculture is highly specialized, dependent on external inputs and responsible for negative environmental impacts. Legume crops are grown on less than 2% of the arable land and more than 70% of the demand for protein feed supplement is imported from overseas. The integration of legumes into cropping systems has the potential to contribute to the transition to a more resource-efficient agriculture and reduce the current protein deficit. Legume crops influence the production of other crops in the rotation making it difficult to evaluate the overall agronomic effects of legumes in cropping systems. A novel assessment framework was developed and applied in five case study regions across Europe with the objective of evaluating trade-offs between economic and environmental effects of integrating legumes into cropping systems. Legumes resulted in positive and negative impacts when integrated into various cropping systems across the case studies. On average, cropping systems with legumes reduced nitrous oxide emissions by 18 and 33% and N fertilizer use by 24 and 38% in arable and forage systems, respectively, compared to systems without legumes. Nitrate leaching was similar with and without legumes in arable systems and reduced by 22% in forage systems. However, grain legumes reduced gross margins in 3 of 5 regions. Forage legumes increased gross margins in 3 of 3 regions. Among the cropping systems with legumes, systems could be identified that had both relatively high economic returns and positive environmental impacts. Thus, increasing the cultivation of legumes could lead to economic competitive cropping systems and positive environmental impacts, but achieving this aim requires the development of novel management strategies informed by the involvement of advisors and farmers.

Compatibility between Legumes and Rhizobia for the Establishment of a Successful Nitrogen-Fixing Symbiosis

PubMed Central

Clúa, Joaquín; Roda, Carla

2018-01-01

The root nodule symbiosis established between legumes and rhizobia is an exquisite biological interaction responsible for fixing a significant amount of nitrogen in terrestrial ecosystems. The success of this interaction depends on the recognition of the right partner by the plant within the richest microbial ecosystems on Earth, the soil. Recent metagenomic studies of the soil biome have revealed its complexity, which includes microorganisms that affect plant fitness and growth in a beneficial, harmful, or neutral manner. In this complex scenario, understanding the molecular mechanisms by which legumes recognize and discriminate rhizobia from pathogens, but also between distinct rhizobia species and strains that differ in their symbiotic performance, is a considerable challenge. In this work, we will review how plants are able to recognize and select symbiotic partners from a vast diversity of surrounding bacteria. We will also analyze recent advances that contribute to understand changes in plant gene expression associated with the outcome of the symbiotic interaction. These aspects of nitrogen-fixing symbiosis should contribute to translate the knowledge generated in basic laboratory research into biotechnological advances to improve the efficiency of the nitrogen-fixing symbiosis in agronomic systems. PMID:29495432

Nitrogen-fixing legume tree species for the reclamation of severely degraded lands in Brazil.

PubMed

Chaer, Guilherme Montandon; Resende, Alexander Silva; Campello, Eduardo Francia Carneiro; de Faria, Sergio Miana; Boddey, Robert Michael

2011-02-01

The main challenges faced in the reclamation of severely degraded lands are in the management of the systems and finding plant species that will grow under the harsh conditions common in degraded soils. This is especially important in extremely adverse situations found in some substrates from mining activities or soils that have lost their upper horizons. Under these conditions, recolonization of the area by native vegetation through natural succession processes may be extremely limited. Once the main physical and chemical factors restrictive to plant growth are corrected or attenuated, the introduction of leguminous trees able to form symbioses with nodulating N₂-fixing bacteria and arbuscular mycorrhizal fungi constitutes an efficient strategy to accelerate soil reclamation and initiate natural succession. These symbioses give the legume species a superior capacity to grow quickly in poor substrates and to withstand the harsh conditions presented in degraded soils. In this article we describe several successful results in Brazil using N₂-fixing legume tree species for reclamation of areas degraded by soil erosion, construction and mining activities, emphasizing the potential of the technique to recover soil organic matter levels and restore ecosystem biodiversity and other environmental functions.

Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant.

PubMed

Horváth, Beatrix; Domonkos, Ágota; Kereszt, Attila; Szűcs, Attila; Ábrahám, Edit; Ayaydin, Ferhan; Bóka, Károly; Chen, Yuhui; Chen, Rujin; Murray, Jeremy D; Udvardi, Michael K; Kondorosi, Éva; Kaló, Péter

2015-12-08

Host compatible rhizobia induce the formation of legume root nodules, symbiotic organs within which intracellular bacteria are present in plant-derived membrane compartments termed symbiosomes. In Medicago truncatula nodules, the Sinorhizobium microsymbionts undergo an irreversible differentiation process leading to the development of elongated polyploid noncultivable nitrogen fixing bacteroids that convert atmospheric dinitrogen into ammonia. This terminal differentiation is directed by the host plant and involves hundreds of nodule specific cysteine-rich peptides (NCRs). Except for certain in vitro activities of cationic peptides, the functional roles of individual NCR peptides in planta are not known. In this study, we demonstrate that the inability of M. truncatula dnf7 mutants to fix nitrogen is due to inactivation of a single NCR peptide, NCR169. In the absence of NCR169, bacterial differentiation was impaired and was associated with early senescence of the symbiotic cells. Introduction of the NCR169 gene into the dnf7-2/NCR169 deletion mutant restored symbiotic nitrogen fixation. Replacement of any of the cysteine residues in the NCR169 peptide with serine rendered it incapable of complementation, demonstrating an absolute requirement for all cysteines in planta. NCR169 was induced in the cell layers in which bacteroid elongation was most pronounced, and high expression persisted throughout the nitrogen-fixing nodule zone. Our results provide evidence for an essential role of NCR169 in the differentiation and persistence of nitrogen fixing bacteroids in M. truncatula.

Loss of the nodule-specific cysteine rich peptide, NCR169, abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant

PubMed Central

Horváth, Beatrix; Domonkos, Ágota; Szűcs, Attila; Ábrahám, Edit; Ayaydin, Ferhan; Bóka, Károly; Chen, Yuhui; Chen, Rujin; Murray, Jeremy D.; Udvardi, Michael K.; Kondorosi, Éva; Kaló, Péter

2015-01-01

Host compatible rhizobia induce the formation of legume root nodules, symbiotic organs within which intracellular bacteria are present in plant-derived membrane compartments termed symbiosomes. In Medicago truncatula nodules, the Sinorhizobium microsymbionts undergo an irreversible differentiation process leading to the development of elongated polyploid noncultivable nitrogen fixing bacteroids that convert atmospheric dinitrogen into ammonia. This terminal differentiation is directed by the host plant and involves hundreds of nodule specific cysteine-rich peptides (NCRs). Except for certain in vitro activities of cationic peptides, the functional roles of individual NCR peptides in planta are not known. In this study, we demonstrate that the inability of M. truncatula dnf7 mutants to fix nitrogen is due to inactivation of a single NCR peptide, NCR169. In the absence of NCR169, bacterial differentiation was impaired and was associated with early senescence of the symbiotic cells. Introduction of the NCR169 gene into the dnf7-2/NCR169 deletion mutant restored symbiotic nitrogen fixation. Replacement of any of the cysteine residues in the NCR169 peptide with serine rendered it incapable of complementation, demonstrating an absolute requirement for all cysteines in planta. NCR169 was induced in the cell layers in which bacteroid elongation was most pronounced, and high expression persisted throughout the nitrogen-fixing nodule zone. Our results provide evidence for an essential role of NCR169 in the differentiation and persistence of nitrogen fixing bacteroids in M. truncatula. PMID:26401023

Organogenic nodule development in hop (Humulus lupulus L.): Transcript and metabolic responses

PubMed Central

Fortes, Ana M; Santos, Filipa; Choi, Young H; Silva, Marta S; Figueiredo, Andreia; Sousa, Lisete; Pessoa, Fernando; Santos, Bartolomeu A; Sebastiana, Mónica; Palme, Klaus; Malhó, Rui; Verpoorte, Rob; Pais, Maria S

2008-01-01

Background Hop (Humulus lupulus L.) is an economically important plant forming organogenic nodules which can be used for genetic transformation and micropropagation. We are interested in the mechanisms underlying reprogramming of cells through stress and hormone treatments. Results An integrated molecular and metabolomic approach was used to investigate global gene expression and metabolic responses during development of hop's organogenic nodules. Transcript profiling using a 3,324-cDNA clone array revealed differential regulation of 133 unigenes, classified into 11 functional categories. Several pathways seem to be determinant in organogenic nodule formation, namely defense and stress response, sugar and lipid metabolism, synthesis of secondary metabolites and hormone signaling. Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, lipid and sugar metabolism and secondary metabolism in organogenic nodule formation. Conclusion The expression profile of genes pivotal for energy metabolism, together with metabolites profile, suggested that these morphogenic structures gain energy through a heterotrophic, transport-dependent and sugar-degrading anaerobic metabolism. Polyamines and auxins are likely to be involved in the regulation of expression of many genes related to organogenic nodule formation. These results represent substantial progress toward a better understanding of this complex developmental program and reveal novel information regarding morphogenesis in plants. PMID:18823540

Molecular cloning of the BLADE-ON-PETIOLE gene and expression analyses during nodule development in Lupinus luteus.

PubMed

Frankowski, Kamil; Wilmowicz, Emilia; Kućko, Agata; Zienkiewicz, Agnieszka; Zienkiewicz, Krzysztof; Kopcewicz, Jan

2015-05-01

The BLADE-ON-PETIOLE (BOP) genes have been recently shown to play an essential role in many physiological processes, including embryogenesis, meristem determinacy, leaf patterning and nodule development. In our research we used Lupinus luteus, a plant with great agronomic potential due to its high protein content and nitrogen fixation ability. In this work, LlBOP in L. luteus was identified for the first time and its expression during nodule development was analyzed. The high expression levels of LlBOP and LlLbI (LEGHEMOGLOBIN), essential to nitrogen-fixing symbiosis, were noted in the developing root nodules and were correlated with the occurrence of leghemoglobin. All of these data indicate that LlBOP is an important regulator of root nodule formation and functioning in L. luteus. Copyright © 2015 Elsevier GmbH. All rights reserved.

Biogeography of a Novel Ensifer meliloti Clade Associated with the Australian Legume Trigonella suavissima

PubMed Central

Elia, Patrick; Brockwell, John; Golemboski, Daniel; van Berkum, Peter

2017-01-01

ABSTRACT Here, we describe a novel clade within Ensifer meliloti and consider how geographic and ecological isolation contributed to the limited distribution of this group. Members of the genus Ensifer are best known for their ability to form nitrogen-fixing symbioses with forage legumes of three related genera, Medicago L., Melilotus Mill., and Trigonella L., which are members of the tribe Trifolieae. These legumes have a natural distribution extending from the Mediterranean Basin through western Asia, where there is an unsurpassed number of species belonging to these genera. Trigonella suavissima L. is unusual in that it is the only species in the tribe Trifolieae that is native to Australia. We compared the genetic diversity and taxonomic placement of rhizobia nodulating T. suavissima with those of members of an Ensifer reference collection. Our goal was to determine if the T. suavissima rhizobial strains, like their plant host, are naturally limited to the Australian continent. We used multilocus sequence analysis to estimate the genetic relatedness of 56 T. suavissima symbionts to 28 Ensifer reference strains. Sequence data were partitioned according to the replicons in which the loci are located. The results were used to construct replicon-specific phylogenetic trees. In both the chromosomal and chromid trees, the Australian strains formed a distinct clade within E. meliloti. The strains also shared few alleles with Ensifer reference strains from other continents. Carbon source utilization assays revealed that the strains are also unusual in their ability to utilize 2-oxoglutarate as a sole carbon source. A strategy was outlined for locating similar strains elsewhere. IMPORTANCE In this study, we employed a biogeographical approach to investigate the origins of a symbiotic relationship between an Australian legume and its nitrogen-fixing rhizobia. The question of the ancestral origins of these symbionts is based on the observation that the legume host is not

Effects, tolerance mechanisms and management of salt stress in grain legumes.

PubMed

Farooq, Muhammad; Gogoi, Nirmali; Hussain, Mubshar; Barthakur, Sharmistha; Paul, Sreyashi; Bharadwaj, Nandita; Migdadi, Hussein M; Alghamdi, Salem S; Siddique, Kadambot H M

2017-09-01

Salt stress is an ever-present threat to crop yields, especially in countries with irrigated agriculture. Efforts to improve salt tolerance in crop plants are vital for sustainable crop production on marginal lands to ensure future food supplies. Grain legumes are a fascinating group of plants due to their high grain protein contents and ability to fix biological nitrogen. However, the accumulation of excessive salts in soil and the use of saline groundwater are threatening legume production worldwide. Salt stress disturbs photosynthesis and hormonal regulation and causes nutritional imbalance, specific ion toxicity and osmotic effects in legumes to reduce grain yield and quality. Understanding the responses of grain legumes to salt stress and the associated tolerance mechanisms, as well as assessing management options, may help in the development of strategies to improve the performance of grain legumes under salt stress. In this manuscript, we discuss the effects, tolerance mechanisms and management of salt stress in grain legumes. The principal inferences of the review are: (i) salt stress reduces seed germination (by up to more than 50%) either by inhibiting water uptake and/or the toxic effect of ions in the embryo, (ii) salt stress reduces growth (by more than 70%), mineral uptake, and yield (by 12-100%) due to ion toxicity and reduced photosynthesis, (iii) apoplastic acidification is a good indicator of salt stress tolerance, (iv) tolerance to salt stress in grain legumes may develop through excretion and/or compartmentalization of toxic ions, increased antioxidant capacity, accumulation of compatible osmolytes, and/or hormonal regulation, (v) seed priming and nutrient management may improve salt tolerance in grain legumes, (vi) plant growth promoting rhizobacteria and arbuscular mycorrhizal fungi may help to improve salt tolerance due to better plant nutrient availability, and (vii) the integration of screening, innovative breeding, and the development of

Metabolic features involved in drought stress tolerance mechanisms in peanut nodules and their contribution to biological nitrogen fixation.

PubMed

Furlan, Ana Laura; Bianucci, Eliana; Castro, Stella; Dietz, Karl-Josef

2017-10-01

Legumes belong to the most important crops worldwide. They increase soil fertility due their ability to establish symbiotic associations with soil microorganisms, known as rhizobia, capable of fixing nitrogen from the atmosphere. However, they are frequently exposed to abiotic stress conditions in particular drought. Such adverse conditions impair the biological nitrogen fixation (BNF) and depend largely on the legume. Therefore, two peanut cultivars with contrasting tolerance to drought, namely the more tolerant EC-98 and the sensitive Granoleico, were investigated to elucidate the relative contribution of BNF to the tolerance to drought. The tolerant cultivar EC-98 sustained growth and BNF similar to the control condition despite the reduced water potential and photosynthesis, suggesting the functioning of distinct metabolic pathways that contributed to enhance the tolerance. The biochemical and metabolomics approaches revealed that nodules from the tolerant cultivar accumulated trehalose, proline and gamma-aminobutyric acid (GABA), metabolites with known function in protecting against drought stress. The amide metabolism was severely affected in nodules from the sensitive cultivar Granoleico as revealed by the low content of asparagine and glutamine in the drought stressed plants. The sensitive cultivar upon rehydration was unable to re-establish a metabolism similar to well-watered plants. This was evidenced by the low level of metabolites and, transcripts and specific activities of enzymes from the carbon (sucrose synthase) and nitrogen (glutamine synthetase) metabolism which decreased below the values of control plants. Therefore, the increased content of metabolites with protective functions under drought stress likely is crucial for the full restoration upon rehydration. Smaller changes of drought stress-related metabolites in nodule are another trait that contributes to the effective control of BNF in the tolerant peanut cultivar (EC-98). Copyright © 2017

Accelerating Genetic Gains in Legumes for the Development of Prosperous Smallholder Agriculture: Integrating Genomics, Phenotyping, Systems Modelling and Agronomy.

PubMed

Varshney, Rajeev K; Thudi, Mahendar; Pandey, Manish K; Tardieu, Francois; Ojiewo, Chris; Vadez, Vincent; Whitbread, Anthony M; Siddique, Kadambot H M; Nguyen, Henry T; Carberry, Peter S; Bergvinson, David

2018-03-05

Grain legumes form an important component of the human diet, feed for livestock and replenish soil fertility through biological nitrogen fixation. Globally, the demand for food legumes is increasing as they complement cereals in protein requirements and possess a high percentage of digestible protein. Climate change has enhanced the frequency and intensity of drought stress that is posing serious production constraints, especially in rainfed regions where most legumes are produced. Genetic improvement of legumes, like other crops, is mostly based on pedigree and performance-based selection over the last half century. For achieving faster genetic gains in legumes in rainfed conditions, this review article proposes the integration of modern genomics approaches, high throughput phenomics and simulation modelling as support for crop improvement that leads to improved varieties that perform with appropriate agronomy. Selection intensity, generation interval and improved operational efficiencies in breeding are expected to further enhance the genetic gain in experiment plots. Improved seed access to farmers, combined with appropriate agronomic packages in farmers' fields, will deliver higher genetic gains. Enhanced genetic gains including not only productivity but also nutritional and market traits will increase the profitability of farmers and the availability of affordable nutritious food especially in developing countries.

Potential of legume-based grassland–livestock systems in Europe: a review

PubMed Central

Lüscher, A; Mueller-Harvey, I; Soussana, J F; Rees, R M; Peyraud, J L

2014-01-01

European grassland-based livestock production systems face the challenge of producing more meat and milk to meet increasing world demands and to achieve this using fewer resources. Legumes offer great potential for achieving these objectives. They have numerous features that can act together at different stages in the soil–plant–animal–atmosphere system, and these are most effective in mixed swards with a legume proportion of 30–50%. The resulting benefits include reduced dependence on fossil energy and industrial N-fertilizer, lower quantities of harmful emissions to the environment (greenhouse gases and nitrate), lower production costs, higher productivity and increased protein self-sufficiency. Some legume species offer opportunities for improving animal health with less medication, due to the presence of bioactive secondary metabolites. In addition, legumes may offer an adaptation option to rising atmospheric CO2 concentrations and climate change. Legumes generate these benefits at the level of the managed land-area unit and also at the level of the final product unit. However, legumes suffer from some limitations, and suggestions are made for future research to exploit more fully the opportunities that legumes can offer. In conclusion, the development of legume-based grassland–livestock systems undoubtedly constitutes one of the pillars for more sustainable and competitive ruminant production systems, and it can be expected that forage legumes will become more important in the future. PMID:26300574

Responses of symbiotic nitrogen-fixing common bean to aluminum toxicity and delineation of nodule responsive microRNAs.

PubMed

Mendoza-Soto, Ana B; Naya, Loreto; Leija, Alfonso; Hernández, Georgina

2015-01-01

Aluminum (Al) toxicity is widespread in acidic soils where the common bean (Phaseolus vulgaris), the most important legume for human consumption, is produced and it is a limiting factor for crop production and symbiotic nitrogen fixation. We characterized the nodule responses of common bean plants inoculated with Rhizobioum tropici CIAT899 and the root responses of nitrate-fertilized plants exposed to excess Al in low pH, for long or short periods. A 43-50% reduction in nitrogenase activity indicates that Al toxicity (Alt) highly affected nitrogen fixation in common bean. Bean roots and nodules showed characteristic symptoms for Alt. In mature nodules Al accumulation and lipoperoxidation were observed in the infected zone, while callose deposition and cell death occurred mainly in the nodule cortex. Regulatory mechanisms of plant responses to metal toxicity involve microRNAs (miRNAs) along other regulators. Using a miRNA-macroarray hybridization approach we identified 28 (14 up-regulated) Alt nodule-responsive miRNAs. We validated (quantitative reverse transcriptase-PCR) the expression of eight nodule responsive miRNAs in roots and in nodules exposed to high Al for long or short periods. The inverse correlation between the target and miRNA expression ratio (stress:control) was observed in every case. Generally, miRNAs showed a higher earlier response in roots than in nodules. Some of the common bean Alt-responsive miRNAs identified has also been reported as differentially expressed in other plant species subjected to similar stress condition. miRNA/target nodes analyzed in this work are known to be involved in relevant signaling pathways, thus we propose that the participation of miR164/NAC1 (NAM/ATAF/CUC transcription factor) and miR393/TIR1 (TRANSPORT INHIBITOR RESPONSE 1-like protein) in auxin and of miR170/SCL (SCARECROW-like protein transcription factor) in gibberellin signaling is relevant for common bean response/adaptation to Al stress. Our data provide a

Responses of symbiotic nitrogen-fixing common bean to aluminum toxicity and delineation of nodule responsive microRNAs

PubMed Central

Mendoza-Soto, Ana B.; Naya, Loreto; Leija, Alfonso; Hernández, Georgina

2015-01-01

Aluminum (Al) toxicity is widespread in acidic soils where the common bean (Phaseolus vulgaris), the most important legume for human consumption, is produced and it is a limiting factor for crop production and symbiotic nitrogen fixation. We characterized the nodule responses of common bean plants inoculated with Rhizobioum tropici CIAT899 and the root responses of nitrate-fertilized plants exposed to excess Al in low pH, for long or short periods. A 43–50% reduction in nitrogenase activity indicates that Al toxicity (Alt) highly affected nitrogen fixation in common bean. Bean roots and nodules showed characteristic symptoms for Alt. In mature nodules Al accumulation and lipoperoxidation were observed in the infected zone, while callose deposition and cell death occurred mainly in the nodule cortex. Regulatory mechanisms of plant responses to metal toxicity involve microRNAs (miRNAs) along other regulators. Using a miRNA-macroarray hybridization approach we identified 28 (14 up-regulated) Alt nodule-responsive miRNAs. We validated (quantitative reverse transcriptase-PCR) the expression of eight nodule responsive miRNAs in roots and in nodules exposed to high Al for long or short periods. The inverse correlation between the target and miRNA expression ratio (stress:control) was observed in every case. Generally, miRNAs showed a higher earlier response in roots than in nodules. Some of the common bean Alt-responsive miRNAs identified has also been reported as differentially expressed in other plant species subjected to similar stress condition. miRNA/target nodes analyzed in this work are known to be involved in relevant signaling pathways, thus we propose that the participation of miR164/NAC1 (NAM/ATAF/CUC transcription factor) and miR393/TIR1 (TRANSPORT INHIBITOR RESPONSE 1-like protein) in auxin and of miR170/SCL (SCARECROW-like protein transcription factor) in gibberellin signaling is relevant for common bean response/adaptation to Al stress. Our data provide a

Hemoglobin LjGlb1-1 is involved in nodulation and regulates the level of nitric oxide in the Lotus japonicus-Mesorhizobium loti symbiosis.

PubMed

Fukudome, Mitsutaka; Calvo-Begueria, Laura; Kado, Tomohiro; Osuki, Ken-Ichi; Rubio, Maria Carmen; Murakami, Ei-Ichi; Nagata, Maki; Kucho, Ken-Ichi; Sandal, Niels; Stougaard, Jens; Becana, Manuel; Uchiumi, Toshiki

2016-09-01

Leghemoglobins transport and deliver O2 to the symbiosomes inside legume nodules and are essential for nitrogen fixation. However, the roles of other hemoglobins (Hbs) in the rhizobia-legume symbiosis are unclear. Several Lotus japonicus mutants affecting LjGlb1-1, a non-symbiotic class 1 Hb, have been used to study the function of this protein in symbiosis. Two TILLING alleles with single amino acid substitutions (A102V and E127K) and a LORE1 null allele with a retrotransposon insertion in the 5'-untranslated region (96642) were selected for phenotyping nodulation. Plants of all three mutant lines showed a decrease in long infection threads and nodules, and an increase in incipient infection threads. About 4h after inoculation, the roots of mutant plants exhibited a greater transient accumulation of nitric oxide (NO) than did the wild-type roots; nevertheless, in vitro NO dioxygenase activities of the wild-type, A102V, and E127K proteins were similar, suggesting that the mutated proteins are not fully functional in vivo The expression of LjGlb1-1, but not of the other class 1 Hb of L. japonicus (LjGlb1-2), was affected during infection of wild-type roots, further supporting a specific role for LjGlb1-1. In conclusion, the LjGlb1-1 mutants reveal that this protein is required during rhizobial infection and regulates NO levels. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Rhizobial Nodulation Factors Stimulate Mycorrhizal Colonization of Nodulating and Nonnodulating Soybeans.

PubMed

Xie, Z. P.; Staehelin, C.; Vierheilig, H.; Wiemken, A.; Jabbouri, S.; Broughton, W. J.; Vogeli-Lange, R.; Boller, T.

1995-08-01

Legumes form tripartite symbiotic associations with noduleinducing rhizobia and vesicular-arbuscular mycorrhizal fungi. Co-inoculation of soybean (Glycine max [L.] Merr.) roots with Bradyrhizobium japonicum 61-A-101 considerably enhanced colonization by the mycorrhizal fungus Glomus mosseae. A similar stimulatory effect on mycorrhizal colonization was also observed in nonnodulating soybean mutants when inoculated with Bradyrhizobium japonicum and in wild-type soybean plants when inoculated with ineffective rhizobial strains, indicating that a functional rhizobial symbiosis is not necessary for enhanced mycorrhiza formation. Inoculation with the mutant Rhizobium sp. NGR[delta]nodABC, unable to produce nodulation (Nod) factors, did not show any effect on mycorrhiza. Highly purified Nod factors also increased the degree of mycorrhizal colonization. Nod factors from Rhizobium sp. NGR234 differed in their potential to promote fungal colonization. The acetylated factor NodNGR-V (MeFuc, Ac), added at concentrations as low as 10-9 M, was active, whereas the sulfated factor, NodNGR-V (MeFuc, S), was inactive. Several soybean flavonoids known to accumulate in response to the acetylated Nod factor showed a similar promoting effect on mycorrhiza. These results suggest that plant flavonoids mediate the Nod factor-induced stimulation of mycorrhizal colonization in soybean roots.

Rhizobial Nodulation Factors Stimulate Mycorrhizal Colonization of Nodulating and Nonnodulating Soybeans.

PubMed Central

Xie, Z. P.; Staehelin, C.; Vierheilig, H.; Wiemken, A.; Jabbouri, S.; Broughton, W. J.; Vogeli-Lange, R.; Boller, T.

1995-01-01

Legumes form tripartite symbiotic associations with noduleinducing rhizobia and vesicular-arbuscular mycorrhizal fungi. Co-inoculation of soybean (Glycine max [L.] Merr.) roots with Bradyrhizobium japonicum 61-A-101 considerably enhanced colonization by the mycorrhizal fungus Glomus mosseae. A similar stimulatory effect on mycorrhizal colonization was also observed in nonnodulating soybean mutants when inoculated with Bradyrhizobium japonicum and in wild-type soybean plants when inoculated with ineffective rhizobial strains, indicating that a functional rhizobial symbiosis is not necessary for enhanced mycorrhiza formation. Inoculation with the mutant Rhizobium sp. NGR[delta]nodABC, unable to produce nodulation (Nod) factors, did not show any effect on mycorrhiza. Highly purified Nod factors also increased the degree of mycorrhizal colonization. Nod factors from Rhizobium sp. NGR234 differed in their potential to promote fungal colonization. The acetylated factor NodNGR-V (MeFuc, Ac), added at concentrations as low as 10-9 M, was active, whereas the sulfated factor, NodNGR-V (MeFuc, S), was inactive. Several soybean flavonoids known to accumulate in response to the acetylated Nod factor showed a similar promoting effect on mycorrhiza. These results suggest that plant flavonoids mediate the Nod factor-induced stimulation of mycorrhizal colonization in soybean roots. PMID:12228558

Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov., isolated from root nodules of different agroforestry legume trees.

PubMed

Degefu, Tulu; Wolde-Meskel, Endalkachew; Liu, Binbin; Cleenwerck, Ilse; Willems, Anne; Frostegård, Åsa

2013-05-01

A total of 18 strains, representing members of the genus Mesorhizobium, obtained from root nodules of woody legumes growing in Ethiopia, have been previously shown, by multilocus sequence analysis (MLSA) of five housekeeping genes, to form three novel genospecies. In the present study, the phylogenetic relationship between representative strains of these three genospecies and the type strains of their closest phylogenetic neighbours Mesorhizobium plurifarium, Mesorhizobium amorphae, Mesorhizobium septentrionale and Mesorhizobium huakuii was further evaluated using a polyphasic taxonomic approach. In line with our earlier MLSA of other housekeeping genes, the phylogenetic trees derived from the atpD and glnII genes grouped the test strains into three well-supported, distinct lineages that exclude all defined species of the genus Mesorhizobium. The DNA-DNA relatedness between the representative strains of genospecies I-III and the type strains of their closest phylogenetic neighbours was low (≤59 %). They differed from each other and from their closest phylogenetic neighbours by the presence/absence of several fatty acids, or by large differences in the relative amounts of particular fatty acids. While showing distinctive features, they were generally able to utilize a wide range of substrates as sole carbon and nitrogen sources. The strains belonging to genospecies I, II and III therefore represent novel species for which we propose the names Mesorhizobium shonense sp. nov., Mesorhizobium hawassense sp. nov. and Mesorhizobium abyssinicae sp. nov. The isolates AC39a(T) ( = LMG 26966(T) = HAMBI 3295(T)), AC99b(T) ( = LMG 26968(T) = HAMBI 3301(T)) and AC98c(T) ( = LMG 26967(T) = HAMBI 3306(T)) are proposed as type strains for the respective novel species.

RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2

PubMed Central

Yuan, Song L.; Li, Rong; Chen, Hai F.; Zhang, Chan J.; Chen, Li M.; Hao, Qing N.; Chen, Shui L.; Shan, Zhi H.; Yang, Zhong L.; Zhang, Xiao J.; Qiu, De Z.; Zhou, Xin A.

2017-01-01

Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages. PMID:28169364

An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula1[W

PubMed Central

Cabeza, Ricardo; Koester, Beke; Liese, Rebecca; Lingner, Annika; Baumgarten, Vanessa; Dirks, Jan; Salinas-Riester, Gabriela; Pommerenke, Claudia; Dittert, Klaus; Schulze, Joachim

2014-01-01

The mechanism through which nitrate reduces the activity of legume nodules is controversial. The objective of the study was to follow Medicago truncatula nodule activity after nitrate provision continuously and to identify molecular mechanisms, which down-regulate the activity of the nodules. Nodule H2 evolution started to decline after about 4 h of nitrate application. At that point in time, a strong shift in nodule gene expression (RNA sequencing) had occurred (1,120 differentially expressed genes). The most pronounced effect was the down-regulation of 127 genes for nodule-specific cysteine-rich peptides. Various other nodulins were also strongly down-regulated, in particular all the genes for leghemoglobins. In addition, shifts in the expression of genes involved in cellular iron allocation and mitochondrial ATP synthesis were observed. Furthermore, the expression of numerous genes for the formation of proteins and glycoproteins with no obvious function in nodules (e.g. germins, patatin, and thaumatin) was strongly increased. This occurred in conjunction with an up-regulation of genes for proteinase inhibitors, in particular those containing the Kunitz domain. The additionally formed proteins might possibly be involved in reducing nodule oxygen permeability. Between 4 and 28 h of nitrate exposure, a further reduction in nodule activity occurred, and the number of differentially expressed genes almost tripled. In particular, there was a differential expression of genes connected with emerging senescence. It is concluded that nitrate exerts rapid and manifold effects on nitrogenase activity. A certain degree of nitrate tolerance might be achieved when the down-regulatory effect on late nodulins can be alleviated. PMID:24285852

Phosphorus acquisition and utilisation in crop legumes under global change.

PubMed

Pang, Jiayin; Ryan, Megan H; Lambers, Hans; Siddique, Kadambot Hm

2018-05-28

Improving phosphorus (P)-use efficiency in legumes is a worldwide challenge in the face of an increasing world population, dwindling global rock phosphate reserves, the relatively high P demand of legumes and global change. This review focuses on P acquisition of crop legumes in response to climate change. We advocate further studies on: firstly, the response of carboxylate exudation, mycorrhizas and root morphology to climate change and their role in P acquisition as dependent on edaphic factors; secondly, developing intercropping systems with a combination of a legume and another crop species to enhance P acquisition; and thirdly, the impact of the interactions of the major climate change factors on P acquisition in the field. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of GH replacement therapy on thyroid volume and nodule development in GH deficient adults: a retrospective cohort study.

PubMed

Curtò, Lorenzo; Giovinazzo, Salvatore; Alibrandi, Angela; Campennì, Alfredo; Trimarchi, Francesco; Cannavò, Salvatore; Ruggeri, Rosaria Maddalena

2015-05-01

Despite the well-known effects of GH/IGF1 signaling on the thyroid, few data are available on the risk of developing nodular goiter in hypopituitary subjects during GH replacement therapy (GHRT). We aimed to define the effects of GH therapy on thyroid volume (TV) and nodular growth. The records of 96 subjects (47 males and 49 females, median age 48 years) with GH deficit (GHD) were investigated. Seventy also had central hypothyroidism (CH). At the time of our retrospective evaluation, median treatment duration was 5 years. Pre-treatment TV was smaller in GHD patients than in healthy subjects (P=0.030). During GH treatment, TV significantly increased (P=0.016 for the entire group and P=0.014 in euthyroid GHD patients). Before starting GH therapy, 17 patients harbored thyroid nodules. During GH therapy, nodule size increased slightly in seven patients, and new thyroid nodules occurred in nine patients. Among the 79 patients without pre-existing thyroid nodules, 17 developed one or more nodules. There was no difference in the prevalence of CH in GHD patients with or without thyroid nodules (P=0.915; P=0.841, when patients with pre-therapy nodular goiter were excluded), the main predictor for nodule development being serum IGF1 (P=0.038). GHRT is associated with TV's increase in GHD patients. Thyroid nodules developed in 27% of patients, mainly in relation to pre-therapy IGF1 levels, independently of normal or impaired TSH stimulation. © 2015 European Society of Endocrinology.

A Comparative Nitrogen Balance and Productivity Analysis of Legume and Non-legume Supported Cropping Systems: The Potential Role of Biological Nitrogen Fixation.

PubMed

Iannetta, Pietro P M; Young, Mark; Bachinger, Johann; Bergkvist, Göran; Doltra, Jordi; Lopez-Bellido, Rafael J; Monti, Michele; Pappa, Valentini A; Reckling, Moritz; Topp, Cairistiona F E; Walker, Robin L; Rees, Robert M; Watson, Christine A; James, Euan K; Squire, Geoffrey R; Begg, Graham S

2016-01-01

The potential of biological nitrogen fixation (BNF) to provide sufficient N for production has encouraged re-appraisal of cropping systems that deploy legumes. It has been argued that legume-derived N can maintain productivity as an alternative to the application of mineral fertilizer, although few studies have systematically evaluated the effect of optimizing the balance between legumes and non N-fixing crops to optimize production. In addition, the shortage, or even absence in some regions, of measurements of BNF in crops and forages severely limits the ability to design and evaluate new legume-based agroecosystems. To provide an indication of the magnitude of BNF in European agriculture, a soil-surface N-balance approach was applied to historical data from 8 experimental cropping systems that compared legume and non-legume crop types (e.g., grains, forages and intercrops) across pedoclimatic regions of Europe. Mean BNF for different legume types ranged from 32 to 115 kg ha -1 annually. Output in terms of total biomass (grain, forage, etc.) was 30% greater in non-legumes, which used N to produce dry matter more efficiently than legumes, whereas output of N was greater from legumes. When examined over the crop sequence, the contribution of BNF to the N-balance increased to reach a maximum when the legume fraction was around 0.5 (legume crops were present in half the years). BNF was lower when the legume fraction increased to 0.6-0.8, not because of any feature of the legume, but because the cropping systems in this range were dominated by mixtures of legume and non-legume forages to which inorganic N as fertilizer was normally applied. Forage (e.g., grass and clover), as opposed to grain crops in this range maintained high outputs of biomass and N. In conclusion, BNF through grain and forage legumes has the potential to generate major benefit in terms of reducing or dispensing with the need for mineral N without loss of total output.

Interactions between ethylene, gibberellins, and brassinosteroids in the development of rhizobial and mycorrhizal symbioses of pea.

PubMed

Foo, Eloise; McAdam, Erin L; Weller, James L; Reid, James B

2016-04-01

The regulation of arbuscular mycorrhizal development and nodulation involves complex interactions between the plant and its microbial symbionts. In this study, we use the recently identified ethylene-insensitive ein2 mutant in pea (Pisum sativum L.) to explore the role of ethylene in the development of these symbioses. We show that ethylene acts as a strong negative regulator of nodulation, confirming reports in other legumes. Minor changes in gibberellin1 and indole-3-acetic acid levels in ein2 roots appear insufficient to explain the differences in nodulation. Double mutants produced by crosses between ein2 and the severely gibberellin-deficient na and brassinosteroid-deficient lk mutants showed increased nodule numbers and reduced nodule spacing compared with the na and lk single mutants, but nodule numbers and spacing were typical of ein2 plants, suggesting that the reduced number of nodules innaandlkplants is largely due to the elevated ethylene levels previously reported in these mutants. We show that ethylene can also negatively regulate mycorrhizae development when ethylene levels are elevated above basal levels, consistent with a role for ethylene in reducing symbiotic development under stressful conditions. In contrast to the hormone interactions in nodulation, ein2 does not override the effect of lk or na on the development of arbuscular mycorrhizae, suggesting that brassinosteroids and gibberellins influence this process largely independently of ethylene. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Wild peanut Arachis duranensis are nodulated by diverse and novel Bradyrhizobium species in acid soils.

PubMed

Chen, Jing Yu; Gu, Jun; Wang, En Tao; Ma, Xing Xian; Kang, Shi Tong; Huang, Ling Zi; Cao, Xue Ping; Li, Liang Bing; Wu, Yan Ling

2014-10-01

Aiming at learning the microsymbionts of Arachis duranensis, a diploid ancestor of cultivated peanut, genetic and symbiotic characterization of 32 isolates from root nodules of this plant grown in its new habitat Guangzhou was performed. Based upon the phylogeny of 16S rRNA, atpD and recA genes, diverse bacteria belonging to Bradyrhizobium yuanmingense, Bradyrhizobium elkanii, Bradyrhizobium iriomotense and four new lineages of Bradyrhizobium (19 isolates), Rhizobium/Agrobacterium (9 isolates), Herbaspirillum (2 isolates) and Burkholderia (2 isolates) were defined. In the nodulation test on peanut, only the bradyrhizobial strains were able to induce effective nodules. Phylogeny of nodC divided the Bradyrhizobium isolates into four lineages corresponding to the grouping results in phylogenetic analysis of housekeeping genes, suggesting that this symbiosis gene was mainly maintained by vertical gene transfer. These results demonstrate that A. duranensis is a promiscuous host preferred the Bradyrhizobium species with different symbiotic gene background as microsymbionts, and that it might have selected some native rhizobia, especially the novel lineages Bradyrhizobium sp. I and sp. II, in its new habitat Guangzhou. These findings formed a basis for further study on adaptation and evolution of symbiosis between the introduced legumes and the indigenous rhizobia. Copyright © 2014 Elsevier GmbH. All rights reserved.

Effect of nano-zinc oxide on nitrogenase activity in legumes: an interplay of concentration and exposure time

NASA Astrophysics Data System (ADS)

Kumar, Praveen; Burman, Uday; Santra, P.

2015-07-01

Experiments were carried out to study the effect of zinc oxide nanoparticles (nano-ZnO) on nitrogenase activity in legumes. In the first experiment, nodulated roots of cluster bean, moth bean, green gram and cowpea were dipped in Hoagland solution containing 1.5 and 10 μg mL-1 of nano-ZnO for 24 h. Nitrogenase activity in cluster bean, green gram and cowpea roots increased after dipping in solution containing 1.5 μg mL-1 nano-ZnO, but decreased in roots dipped in solution containing 10 μg mL-1 nano-ZnO. However, in moth bean roots, nitrogenase activity decreased after dipping in solution containing either concentration of nano-ZnO. In the second experiment, nodulated roots of green gram were dipped in Hoagland solution containing 1, 4, 6, 8 and 10 μg mL-1 nano-ZnO for 6-30 h before estimating nitrogenase activity. Results showed that an interactive effect of nano-ZnO concentration and exposure time influenced nitrogenase activity. The possible reasons behind this effect have been discussed. A model [ A = 3.44 + 0.46 t - 0.01 t 2 - 0.002 tc 2 ( R 2 = 0.81)] involving linear and power components was developed to simulate the response of nitrogenase activity in green gram roots to the concentration and exposure time of nano-ZnO.

Athlete's nodule.

PubMed

Uchiyama, Masaki; Tsuboi, Ryoji; Mitsuhashi, Yoshihiko

2009-11-01

Three cases of athlete's nodule on the feet are reported. In case 1, a 30-year-old man, who had been an amateur football player, presented with nodules on the lateral side of the feet and on the right lateral malleolus with a duration of 1 year. In case 2, a 22-year-old man, who had participated in karate and track-and-field, presented with nodules on the lateral side of the feet and on the right lateral malleolus with a duration of 10 years. In case 3, a 25-year-old man, who had skied, presented with a nodule on the right lateral malleolus with a duration of 4 years. The biopsy specimens from the lesion demonstrated hyperkeratosis, acanthosis of the epidermis and thickness of the dermis. In 1991, Cohen et al. proposed the concept of athlete's nodule which indicated an acquired cutaneous nodule caused by chronic stimuli with sports. Histopathology of the athlete's nodule shows hypertrophy of the epidermis and dermis. To the best of our knowledge the term "athlete's nodule" has not been used in Japan, but it is a useful term to refer to the lesion induced by athletics or the use of sporting equipment.

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

PubMed Central

Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

2016-01-01

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: application to the identification of Lupinus nodulating strains.

PubMed

Sánchez-Juanes, Fernando; Ferreira, Laura; Alonso de la Vega, Pablo; Valverde, Angel; Barrios, Milagros León; Rivas, Raúl; Mateos, Pedro F; Martínez-Molina, Eustoquio; González-Buitrago, José Manuel; Trujillo, Martha E; Velázquez, Encarna

2013-12-01

Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species. Copyright © 2013. Published by Elsevier GmbH.

Glutamine Synthetase Is a Molecular Target of Nitric Oxide in Root Nodules of Medicago truncatula and Is Regulated by Tyrosine Nitration1[W][OA

PubMed Central

Melo, Paula M.; Silva, Liliana S.; Ribeiro, Isa; Seabra, Ana R.; Carvalho, Helena G.

2011-01-01

Nitric oxide (NO) is emerging as an important regulatory player in the Rhizobium-legume symbiosis, but its biological role in nodule functioning is still far from being understood. To unravel the signal transduction cascade and ultimately NO function, it is necessary to identify its molecular targets. This study provides evidence that glutamine synthetase (GS), a key enzyme for root nodule metabolism, is a molecular target of NO in root nodules of Medicago truncatula, being regulated by tyrosine (Tyr) nitration in relation to active nitrogen fixation. In vitro studies, using purified recombinant enzymes produced in Escherichia coli, demonstrated that the M. truncatula nodule GS isoenzyme (MtGS1a) is subjected to NO-mediated inactivation through Tyr nitration and identified Tyr-167 as the regulatory nitration site crucial for enzyme inactivation. Using a sandwich enzyme-linked immunosorbent assay, it is shown that GS is nitrated in planta and that its nitration status changes in relation to active nitrogen fixation. In ineffective nodules and in nodules fed with nitrate, two conditions in which nitrogen fixation is impaired and GS activity is reduced, a significant increase in nodule GS nitration levels was observed. Furthermore, treatment of root nodules with the NO donor sodium nitroprusside resulted in increased in vivo GS nitration accompanied by a reduction in GS activity. Our results support a role of NO in the regulation of nitrogen metabolism in root nodules and places GS as an important player in the process. We propose that the NO-mediated GS posttranslational inactivation is related to metabolite channeling to boost the nodule antioxidant defenses in response to NO. PMID:21914816

Small Nodules Localization on CT Images of Lungs

NASA Astrophysics Data System (ADS)

Snezhko, E. V.; Kharuzhyk, S. A.; Tuzikov, A. V.; Kovalev, V. A.

2017-05-01

According to the World Health Organization (WHO) lung cancer remains the leading cause of death of men among all malignant tumors [1, 2]. One of the reasons of such a statistics is the fact that the lung cancer is hardly diagnosed on the yearly stages when it is almost asymptomatic. The purpose of this paper is to present a Computer-Aided Diagnosis (CAD) software developed for assistance of early detection of nodules in CT lung images including solitary pulmonary nodules (SPN) as well as multiple nodules. The efficiency of nodule localization was intended to be as high as the level of the best practice. The software developed supports several functions including lungs segmentation, selection of nodule candidates and nodule candidates filtering.

A Comparative Nitrogen Balance and Productivity Analysis of Legume and Non-legume Supported Cropping Systems: The Potential Role of Biological Nitrogen Fixation

PubMed Central

Iannetta, Pietro P. M.; Young, Mark; Bachinger, Johann; Bergkvist, Göran; Doltra, Jordi; Lopez-Bellido, Rafael J.; Monti, Michele; Pappa, Valentini A.; Reckling, Moritz; Topp, Cairistiona F. E.; Walker, Robin L.; Rees, Robert M.; Watson, Christine A.; James, Euan K.; Squire, Geoffrey R.; Begg, Graham S.

2016-01-01

The potential of biological nitrogen fixation (BNF) to provide sufficient N for production has encouraged re-appraisal of cropping systems that deploy legumes. It has been argued that legume-derived N can maintain productivity as an alternative to the application of mineral fertilizer, although few studies have systematically evaluated the effect of optimizing the balance between legumes and non N-fixing crops to optimize production. In addition, the shortage, or even absence in some regions, of measurements of BNF in crops and forages severely limits the ability to design and evaluate new legume–based agroecosystems. To provide an indication of the magnitude of BNF in European agriculture, a soil-surface N-balance approach was applied to historical data from 8 experimental cropping systems that compared legume and non-legume crop types (e.g., grains, forages and intercrops) across pedoclimatic regions of Europe. Mean BNF for different legume types ranged from 32 to 115 kg ha−1 annually. Output in terms of total biomass (grain, forage, etc.) was 30% greater in non-legumes, which used N to produce dry matter more efficiently than legumes, whereas output of N was greater from legumes. When examined over the crop sequence, the contribution of BNF to the N-balance increased to reach a maximum when the legume fraction was around 0.5 (legume crops were present in half the years). BNF was lower when the legume fraction increased to 0.6–0.8, not because of any feature of the legume, but because the cropping systems in this range were dominated by mixtures of legume and non-legume forages to which inorganic N as fertilizer was normally applied. Forage (e.g., grass and clover), as opposed to grain crops in this range maintained high outputs of biomass and N. In conclusion, BNF through grain and forage legumes has the potential to generate major benefit in terms of reducing or dispensing with the need for mineral N without loss of total output. PMID:27917178

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island

PubMed Central

Ling, Jun; Wang, Hui; Wu, Ping; Li, Tao; Tang, Yu; Naseer, Nawar; Zheng, Huiming; Masson-Boivin, Catherine; Zhong, Zengtao

2016-01-01

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICEAc) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICEAc-located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity. PMID:27849579

Plant nodulation inducers enhance horizontal gene transfer of Azorhizobium caulinodans symbiosis island.

PubMed

Ling, Jun; Wang, Hui; Wu, Ping; Li, Tao; Tang, Yu; Naseer, Nawar; Zheng, Huiming; Masson-Boivin, Catherine; Zhong, Zengtao; Zhu, Jun

2016-11-29

Horizontal gene transfer (HGT) of genomic islands is a driving force of bacterial evolution. Many pathogens and symbionts use this mechanism to spread mobile genetic elements that carry genes important for interaction with their eukaryotic hosts. However, the role of the host in this process remains unclear. Here, we show that plant compounds inducing the nodulation process in the rhizobium-legume mutualistic symbiosis also enhance the transfer of symbiosis islands. We demonstrate that the symbiosis island of the Sesbania rostrata symbiont, Azorhizobium caulinodans, is an 87.6-kb integrative and conjugative element (ICE Ac ) that is able to excise, form a circular DNA, and conjugatively transfer to a specific site of gly-tRNA gene of other rhizobial genera, expanding their host range. The HGT frequency was significantly increased in the rhizosphere. An ICE Ac -located LysR-family transcriptional regulatory protein AhaR triggered the HGT process in response to plant flavonoids that induce the expression of nodulation genes through another LysR-type protein, NodD. Our study suggests that rhizobia may sense rhizosphere environments and transfer their symbiosis gene contents to other genera of rhizobia, thereby broadening rhizobial host-range specificity.

Thyroid Nodules

MedlinePlus

... the thyroid and see if the nodule is solid or filled with fluid (cystic). Although this test cannot tell if the nodule is cancerous, it is very useful to guide the needle to remove (aspirate) cells from nodules. This procedure is called “ultrasound-guided ...

Long-distance transport of signals during symbiosis

PubMed Central

Xie, Zhi-Ping; Illana, Antonio

2011-01-01

Legumes enter nodule symbioses with nitrogen-fixing bacteria (rhizobia), whereas most flowering plants establish symbiotic associations with arbuscular mycorrhizal (AM) fungi. Once first steps of symbiosis are initiated, nodule formation and mycorrhization in legumes is negatively controlled by a shoot-derived inhibitor (SDI), a phenomenon termed autoregulation. According to current views, autoregulation of nodulation and mycorrhization in legumes is regulated in a similar way. CLE peptides induced in response to rhizobial nodulation signals (Nod factors) have been proposed to represent the ascending long-distance signals to the shoot. Although not proven yet, these CLE peptides are likely perceived by leucine-rich repeat (LRR) autoregulation receptor kinases in the shoot. Autoregulation of mycorrhization in non-legumes is reminiscent to the phenomenon of “systemic acquired resistance” in plant-pathogen interactions. PMID:21455020

Potential of Rice Stubble as a Reservoir of Bradyrhizobial Inoculum in Rice-Legume Crop Rotation

PubMed Central

Piromyou, Pongdet; Greetatorn, Teerana; Teamtisong, Kamonluck; Tittabutr, Panlada; Boonkerd, Nantakorn

2017-01-01

. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobia. However, the NO-producing strains should be of concern due to a possible deleterious effect of NO on rice growth. In addition, this study reports the application of endophytic bradyrhizobia in rice stubbles, and the rice stubbles were used directly as an inoculum for a leguminous plant (mung bean). The degradation of rice stubbles leads to an increased number of SUTN9-2 in the soil and may result in increased mung bean nodulation. Therefore, the persistence of endophytic bradyrhizobia in rice tissues can be developed to use rice stubbles as an inoculum for mung bean in a rice-legume crop rotation system. PMID:28916558

Potential of Rice Stubble as a Reservoir of Bradyrhizobial Inoculum in Rice-Legume Crop Rotation.

PubMed

Piromyou, Pongdet; Greetatorn, Teerana; Teamtisong, Kamonluck; Tittabutr, Panlada; Boonkerd, Nantakorn; Teaumroong, Neung

2017-11-15

. These characteristics may play an important role in rice growth promotion by endophytic bradyrhizobia. However, the NO-producing strains should be of concern due to a possible deleterious effect of NO on rice growth. In addition, this study reports the application of endophytic bradyrhizobia in rice stubbles, and the rice stubbles were used directly as an inoculum for a leguminous plant (mung bean). The degradation of rice stubbles leads to an increased number of SUTN9-2 in the soil and may result in increased mung bean nodulation. Therefore, the persistence of endophytic bradyrhizobia in rice tissues can be developed to use rice stubbles as an inoculum for mung bean in a rice-legume crop rotation system. Copyright © 2017 American Society for Microbiology.

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins

PubMed Central

Frederix, Marijke; Edwards, Anne; Swiderska, Anna; Stanger, Andrew; Karunakaran, Ramakrishnan; Williams, Alan; Abbruscato, Pamela; Sanchez-Contreras, Maria; Poole, Philip S; Downie, J Allan

2014-01-01

In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots. PMID:24942546

RbohB, a Phaseolus vulgaris NADPH oxidase gene, enhances symbiosome number, bacteroid size, and nitrogen fixation in nodules and impairs mycorrhizal colonization.

PubMed

Arthikala, Manoj-Kumar; Sánchez-López, Rosana; Nava, Noreide; Santana, Olivia; Cárdenas, Luis; Quinto, Carmen

2014-05-01

The reactive oxygen species (ROS) generated by respiratory burst oxidative homologs (Rbohs) are involved in numerous plant cell signaling processes, and have critical roles in the symbiosis between legumes and nitrogen-fixing bacteria. Previously, down-regulation of RbohB in Phaseolus vulgaris was shown to suppress ROS production and abolish Rhizobium infection thread (IT) progression, but also to enhance arbuscular mycorrhizal fungal (AMF) colonization. Thus, Rbohs function both as positive and negative regulators. Here, we assessed the effect of enhancing ROS concentrations, by overexpressing PvRbohB, on the P. vulgaris--rhizobia and P. vulgaris--AMF symbioses. We estimated superoxide concentrations in hairy roots overexpressing PvRbohB, determined the status of early and late events of both Rhizobium and AMF interactions in symbiont-inoculated roots, and analyzed the nodule ultrastructure of transgenic plants overexpressing PvRbohB. Overexpression of PvRbohB significantly enhanced ROS production, the formation of ITs, nodule biomass, and nitrogen-fixing activity, and increased the density of symbiosomes in nodules, and the density and size of bacteroides in symbiosomes. Furthermore, PvCAT, early nodulin, PvSS1, and PvGOGAT transcript abundances were elevated in these nodules. By contrast, mycorrhizal colonization was reduced in roots that overexpressed RbohB. Overexpression of PvRbohB augmented nodule efficiency by enhancing nitrogen fixation and delaying nodule senescence, but impaired AMF colonization. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Manganese nodules

USGS Publications Warehouse

Hein, James R.; Harff, Jan; Petersen, Sven; Thiede, Jorn

2016-01-01

The existence of manganese (Mn) nodules (Figure 1) has been known since the late 1800s when they were collected during the Challenger expedition of 1873–1876. However, it was not until after WWII that nodules were further studied in detail for their ability to adsorb metals from seawater. Many of the early studies did not distinguish Mn nodules from Mn crusts. Economic interest in Mn nodules began in the late 1950s and early 1960s when John Mero finished his Ph.D. thesis on this subject, which was published in the journal Economic Geology (Mero, 1962) and later as a book (Mero, 1965). By the mid-1970s, large consortia had formed to search for and mine Mn nodules that occur between the Clarion and Clipperton fracture zones (CCZ) in the NE Pacific (Figure 2). This is still the area considered of greatest economic potential in the global ocean because of high nickel (Ni), copper (Cu), and Mn contents and the dense distribution of nodules in the area. While the mining of nodules was fully expected to begin in the late 1970s or early 1980s, this never occurred due to a downturn in the price of metals on the global market. Since then, many research cruises have been undertaken to study the CCZ nodules, and now 15 contracts for exploration sites have been given or are pending by the International Seabed Authority (ISA). Many books and science journal articles have been published summarizing the early work (e.g., Baturin, 1988; Halbach et al., 1988), and research has continued to the present day (e.g., ISA, 1999; ISA, 2010). Although the initial attraction for nodules was their high Ni, Cu, and Mn contents, subsequent work has shown that nodules host large quantities of other critical metals needed for high-tech, green-tech, and energy applications (Hein et al., 2013; Hein and Koschinsky, 2014).

Legume presence reduces the decomposition rate of non-legume roots, role of plant traits?

NASA Astrophysics Data System (ADS)

De Deyn, Gerlinde B.; Saar, Sirgi; Barel, Janna; Semchenko, Marina

2016-04-01

Plant litter traits are known to play an important role in the rate of litter decomposition and mineralization, both for aboveground and belowground litter. However also the biotic and abiotic environment in which the litter decomposes plays a significant role in the rate of decomposition. The presence of living plants may accelerate litter decomposition rates via a priming effects. The size of this effect is expected to be related to the traits of the litter. In this study we focus on root litter, given that roots and their link to ecosystem processes have received relatively little attention in trait-based research. To test the effect of a growing legume plant on root decomposition and the role of root traits in this we used dead roots of 7 different grassland species (comprising grasses, a forb and legumes), determined their C, N, P content and quantified litter mass loss after eight weeks of incubation in soil with and without white clover. We expected faster root decomposition with white clover, especially for root litter with low N content. In contrast we found slower decomposition of grass and forb roots which were poor in N (negative priming) in presence of white clover, while decomposition rates of legume roots were not affected by the presence of white clover. Overall we found that root decomposition can be slowed down in the presence of a living plant and that this effect depends on the traits of the decomposing roots, with a pronounced reduction in root litter poor in N and P, but not in the relatively nutrient-rich legume root litters. The negative priming effect of legume plants on non-legume litter decomposition may have resulted from preferential substrate utilisation by soil microbes.

Legume Lectins: Proteins with Diverse Applications

PubMed Central

Lagarda-Diaz, Irlanda; Guzman-Partida, Ana Maria; Vazquez-Moreno, Luz

2017-01-01

Lectins are a diverse class of proteins distributed extensively in nature. Among these proteins; legume lectins display a variety of interesting features including antimicrobial; insecticidal and antitumor activities. Because lectins recognize and bind to specific glycoconjugates present on the surface of cells and intracellular structures; they can serve as potential target molecules for developing practical applications in the fields of food; agriculture; health and pharmaceutical research. This review presents the current knowledge of the main structural characteristics of legume lectins and the relationship of structure to the exhibited specificities; provides an overview of their particular antimicrobial; insecticidal and antitumor biological activities and describes possible applications based on the pattern of recognized glyco-targets. PMID:28604616

Cross-reactivity of a new food ingredient, dun pea, with legumes, and risk of anaphylaxis in legume allergic children.

PubMed

Richard, C; Jacquenet, S; Sergeant, P; Moneret-Vautrin, D A

2015-07-01

Legume allergy is the fifth food allergy in Europe. The dun pea (Pisum sativum sativum var. arvense), a pea belonging to the same subspecies as green pea, has been recently introduced as an ingredient in the human food industry. The aims of this study were to evaluate the cross-reactivity between dun pea and other legumes and to search for modification of allergenicity induced by food technologies. A series of 36 patients with legume and/or peanut allergy was studied. They underwent skin tests to peanut and a panel of legumes including dun pea. Specific IgE to dun pea and cross-reactivity to peanut allergens, particularly to Ara h 1, were evaluated by ELISA. Proteins and allergens of different pea extracts were studied by SDS-PAGE and immunoblots. In France and Belgium, 7.7% of severe food anaphylaxis cases were due to legumes. Patients with isolated legume allergy had positive prick tests to dun pea, whereas patients with isolated peanut allergy had negative prick tests. Cross-reactivity between sIgE to peanut and dun pea was observed, and more frequently than expected (96%) peanut-allergic patients with legume sensitization or allergy had sIgE to Ara h 1. Analysis of dun pea allergens suggested that protein epitopes were presented differently in dun pea seeds, isolate and flour. This study identifies, for the first time, a risk of dun pea allergy in legume-allergic patients and in a subset of peanut-allergic patients.

A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.

PubMed

Pislariu, Catalina I; Murray, Jeremy D; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; Benedito, Vagner A; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S; Chen, Rujin; Udvardi, Michael K

2012-08-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

Legume carotenoids.

PubMed

Sri Kantha, S; Erdman, J W

1987-01-01

In recent years, the results of research studies have suggested a positive beneficial relationship between a vegetarian-based diet and low incidence of diseases, including coronary heart disease, cancer, obesity, dental caries, and osteoporosis. beta-Carotene has specifically been suggested as a nutrient with antitumorigenic properties. In this regard there is a need to evaluate the carotenoid content of foods. Legumes are one of the staple components of a vegetarian diet. This review specifically surveys the prevalence of carotenoids in food and forage legumes. In addition, the methods available for carotenoid analysis are discussed; factors affecting the determination of carotenoid content during maturation, germination, processing and storage are identified; research areas which have been inadequately explored are identified; and suggestions are made for future lines of investigation.

Early nodule senescence is activated in symbiotic mutants of pea (Pisum sativum L.) forming ineffective nodules blocked at different nodule developmental stages.

PubMed

Serova, Tatiana A; Tsyganova, Anna V; Tsyganov, Viktor E

2018-04-03

Plant symbiotic mutants are useful tool to uncover the molecular-genetic mechanisms of nodule senescence. The pea (Pisum sativum L.) mutants SGEFix - -1 (sym40), SGEFix - -3 (sym26), and SGEFix - -7 (sym27) display an early nodule senescence phenotype, whereas the mutant SGEFix - -2 (sym33) does not show premature degradation of symbiotic structures, but its nodules show an enhanced immune response. The nodules of these mutants were compared with each other and with those of the wild-type SGE line using seven marker genes that are known to be activated during nodule senescence. In wild-type SGE nodules, transcript levels of all of the senescence-associated genes were highest at 6 weeks after inoculation (WAI). The senescence-associated genes showed higher transcript abundance in mutant nodules than in wild-type nodules at 2 WAI and attained maximum levels in the mutant nodules at 4 WAI. Immunolocalization analyses showed that the ethylene precursor 1-aminocyclopropane-1-carboxylate accumulated earlier in the mutant nodules than in wild-type nodules. Together, these results showed that nodule senescence was activated in ineffective nodules blocked at different developmental stages in pea lines that harbor mutations in four symbiotic genes.

miR396 affects mycorrhization and root meristem activity in the legume Medicago truncatula.

PubMed

Bazin, Jérémie; Khan, Ghazanfar Abbas; Combier, Jean-Philippe; Bustos-Sanmamed, Pilar; Debernardi, Juan Manuel; Rodriguez, Ramiro; Sorin, Céline; Palatnik, Javier; Hartmann, Caroline; Crespi, Martin; Lelandais-Brière, Christine

2013-06-01

The root system is crucial for acquisition of resources from the soil. In legumes, the efficiency of mineral and water uptake by the roots may be reinforced due to establishment of symbiotic relationships with mycorrhizal fungi and interactions with soil rhizobia. Here, we investigated the role of miR396 in regulating the architecture of the root system and in symbiotic interactions in the model legume Medicago truncatula. Analyses with promoter-GUS fusions suggested that the mtr-miR396a and miR396b genes are highly expressed in root tips, preferentially in the transition zone, and display distinct expression profiles during lateral root and nodule development. Transgenic roots of composite plants that over-express the miR396b precursor showed lower expression of six growth-regulating factor genes (MtGRF) and two bHLH79-like target genes, as well as reduced growth and mycorrhizal associations. miR396 inactivation by mimicry caused contrasting tendencies, with increased target expression, higher root biomass and more efficient colonization by arbuscular mycorrhizal fungi. In contrast to MtbHLH79, repression of three GRF targets by RNA interference severely impaired root growth. Early activation of mtr-miR396b, concomitant with post-transcriptional repression of MtGRF5 expression, was also observed in response to exogenous brassinosteroids. Growth limitation in miR396 over-expressing roots correlated with a reduction in cell-cycle gene expression and the number of dividing cells in the root apical meristem. These results link the miR396 network to the regulation of root growth and mycorrhizal associations in plants. © 2013 The Authors The Plant Journal © 2013 John Wiley & Sons Ltd.

Legume-rhizobia signal exchange: promiscuity and environmental effects.

PubMed

Lira, Mario A; Nascimento, Luciana R S; Fracetto, Giselle G M

2015-01-01

Although signal exchange between legumes and their rhizobia is among the best-known examples of this biological process, most of the more characterized data comes from just a few legume species and environmental stresses. Although a relative wealth of information is available for some model legumes and some of the major pulses such as soybean, little is known about tropical legumes. This relative disparity in current knowledge is also apparent in the research on the effects of environmental stress on signal exchange; cool-climate stresses, such as low-soil temperature, comprise a relatively large body of research, whereas high-temperature stresses and drought are not nearly as well understood. Both tropical legumes and their environmental stress-induced effects are increasingly important due to global population growth (the demand for protein), climate change (increasing temperatures and more extreme climate behavior), and urbanization (and thus heavy metals). This knowledge gap for both legumes and their environmental stresses is compounded because whereas most temperate legume-rhizobia symbioses are relatively specific and cultivated under relatively stable environments, the converse is true for tropical legumes, which tend to be promiscuous, and grow in highly variable conditions. This review will clarify some of this missing information and highlight fields in which further research would benefit our current knowledge.

Inactivation Methods of Trypsin Inhibitor in Legumes: A Review.

PubMed

Avilés-Gaxiola, Sara; Chuck-Hernández, Cristina; Serna Saldívar, Sergio O

2018-01-01

Seed legumes have played a major role as a crop worldwide, being cultivated on about 12% to 15% of Earth's arable land; nevertheless, their use is limited by, among other things, the presence of several antinutritional factors (ANFs - naturally occurring metabolites that the plant produces to protect itself from pest attacks.) Trypsin inhibitors (TIs) are one of the most relevant ANFs because they reduce digestion and absorption of dietary proteins. Several methods have been developed in order to inactivate TIs, and of these, thermal treatments are the most commonly used. They cause loss of nutrients, affect functional properties, and require high amounts of energy. Given the above, new processes have emerged to improve the nutritional quality of legumes while trying to solve the problems caused by the use of thermal treatments. This review examines and discusses the methods developed by researchers to inactivate TI present in legumes and their effects over nutritional and functional properties. © 2017 Institute of Food Technologists®.

Soybean nodulation and symbiotic nitrogen fixation in response to soil compaction and mulching

NASA Astrophysics Data System (ADS)

Siczek, A.; Lipiec, J.

2009-04-01

Symbiotic nitrogen fixation by legume crops such as soybean plays a key role in supplying nitrogen for agricultural systems. In symbiotic associations with Bradyrhizobium japonicum soybean can fix up to 200 kg N ha-1 yr-1. This reduces the need for expensive and often environmentally harmful because of leaching nitrogen fertilization. However both soybean nodulation and nitrogen fixation are sensitive to soil conditions. One of the critical soil constraints is soil compaction. Increasing use of heavy equipment and intensive cropping in modern agriculture leads to excessive soil compaction. Compaction often is found as a result of field operations that have to be performed in a very short period of time and when soils are wet and more susceptible to compaction. This results in unfavourable water content, temperature, aeration, pore size distribution, strength for plant growth and microbial activity. The surface mulching can alleviate the adverse effect of the environmental factors on soil by decreasing fluctuation of soil temperature, increasing moisture by controlling evaporation from the soil surface, decreasing bulk density, preventing soil crusting. The effect of mulch on soil conditions largely depends on soil compaction and weather conditions during growing season. The positive effect of the straw mulch on soil moisture has been seen under seasons with insufficient rainfalls. However thicker layers of mulch can act as diffusion barrier, especially when the mulch is wet. Additionally, low soil temperature prevalent during early spring under mulch can impede development of nodule, nodule size and delay onset of nodulation. The aim of this study was to determine the effect of the straw mulch on nodulation and nitrogen fixation of soybean in variously compacted soil. The experimental field was 192 m2and was divided into three parts composed of 6 micro-plots with area 7 m2. Three degrees of soil compaction obtained in each field part through tractor passes were

Comparison of the Nodule vs. Root Transcriptome of the Actinorhizal Plant Datisca glomerata: Actinorhizal Nodules Contain a Specific Class of Defensins

PubMed Central

Santos, Patricia; Plaszczyca, Marian; Pawlowski, Katharina

2013-01-01

Actinorhizal root nodule symbioses are very diverse, and the symbiosis of Datisca glomerata has previously been shown to have many unusual aspects. In order to gain molecular information on the infection mechanism, nodule development and nodule metabolism, we compared the transcriptomes of D. glomerata roots and nodules. Root and nodule libraries representing the 3′-ends of cDNAs were subjected to high-throughput parallel 454 sequencing. To identify the corresponding genes and to improve the assembly, Illumina sequencing of the nodule transcriptome was performed as well. The evaluation revealed 406 differentially regulated genes, 295 of which (72.7%) could be assigned a function based on homology. Analysis of the nodule transcriptome showed that genes encoding components of the common symbiosis signaling pathway were present in nodules of D. glomerata, which in combination with the previously established function of SymRK in D. glomerata nodulation suggests that this pathway is also active in actinorhizal Cucurbitales. Furthermore, comparison of the D. glomerata nodule transcriptome with nodule transcriptomes from actinorhizal Fagales revealed a new subgroup of nodule-specific defensins that might play a role specific to actinorhizal symbioses. The D. glomerata members of this defensin subgroup contain an acidic C-terminal domain that was never found in plant defensins before. PMID:24009681

Natural History of Pulmonary Subsolid Nodules: A Prospective Multicenter Study.

PubMed

Kakinuma, Ryutaro; Noguchi, Masayuki; Ashizawa, Kazuto; Kuriyama, Keiko; Maeshima, Akiko Miyagi; Koizumi, Naoya; Kondo, Tetsuro; Matsuguma, Haruhisa; Nitta, Norihisa; Ohmatsu, Hironobu; Okami, Jiro; Suehisa, Hiroshi; Yamaji, Taiki; Kodama, Ken; Mori, Kiyoshi; Yamada, Kouzo; Matsuno, Yoshihiro; Murayama, Sadayuki; Murata, Kiyoshi

2016-07-01

The purpose of this study was to evaluate the natural course of the progression of pulmonary subsolid nodules (SSNs). Eight facilities participated in this study. A total of 795 patients with 1229 SSNs were assessed for the frequency of invasive adenocarcinomas. SSNs were classified into three categories: pure ground-glass nodules (PGGNs), heterogeneous GGNs (HGGNs) (solid component detected only in lung windows), and part-solid nodules. The mean prospective follow-up period was 4.3 ± 2.5 years. SSNs were classified at baseline as follows: 1046 PGGNs, 81 HGGNs, and 102 part-solid nodules. Among the 1046 PGGNs, 13 (1.2%) developed into HGGNs and 56 (5.4%) developed into part-solid nodules. Among the 81 HGGNs, 16 (19.8%) developed into part-solid nodules. Thus, the SSNs at the final follow-up were classified as follows: 977 PGGNs, 78 HGGNs, and 174 part-solid nodules. Of the 977 PGGNs, 35 were resected (nine minimally invasive adenocarcinomas [MIAs], 21 adenocarcinomas in situ [AIS], and five atypical adenomatous hyperplasias). Of the 78 HGGNs, seven were resected (five MIAs and two AIS). Of the 174 part-solid nodules, 49 were resected (12 invasive adenocarcinomas, 26 MIAs, 10 AIS, and one adenomatous hyperplasia). For the PGGNs, the mean period until their development into part-solid nodules was 3.8 ± 2.0 years, whereas the mean period for the HGGNs was 2.1 ± 2.3 years (p = 0.0004). This study revealed the frequencies and periods of development from PGGNs and HGGNs into part-solid nodules. Invasive adenocarcinomas were diagnosed only among the part-solid nodules, corresponding to 1% of all 1229 SSNs. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Mutation of praR in Rhizobium leguminosarum enhances root biofilms, improving nodulation competitiveness by increased expression of attachment proteins.

PubMed

Frederix, Marijke; Edwards, Anne; Swiderska, Anna; Stanger, Andrew; Karunakaran, Ramakrishnan; Williams, Alan; Abbruscato, Pamela; Sanchez-Contreras, Maria; Poole, Philip S; Downie, J Allan

2014-08-01

In Rhizobium leguminosarum bv. viciae, quorum-sensing is regulated by CinR, which induces the cinIS operon. CinI synthesizes an AHL, whereas CinS inactivates PraR, a repressor. Mutation of praR enhanced biofilms in vitro. We developed a light (lux)-dependent assay of rhizobial attachment to roots and demonstrated that mutation of praR increased biofilms on pea roots. The praR mutant out-competed wild-type for infection of pea nodules in mixed inoculations. Analysis of gene expression by microarrays and promoter fusions revealed that PraR represses its own transcription and mutation of praR increased expression of several genes including those encoding secreted proteins (the adhesins RapA2, RapB and RapC, two cadherins and the glycanase PlyB), the polysaccharide regulator RosR, and another protein similar to PraR. PraR bound to the promoters of several of these genes indicating direct repression. Mutations in rapA2, rapB, rapC, plyB, the cadherins or rosR did not affect the enhanced root attachment or nodule competitiveness of the praR mutant. However combinations of mutations in rapA, rapB and rapC abolished the enhanced attachment and nodule competitiveness. We conclude that relief of PraR-mediated repression determines a lifestyle switch allowing the expression of genes that are important for biofilm formation on roots and the subsequent initiation of infection of legume roots. © 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

Medicago truncatula natural resistance-associated macrophage Protein1 is required for iron uptake by rhizobia-infected nodule cells.

PubMed

Tejada-Jiménez, Manuel; Castro-Rodríguez, Rosario; Kryvoruchko, Igor; Lucas, M Mercedes; Udvardi, Michael; Imperial, Juan; González-Guerrero, Manuel

2015-05-01

Iron is critical for symbiotic nitrogen fixation (SNF) as a key component of multiple ferroproteins involved in this biological process. In the model legume Medicago truncatula, iron is delivered by the vasculature to the infection/maturation zone (zone II) of the nodule, where it is released to the apoplast. From there, plasma membrane iron transporters move it into rhizobia-containing cells, where iron is used as the cofactor of multiple plant and rhizobial proteins (e.g. plant leghemoglobin and bacterial nitrogenase). MtNramp1 (Medtr3g088460) is the M. truncatula Natural Resistance-Associated Macrophage Protein family member, with the highest expression levels in roots and nodules. Immunolocalization studies indicate that MtNramp1 is mainly targeted to the plasma membrane. A loss-of-function nramp1 mutant exhibited reduced growth compared with the wild type under symbiotic conditions, but not when fertilized with mineral nitrogen. Nitrogenase activity was low in the mutant, whereas exogenous iron and expression of wild-type MtNramp1 in mutant nodules increased nitrogen fixation to normal levels. These data are consistent with a model in which MtNramp1 is the main transporter responsible for apoplastic iron uptake by rhizobia-infected cells in zone II. © 2015 American Society of Plant Biologists. All Rights Reserved.

The role of the testa during development and in establishment of dormancy of the legume seed

PubMed Central

Smýkal, Petr; Vernoud, Vanessa; Blair, Matthew W.; Soukup, Aleš; Thompson, Richard D.

2014-01-01

Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the “domestication syndrome.” Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. myeloblastosis family of transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa color in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defense against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on

Neglecting legumes has compromised human health and sustainable food production.

PubMed

Foyer, Christine H; Lam, Hon-Ming; Nguyen, Henry T; Siddique, Kadambot H M; Varshney, Rajeev K; Colmer, Timothy D; Cowling, Wallace; Bramley, Helen; Mori, Trevor A; Hodgson, Jonathan M; Cooper, James W; Miller, Anthony J; Kunert, Karl; Vorster, Juan; Cullis, Christopher; Ozga, Jocelyn A; Wahlqvist, Mark L; Liang, Yan; Shou, Huixia; Shi, Kai; Yu, Jingquan; Fodor, Nandor; Kaiser, Brent N; Wong, Fuk-Ling; Valliyodan, Babu; Considine, Michael J

2016-08-02

The United Nations declared 2016 as the International Year of Pulses (grain legumes) under the banner 'nutritious seeds for a sustainable future'. A second green revolution is required to ensure food and nutritional security in the face of global climate change. Grain legumes provide an unparalleled solution to this problem because of their inherent capacity for symbiotic atmospheric nitrogen fixation, which provides economically sustainable advantages for farming. In addition, a legume-rich diet has health benefits for humans and livestock alike. However, grain legumes form only a minor part of most current human diets, and legume crops are greatly under-used. Food security and soil fertility could be significantly improved by greater grain legume usage and increased improvement of a range of grain legumes. The current lack of coordinated focus on grain legumes has compromised human health, nutritional security and sustainable food production.

Control of the ethylene signaling pathway prevents plant defenses during intracellular accommodation of the rhizobia.

PubMed

Berrabah, Fathi; Balliau, Thierry; Aït-Salem, El Hosseyn; George, Jeoffrey; Zivy, Michel; Ratet, Pascal; Gourion, Benjamin

2018-04-18

Massive intracellular populations of symbiotic bacteria, referred to as rhizobia, are housed in legume root nodules. Little is known about the mechanisms preventing the development of defense in these organs although genes such as SymCRK and DNF2 of the model legume Medicago truncatula are required for this control after rhizobial internalization in host nodule cells. Here we investigated the molecular basis of the symbiotic control of immunity. Proteomic analysis was performed to compare functional (wild-type) and defending nodules (symCRK). Based on the results, the control of plant immunity during the functional step of the symbiosis was further investigated by biochemical and pharmacological approaches as well as by transcript and histology analysis. Ethylene was identified as a potential signal inducing plant defenses in symCRK nodules. Involvement of this phytohormone in symCRK and dnf2-developed defenses and in the death of intracellular rhizobia was confirmed. This negative effect of ethylene depended on the M. truncatula sickle gene and was also observed in the legume Lotus japonicus. Together, these data indicate that prevention of ethylene-triggered defenses is crucial for the persistence of endosymbiosis and that the DNF2 and SymCRK genes are required for this process. © 2018 CNRS New Phytologist © 2018 New Phytologist Trust.

Discovery of novel plant interaction determinants from the genomes of 163 root nodule bacteria

DOE PAGES

Seshadri, Rekha; Reeve, Wayne G.; Ardley, Julie K.; ...

2015-11-20

Root nodule bacteria (RNB) or “rhizobia” are a type of plant growth promoting bacteria, typified by their ability to fix nitrogen for their plant host, fixing nearly 65% of the nitrogen currently utilized in sustainable agricultural production of legume crops and pastures. In this study, we sequenced the genomes of 110 RNB from diverse hosts and biogeographical regions, and undertook a global exploration of all available RNB genera with the aim of identifying novel genetic determinants of symbiotic association and plant growth promotion. Specifically, we performed a subtractive comparative analysis with non-RNB genomes, employed relevant transcriptomic data, and leveraged phylogeneticmore » distribution patterns and sequence signatures based on known precepts of symbioticand host-microbe interactions. A total of 184 protein families were delineated, including known factors for nodulation and nitrogen fixation, and candidates with previously unexplored functions, for which a role in host-interaction, -regulation, biocontrol, and more, could be posited. Lastly, these analyses expand our knowledge of the RNB purview and provide novel targets for strain improvement in the ultimate quest to enhance plant productivity and agricultural sustainability.« less

Subsolid pulmonary nodules: imaging evaluation and strategic management.

PubMed

Godoy, Myrna C B; Sabloff, Bradley; Naidich, David P

2012-07-01

Given the higher rate of malignancy of subsolid pulmonary nodules and the considerably lower growth rate of ground-glass nodules (GGNs), dedicated standardized guidelines for management of these nodules have been proposed, including long-term low-dose computed tomography (CT) follow-up (≥3 years). Physicians must be familiar with the strategic management of subsolid pulmonary nodules, and should be able to identify imaging features that suggest invasive adenocarcinoma requiring a more aggressive management. Low-dose CT screening studies for early detection of lung cancer have increased our knowledge of pulmonary nodules, and in particular our understanding of the strong although imperfect correlation of the subsolid pulmonary nodules, including pure GGNs and part-solid nodules, with the spectrum of preinvasive to invasive lung adenocarcinoma. Serial CT imaging has shown stepwise progression in a subset of these nodules, characterized by increase in size and density of pure GGNs and development of a solid component, the latter usually indicating invasive adenocarcinoma. There is close correlation between the CT features of subsolid nodules (SSNs) and the spectrum of lung adenocarcinoma. Standardized guidelines are suggested for management of SSNs.

[Production of inhibiting plant growth and development hormones by pathogenic for legumes Pseudomonas genus bacteria].

PubMed

Dankevich, L A

2013-01-01

It has been studied the ability of pathogenic for legumes pathovars of Pseudomonas genus to produce ethylene and abscisic acid in vitro. A direct correlation between the level of ethylene production by agent of bacterial pea burn--Pseudomonas syringae pv. pisi and level of its aggressiveness for plants has been found. It is shown that the amount of abscisic acid synthesized by pathogenic for legumes Pseudomonas genus bacteria correlates with their aggressiveness for plants.

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE PAGES

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter; ...

2015-10-16

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

High-quality permanent draft genome sequence of the Mimosa asperata - nodulating Cupriavidus sp. strain AMP6

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Meyer, Sofie E.; Parker, Matthew; Van Berkum, Peter

Cupriavidus sp. strain AMP6 is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from a root nodule of Mimosa asperata collected in Santa Ana National Wildlife Refuge, Texas, in 2005. Mimosa asperata is the only legume described so far to exclusively associates with Cupriavidus symbionts. Furthermore, strain AMP6 represents an early-diverging lineage within the symbiotic Cupriavidus group and has the capacity to develop an effective nitrogen-fixing symbiosis with three other species of Mimosa. Here, we describe the genome of Cupriavidus sp. strain AMP6 which enables comparative analyses of symbiotic trait evolution in this genus; the general features, together withmore » sequence and annotation are further discussed. Finally, the 7,579,563 bp high-quality permanent draft genome is arranged in 260 scaffolds of 262 contigs, contains 7,033 protein-coding genes and 97 RNA-only encoding genes, and is part of the GEBA-RNB project proposal.« less

Early signaling, synthesis, transport and metabolism of ureides.

PubMed

Baral, Bikash; Teixeira da Silva, Jaime A; Izaguirre-Mayoral, Maria Luisa

2016-04-01

The symbiosis between α nitrogen (N2)-fixing Proteobacteria (family Rhizobiaceae) and legumes belonging to the Fabaceae (a single phylogenetic group comprising three subfamilies: Caesalpinioideae, Mimosoideae and Papilionoideae) results in the formation of a novel root structure called a nodule, where atmospheric N2 is fixed into NH3(+). In the determinate type of nodules harbored by Rhizobium-nodulated Fabaceae species, newly synthesized NH3(+) is finally converted into allantoin (C4H6N4O3) and allantoic acid (C4H8N4O4) (ureides) through complex pathways involving at least 20 different enzymes that act synchronously in two types of nodule cells with contrasting ultrastructure, including the tree nodule cell organelles. Newly synthesized ureides are loaded into the network of nodule-root xylem vessels and transported to aerial organs by the transpirational water current. Once inside the leaves, ureides undergo an enzymatically driven reverse process to yield NH4(+) that is used for growth. This supports the role of ureides as key nitrogen (N)-compounds for the growth and yield of legumes nodulated by Rhizobium that grow in soils with a low N content. Thus, a concrete understanding of the mechanisms underlying ureide biogenesis and catabolism in legumes may help agrobiologists to achieve greater agricultural discoveries. In this review we focus on the transmembranal and transorganellar symplastic and apoplastic movement of N-precursors within the nodules, as well as on the occurrence, localization and properties of enzymes and genes involved in the biogenesis and catabolism of ureides. The synthesis and transport of ureides are not unique events in Rhizobium-nodulated N2-fixing legumes. Thus, a brief description of the synthesis and catabolism of ureides in non-legumes was included for comparison. The establishment of the symbiosis, nodule organogenesis and the plant's control of nodule number, synthesis and translocation of ureides via feed-back inhibition

Development of local complexity metrics to quantify the effect of anatomical noise on detectability of lung nodules in chest CT imaging

NASA Astrophysics Data System (ADS)

Solomon, Justin; Rubin, Geoffrey; Smith, Taylor; Harrawood, Brian; Choudhury, Kingshuk Roy; Samei, Ehsan

2017-03-01

The purpose of this study was to develop metrics of local anatomical complexity and compare them with detectability of lung nodules in CT. Data were drawn retrospectively from a published perception experiment in which detectability was assessed in cases enriched with virtual nodules (13 radiologists x 157 total nodules = 2041 responses). A local anatomical complexity metric called the distractor index was developed, defined as the Gaussian weighted proportion (i.e., average) of distracting local voxels (50 voxels in-plane, 5 slices). A distracting voxel was classified by thresholding image data that had been selectively filtered to enhance nodule-like features. The distractor index was measured for each nodule location in the nodule-free images. The local pixel standard deviation (STD) was also measured for each nodule. Other confounding factors of search fraction (proportion of lung voxels to total voxels in the given slice) and peripheral distance (defined as the 3D distance of the nodule from the trachea bifurcation) were measured. A generalized linear mixed-effects statistical model (no interaction terms, probit link function, random reader term) was fit to the data to determine the influence of each metric on detectability. In order of decreasing effect size: distractor index, STD, and search fraction all significantly affected detectability (P < 0.001). Distance to the trachea did not have a significant effect (P < 0.05). These data demonstrate that local lung complexity degrades detection of lung nodules and the distractor index could serve as a good surrogate metric to quantify anatomical complexity.

Nodulation and Delayed Nodule Senescence: Strategies of Two Bradyrhizobium Japonicum Isolates with High Capacity to Fix Nitrogen.

PubMed

López, Silvina M Y; Sánchez, Ma Dolores Molina; Pastorino, Graciela N; Franco, Mario E E; García, Nicolás Toro; Balatti, Pedro A

2018-03-15

The purpose of this work was to study further two Bradyrhizobium japonicum strains with high nitrogen-fixing capacity that were identified within a collection of approximately 200 isolates from the soils of Argentina. Nodulation and nitrogen-fixing capacity and the level of expression of regulatory as well as structural genes of nitrogen fixation and the 1-aminocyclopropane-1-carboxylate (ACC) deaminase gene of the isolates were compared with that of E109-inoculated plants. Both isolates of B. japonicum, 163 and 366, were highly efficient to fix nitrogen compared to commercial strain E109. Isolate 366 developed a higher number and larger biomass of nodules and because of this fixed more nitrogen. Isolate 163 developed the same number and nodule biomass than E109. However, nodules developed by isolate 163 had red interiors for a longer period, had a higher leghemoglobin content, and presented high levels of expression of acdS gene, that codes for an ACC deaminase. In conclusion, naturalized rhizobia of the soils of Argentina hold a diverse population that might be the source of highly active nitrogen-fixing rhizobia, a process that appears to be based on different strategies.

Improved pulmonary nodule classification utilizing quantitative lung parenchyma features.

PubMed

Dilger, Samantha K N; Uthoff, Johanna; Judisch, Alexandra; Hammond, Emily; Mott, Sarah L; Smith, Brian J; Newell, John D; Hoffman, Eric A; Sieren, Jessica C

2015-10-01

Current computer-aided diagnosis (CAD) models for determining pulmonary nodule malignancy characterize nodule shape, density, and border in computed tomography (CT) data. Analyzing the lung parenchyma surrounding the nodule has been minimally explored. We hypothesize that improved nodule classification is achievable by including features quantified from the surrounding lung tissue. To explore this hypothesis, we have developed expanded quantitative CT feature extraction techniques, including volumetric Laws texture energy measures for the parenchyma and nodule, border descriptors using ray-casting and rubber-band straightening, histogram features characterizing densities, and global lung measurements. Using stepwise forward selection and leave-one-case-out cross-validation, a neural network was used for classification. When applied to 50 nodules (22 malignant and 28 benign) from high-resolution CT scans, 52 features (8 nodule, 39 parenchymal, and 5 global) were statistically significant. Nodule-only features yielded an area under the ROC curve of 0.918 (including nodule size) and 0.872 (excluding nodule size). Performance was improved through inclusion of parenchymal (0.938) and global features (0.932). These results show a trend toward increased performance when the parenchyma is included, coupled with the large number of significant parenchymal features that support our hypothesis: the pulmonary parenchyma is influenced differentially by malignant versus benign nodules, assisting CAD-based nodule characterizations.

Complete Genome sequence of Burkholderia phymatum STM815T, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

PubMed Central

Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud; Booth, Kristina; Vriezen, Jan A.C.; Melkonian, Rémy; James, Euan K.; Young, J. Peter W.; Bena, Gilles; Hauser, Loren; Land, Miriam; Kyrpides, Nikos; Bruce, David; Chain, Patrick; Copeland, Alex; Pitluck, Sam; Woyke, Tanja; Lizotte-Waniewski, Michelle; Bristow, Jim; Riley, Margaret

2014-01-01

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp) and a plasmid hosting the symbiotic functions (595,108 bp). PMID:25197461

Digital tomosynthesis for evaluating metastatic lung nodules: nodule visibility, learning curves, and reading times.

PubMed

Lee, Kyung Hee; Goo, Jin Mo; Lee, Sang Min; Park, Chang Min; Bahn, Young Eun; Kim, Hyungjin; Song, Yong Sub; Hwang, Eui Jin

2015-01-01

To evaluate nodule visibility, learning curves, and reading times for digital tomosynthesis (DT). We included 80 patients who underwent computed tomography (CT) and DT before pulmonary metastasectomy. One experienced chest radiologist annotated all visible nodules on thin-section CT scans using computer-aided detection software. Two radiologists used CT as the reference standard and retrospectively graded the visibility of nodules on DT. Nodule detection performance was evaluated in four sessions of 20 cases each by six readers. After each session, readers were unblinded to the DT images by revealing the true-positive markings and were instructed to self-analyze their own misreads. Receiver-operating-characteristic curves were determined. Among 414 nodules on CT, 53.3% (221/414) were visible on DT. The main reason for not seeing a nodule on DT was small size (93.3%, ≤ 5 mm). DT revealed a substantial number of malignant nodules (84.1%, 143/170). The proportion of malignant nodules among visible nodules on DT was significantly higher (64.7%, 143/221) than that on CT (41.1%, 170/414) (p < 0.001). Area under the curve (AUC) values at the initial session were > 0.8, and the average detection rate for malignant nodules was 85% (210/246). The inter-session analysis of the AUC showed no significant differences among the readers, and the detection rate for malignant nodules did not differ across sessions. A slight improvement in reading times was observed. Most malignant nodules > 5 mm were visible on DT. As nodule detection performance was high from the initial session, DT may be readily applicable for radiology residents and board-certified radiologists.

Noncalcified Lung Nodules: Volumetric Assessment with Thoracic CT

PubMed Central

Gavrielides, Marios A.; Kinnard, Lisa M.; Myers, Kyle J.; Petrick, Nicholas

2009-01-01

Lung nodule volumetry is used for nodule diagnosis, as well as for monitoring tumor response to therapy. Volume measurement precision and accuracy depend on a number of factors, including image-acquisition and reconstruction parameters, nodule characteristics, and the performance of algorithms for nodule segmentation and volume estimation. The purpose of this article is to provide a review of published studies relevant to the computed tomographic (CT) volumetric analysis of lung nodules. A number of underexamined areas of research regarding volumetric accuracy are identified, including the measurement of nonsolid nodules, the effects of pitch and section overlap, and the effect of respiratory motion. The need for public databases of phantom scans, as well as of clinical data, is discussed. The review points to the need for continued research to examine volumetric accuracy as a function of a multitude of interrelated variables involved in the assessment of lung nodules. Understanding and quantifying the sources of volumetric measurement error in the assessment of lung nodules with CT would be a first step toward the development of methods to minimize that error through system improvements and to correctly account for any remaining error. © RSNA, 2009 PMID:19332844

Development of a Blood-Based Biomarker Panel for Indeterminate Lung Nodules

DTIC Science & Technology

2016-09-01

Taguchi CONTRACTING ORGANIZATION: University of Texas MD Anderson Cancer Center Houston, TX 77030 REPORT DATE: September 2016 TYPE OF REPORT...PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER University of Texas MD Anderson Cancer Center Rene...protein, autoantibody and microRNA) to distinguish malignant lung nodules from benign lung nodules. We have so far assayed 20 protein markers, 122

High intensity, short duration rotational grazing on reclaimed cool season fescue/legume pastures: I. System development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erickson, W.R.; Carlson, K.E.

The Pittsburg & Midway Coal Mining Co.`s ({open_quotes}P&M{close_quotes}) Midway Mine lies 50 miles south of Kansas City, Kansas, straddling the border of Kansas and Missouri. P&M actively mined the area until 1989, when the mine was closed and reclaimed. Approximately 3,750 acres of surface mined land were topsoiled and revegetated to cool season fescue/legume pasture. Various pasture management methods are being utilized to meet reclamation success standards and achieve final bond release. The effectiveness and costs of various cool season fescue/legume pasture management methods are evaluated and contrasted. These methods include sharecropping, bush hogging, burning and livestock grazing. It presentsmore » guidelines used to develop a site specific rotational livestock grazing programs with land owners or contractors, and local, state and federal agencies. Rotational grazing uses both cow/calf or feeder livestock operations. Key managerial elements used to control grazing activities, either by the landowner or a contractor, are reviewed. Methods used to determine stocking levels for successful rotational grazing on this type of pasture are presented. Rotational grazing of livestock has proven to be the most effective method for managing established cool season fescue/legume pastures at this site. Initial stocking rates of 1 A.U.M. per 5 acres have been modified to a current stocking rate of 1 A.U.M. per 2.5 acres. Supporting physical and chemical data are presented and discussed.« less

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes

PubMed Central

Singh, Vikash K.; Jain, Mukesh; Garg, Rohini

2014-01-01

Growth hormone auxin regulates various cellular processes by altering the expression of diverse genes in plants. Among various auxin-responsive genes, GH3 genes maintain endogenous auxin homeostasis by conjugating excess of auxin with amino acids. GH3 genes have been characterized in many plant species, but not in legumes. In the present work, we identified members of GH3 gene family and analyzed their chromosomal distribution, gene structure, gene duplication and phylogenetic analysis in different legumes, including chickpea, soybean, Medicago, and Lotus. A comprehensive expression analysis in different vegetative and reproductive tissues/stages revealed that many of GH3 genes were expressed in a tissue-specific manner. Notably, chickpea CaGH3-3, soybean GmGH3-8 and -25, and Lotus LjGH3-4, -5, -9 and -18 genes were up-regulated in root, indicating their putative role in root development. In addition, chickpea CaGH3-1 and -7, and Medicago MtGH3-7, -8, and -9 were found to be highly induced under drought and/or salt stresses, suggesting their role in abiotic stress responses. We also observed the examples of differential expression pattern of duplicated GH3 genes in soybean, indicating their functional diversification. Furthermore, analyses of three-dimensional structures, active site residues and ligand preferences provided molecular insights into function of GH3 genes in legumes. The analysis presented here would help in investigation of precise function of GH3 genes in legumes during development and stress conditions. PMID:25642236

Central focused convolutional neural networks: Developing a data-driven model for lung nodule segmentation.

PubMed

Wang, Shuo; Zhou, Mu; Liu, Zaiyi; Liu, Zhenyu; Gu, Dongsheng; Zang, Yali; Dong, Di; Gevaert, Olivier; Tian, Jie

2017-08-01

Accurate lung nodule segmentation from computed tomography (CT) images is of great importance for image-driven lung cancer analysis. However, the heterogeneity of lung nodules and the presence of similar visual characteristics between nodules and their surroundings make it difficult for robust nodule segmentation. In this study, we propose a data-driven model, termed the Central Focused Convolutional Neural Networks (CF-CNN), to segment lung nodules from heterogeneous CT images. Our approach combines two key insights: 1) the proposed model captures a diverse set of nodule-sensitive features from both 3-D and 2-D CT images simultaneously; 2) when classifying an image voxel, the effects of its neighbor voxels can vary according to their spatial locations. We describe this phenomenon by proposing a novel central pooling layer retaining much information on voxel patch center, followed by a multi-scale patch learning strategy. Moreover, we design a weighted sampling to facilitate the model training, where training samples are selected according to their degree of segmentation difficulty. The proposed method has been extensively evaluated on the public LIDC dataset including 893 nodules and an independent dataset with 74 nodules from Guangdong General Hospital (GDGH). We showed that CF-CNN achieved superior segmentation performance with average dice scores of 82.15% and 80.02% for the two datasets respectively. Moreover, we compared our results with the inter-radiologists consistency on LIDC dataset, showing a difference in average dice score of only 1.98%. Copyright © 2017. Published by Elsevier B.V.

Benign and malignant thyroid nodules after neck irradiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fjaelling, M.T.; Tisell, L.E.; Carlsson, S.

1986-09-15

A total of 444 persons were examined for the presence of thyroid nodules on average of 43 years after having been treated with x-rays for cervical tuberculous adenitis. Of this total, 101 subjects had undergone surgery for thyroid nodules: 25 for carcinoma (6%) and 76 for benign nodules (17%). Carcinoma occurred with the same frequency in multinodular and uninodular glands. Because of the uneven age distribution in the current series, it could not be decided whether there was a higher susceptibility of the young thyroid to the induction of thyroid carcinoma or benign nodules. The dosage range for the wholemore » series was 0.40 to 50.90 Gy (40-5090 rad). There was a positive correlation between the absorbed radiation dose and the probability of developing benign and malignant thyroid nodules, even after doses of 20 Gy or more. The risk of developing thyroid carcinoma was equal for men and women, while the female-to-male ratio for benign nodules was 2.9:1, indicating that risk factors associated with females are of less importance in irradiated than in nonirradiated populations. The median latency for carcinoma was 40 years, suggesting that the increased risk of thyroid carcinoma after irradiation remains for the rest of the patient's life.« less

Electron Microscopy of the Infection and Subsequent Development of Soybean Nodule Cells

PubMed Central

Goodchild, D. J.; Bergersen, F. J.

1966-01-01

Goodchild, D. J. (Commonwealth Scientific and Industrial Research Organization, Canberra, Australia), and F. J. Bergersen. Electron microscopy of the infection and subsequent development of soybean nodule cells. J. Bacteriol. 92:204–213. 1966—Electron microscopy of thin sections of the developing central tissue cells of young soybean root nodules has shown that infection is initiated by a few infection threads which penetrate cells of the young central tissue. Extension growth of the threads may be a result of pressure developed from the growth of the bacteria within the threads. Release of bacteria from a thread is preceded by the development on an infection thread of a bulge with a cellulose-free membrane-bounded extension; bacteria move from this into the host cells by an endocytotic process and remain enclosed in an infection vacuole which is bounded by a membrane of host-cell origin. Multiplication of the intracellular bacteria takes place within these vacuoles. Until the host cell becomes filled with bacteria, the vacuoles separate into discrete units at each division. Later, division of the bacteria occurs within each vacuole, thus leading to the mature structure of the central tissue cells in which several bacteria are enclosed within each membrane-bounded unit. Images PMID:5949564

Phytochelatin synthases of the model legume Lotus japonicus. A small multigene family with differential response to cadmium and alternatively spliced variants.

PubMed

Ramos, Javier; Clemente, Maria R; Naya, Loreto; Loscos, Jorge; Pérez-Rontomé, Carmen; Sato, Shusei; Tabata, Satoshi; Becana, Manuel

2007-03-01

The biosynthesis of phytochelatins and homophytochelatins has been studied in nodulated plants of the model legume Lotus (Lotus japonicus). In the first 6 to 24 h of treatment with cadmium (Cd), roots started to synthesize elevated amounts of both polypeptides, with a concomitant increase of glutathione and a decrease of homoglutathione, indicating the presence of active phytochelatin synthase (PCS) genes. Screening of transformation-competent artificial chromosome libraries allowed identification of a cluster of three genes, LjPCS1, LjPCS2, and LjPCS3, which were mapped at 69.0 cM on chromosome 1. The genes differ in exon-intron composition and responsiveness to Cd. Gene structures and phylogenetic analysis of the three protein products, LjPCS1-8R, LjPCS2-7N, and LjPCS3-7N, are consistent with two sequential gene duplication events during evolution of vascular plants. Two sites for alternative splicing in the primary transcripts were identified. One of them, involving intron 2 of the LjPCS2 gene, was confirmed by the finding of the two predicted mRNAs, encoding LjPCS2-7R in roots and LjPCS2-7N in nodules. The amino acid sequences of LjPCS2-7R (or LjPCS2-7N) and LjPCS3-7N share 90% identity, but have only 43% to 59% identity with respect to the typical PCS1 enzymes of Lotus and other plants. The unusual LjPCS2-7N and LjPCS3-7N proteins conferred Cd tolerance when expressed in yeast (Saccharomyces cerevisiae) cells, whereas the alternatively spliced form, LjPCS2-7R, differing only in a five-amino acid motif (GRKWK) did not. These results unveil complex regulatory mechanisms of PCS expression in legume tissues in response to heavy metals and probably to other developmental and environmental factors.

Remodeling of the Infection Chamber before Infection Thread Formation Reveals a Two-Step Mechanism for Rhizobial Entry into the Host Legume Root Hair1

PubMed Central

Teillet, Alice; Chabaud, Mireille; Ivanov, Sergey; Genre, Andrea; Limpens, Erik; de Carvalho-Niebel, Fernanda; Barker, David G.

2015-01-01

In many legumes, root entry of symbiotic nitrogen-fixing rhizobia occurs via host-constructed tubular tip-growing structures known as infection threads (ITs). Here, we have used a confocal microscopy live-tissue imaging approach to investigate early stages of IT formation in Medicago truncatula root hairs (RHs) expressing fluorescent protein fusion reporters. This has revealed that ITs only initiate 10 to 20 h after the completion of RH curling, by which time major modifications have occurred within the so-called infection chamber, the site of bacterial entrapment. These include the accumulation of exocytosis (M. truncatula Vesicle-Associated Membrane Protein721e)- and cell wall (M. truncatula EARLY NODULIN11)-associated markers, concomitant with radial expansion of the chamber. Significantly, the infection-defective M. truncatula nodule inception-1 mutant is unable to create a functional infection chamber. This underlines the importance of the NIN-dependent phase of host cell wall remodeling that accompanies bacterial proliferation and precedes IT formation, and leads us to propose a two-step model for rhizobial infection initiation in legume RHs. PMID:25659382

A global experimental dataset for assessing grain legume production

PubMed Central

Cernay, Charles; Pelzer, Elise; Makowski, David

2016-01-01

Grain legume crops are a significant component of the human diet and animal feed and have an important role in the environment, but the global diversity of agricultural legume species is currently underexploited. Experimental assessments of grain legume performances are required, to identify potential species with high yields. Here, we introduce a dataset including results of field experiments published in 173 articles. The selected experiments were carried out over five continents on 39 grain legume species. The dataset includes measurements of grain yield, aerial biomass, crop nitrogen content, residual soil nitrogen content and water use. When available, yields for cereals and oilseeds grown after grain legumes in the crop sequence are also included. The dataset is arranged into a relational database with nine structured tables and 198 standardized attributes. Tillage, fertilization, pest and irrigation management are systematically recorded for each of the 8,581 crop*field site*growing season*treatment combinations. The dataset is freely reusable and easy to update. We anticipate that it will provide valuable information for assessing grain legume production worldwide. PMID:27676125

Effects of lasalocid or monensin on legume or grain (feedlot) bloat.

PubMed

Bartley, E E; Nagaraja, T G; Pressman, E S; Dayton, A D; Katz, M P; Fina, L R

1983-06-01

Doses of .66 to .99 mg monensin/kg body weight reduced legume bloat in cattle about 66% when compared with pretreatment bloat scores. Similar doses of lasalocid reduced legume bloat about 26%. A dose of 44 mg poloxalene/kg body weight (recommended dose for field use) reduced legume bloat 100%. Monensin or lasalocid combined with 25 or 50% of the recommended dose of poloxalene reduced bloat under that of the antibiotics alone, but did not achieve 100% reduction. The antibiotic thiopeptin provided no preventive effect on legume bloat. Lasalocid, monensin or an experimental polyether antibiotic (X-14,547 A) at a dose of 1.32 mg/kg body weight when tested on cattle bloated on high grain diets reduced bloat by 92, 64 and 25%, respectively. Lasalocid at .66 mg/kg effectively prevented bloat from developing when given to animals before the feeding of high grain diets; however, a 1.32-mg dose was required to control bloat in cattle that were already bloating before they were given lasalocid. A dose of 1.32 mg salinomycin was ineffective in controlling grain bloat.

Solitary pulmonary nodule

MedlinePlus

Lung cancer - solitary nodule; Infectious granuloma - pulmonary nodule; SPN ... such as aspergillosis , coccidioidomycosis , cryptococcosis , or histoplasmosis Primary lung cancer is the most common cause of cancerous (malignant) ...

Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moulin, Lionel; Klonowska, Agnieszka; Caroline, Bournaud

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T, was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a megaplasmid (1,904,893 bp)more » and a plasmid hosting the symbiotic functions (595,108 bp).« less

Are common symbiosis genes required for endophytic rice-rhizobial interactions?

PubMed

Chen, Caiyan; Zhu, Hongyan

2013-09-01

Legume plants are able to establish root nodule symbioses with nitrogen-fixing bacteria, called rhizobia. Recent studies revealed that the root nodule symbiosis has co-opted the signaling pathway that mediates the ancestral mycorrhizal symbiosis that occurs in most land plants. Despite being unable to induce nodulation, rhizobia have been shown to be able to infect and colonize the roots of non-legumes such as rice. One fascinating question is whether establishment of such associations requires the common symbiosis (Sym) genes that are essential for infection of plant cells by mycorrhizal fungi and rhizobia in legumes. Here, we demonstrated that the common Sym genes are not required for endophytic colonization of rice roots by nitrogen-fixing rhizobia.

Multicellular contractility contributes to the emergence of mesothelioma nodules

NASA Astrophysics Data System (ADS)

Czirok, Andras

Malignant pleural mesothelioma (MPM) nodules arise from the mesothelial lining of the pleural cavity by a poorly understood mechanism. We demonstrate that macroscopic multicellular aggregates, reminiscent of the MPM nodules found in patients, develop when MPM cell lines are cultured at high cell densities for several weeks. Surprisingly, the nodule-like aggregates do not arise by excessive local cell proliferation, but by myosin II-driven cell contractility. Contractile nodules contain prominent actin cables that can span several cells. Several features of the in vitro MPM nodule development can be explained by a computational model that assumes uniform and steady intercellular contractile forces within a monolayer of cells, and a mechanical load-dependent lifetime of cell-cell contacts. The model behaves as a self-tensioned Maxwell fluid and exhibits an instability that leads to pattern formation. Altogether, our findings suggest that inhibition of the actomyosin system may provide a hitherto not utilized therapeutic approach to affect MPM growth. NIH R01-GM102801.

Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads

PubMed Central

Yano, Koji; Aoki, Seishiro; Liu, Meng; Umehara, Yosuke; Suganuma, Norio; Iwasaki, Wataru; Sato, Shusei; Soyano, Takashi; Kouchi, Hiroshi

2017-01-01

Abstract Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint. PMID:28028038

A deep-learning based automatic pulmonary nodule detection system

NASA Astrophysics Data System (ADS)

Zhao, Yiyuan; Zhao, Liang; Yan, Zhennan; Wolf, Matthias; Zhan, Yiqiang

2018-02-01

Lung cancer is the deadliest cancer worldwide. Early detection of lung cancer is a promising way to lower the risk of dying. Accurate pulmonary nodule detection in computed tomography (CT) images is crucial for early diagnosis of lung cancer. The development of computer-aided detection (CAD) system of pulmonary nodules contributes to making the CT analysis more accurate and with more efficiency. Recent studies from other groups have been focusing on lung cancer diagnosis CAD system by detecting medium to large nodules. However, to fully investigate the relevance between nodule features and cancer diagnosis, a CAD that is capable of detecting nodules with all sizes is needed. In this paper, we present a deep-learning based automatic all size pulmonary nodule detection system by cascading two artificial neural networks. We firstly use a U-net like 3D network to generate nodule candidates from CT images. Then, we use another 3D neural network to refine the locations of the nodule candidates generated from the previous subsystem. With the second sub-system, we bring the nodule candidates closer to the center of the ground truth nodule locations. We evaluate our system on a public CT dataset provided by the Lung Nodule Analysis (LUNA) 2016 grand challenge. The performance on the testing dataset shows that our system achieves 90% sensitivity with an average of 4 false positives per scan. This indicates that our system can be an aid for automatic nodule detection, which is beneficial for lung cancer diagnosis.

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses.

PubMed

van Velzen, Robin; Holmer, Rens; Bu, Fengjiao; Rutten, Luuk; van Zeijl, Arjan; Liu, Wei; Santuari, Luca; Cao, Qingqin; Sharma, Trupti; Shen, Defeng; Roswanjaya, Yuda; Wardhani, Titis A K; Kalhor, Maryam Seifi; Jansen, Joelle; van den Hoogen, Johan; Güngör, Berivan; Hartog, Marijke; Hontelez, Jan; Verver, Jan; Yang, Wei-Cai; Schijlen, Elio; Repin, Rimi; Schilthuizen, Menno; Schranz, M Eric; Heidstra, Renze; Miyata, Kana; Fedorova, Elena; Kohlen, Wouter; Bisseling, Ton; Smit, Sandra; Geurts, Rene

2018-05-15

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION ( NIN ) and RHIZOBIUM-DIRECTED POLAR GROWTH ( RPG ). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN , RPG , and NOD FACTOR PERCEPTION Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants. Copyright © 2018 the Author(s). Published by PNAS.

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses

PubMed Central

Holmer, Rens; Bu, Fengjiao; Rutten, Luuk; van Zeijl, Arjan; Liu, Wei; Santuari, Luca; Cao, Qingqin; Sharma, Trupti; Shen, Defeng; Roswanjaya, Yuda; Wardhani, Titis A. K.; Kalhor, Maryam Seifi; Jansen, Joelle; van den Hoogen, Johan; Güngör, Berivan; Hartog, Marijke; Hontelez, Jan; Verver, Jan; Schijlen, Elio; Repin, Rimi; Schilthuizen, Menno; Heidstra, Renze; Miyata, Kana; Fedorova, Elena; Kohlen, Wouter; Bisseling, Ton; Smit, Sandra

2018-01-01

Nodules harboring nitrogen-fixing rhizobia are a well-known trait of legumes, but nodules also occur in other plant lineages, with rhizobia or the actinomycete Frankia as microsymbiont. It is generally assumed that nodulation evolved independently multiple times. However, molecular-genetic support for this hypothesis is lacking, as the genetic changes underlying nodule evolution remain elusive. We conducted genetic and comparative genomics studies by using Parasponia species (Cannabaceae), the only nonlegumes that can establish nitrogen-fixing nodules with rhizobium. Intergeneric crosses between Parasponia andersonii and its nonnodulating relative Trema tomentosa demonstrated that nodule organogenesis, but not intracellular infection, is a dominant genetic trait. Comparative transcriptomics of P. andersonii and the legume Medicago truncatula revealed utilization of at least 290 orthologous symbiosis genes in nodules. Among these are key genes that, in legumes, are essential for nodulation, including NODULE INCEPTION (NIN) and RHIZOBIUM-DIRECTED POLAR GROWTH (RPG). Comparative analysis of genomes from three Parasponia species and related nonnodulating plant species show evidence of parallel loss in nonnodulating species of putative orthologs of NIN, RPG, and NOD FACTOR PERCEPTION. Parallel loss of these symbiosis genes indicates that these nonnodulating lineages lost the potential to nodulate. Taken together, our results challenge the view that nodulation evolved in parallel and raises the possibility that nodulation originated ∼100 Mya in a common ancestor of all nodulating plant species, but was subsequently lost in many descendant lineages. This will have profound implications for translational approaches aimed at engineering nitrogen-fixing nodules in crop plants. PMID:29717040

Microgravity Effects on the Early Events of Biological Nitrogen Fixation in Medicago Truncatula: Results from the SyNRGE Experiment

NASA Astrophysics Data System (ADS)

Stutte, Gary W.; Roberts, Michael S.

2013-02-01

SyNRGE (Symbiotic Nodulation in a Reduced Gravity Environment) was a sortie mission on STS-135 in the Biological Research in Canisters (BRIC) hardware to study the effect of μg on a plant-microbe symbiosis resulting in biological nitrogen fixation. Medicago truncatula, a model species for the legume family, was inoculated with its bacterial symbiont, Sinorhizobium meliloti, to observe early biomolecular events associated with infection and nodulation in Petri Dish Fixation Units (PDFU’s). Two sets of experiments were conducted in orbit and in 24-hour delayed ground controls. Experiments were designed to determine if S. meliloti would infect M. truncatula and initiate biomolecular changes associated with nodule formation and if the μg environment altered the host plant and/or bacteria to induce nodule formation upon return to 1g. Initial analysis results demonstrate that the legumes and bacteria cultivated in μg have potential to develop a symbiotic interaction, but suggest that μg alters their ability to form nodules upon return to 1g. (Research supported by NASA ESMD/ Advance Capabilities Division grant NNX10AR09A)

Enhancing Legume Ecosystem Services through an Understanding of Plant-Pollinator Interplay.

PubMed

Suso, María J; Bebeli, Penelope J; Christmann, Stefanie; Mateus, Célia; Negri, Valeria; Pinheiro de Carvalho, Miguel A A; Torricelli, Renzo; Veloso, Maria M

2016-01-01

Legumes are bee-pollinated, but to a different extent. The importance of the plant-pollinator interplay (PPI), in flowering crops such as legumes lies in a combination of the importance of pollination for the production service and breeding strategies, plus the increasing urgency in mitigating the decline of pollinators through the development and implementation of conservation measures. To realize the full potential of the PPI, a multidisciplinary approach is required. This article assembles an international team of genebank managers, geneticists, plant breeders, experts on environmental governance and agro-ecology, and comprises several sections. The contributions in these sections outline both the state of the art of knowledge in the field and the novel aspects under development, and encompass a range of reviews, opinions and perspectives. The first three sections explore the role of PPI in legume breeding strategies. PPI based approaches to crop improvement can make it possible to adapt and re-design breeding strategies to meet both goals of: (1) optimal productivity, based on an efficient use of pollinators, and (2) biodiversity conservation. The next section deals with entomological aspects and focuses on the protection of the "pest control service" and pollinators in legume crops. The final section addresses general approaches to encourage the synergy between food production and pollination services at farmer field level. Two basic approaches are proposed: (a) Farming with Alternative Pollinators and (b) Crop Design System.

A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation1[W][OA

PubMed Central

Pislariu, Catalina I.; D. Murray, Jeremy; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; A. Benedito, Vagner; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E.; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Chen, Rujin; Udvardi, Michael K.

2012-01-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging. PMID:22679222

Late Embryogenesis Abundant (LEA) proteins in legumes

PubMed Central

Battaglia, Marina; Covarrubias, Alejandra A.

2013-01-01

Plants are exposed to different external conditions that affect growth, development, and productivity. Water deficit is one of these adverse conditions caused by drought, salinity, and extreme temperatures. Plants have developed different responses to prevent, ameliorate or repair the damage inflicted by these stressful environments. One of these responses is the activation of a set of genes encoding a group of hydrophilic proteins that typically accumulate to high levels during seed dehydration, at the last stage of embryogenesis, hence named Late Embryogenesis Abundant (LEA) proteins. LEA proteins also accumulate in response to water limitation in vegetative tissues, and have been classified in seven groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. These proteins are widely distributed in the plant kingdom, from ferns to angiosperms, suggesting a relevant role in the plant response to this unfavorable environmental condition. In this review, we analyzed the LEA proteins from those legumes whose complete genomes have been sequenced such as Phaseolus vulgaris, Glycine max, Medicago truncatula, Lotus japonicus, Cajanus cajan, and Cicer arietinum. Considering their distinctive motifs, LEA proteins from the different groups were identified, and their sequence analysis allowed the recognition of novel legume specific motifs. Moreover, we compile their transcript accumulation patterns based on publicly available data. In spite of the limited information on these proteins in legumes, the analysis and data compiled here confirm the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions. PMID:23805145

Beans and Other Legumes: Types and Cooking Tips

MedlinePlus

... Nutrition and healthy eating Want to add nutritious beans and legumes to your diet but aren't ... Staff Legumes — a class of vegetables that includes beans, peas and lentils — are among the most versatile ...

Legume crops phylogeny and genetic diversity for science and breeding

USDA-ARS?s Scientific Manuscript database

Economically, legumes (Fabaceae) represent the second most important family of crop plants after the grass family, Poaceae. Grain legumes account for 27% of world crop production and provide 33% of the dietary protein consumed by humans, while pasture and forage legumes provide vital part of animal ...

Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes.

PubMed

Wang, Zhihui; Cheng, Ke; Wan, Liyun; Yan, Liying; Jiang, Huifang; Liu, Shengyi; Lei, Yong; Liao, Boshou

2015-12-10

Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a-d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. In summary, this genome-wide identification, characterization and expression analysis of

24-Epibrassinolide ameliorates salt stress effects in the symbiosis Medicago truncatula-Sinorhizobium meliloti and regulates the nodulation in cross-talk with polyamines.

PubMed

López-Gómez, Miguel; Hidalgo-Castellanos, Javier; Lluch, Carmen; Herrera-Cervera, José A

2016-11-01

Brassinosteroids (BRs) are steroid plant hormones that have been shown to be involved in the response to salt stress in cross-talk with other plant growth regulators such as polyamines (PAs). In addition, BRs are involved in the regulation of the nodulation in the rhizobium-legume symbiosis through the alteration of the PAs content in leaves. In this work, we have studied the effect of exogenous 24-epibrassinolide (EBL) in the response to salinity of nitrogen fixation in the symbiosis Medicago truncatula-Sinorhizobium meliloti. Foliar spraying of EBL restored the growth of plants subjected to salt stress and provoked an increment of the nitrogenase activity. In general, PAs levels in leaves and nodules decreased by the salt and EBL treatments, however, the co-treatment with NaCl and EBL augmented the foliar spermine (Spm) concentration. This increment of the Spm levels was followed by a reduction of the membrane oxidative damage and a diminution of the proline accumulation. The effect of BRs on the symbiotic interaction was evaluated by the addition of 0.01, 0.1 and 0.5 μM EBL to the growing solution, which provoked a reduction of the nodule number and an increment of the PAs levels in shoot. In conclusion, foliar treatment with EBL had a protective effect against salt stress in the M. truncatula-S. meliloti symbiosis mediated by an increment of the Spm levels. Treatment of roots with EBL incremented PAs levels in shoot and reduced the nodule number which suggests a cross-talk between PAs and BRs in the nodule suppression and the protection against salt stress. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Botulinum toxin in the treatment of vocal fold nodules.

PubMed

Allen, Jacqui E; Belafsky, Peter C

2009-12-01

Promising new techniques in the management of vocal fold nodules have been developed in the past 2 years. Simultaneously, the therapeutic use of botulinum toxin has rapidly expanded. This review explores the use of botulinum toxin in treatment of vocal nodules and summarizes current therapeutic concepts. New microsurgical instruments and techniques, refinements in laser technology, radiosurgical excision and steroid intralesional injections are all promising new techniques in the management of vocal nodules. Botulinum toxin-induced 'voice rest' is a new technique we have employed in patients with recalcitrant nodules. Successful resolution of nodules is possible with this technique, without the risk of vocal fold scarring inherent in dissection/excision techniques. Botulinum toxin usage is exponentially increasing, and large-scale, long-term studies demonstrate its safety profile. Targeted vocal fold temporary paralysis induced by botulinum toxin injection is a new, well tolerated and efficacious treatment in patients with persistent vocal fold nodules.

Detection of pulmonary nodule growth with dose reduced chest tomosynthesis: a human observer study using simulated nodules

NASA Astrophysics Data System (ADS)

Söderman, Christina; Johnsson, Ã. se; Vikgren, Jenny; Rossi Norrlund, Rauni; Molnar, David; Mirzai, Maral; Svalkvist, Angelica; Mânsson, Lars Gunnar; Bâth, Magnus

2016-03-01

Chest tomosynthesis may be a suitable alternative to computed tomography for the clinical task of follow up of pulmonary nodules. The aim of the present study was to investigate the detection of pulmonary nodule growth suggestive of malignancy using chest tomosynthesis. Previous studies have indicated remained levels of detection of pulmonary nodules at dose levels corresponding to that of a conventional lateral radiograph, approximately 0.04 mSv, which motivated to perform the present study this dose level. Pairs of chest tomosynthesis image sets, where the image sets in each pair were acquired of the same patient at two separate occasions, were included in the study. Simulated nodules with original diameters of approximately 8 mm were inserted in the pairs of image sets, simulating situations where the nodule had remained stable in size or increased isotropically in size between the two different imaging occasions. Four different categories of nodule growth were included, corresponding to a volume increase of approximately 21 %, 68 %, 108 % and 250 %. All nodules were centered in the depth direction in the tomosynthesis images. All images were subjected to a simulated dose reduction, resulting in images corresponding to an effective dose of 0.04 mSv. Four observers were given the task of rating their confidence that the nodule was stable in size or not on a five-level rating scale. This was done both before any size measurements were made of the nodule as well as after measurements were performed. Using Receiver operating characteristic analysis, the rating data for the nodules that were stable in size was compared to the rating data for the nodules simulated to have increased in size. Statistically significant differences between the rating distributions for the stable nodules and all of the four nodule growth categories were found. For the three largest nodule growths, nearly perfect detection of nodule growth was seen. In conclusion, the present study

Evaluation of the 95% limits of agreement of the volumes of 5-year clinically stable solid nodules for the development of a follow-up system for indeterminate solid nodules in CT lung cancer screening

PubMed Central

Muramatsu, Yukio; Yamamichi, Junta; Gomi, Shiho; Oubel, Estanislao; Moriyama, Noriyuki

2018-01-01

Background This study sought to evaluate the 95% limits of agreement of the volumes of 5-year clinically stable solid nodules for the development of a follow-up system for indeterminate solid nodules. Methods The volumes of 226 solid nodules that had been clinically stable for 5 years were measured in 186 patients (53 female never-smokers, 36 male never-smokers, 51 males with <30 pack-years, and 46 males with ≥30 pack-years) using a three-dimensional semiautomated method. Volume changes were evaluated using three methods: percent change, proportional change and growth rate. The 95% limits of agreement were evaluated using the Bland-Altman method. Results The 95% limits of agreement were as follows: range of percent change, from ±34.5% to ±37.8%; range of proportional change, from ±34.1% to ±36.8%; and range of growth rate, from ±39.2% to ±47.4%. Percent change-based, proportional change-based, and growth rate-based diagnoses of an increase or decrease in ten solid nodules were made at a mean of 302±402, 367±455, and 329±496 days, respectively, compared with a clinical diagnosis made at 809±616 days (P<0.05). Conclusions The 95% limits of agreement for volume change in 5-year stable solid nodules may enable the detection of an increase or decrease in the solid nodule at an earlier stage than that enabled by a clinical diagnosis, possibly contributing to the development of a follow-up system for reducing the number of additional Computed tomography (CT) scans performed during the follow-up period. PMID:29600047

Evaluation of the 95% limits of agreement of the volumes of 5-year clinically stable solid nodules for the development of a follow-up system for indeterminate solid nodules in CT lung cancer screening.

PubMed

Kakinuma, Ryutaro; Muramatsu, Yukio; Yamamichi, Junta; Gomi, Shiho; Oubel, Estanislao; Moriyama, Noriyuki

2018-01-01

This study sought to evaluate the 95% limits of agreement of the volumes of 5-year clinically stable solid nodules for the development of a follow-up system for indeterminate solid nodules. The volumes of 226 solid nodules that had been clinically stable for 5 years were measured in 186 patients (53 female never-smokers, 36 male never-smokers, 51 males with <30 pack-years, and 46 males with ≥30 pack-years) using a three-dimensional semiautomated method. Volume changes were evaluated using three methods: percent change, proportional change and growth rate. The 95% limits of agreement were evaluated using the Bland-Altman method. The 95% limits of agreement were as follows: range of percent change, from ±34.5% to ±37.8%; range of proportional change, from ±34.1% to ±36.8%; and range of growth rate, from ±39.2% to ±47.4%. Percent change-based, proportional change-based, and growth rate-based diagnoses of an increase or decrease in ten solid nodules were made at a mean of 302±402, 367±455, and 329±496 days, respectively, compared with a clinical diagnosis made at 809±616 days (P<0.05). The 95% limits of agreement for volume change in 5-year stable solid nodules may enable the detection of an increase or decrease in the solid nodule at an earlier stage than that enabled by a clinical diagnosis, possibly contributing to the development of a follow-up system for reducing the number of additional Computed tomography (CT) scans performed during the follow-up period.

Growth, nitrogen accumulation and nitrogen transfer by legume species established on mine spoils

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jefferies, R.A.; Bradshaw, A.D.; Putwain, P.D.

1981-12-01

Nitrogen deficiency is an important factor limiting plant growth on many types of mine and mineral spoils. One method of overcoming this problem is to use legume species which are able to accumulate nitrogen in such spoils. The growth, nitrogen accumulation and nitrogen transfer to a companion species was compared in contrasting legume species established on colliery spoil and on sand waste from the extraction of china clay. Legumes can be effective means of accumulating nitrogen in such spoils with rates as high as 295 kg N ha/sup -1/ yr/sup -1/ being measured for Lupinus perennis sown on sand waste.more » Nitrogen transfer from legumes to a companion grass was also apparent. Trifolium repens sown on colliery spoil increased the nitrogen content of the companion grass by 76 kg ha/sup -1/ within 2 yr of sowing. It is concluded that a wider range of legume species than conventionally used is available, offering greater tolerance of the extreme conditions of mine spoils combined with high rates of nitrogen accumulation. It is necessary to develop reclamation strategies which incorporate such species.« less

Interstitial laser photocoagulation for benign thyroid nodules: time to treat large nodules.

PubMed

Amabile, Gerardo; Rotondi, Mario; Pirali, Barbara; Dionisio, Rosa; Agozzino, Lucio; Lanza, Michele; Buonanno, Luciano; Di Filippo, Bruno; Fonte, Rodolfo; Chiovato, Luca

2011-09-01

Interstitial laser photocoagulation (ILP) is a new therapeutic option for the ablation of non-functioning and hyper-functioning benign thyroid nodules. Amelioration of the ablation procedure currently allows treating large nodules. Aim of this study was to evaluate the therapeutic efficacy of ILP, performed according to a modified protocol of ablation, in patients with large functioning and non-functioning thyroid nodules and to identify the best parameters for predicting successful outcome in hyperthyroid patients. Fifty-one patients with non-functioning thyroid nodules (group 1) and 26 patients with hyperfunctioning thyroid nodules (group 2) were enrolled. All patients had a nodular volume ≥40 ml. Patients were addressed to 1-3 cycles of ILP. A cycle consisted of three ILP sessions, each lasting 5-10 minutes repeated at an interval of 1 month. After each cycle of ILP patients underwent thyroid evaluation. A nodule volume reduction, expressed as percentage of the basal volume, significantly occurred in both groups (F = 190.4; P < 0.0001 for group 1 and F = 100.2; P < 0.0001 for group 2). Receiver-operator-characteristic (ROC) curves were constructed for: (i) percentage of volume reduction; (ii) difference in nodule volume; (iii) total amount of energy delivered expressed in Joule. ROC curves identified the percentage of volume reduction as the best parameter predicting a normalized serum TSH (area under the curve 0.962; P < 0.0001). Intraoperative complications consisted in: (i) mild pain occurring in five (6.5%) patients, (ii) vasovagal reaction in two (2.6%) patients, (iii) fever within 24 hours from ILP in five (6.5%) patients. No major complications including persistent pain, laringeal nerve dysfunction, hypoparathyroidism, pseudocystic transformation, and/or neck fascitis were observed. ILP represents a valid alternative to surgery also for large benign thyroid nodules, both in terms of nodule size reduction and cure of

[Manifestation of Dupuytren nodules following fracture of the distal radius].

PubMed

Wichelhaus, Alice; Wendt, M; Mielsch, N; Gradl, G; Mittlmeier, T

2015-02-01

The aim of this study is to evaluate the incidence of post-traumatic development of Dupuytren nodules in distal radius fractures treated operatively. In 2 prospective randomised studies for operative treatment of distal radius fractures, the formation of Dupuytren nodules was registered. One of the exclusion criteria was a pre-existing Dupuytren's disease at the date of trauma. In addition to the notification of the development of Dupuytren nodules, signs of a complex regional pain syndrome were registered as well as the wrist function, level of pain and grip strength. The Castaing and the Gartland and Werley scores were assessed. The clinical outcomes of patients with and without Dupuytren nodules were compared. 239 of 275 (87%) of the patients could be examined 1 year after the operation, consisting of 32 men and 207 women with a median age of 64.2 years. The patients with Dupuytren nodules were re-evaluated after 16-60 months (median 41.8) for progression of the disease. 21 patients (8.7%) developed changes of the palmar aponeurosis. In 20 patients nodules were stated, one patient showed a cord at the fourth ray of the injured hand. 19 out of 21 patients were female (90.5%). At re-evaluation after 41.8 months (16-60) progression could not be noted nor could similar changes be seen on the contralateral side. Patients with Dupuytren nodules were not handicapped in their hand function. 3 patients (14.3%) revealed a positive family history for Dupuytren's disease. Abuse of alcohol or diabetes was not present in any of the patients with Dupuytren nodules, 7 (33%) were smokers. The occurrence of Dupyutren nodules can be triggered by a trauma or operation. It may be speculated that these nodules are an entity of their own as no progression of the contracture could be seen during the follow-up period. © Georg Thieme Verlag KG Stuttgart · New York.

Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters1[W][OA

PubMed Central

Benedito, Vagner A.; Li, Haiquan; Dai, Xinbin; Wandrey, Maren; He, Ji; Kaundal, Rakesh; Torres-Jerez, Ivone; Gomez, S. Karen; Harrison, Maria J.; Tang, Yuhong; Zhao, Patrick X.; Udvardi, Michael K.

2010-01-01

Transporters move hydrophilic substrates across hydrophobic biological membranes and play key roles in plant nutrition, metabolism, and signaling and, consequently, in plant growth, development, and responses to the environment. To initiate and support systematic characterization of transporters in the model legume Medicago truncatula, we identified 3,830 transporters and classified 2,673 of these into 113 families and 146 subfamilies. Analysis of gene expression data for 2,611 of these transporters identified 129 that are expressed in an organ-specific manner, including 50 that are nodule specific and 36 specific to mycorrhizal roots. Further analysis uncovered 196 transporters that are induced at least 5-fold during nodule development and 44 in roots during arbuscular mycorrhizal symbiosis. Among the nodule- and mycorrhiza-induced transporter genes are many candidates for known transport activities in these beneficial symbioses. The data presented here are a unique resource for the selection and functional characterization of legume transporters. PMID:20023147

The C2H2 transcription factor regulator of symbiosome differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in Medicago truncatula.

PubMed

Sinharoy, Senjuti; Torres-Jerez, Ivone; Bandyopadhyay, Kaustav; Kereszt, Attila; Pislariu, Catalina I; Nakashima, Jin; Benedito, Vagner A; Kondorosi, Eva; Udvardi, Michael K

2013-09-01

Transcription factors (TFs) are thought to regulate many aspects of nodule and symbiosis development in legumes, although few TFs have been characterized functionally. Here, we describe regulator of symbiosome differentiation (RSD) of Medicago truncatula, a member of the Cysteine-2/Histidine-2 (C2H2) family of plant TFs that is required for normal symbiosome differentiation during nodule development. RSD is expressed in a nodule-specific manner, with maximal transcript levels in the bacterial invasion zone. A tobacco (Nicotiana tabacum) retrotransposon (Tnt1) insertion rsd mutant produced nodules that were unable to fix nitrogen and that contained incompletely differentiated symbiosomes and bacteroids. RSD protein was localized to the nucleus, consistent with a role of the protein in transcriptional regulation. RSD acted as a transcriptional repressor in a heterologous yeast assay. Transcriptome analysis of an rsd mutant identified 11 genes as potential targets of RSD repression. RSD interacted physically with the promoter of one of these genes, VAMP721a, which encodes vesicle-associated membrane protein 721a. Thus, RSD may influence symbiosome development in part by repressing transcription of VAMP721a and modifying vesicle trafficking in nodule cells. This establishes RSD as a TF implicated directly in symbiosome and bacteroid differentiation and a transcriptional regulator of secretory pathway genes in plants.

Crops, Nitrogen, Water: Are Legumes Friend, Foe, or Misunderstood Ally?

PubMed

Adams, Mark A; Buchmann, Nina; Sprent, Janet; Buckley, Thomas N; Turnbull, Tarryn L

2018-06-01

Biological nitrogen fixation (BNF) by crop legumes reduces demand for industrial nitrogen fixation (INF). Nonetheless, rates of BNF in agriculture remain low, with strong negative feedback to BNF from reactive soil nitrogen (N) and drought. We show that breeding for yield has resulted in strong relationships between photosynthesis and leaf N in non-leguminous crops, whereas grain legumes show strong relations between leaf N and water use efficiency (WUE). We contrast these understandings with other studies that draw attention to the water costs of grain legume crops, and their potential for polluting the biosphere with N. We propose that breeding grain legumes for reduced stomatal conductance can increase WUE without compromising production or BNF. Legume crops remain a better bet than relying on INF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Tripartite symbiosis of Sophora tomentosa, rhizobia and arbuscular mycorhizal fungi.

PubMed

Toma, Maíra Akemi; Soares de Carvalho, Teotonio; Azarias Guimarães, Amanda; Martins da Costa, Elaine; Savana da Silva, Jacqueline; de Souza Moreira, Fatima Maria

Sophora tomentosa is a pantropical legume species with potential for recovery of areas degraded by salinization, and for stabilization of sand dunes. However, few studies on this species have been carried out, and none regarding its symbiotic relationship with beneficial soil microorganisms. Therefore, this study aimed to evaluate the diversity of nitrogen-fixing bacteria isolated from nodules of Sophora tomentosa, and to analyze the occurrence of colonization of arbuscular mycorrhizal fungi on the roots of this legume in seafront soil. Thus, seeds, root nodules, and soil from the rhizosphere of Sophora tomentosa were collected. From the soil samples, trap cultures with this species were established to extract spores and to evaluate arbuscular mycorhizal fungi colonization in legume roots, as well as to capture rhizobia. Rhizobia strains were isolated from nodules collected in the field or from the trap cultures. Representative isolates of the groups obtained in the similarity dendrogram, based on phenotypic characteristics, had their 16S rRNA genes sequenced. The legume species showed nodules with indeterminate growth, and reddish color, distributed throughout the root. Fifty-one strains of these nodules were isolated, of which 21 were classified in the genus Bacillus, Brevibacillus, Paenibacillus, Rhizobium and especially Sinorhizobium. Strains closely related to Sinorhizobium adhaerens were the predominant bacteria in nodules. The other genera found, with the exception of Rhizobium, are probably endophytic bacteria in the nodules. Arbuscular mycorrhizal fungi was observed colonizing the roots, but arbuscular mycorhizal fungi spores were not found in the trap cultures. Therefore Sophora tomentosa is associated with both arbuscular mycorhizal fungi and nodulating nitrogen-fixing bacteria. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Novel Cupriavidus Strains Isolated from Root Nodules of Native Uruguayan Mimosa Species

PubMed Central

James, Euan K.; Rios, Cecilia; Iriarte, Andrés; Sandes, Laura; Zabaleta, María; Battistoni, Federico; Fabiano, Elena

2016-01-01

ABSTRACT The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus. However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis. Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found. IMPORTANCE With the aim of exploring the diversity of rhizobia associated with native Mimosa species, symbionts were isolated from root nodules on five Mimosa species that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genus Mimosa, Brazil and Mexico, where it is mainly associated with Burkholderia and Rhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genus Cupriavidus. Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic species C. taiwanensis, but instead they were related to other Cupriavidus species such as C

Novel Cupriavidus Strains Isolated from Root Nodules of Native Uruguayan Mimosa Species.

PubMed

Platero, Raúl; James, Euan K; Rios, Cecilia; Iriarte, Andrés; Sandes, Laura; Zabaleta, María; Battistoni, Federico; Fabiano, Elena

2016-06-01

The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found. With the aim of exploring the diversity of rhizobia associated with native Mimosa species, symbionts were isolated from root nodules on five Mimosa species that are native to a region in southern Uruguay, Sierra del Abra de Zabaleta. In contrast to data obtained in the major centers of diversification of the genus Mimosa, Brazil and Mexico, where it is mainly associated with Burkholderia and Rhizobium/Ensifer, respectively, the present study has shown that all the isolated symbiotic bacteria belonged to the genus Cupriavidus Interestingly, none of nodules contained bacteria belonging to the well-described symbiotic species C. taiwanensis, but instead they were related to other Cupriavidus species such as C. necator and C

Phytoremediation of heavy and transition metals aided by legume-rhizobia symbiosis.

PubMed

Hao, X; Taghavi, S; Xie, P; Orbach, M J; Alwathnani, H A; Rensing, C; Wei, G

2014-01-01

Legumes are important for nitrogen cycling in the environment and agriculture due to the ability of nitrogen fixation by rhizobia. In this review, we introduce an important and potential role of legume-rhizobia symbiosis in aiding phytoremediation of some metal contaminated soils as various legumes have been found to be the dominant plant species in metal contaminated areas. Resistant rhizobia used for phytoremediation could act on metals directly by chelation, precipitation, transformation, biosorption and accumulation. Moreover, the plant growth promoting (PGP) traits of rhizobia including nitrogen fixation, phosphorus solubilization, phytohormone synthesis, siderophore release, and production of ACC deaminase and the volatile compounds of acetoin and 2, 3-butanediol may facilitate legume growth while lessening metal toxicity. The benefits of using legumes inoculated with naturally resistant rhizobia or recombinant rhizobia with enhanced resistance, as well as co-inoculation with other plant growth promoting bacteria (PGPB) are discussed. However, the legume-rhizobia symbiosis appears to be sensitive to metals, and the effect of metal toxicity on the interaction between legumes and rhizobia is not clear. Therefore, to obtain the maximum benefits from legumes assisted by rhizobia for phytoremediation of metals, it is critical to have a good understanding of interactions between PGP traits, the symbiotic plant-rhizobia relationship and metals.

Vasculature surrounding a nodule: A novel lung cancer biomarker.

PubMed

Wang, Xiaohua; Leader, Joseph K; Wang, Renwei; Wilson, David; Herman, James; Yuan, Jian-Min; Pu, Jiantao

2017-12-01

To investigate whether the vessels surrounding a nodule depicted on non-contrast, low-dose computed tomography (LDCT) can discriminate benign and malignant screen detected nodules. We collected a dataset consisting of LDCT scans acquired on 100 subjects from the Pittsburgh Lung Screening study (PLuSS). Fifty subjects were diagnosed with lung cancer and 50 subjects had suspicious nodules later proven benign. For the lung cancer cases, the location of the malignant nodule in the LDCT scans was known; while for the benign cases, the largest nodule in the LDCT scan was used in the analysis. A computer algorithm was developed to identify surrounding vessels and quantify the number and volume of vessels that were connected or near the nodule. A nonparametric receiver operating characteristic (ROC) analysis was performed based on a single nodule per subject to assess the discriminability of the surrounding vessels to provide a lung cancer diagnosis. Odds ratio (OR) were computed to determine the probability of a nodule being lung cancer based on the vessel features. The areas under the ROC curves (AUCs) for vessel count and vessel volume were 0.722 (95% CI=0.616-0.811, p<0.01) and 0.676 (95% CI=0.565-0.772), respectively. The number of vessels attached to a nodule was significantly higher in the lung cancer group 9.7 (±9.6) compared to the non-lung cancer group 4.0 (±4.3) CONCLUSION: Our preliminary results showed that malignant nodules are often surrounded by more vessels compared to benign nodules, suggesting that the surrounding vessel characteristics could serve as lung cancer biomarker for indeterminate nodules detected during LDCT lung cancer screening using only the information collected during the initial visit. Copyright © 2017 Elsevier B.V. All rights reserved.

The pea Sym37 receptor kinase gene controls infection-thread initiation and nodule development.

PubMed

Zhukov, Vladimir; Radutoiu, Simona; Madsen, Lene H; Rychagova, Tamara; Ovchinnikova, Evgenia; Borisov, Alex; Tikhonovich, Igor; Stougaard, Jens

2008-12-01

Phenotypic characterization of pea symbiotic mutants has provided a detailed description of the symbiosis with Rhizobium leguminosarum bv. viciae strains. We show here that two allelic non-nodulating pea mutants, RisNod4 and K24, are affected in the PsSym37 gene, encoding a LysM receptor kinase similar to Lotus japonicus NFR1 and Medicago truncatula LYK3. Phenotypic analysis of RisNod4 and K24 suggests a role for the SYM37 in regulation of infection-thread initiation and nodule development from cortical-cell division foci. We show that RisNod4 plants carrying an L to F substitution in the LysM1 domain display a restrictive symbiotic phenotype comparable to the PsSym2(A) lines that distinguish 'European' and 'Middle East' Rhizobium leguminosarum bv. viciae strains. RisNod4 mutants develop nodules only in the presence of a 'Middle East' Rhizobium strain producing O-acetylated Nod factors indicating the SYM37 involvement in Nod-factor recognition. Along with the PsSym37, a homologous LysM receptor kinase gene, PsK1, was isolated and characterized. We show that PsK1 and PsSym37 are genetically linked to each other and to the PsSym2 locus. Allelic complementation analyses and sequencing of the extracellular regions of PsSym37 and PsK1 in several 'European' and 'Afghan' pea cultivars point towards PsK1 as possible candidate for the elusive PsSym2 gene.

Enhancing Legume Ecosystem Services through an Understanding of Plant–Pollinator Interplay

PubMed Central

Suso, María J.; Bebeli, Penelope J.; Christmann, Stefanie; Mateus, Célia; Negri, Valeria; Pinheiro de Carvalho, Miguel A. A.; Torricelli, Renzo; Veloso, Maria M.

2016-01-01

Legumes are bee-pollinated, but to a different extent. The importance of the plant–pollinator interplay (PPI), in flowering crops such as legumes lies in a combination of the importance of pollination for the production service and breeding strategies, plus the increasing urgency in mitigating the decline of pollinators through the development and implementation of conservation measures. To realize the full potential of the PPI, a multidisciplinary approach is required. This article assembles an international team of genebank managers, geneticists, plant breeders, experts on environmental governance and agro-ecology, and comprises several sections. The contributions in these sections outline both the state of the art of knowledge in the field and the novel aspects under development, and encompass a range of reviews, opinions and perspectives. The first three sections explore the role of PPI in legume breeding strategies. PPI based approaches to crop improvement can make it possible to adapt and re-design breeding strategies to meet both goals of: (1) optimal productivity, based on an efficient use of pollinators, and (2) biodiversity conservation. The next section deals with entomological aspects and focuses on the protection of the “pest control service” and pollinators in legume crops. The final section addresses general approaches to encourage the synergy between food production and pollination services at farmer field level. Two basic approaches are proposed: (a) Farming with Alternative Pollinators and (b) Crop Design System. PMID:27047514

MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula.

PubMed

Ryu, Hojin; Laffont, Carole; Frugier, Florian; Hwang, Ildoo

2017-01-01

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula . The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN . We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors.

MAP Kinase-Mediated Negative Regulation of Symbiotic Nodule Formation in Medicago truncatula

PubMed Central

Ryu, Hojin; Laffont, Carole; Frugier, Florian; Hwang, Ildoo

2017-01-01

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events in plants, including stress responses, innate immunity, hormone signaling, and cell specificity. MAPK-mediated stress signaling is also known to negatively regulate nitrogen-fixing symbiotic interactions, but the molecular mechanism of the MAPK signaling cascades underlying the symbiotic nodule development remains largely unknown. We show that the MtMKK5-MtMPK3/6 signaling module negatively regulates the early symbiotic nodule formation, probably upstream of ERN1 (ERF Required for Nodulation 1) and NSP1 (Nod factor Signaling Pathway 1) in Medicago truncatula. The overexpression of MtMKK5 stimulated stress and defense signaling pathways but also reduced nodule formation in M. truncatula roots. Conversely, a MAPK specific inhibitor, U0126, enhanced nodule formation and the expression of an early nodulation marker gene, MtNIN. We found that MtMKK5 directly activates MtMPK3/6 by phosphorylating the TEY motif within the activation loop and that the MtMPK3/6 proteins physically interact with the early nodulation-related transcription factors ERN1 and NSP1. These data suggest that the stress signaling-mediated MtMKK5/MtMPK3/6 module suppresses symbiotic nodule development via the action of early nodulation transcription factors. PMID:28152300

[Diagnostic work-up of pulmonary nodules : Management of pulmonary nodules detected with low‑dose CT screening].

PubMed

Wormanns, D

2016-09-01

Pulmonary nodules are the most frequent pathological finding in low-dose computed tomography (CT) scanning for early detection of lung cancer. Early stages of lung cancer are often manifested as pulmonary nodules; however, the very commonly occurring small nodules are predominantly benign. These benign nodules are responsible for the high percentage of false positive test results in screening studies. Appropriate diagnostic algorithms are necessary to reduce false positive screening results and to improve the specificity of lung cancer screening. Such algorithms are based on some of the basic principles comprehensively described in this article. Firstly, the diameter of nodules allows a differentiation between large (>8 mm) probably malignant and small (<8 mm) probably benign nodules. Secondly, some morphological features of pulmonary nodules in CT can prove their benign nature. Thirdly, growth of small nodules is the best non-invasive predictor of malignancy and is utilized as a trigger for further diagnostic work-up. Non-invasive testing using positron emission tomography (PET) and contrast enhancement as well as invasive diagnostic tests (e.g. various procedures for cytological and histological diagnostics) are briefly described in this article. Different nodule morphology using CT (e.g. solid and semisolid nodules) is associated with different biological behavior and different algorithms for follow-up are required. Currently, no obligatory algorithm is available in German-speaking countries for the management of pulmonary nodules, which reflects the current state of knowledge. The main features of some international and American recommendations are briefly presented in this article from which conclusions for the daily clinical use are derived.

The C2H2 Transcription Factor REGULATOR OF SYMBIOSOME DIFFERENTIATION Represses Transcription of the Secretory Pathway Gene VAMP721a and Promotes Symbiosome Development in Medicago truncatula[W][OPEN

PubMed Central

Sinharoy, Senjuti; Torres-Jerez, Ivone; Bandyopadhyay, Kaustav; Kereszt, Attila; Pislariu, Catalina I.; Nakashima, Jin; Benedito, Vagner A.; Kondorosi, Eva; Udvardi, Michael K.

2013-01-01

Transcription factors (TFs) are thought to regulate many aspects of nodule and symbiosis development in legumes, although few TFs have been characterized functionally. Here, we describe REGULATOR OF SYMBIOSOME DIFFERENTIATION (RSD) of Medicago truncatula, a member of the Cysteine-2/Histidine-2 (C2H2) family of plant TFs that is required for normal symbiosome differentiation during nodule development. RSD is expressed in a nodule-specific manner, with maximal transcript levels in the bacterial invasion zone. A tobacco (Nicotiana tabacum) retrotransposon (Tnt1) insertion rsd mutant produced nodules that were unable to fix nitrogen and that contained incompletely differentiated symbiosomes and bacteroids. RSD protein was localized to the nucleus, consistent with a role of the protein in transcriptional regulation. RSD acted as a transcriptional repressor in a heterologous yeast assay. Transcriptome analysis of an rsd mutant identified 11 genes as potential targets of RSD repression. RSD interacted physically with the promoter of one of these genes, VAMP721a, which encodes vesicle-associated membrane protein 721a. Thus, RSD may influence symbiosome development in part by repressing transcription of VAMP721a and modifying vesicle trafficking in nodule cells. This establishes RSD as a TF implicated directly in symbiosome and bacteroid differentiation and a transcriptional regulator of secretory pathway genes in plants. PMID:24082011

Transcriptome Profiling of Lotus japonicus Roots During Arbuscular Mycorrhiza Development and Comparison with that of Nodulation

PubMed Central

Deguchi, Yuichi; Banba, Mari; Shimoda, Yoshikazu; Chechetka, Svetlana A.; Suzuri, Ryota; Okusako, Yasuhiro; Ooki, Yasuhiro; Toyokura, Koichi; Suzuki, Akihiro; Uchiumi, Toshiki; Higashi, Shiro; Abe, Mikiko; Kouchi, Hiroshi; Izui, Katsura; Hata, Shingo

2007-01-01

Abstract To better understand the molecular responses of plants to arbuscular mycorrhizal (AM) fungi, we analyzed the differential gene expression patterns of Lotus japonicus, a model legume, with the aid of a large-scale cDNA macroarray. Experiments were carried out considering the effects of contaminating microorganisms in the soil inoculants. When the colonization by AM fungi, i.e. Glomus mosseae and Gigaspora margarita, was well established, four cysteine protease genes were induced. In situ hybridization revealed that these cysteine protease genes were specifically expressed in arbuscule-containing inner cortical cells of AM roots. On the other hand, phenylpropanoid biosynthesis-related genes for phenylalanine ammonia-lyase (PAL), chalcone synthase, etc. were repressed in the later stage, although they were moderately up-regulated on the initial association with the AM fungus. Real-time RT–PCR experiments supported the array experiments. To further confirm the characteristic expression, a PAL promoter was fused with a reporter gene and introduced into L. japonicus, and then the transformants were grown with a commercial inoculum of G. mosseae. The reporter activity was augmented throughout the roots due to the presence of contaminating microorganisms in the inoculum. Interestingly, G. mosseae only colonized where the reporter activity was low. Comparison of the transcriptome profiles of AM roots and nitrogen-fixing root nodules formed with Mesorhizobium loti indicated that the PAL genes and other phenylpropanoid biosynthesis-related genes were similarly repressed in the two organs. PMID:17634281

Biological nitrogen fixation in non-legume plants.

PubMed

Santi, Carole; Bogusz, Didier; Franche, Claudine

2013-05-01

Nitrogen is an essential nutrient in plant growth. The ability of a plant to supply all or part of its requirements from biological nitrogen fixation (BNF) thanks to interactions with endosymbiotic, associative and endophytic symbionts, confers a great competitive advantage over non-nitrogen-fixing plants. Because BNF in legumes is well documented, this review focuses on BNF in non-legume plants. Despite the phylogenic and ecological diversity among diazotrophic bacteria and their hosts, tightly regulated communication is always necessary between the microorganisms and the host plant to achieve a successful interaction. Ongoing research efforts to improve knowledge of the molecular mechanisms underlying these original relationships and some common strategies leading to a successful relationship between the nitrogen-fixing microorganisms and their hosts are presented. Understanding the molecular mechanism of BNF outside the legume-rhizobium symbiosis could have important agronomic implications and enable the use of N-fertilizers to be reduced or even avoided. Indeed, in the short term, improved understanding could lead to more sustainable exploitation of the biodiversity of nitrogen-fixing organisms and, in the longer term, to the transfer of endosymbiotic nitrogen-fixation capacities to major non-legume crops.

Phosphatidylinositol 3-kinase function at very early symbiont perception: a local nodulation control under stress conditions?

PubMed

Robert, Germán; Muñoz, Nacira; Alvarado-Affantranger, Xochitl; Saavedra, Laura; Davidenco, Vanina; Rodríguez-Kessler, Margarita; Estrada-Navarrete, Georgina; Sánchez, Federico; Lascano, Ramiro

2018-04-09

Root hair curling is an early and essential morphological change required for the success of the symbiotic interaction between legumes and rhizobia. At this stage rhizobia grow as an infection thread within root hairs and are internalized into the plant cells by endocytosis, where the PI3K enzyme plays important roles. Previous observations show that stress conditions affect early stages of the symbiotic interaction, from 2 to 30 min post-inoculation, which we term as very early host responses, and affect symbiosis establishment. Herein, we demonstrated the relevance of the very early host responses for the symbiotic interaction. PI3K and the NADPH oxidase complex are found to have key roles in the microsymbiont recognition response, modulating the apoplastic and intracellular/endosomal ROS induction in root hairs. Interestingly, compared with soybean mutant plants that do not perceive the symbiont, we demonstrated that the very early symbiont perception under sublethal saline stress conditions induced root hair death. Together, these results highlight not only the importance of the very early host-responses on later stages of the symbiont interaction, but also suggest that they act as a mechanism for local control of nodulation capacity, prior to the abortion of the infection thread, preventing the allocation of resources/energy for nodule formation under unfavorable environmental conditions.

False negative cytology in large thyroid nodules.

PubMed

Giles, Wesley H; Maclellan, Reid A; Gawande, Atul A; Ruan, Daniel T; Alexander, Erik K; Moore, Francis D; Cho, Nancy L

2015-01-01

Controversy exists regarding the accuracy of fine-needle aspiration (FNA) in large thyroid nodules. Recent surgical series have documented false-negative rates ranging from 0.7 to 13 %. We examined the accuracy of benign FNA cytology in patients with thyroid nodules ≥3 cm who underwent surgical resection and identified features characteristic of false-negative results. We retrospectively studied all thyroidectomy specimens between January 2009 and October 2011 and identified nodules ≥3 cm with corresponding benign preoperative FNA cytology. We collected clinical information regarding patient demographics, nodule size, symptoms, sonographic features, FNA results, and final surgical pathology. For comparison, we analyzed nodules <3 cm from this cohort also with benign FNA cytology. A total of 323 nodules with benign preoperative cytology were identified. Eighty-three nodules were <3 cm, 94 nodules were 3-3.9 cm, and 146 nodules were ≥4 cm in size. The false-negative rate was 11.7 % for all nodules ≥3 cm and 4.8 % for nodules <3 cm (p = 0.03). Subgroup analysis of nodules ≥3 cm revealed a false-negative rate of 12.8 % for nodules 3-3.9 cm and 11 % for nodules ≥4 cm. Age ≥55 years and asymptomatic clinical status were the only patient characteristics that reached statistical significance as risk factors. Final pathology of the false-negative specimens consisted mainly of follicular variant of papillary thyroid cancer and follicular thyroid cancer. When referred for thyroidectomy, patients with large thyroid nodules demonstrate a modest, yet significant, false-negative rate despite initial benign aspiration cytology. Therefore, thyroid nodules ≥3 cm may be considered for removal even when referred with benign preoperative cytology.

Function and evolution of a Lotus japonicus AP2/ERF family transcription factor that is required for development of infection threads.

PubMed

Yano, Koji; Aoki, Seishiro; Liu, Meng; Umehara, Yosuke; Suganuma, Norio; Iwasaki, Wataru; Sato, Shusei; Soyano, Takashi; Kouchi, Hiroshi; Kawaguchi, Masayoshi

2017-04-01

Legume-rhizobium symbiosis is achieved by two major events evolutionarily acquired: root hair infection and organogenesis. Infection thread (IT) development is a distinct element for rhizobial infection. Through ITs, rhizobia are efficiently transported from infection foci on root hairs to dividing meristematic cortical cells. To unveil this process, we performed genetic screening using Lotus japonicus MG-20 and isolated symbiotic mutant lines affecting nodulation, root hair morphology, and IT development. Map-based cloning identified an AP2/ERF transcription factor gene orthologous to Medicago truncatula ERN1. LjERN1 was activated in response to rhizobial infection and depended on CYCLOPS and NSP2. Legumes conserve an ERN1 homolog, ERN2, that functions redundantly with ERN1 in M. truncatula. Phylogenetic analysis showed that the lineages of ERN1 and ERN2 genes originated from a gene duplication event in the common ancestor of legume plants. However, genomic analysis suggested the lack of ERN2 gene in the L. japonicus genome, consistent with Ljern1 mutants exhibited a root hair phenotype that is observed in ern1/ern2 double mutants in M. truncatula. Molecular evolutionary analysis suggested that the nonsynonymous/synonymous rate ratios of legume ERN1 genes was almost identical to that of non-legume plants, whereas the ERN2 genes experienced a relaxed selective constraint. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Members of Microvirga and Bradyrhizobium genera are native endosymbiotic bacteria nodulating Lupinus luteus in Northern Tunisian soils.

PubMed

Msaddak, Abdelhakim; Rejili, Mokhtar; Durán, David; Rey, Luis; Imperial, Juan; Palacios, Jose Manuel; Ruiz-Argüeso, Tomas; Mars, Mohamed

2017-06-01

The genetic diversity of bacterial populations nodulating Lupinus luteus (yellow lupine) in Northern Tunisia was examined. Phylogenetic analyses of 43 isolates based on recA and gyrB partial sequences grouped them in three clusters, two of which belong to genus Bradyrhizobium (41 isolates) and one, remarkably, to Microvirga (2 isolates), a genus never previously described as microsymbiont of this lupine species. Representatives of the three clusters were analysed in-depth by multilocus sequence analysis of five housekeeping genes (rrs, recA, glnII, gyrB and dnaK). Surprisingly, the Bradyrhizobium cluster with the two isolates LluI4 and LluTb2 may constitute a new species defined by a separate position between Bradyrhizobium manausense and B. denitrificans. A nodC-based phylogeny identified only two groups: one formed by Bradyrhizobium strains included in the symbiovar genistearum and the other by the Microvirga strains. Symbiotic behaviour of representative isolates was tested, and among the seven legumes inoculated only a difference was observed i.e. the Bradyrhizobium strains nodulated Ornithopus compressus unlike the two strains of Microvirga. On the basis of these data, we conclude that L. luteus root nodule symbionts in Northern Tunisia are mostly strains within the B. canariense/B. lupini lineages, and the remaining strains belong to two groups not previously identified as L. luteus endosymbionts: one corresponding to a new clade of Bradyrhizobium and the other to the genus Microvirga. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Structure and postembryonic development of the intersegmental nodules in the non-muscular joints of the antennae in Rhodnius prolixus.

PubMed

Ospina-Rozo, Bibiana; Forero-Shelton, Manu; Molina, Jorge

2017-03-01

The antennae of Insecta consist of two basal segments and the distal annulated flagellum lacking intrinsic muscles. Non-muscular joints are important to preserve the flexibility and structure of the long heteropteran antennae which bear an intersegmental nodule on each non-muscular joint. Little is known about their properties or function. Here we characterize the structure and postembryonic development of the non-muscular joints of Rhodnius prolixus antennae. Using Scanning Electron Microscopy, we tracked the changes in shape and size of both intersegmental nodules during the course of the hemimetabolous insect life cycle. Using Atomic Force Microscopy, we established a qualitative correlation between the topography of the surface and the rigidity of the joint between pedicel and flagellum. Our results confirmed the presence of two sub-articulations on each non-muscular joint. Also, the two intersegmental nodules have different origins: the one between the two flagellar segments (intraflagelloid) is a sclerite already present from the early nymph, while the nodule between pedicel and flagellum (prebasiflagellite) originates by gradual separation of the proximal end of the basiflagellum during postembryonic development. Various changes occur in the non-muscular joints and segments of the antenna during the life cycle of R. prolixus. Copyright © 2016 Elsevier Ltd. All rights reserved.

Thyroid nodule classification using ultrasound elastography via linear discriminant analysis.

PubMed

Luo, Si; Kim, Eung-Hun; Dighe, Manjiri; Kim, Yongmin

2011-05-01

The non-surgical diagnosis of thyroid nodules is currently made via a fine needle aspiration (FNA) biopsy. It is estimated that somewhere between 250,000 and 300,000 thyroid FNA biopsies are performed in the United States annually. However, a large percentage (approximately 70%) of these biopsies turn out to be benign. Since the aggressive FNA management of thyroid nodules is costly, quantitative risk assessment and stratification of a nodule's malignancy is of value in triage and more appropriate healthcare resources utilization. In this paper, we introduce a new method for classifying the thyroid nodules based on the ultrasound (US) elastography features. Unlike approaches to assess the stiffness of a thyroid nodule by visually inspecting the pseudo-color pattern in the strain image, we use a classification algorithm to stratify the nodule by using the power spectrum of strain rate waveform extracted from the US elastography image sequence. Pulsation from the carotid artery was used to compress the thyroid nodules. Ultrasound data previously acquired from 98 thyroid nodules were used in this retrospective study to evaluate our classification algorithm. A classifier was developed based on the linear discriminant analysis (LDA) and used to differentiate the thyroid nodules into two types: (I) no FNA (observation-only) and (II) FNA. Using our method, 62 nodules were classified as type I, all of which were benign, while 36 nodules were classified as Type-II, 16 malignant and 20 benign, resulting in a sensitivity of 100% and specificity of 75.6% in detecting malignant thyroid nodules. This indicates that our triage method based on US elastography has the potential to substantially reduce the number of FNA biopsies (63.3%) by detecting benign nodules and managing them via follow-up observations rather than an FNA biopsy. Published by Elsevier B.V.

Nonlinear tumor evolution from dysplastic nodules to hepatocellular carcinoma.

PubMed

Joung, Je-Gun; Ha, Sang Yun; Bae, Joon Seol; Nam, Jae-Yong; Gwak, Geum-Youn; Lee, Hae-Ock; Son, Dae-Soon; Park, Cheol-Keun; Park, Woong-Yang

2017-01-10

Dysplastic nodules are premalignant neoplastic nodules found in explanted livers with cirrhosis. Genetic signatures of premalignant dysplastic nodules (DNs) with concurrent hepatocellular carcinoma (HCC) may provide an insight in the molecular evolution of hepatocellular carcinogenesis. We analyzed four patients with multifocal nodular lesions and cirrhotic background by whole-exome sequencing (WES). The genomic profiles of somatic single nucleotide variations (SNV) and copy number variations (CNV) in DNs were compared to those of HCCs. The number and variant allele frequency of somatic SNVs of DNs and HCCs in each patient was identical along the progression of pathological grade. The somatic SNVs in DNs showed little conservation in HCC. Additionally, CNVs showed no conservation. Phylogenetic analysis based on SNVs and copy number profiles indicated a nonlinear segregation pattern, implying independent development of DNs and HCC in each patient. Thus, somatic mutations in DNs may be developed separately from other malignant nodules in the same liver, suggesting a nonlinear model for hepatocarcinogenesis from DNs to HCC.

Legumes steam allergy in childhood: Update of the reported cases.

PubMed

Vitaliti, G; Pavone, P; Spataro, G; Giunta, L; Guglielmo, F; Falsaperla, R

2015-01-01

In the past few decades, the prevalence of allergic diseases has deeply increased, with a key role played by food allergies. Legumes seem to play a major role towards the overall increase in the scenario of food allergy, since they are an appreciated source, consumed worldwide, due to their high protein content, variable amounts of lipids and for the presence of vitamins. In literature there are numerous descriptions of adverse reactions after ingestion of uncooked and cooked legumes. Nevertheless, cases of allergic reactions induced by inhaling vapours from cooking legumes have rarely been described. Herein the authors report an update of the literature data on allergic reactions caused by legume steam inhalation, underlying the possible pathogenic mechanism of these atopic events and the knowledge of literature data in paediatric age. The importance of this review is the focus on the clinical aspects concerning legume vapour allergy, referring to literature data in childhood. Copyright © 2013 SEICAP. Published by Elsevier Espana. All rights reserved.

Legume abundance along successional and rainfall gradients in Neotropical forests.

PubMed

Gei, Maga; Rozendaal, Danaë M A; Poorter, Lourens; Bongers, Frans; Sprent, Janet I; Garner, Mira D; Aide, T Mitchell; Andrade, José Luis; Balvanera, Patricia; Becknell, Justin M; Brancalion, Pedro H S; Cabral, George A L; César, Ricardo Gomes; Chazdon, Robin L; Cole, Rebecca J; Colletta, Gabriel Dalla; de Jong, Ben; Denslow, Julie S; Dent, Daisy H; DeWalt, Saara J; Dupuy, Juan Manuel; Durán, Sandra M; do Espírito Santo, Mário Marcos; Fernandes, G Wilson; Nunes, Yule Roberta Ferreira; Finegan, Bryan; Moser, Vanessa Granda; Hall, Jefferson S; Hernández-Stefanoni, José Luis; Junqueira, André B; Kennard, Deborah; Lebrija-Trejos, Edwin; Letcher, Susan G; Lohbeck, Madelon; Marín-Spiotta, Erika; Martínez-Ramos, Miguel; Meave, Jorge A; Menge, Duncan N L; Mora, Francisco; Muñoz, Rodrigo; Muscarella, Robert; Ochoa-Gaona, Susana; Orihuela-Belmonte, Edith; Ostertag, Rebecca; Peña-Claros, Marielos; Pérez-García, Eduardo A; Piotto, Daniel; Reich, Peter B; Reyes-García, Casandra; Rodríguez-Velázquez, Jorge; Romero-Pérez, I Eunice; Sanaphre-Villanueva, Lucía; Sanchez-Azofeifa, Arturo; Schwartz, Naomi B; de Almeida, Arlete Silva; Almeida-Cortez, Jarcilene S; Silver, Whendee; de Souza Moreno, Vanessa; Sullivan, Benjamin W; Swenson, Nathan G; Uriarte, Maria; van Breugel, Michiel; van der Wal, Hans; Veloso, Maria das Dores Magalhães; Vester, Hans F M; Vieira, Ima Célia Guimarães; Zimmerman, Jess K; Powers, Jennifer S

2018-05-28

The nutrient demands of regrowing tropical forests are partly satisfied by nitrogen-fixing legume trees, but our understanding of the abundance of those species is biased towards wet tropical regions. Here we show how the abundance of Leguminosae is affected by both recovery from disturbance and large-scale rainfall gradients through a synthesis of forest inventory plots from a network of 42 Neotropical forest chronosequences. During the first three decades of natural forest regeneration, legume basal area is twice as high in dry compared with wet secondary forests. The tremendous ecological success of legumes in recently disturbed, water-limited forests is likely to be related to both their reduced leaflet size and ability to fix N 2 , which together enhance legume drought tolerance and water-use efficiency. Earth system models should incorporate these large-scale successional and climatic patterns of legume dominance to provide more accurate estimates of the maximum potential for natural nitrogen fixation across tropical forests.

Automatic Solitary Lung Nodule Detection in Computed Tomography Images Slices

NASA Astrophysics Data System (ADS)

Sentana, I. W. B.; Jawas, N.; Asri, S. A.

2018-01-01

Lung nodule is an early indicator of some lung diseases, including lung cancer. In Computed Tomography (CT) based image, nodule is known as a shape that appears brighter than lung surrounding. This research aim to develop an application that automatically detect lung nodule in CT images. There are some steps in algorithm such as image acquisition and conversion, image binarization, lung segmentation, blob detection, and classification. Data acquisition is a step to taking image slice by slice from the original *.dicom format and then each image slices is converted into *.tif image format. Binarization that tailoring Otsu algorithm, than separated the background and foreground part of each image slices. After removing the background part, the next step is to segment part of the lung only so the nodule can localized easier. Once again Otsu algorithm is use to detect nodule blob in localized lung area. The final step is tailoring Support Vector Machine (SVM) to classify the nodule. The application has succeed detecting near round nodule with a certain threshold of size. Those detecting result shows drawback in part of thresholding size and shape of nodule that need to enhance in the next part of the research. The algorithm also cannot detect nodule that attached to wall and Lung Chanel, since it depend the searching only on colour differences.

Host-secreted antimicrobial peptide enforces symbiotic selectivity in Medicago truncatula.

PubMed

Wang, Qi; Yang, Shengming; Liu, Jinge; Terecskei, Kata; Ábrahám, Edit; Gombár, Anikó; Domonkos, Ágota; Szűcs, Attila; Körmöczi, Péter; Wang, Ting; Fodor, Lili; Mao, Linyong; Fei, Zhangjun; Kondorosi, Éva; Kaló, Péter; Kereszt, Attila; Zhu, Hongyan

2017-06-27

Legumes engage in root nodule symbioses with nitrogen-fixing soil bacteria known as rhizobia. In nodule cells, bacteria are enclosed in membrane-bound vesicles called symbiosomes and differentiate into bacteroids that are capable of converting atmospheric nitrogen into ammonia. Bacteroid differentiation and prolonged intracellular survival are essential for development of functional nodules. However, in the Medicago truncatula - Sinorhizobium meliloti symbiosis, incompatibility between symbiotic partners frequently occurs, leading to the formation of infected nodules defective in nitrogen fixation (Fix - ). Here, we report the identification and cloning of the M. truncatula NFS2 gene that regulates this type of specificity pertaining to S. meliloti strain Rm41. We demonstrate that NFS2 encodes a nodule-specific cysteine-rich (NCR) peptide that acts to promote bacterial lysis after differentiation. The negative role of NFS2 in symbiosis is contingent on host genetic background and can be counteracted by other genes encoded by the host. This work extends the paradigm of NCR function to include the negative regulation of symbiotic persistence in host-strain interactions. Our data suggest that NCR peptides are host determinants of symbiotic specificity in M. truncatula and possibly in closely related legumes that form indeterminate nodules in which bacterial symbionts undergo terminal differentiation.

Occurrence of H2-Uptake Hydrogenases in Bradyrhizobium sp. (Lupinus) and Their Expression in Nodules of Lupinus spp. and Ornithopus compressus1

PubMed Central

Murillo, Jesús; Villa, Ana; Chamber, Manuel; Ruiz-Argüeso, Tomás

1989-01-01

Fifty-four strains of Bradyrhizobium sp. (Lupinus) from worldwide collections were screened by a colony hybridization method for the presence of DNA sequences homologous to the structural genes of the Bradyrhizobium japonicum hydrogenase. Twelve strains exhibited strong colony hybridization signals, and subsequent Southern blot hybridization experiments showed that they fell into two different groups on the basis of the pattern of EcoRI fragments containing the homology to the hup probe. All strains in the first group (UPM860, UPM861, and 750) expressed uptake hydrogenase activity in symbiosis with Lupinus albus, Lupinus angustifolius, Lupinus luteus, and Ornithopus compressus, but both the rate of H2 uptake by bacteroids and the relative efficiency of N2 fixation (RE = 1 - [H2 evolved in air/acetylene reduced]) by nodules were markedly affected by the legume host. L. angustifolius was the less permissive host for hydrogenase expression in symbiosis with the three strains (average RE = 0.76), and O. compressus was the more permissive (average RE = 1.0). None of the strains in the second group expressed hydrogenase activity in lupine nodules, and only one exhibited low H2-uptake activity in symbiosis with O. compressus. The inability of these putative Hup+ strains to induce hydrogenase activity in lupine nodules is discussed on the basis of the legume host effect. Among the 42 strains showing no homology to the B. japonicum hup-specific probe in the colony hybridization assay, 10 were examined in symbiosis with L. angustifolius. The average RE for these strains was 0.51. However, one strain, IM43B, exhibited high RE values (higher than 0.80) and high levels of hydrogenase activity in symbiosis with L. angustifolius, L. albus, and L. luteus. In Southern blot hybridization experiments, no homology was detected between the B. japonicum hup-specific DNA probe and total DNA from vegetative cells or bacteroids from strain IM43B even under low stringency hybridization

Cowpea: a legume crop for a challenging environment.

PubMed

Carvalho, Márcia; Lino-Neto, Teresa; Rosa, Eduardo; Carnide, Valdemar

2017-10-01

Cowpea is a grain legume native from Africa and is a primary source of protein for millions of people in sub-Saharan Africa and other parts of the developing world. The main important characteristics of this crop include a good protein quality with a high nutritional value, its nitrogen-fixing ability, and an ability to be more drought- and heat-tolerant than most of its legume relatives. In a research perspective, studies of cowpea are relatively scarce, despite its relevance to agriculture in the developing world and its resilience to stress. The present review provides an overview of different aspects of cowpea, with a special emphasis on the molecular markers for assessing genetic diversity, as well as on biochemical and transcriptomic data with respect to evaluating cowpea drought stress tolerance. The integration of both datasets will be useful for the improvement of cowpea because research on drought stress tolerance is of major interest for this crop in a challenging environment. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Microbial communities associated with ferromanganese nodules and the surrounding sediments

PubMed Central

Tully, Benjamin J.; Heidelberg, John F.

2013-01-01

The formation and maintenance of deep-sea ferromanganese/polymetallic nodules still remains a mystery 140 years after their discovery. The wealth of rare metals concentrated in these nodules has spurred global interest in exploring the mining potential of these resources. The prevailing theory of abiotic formation has been called into question and the role of microbial metabolisms in nodule development is now an area of active research. To understand the community structure of microbes associated with nodules and their surrounding sediment, we performed targeted sequencing of the V4 hypervariable region of the 16S rRNA gene from three nodules collected from the central South Pacific. Results have shown that the microbial communities of the nodules are significantly distinct from the communities in the surrounding sediments, and that the interiors of the nodules harbor communities different from the exterior. This suggests not only differences in potential metabolisms between the nodule and sediment communities, but also differences in the dominant metabolisms of interior and exterior communities. We identified several operational taxonomic units (OTUs) unique to both the nodule and sediment environments. The identified OTUs were assigned putative taxonomic identifications, including two OTUs only found associated with the nodules, which were assigned to the α-Proteobacteria. Finally, we explored the diversity of the most assigned taxonomic group, the Thaumarchaea MG-1, which revealed novel OTUs compared to previous research from the region and suggests a potential role as a source of fixed carbon for ammonia oxidizing archaea in the environment. PMID:23805131

Localization of the Bacillus subtilis beta-propeller phytase transcripts in nodulated roots of Phaseolus vulgaris supplied with phytate.

PubMed

Maougal, Rim Tinhinen; Bargaz, Adnane; Sahel, Charaf; Amenc, Laurie; Djekoun, Abdelhamid; Plassard, Claude; Drevon, Jean-Jacques

2014-04-01

Soil organic phosphorus (Po) such as phytate, which comprises up to 80 % of total Po, must be hydrolyzed by specific enzymes called phytases to be used by plants. In contrast to plants, bacteria, such as Bacillus subtilis, have the ability to use phytate as the sole source of P due to the excretion of a beta-propeller phytase (BPP). In order to assess whether the B. subtilis BPP could make P available from phytate for the benefit of a nodulated legume, the P-sensitive recombinant inbred line RIL147 of Phaseolus vulgaris was grown under hydroaeroponic conditions with either 12.5 μM phytate (C₆H₁₈O₂₄P₆) or 75 μmol Pi (K₂HPO₄), and inoculated with Rhizobium tropici CIAT899 alone, or co-inoculated with both B. subtilis DSM 10 and CIAT899. The in situ RT-PCR of BPP genes displayed the most intense fluorescent BPP signal on root tips. Some BPP signal was found inside the root cortex and the endorhizosphere of the root tip, suggesting endophytic bacteria expressing BPP. However, the co-inoculation with B. subtilis was associated with a decrease in plant P content, nodulation and the subsequent plant growth. Such a competitive effect of B. subtilis on P acquisition from phytate in symbiotic nitrogen fixation might be circumvented if the rate of inoculation were reasoned in order to avoid the inhibition of nodulation by excess B. subtilis proliferation. It is concluded that B. subtilis BPP gene is expressed in P. vulgaris rhizosphere.

Hormonal regulation of reproductive growth under normal and heat-stress conditions in legume and other model crop species.

PubMed

Ozga, Jocelyn A; Kaur, Harleen; Savada, Raghavendra P; Reinecke, Dennis M

2017-04-01

Legume crops are grown throughout the world and provide an excellent food source of digestible protein and starch, as well as dietary fibre, vitamins, minerals, and flavonoids. Fruit and seeds from legumes are also an important source of vegetables for a well-balanced diet. A trend in elevated temperature as a result of climate change increases the risk of a heat stress-induced reduction in legume crop yield. High temperatures during the crop reproductive development phase are particularly detrimental to fruit/seed production because the growth and development of the reproductive tissues are sensitive to small changes in temperature. Hormones are signalling molecules that play important roles in a plant's ability to integrate different environmental inputs and modify their developmental processes to optimize growth, survival, and reproduction. This review focuses on the hormonal regulation of reproductive development and heat stress-induced alteration of this regulation during (i) pollination, (ii) early fruit set, and (iii) seed development that affects fruit/seed yield in legume and other model crops. Further understanding of hormone-regulated reproductive growth under non-stress and heat-stress conditions can aid in trait selection and the development of gene modification strategies and cultural practices to improve heat tolerance in legume crops contributing to improved food security. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Effects of tropical high tannin non legume and low tannin legume browse mixtures on fermentation parameters and methanogenesis using gas production technique.

PubMed

Seresinhe, T; Madushika, S A C; Seresinhe, Y; Lal, P K; Orskov, E R

2012-10-01

In vitro experiments were conducted to evaluate the suitability of several mixtures of high tanniniferous non legumes with low tanniniferous legumes on in vitro gas production (IVGP), dry matter degradation, Ammonia-N, methane production and microbial population. Eight treatments were examined in a randomized complete block design using four non-legumes and two legumes (Carallia integerrima×Leucaena leucocephala (LL) (Trt 1), C. integerrima×Gliricidia sepium (GS) (Trt 2), Aporosa lindeliyana×LL (Trt 3), A. lindeliyana×GS (Trt 4), Ceiba perntandra×LL (Trt 5), C. perntandra×GS (Trt 6), Artocarpus heterophyllus×LL (Trt 7), A. heterophyllus×GS (Trt 8). The condensed tannin (CT) content of non legumes ranged from 6.2% (Carallia integerrima) to 4.9% (Ceiba perntandra) while the CT of legumes were 1.58% (Leucaena leucocephala) and 0.78% (Gliricidia sepium). Forage mixtures contained more than 14% of crude protein (CP) while the CT content ranged from 2.8% to 4.0% respectively. Differences (p<0.05) were observed in in vitro gas production (IGVP) within treatments over a 48 h period dominated by C. perntandra×G. sepium (Trt 6). The net gas production (p<0.05) was also high with Trt6 followed by A. heterophyllus×L. leucocephala (Trt 7) and A. heterophyllus×G. sepium (Trt 8). Highest (p>0.05) NH3-N (ml/200 mg DM) production was observed with the A. heterophyllus×G. sepium (Trt 8) mixture which may be attributed with it's highest CP content. The correlation between IVGP and CT was 0.675 while IVGP and CP was 0.610. In vitro dry matter degradation (IVDMD) was highest in Trt 8 as well. Methane production ranged from 2.57 to 4.79 (ml/200 mg DM) to be synonimous with IVGP. A higher bacteria population (p<0.05) was found in C. perntandra×G. sepium (Trt 6) followed by Artocarpus heterophyllus+G. sepium (Trt 8) and the same trend was observed with the protozoa population as well. The results show that supplementing high tannin non leguminous forages by incremental

Image-guided decision support system for pulmonary nodule classification in 3D thoracic CT images

NASA Astrophysics Data System (ADS)

Kawata, Yoshiki; Niki, Noboru; Ohmatsu, Hironobu; Kusumoto, Masahiro; Kakinuma, Ryutaro; Mori, Kiyoshi; Yamada, Kozo; Nishiyama, Hiroyuki; Eguchi, Kenji; Kaneko, Masahiro; Moriyama, Noriyuki

2004-05-01

The purpose of this study is to develop an image-guided decision support system that assists decision-making in clinical differential diagnosis of pulmonary nodules. This approach retrieves and displays nodules that exhibit morphological and internal profiles consistent to the nodule in question. It uses a three-dimensional (3-D) CT image database of pulmonary nodules for which diagnosis is known. In order to build the system, there are following issues that should be solved: 1) to categorize the nodule database with respect to morphological and internal features, 2) to quickly search nodule images similar to an indeterminate nodule from a large database, and 3) to reveal malignancy likelihood computed by using similar nodule images. Especially, the first problem influences the design of other issues. The successful categorization of nodule pattern might lead physicians to find important cues that characterize benign and malignant nodules. This paper focuses on an approach to categorize the nodule database with respect to nodule shape and CT density patterns inside nodule.

Nutritive evaluation of legume seeds for ruminant feeding.

PubMed

Ramos-Morales, E; Sanz-Sampelayo, M R; Molina-Alcaide, E

2010-02-01

Chemical composition, rumen degradability and the effect of particle losses, and intestinal digestibility of protein by using in situ-in vitro and in vitro techniques were stated for beans (Vicia faba), lupin (Lupinus albus), vetch (Vicia sativa) and bitter vetch (Vicia ervilia) and four diets including those legume seeds. In addition, the apparent digestibility of experimental diets was determined in goats. The legume seeds showed high protein content (206-319 g/kg dry matter). Effective degradability of protein for legumes and diets varied from 0.80 to 0.87 and 0.76 to 0.82, respectively, decreasing to 0.53-0.76 and 0.61-0.67, respectively, when particle loss was taken into account. Different intestinal digestibility values were obtained with both methodologies without significant relationship between them (y = 1.058-0.463x; R(2)=0.068; RSD = 0.140; p = 0.53). There were no differences in the apparent nutrients and energy digestibility among diets (p > 0.05). These legumes can supply rapidly degradable protein for microbial protein synthesis and contribute to the pool of amino acids available for the synthesis of milk protein and for retention in the body.

Interaction between Orobanche crenata and its Host Legumes: Unsuccessful Haustorial Penetration and Necrosis of the Developing Parasite

PubMed Central

PÉREZ-DE-LUQUE, A.; RUBIALES, D.; CUBERO, J. I.; PRESS, M. C.; SCHOLES, J.; YONEYAMA, K.; TAKEUCHI, Y.; PLAKHINE, D.; JOEL, D. M.

2005-01-01

• Background and Aims Orobanche species represent major constraints to crop production in many parts of the world as they reduce yield and alter root/shoot allometry. Although much is known about the histology and effect of Orobanche spp. on susceptible hosts, less is known about the basis of host resistance to these parasites. In this work, histological aspects related to the resistance of some legumes to Orobanche crenata have been investigated in order to determine which types of resistance responses are involved in the unsuccessful penetration of O. crenata. • Methods Samples of resistance reactions against O. crenata on different genotypes of resistant legumes were collected. The samples were fixed, sectioned and stained using different procedures. Sections were observed using a transmission light microscope and by epi-fluorescence. • Key Results Lignification of endodermal and pericycle host cells seems to prevent parasite intrusion into the root vascular cylinder at early infection stages. But in other cases, established tubercles became necrotic and died. Contrary to some previous studies, it was found that darkening at the infection site in these latter cases does not correspond to death of host tissues, but to the secretion of substances that fill the apoplast in the host–parasite interface and in much of the infected host tissues. The secretions block neighbouring host vessels. This may interfere with the nutrient flux between host and parasite, and may lead to necrosis and death of the developing parasite. • Conclusions The unsuccessful penetration of O. crenata seedlings into legume roots cannot be attributed to cell death in the host. It seems to be associated with lignification of host endodermis and pericycle cells at the penetration site. The accumulation of secretions at the infection site, may lead to the activation of xylem occlusion, another defence mechanism, which may cause further necrosis of established tubercles. PMID:15749751

Non-invasive Characterization of the Histopathologic Features of Pulmonary Nodules of the Lung Adenocarcinoma Spectrum using Computer Aided Nodule Assessment and Risk Yield (CANARY) – a Pilot Study

PubMed Central

Maldonado, Fabien; Boland, Jennifer M.; Raghunath, Sushravya; Aubry, Marie Christine; Bartholmai, Brian J.; deAndrade, Mariza; Hartman, Thomas E.; Karwoski, Ronald A.; Rajagopalan, Srinivasan; Sykes, Anne-Marie; Yang, Ping; Yi, Eunhee S.; Robb, Richard A.; Peikert, Tobias

2013-01-01

Introduction Pulmonary nodules of the adenocarcinoma spectrum are characterized by distinctive morphological and radiological features and variable prognosis. Non-invasive high-resolution computed-tomography (HRCT)-based risk stratification tools are needed to individualize their management. Methods Radiological measurements of histopathologic tissue invasion were developed in a training set of 54 pulmonary nodules of the adenocarcinoma spectrum and validated in 86 consecutively resected nodules. Nodules were isolated and characterized by computer-aided analysis and data were analyzed by Spearman correlation, sensitivity, specificity as well as the positive and negative predictive values. Results Computer Aided Nodule Assessment and Risk Yield (CANARY) can non-invasively characterize pulmonary nodules of the adenocarcinoma spectrum. Unsupervised clustering analysis of HRCT data identified 9 unique exemplars representing the basic radiologic building blocks of these lesions. The exemplar distribution within each nodule correlated well with the proportion of histologic tissue invasion, Spearman R=0.87,p < 0.0001 and 0.89,p < 0.0001 for the training and the validation set, respectively. Clustering of the exemplars in three-dimensional space corresponding to tissue invasion and lepidic growth was used to develop a CANARY decision algorithm, which successfully categorized these pulmonary nodules as “aggressive” (invasive adenocarcinoma) or “indolent” (adenocarcinoma in situ and minimally invasive adenocarcinoma). Sensitivity, specificity, positive predictive value and negative predictive value of this approach for the detection of “aggressive” lesions were 95.4%, 96.8%, 95.4% and 96.8%, respectively in the training set and 98.7%, 63.6%, 94.9% and 87.5%, respectively in the validation set. Conclusion CANARY represents a promising tool to non-invasively risk stratify pulmonary nodules of the adenocarcinoma spectrum. PMID:23486265

Clinical, pathological and thin-section CT features of persistent multiple ground-glass opacity nodules: comparison with solitary ground-glass opacity nodule.

PubMed

Kim, Tae Jung; Goo, Jin Mo; Lee, Kyung Won; Park, Chang Min; Lee, Hyun Ju

2009-05-01

To retrospectively compare the clinical, pathological, and thin-section CT features of persistent multiple ground-glass opacity (GGO) nodules with those of solitary GGO nodules. Histopathologic specimens were obtained from 193 GGO nodules in 136 patients (87 women, 49 men; mean age, 57; age range 33-81). The clinical data, pathologic findings, and thin-section CT features of multiple and solitary GGO nodules were compared by using t-test or Fisher's exact test. Multiple GGO nodules (n=105) included atypical adenomatous hyperplasia (AAH) (n=31), bronchioloalveolar carcinoma (BAC) (n=33), adenocarcinoma (n=34) and focal interstitial fibrosis (n=7). Solitary GGO nodules included AAH (n=8), BAC (n=15), adenocarcinoma (n=55) and focal interstitial fibrosis (n=10). AAH (P=.001) and BAC (P=.029) were more frequent in multiple GGO nodules, whereas adenocarcinoma (P<.001) was more frequent in solitary GGO nodules. Female sex (P<.001), nonsmoker (P=.012) and multiple primary lung cancers (P<.001) were more frequent for multiple GGO nodules, which were smaller (12 mm+/-7.9) than solitary GGO nodules (17 mm+/-8.1) (P<.001). Air-bronchogram (P=.019), bubble-lucency (P=.004), and pleural retraction (P<.001) were more frequent in solitary GGO nodules. There was no postoperative recurrence except for one patient with multiple GGO nodules and one with solitary GGO nodule. Clinical, pathological, and thin-section CT features of persistent multiple GGO nodules were found to differ from those of solitary GGO nodules. Nevertheless, the two nodule types can probably be followed up and managed in a similar manner because their prognoses were found to be similar.

Genome Structure of the Legume, Lotus japonicus

PubMed Central

Sato, Shusei; Nakamura, Yasukazu; Kaneko, Takakazu; Asamizu, Erika; Kato, Tomohiko; Nakao, Mitsuteru; Sasamoto, Shigemi; Watanabe, Akiko; Ono, Akiko; Kawashima, Kumiko; Fujishiro, Tsunakazu; Katoh, Midori; Kohara, Mitsuyo; Kishida, Yoshie; Minami, Chiharu; Nakayama, Shinobu; Nakazaki, Naomi; Shimizu, Yoshimi; Shinpo, Sayaka; Takahashi, Chika; Wada, Tsuyuko; Yamada, Manabu; Ohmido, Nobuko; Hayashi, Makoto; Fukui, Kiichi; Baba, Tomoya; Nakamichi, Tomoko; Mori, Hirotada; Tabata, Satoshi

2008-01-01

The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes. PMID:18511435

Can Lung Nodules Be Cancerous?

MedlinePlus

... Pulmonary nodules. Rochester, Minn.: Mayo Foundation for Medical Education and Research; 2015. Weinberger SE, et al. Diagnostic evaluation and management of the solitary pulmonary nodule. http:// ...

Thyroid nodules.

PubMed

Knox, Mark A

2013-08-01

Thyroid nodules are a common finding in the general population. They may present with symptoms of pressure in the neck or may be discovered during physical examination. Although the risk of cancer is small, it is the main reason for workup of these lesions. Measurement of thyroid-stimulating hormone can identify conditions that may cause hyperfunctioning of the thyroid. For all other conditions, ultrasonography and fine-needle aspiration are central to the diagnosis. Lesions larger than 1 cm should be biopsied. Lesions with features suggestive of malignancy and those in patients with risk factors for thyroid cancer should be biopsied, regardless of size. Smaller lesions and those with benign histology can be followed and reevaluated if they grow. The evaluation of thyroid nodules in euthyroid and hypothyroid pregnant women is the same as in other adults. Thyroid nodules are uncommon in children, but the malignancy rate is much higher than in adults. Fine-needle aspiration is less accurate in children, so more aggressive surgical excision may be preferable.

Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens.

PubMed

Jiao, Yin Shan; Yan, Hui; Ji, Zhao Jun; Liu, Yuan Hui; Sui, Xin Hua; Wang, En Tao; Guo, Bao Lin; Chen, Wen Xin; Chen, Wen Feng

2015-02-01

Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus Rhizobium based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to Rhizobium leguminosarum USDA 2370(T) (95.6 % similarity for group I) and Rhizobium phaseoli ATCC 14482(T) (93.4 % similarity for group II) in multilocus sequence analysis. In DNA-DNA hybridization experiments, the reference strains CCBAU 03386(T) (group I) and CCBAU 03470(T) (group II) showed levels of relatedness of 17.9-57.8 and 11.0-42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386(T) and CCBAU 03470(T) contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo ω8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 ω6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus Rhizobium were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386(T) = E5(T) = LMG 27901(T) = HAMBI 3615(T)) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470(T) = C-5-1(T) = LMG 27898(T) = HAMBI 3510(T)), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli. © 2015 IUMS.

Diagnosis and management of solitary pulmonary nodules.

PubMed

Jeong, Yeon Joo; Lee, Kyung Soo; Kwon, O Jung

2008-12-01

The advent of computed tomography (CT) screening with or without the help of computer-aided detection systems has increased the detection rate of solitary pulmonary nodules (SPNs), including that of early peripheral lung cancer. Helical dynamic (HD)CT, providing the information on morphologic and hemodynamic characteristics with high specificity and reasonably high accuracy, can be used for the initial assessment of SPNs. (18)F-fluorodeoxyglucose PET/CT is more sensitive at detecting malignancy than HDCT. Therefore, PET/CT may be selectively performed to characterize SPNs when HDCT gives an inconclusive diagnosis. Serial volume measurements are currently the most reliable methods for the tissue characterization of subcentimeter nodules. When malignant nodule is highly suspected for subcentimeter nodules, video-assisted thoracoscopic surgery nodule removal after nodule localization using the pulmonary nodule-marker system may be performed for diagnosis and treatment.

[Nodulation competitiveness of nodule bacteria: Genetic control and adaptive significance].

PubMed

Onishchuk, O P; Vorobyov, N I; Provorov, N A

2017-01-01

The most recent data on the system of cmp (competitiveness) genes that determine the nodulation competitiveness of rhizobial strains, i.e., the ability to compete for nodule formation in leguminous plants, is analyzed. Three genetic approaches for the construction of economically valuable strains of rhizobia are proposed: the amplification of positive regulators of competitiveness, the inactivation of the negative regulators of this trait, and the introduction of efficient competitiveness factors into strains capable of active nitrogen fixation.

[Thyroid nodules and differentiated thyroid cancer: Brazilian consensus].

PubMed

Maia, Ana Luiza; Ward, Laura S; Carvalho, Gisah A; Graf, Hans; Maciel, Rui M B; Maciel, Léa M Zanini; Rosário, Pedro W; Vaisman, Mario

2007-07-01

Thyroid nodules are a common manifestation of thyroid diseases. It is estimated that approximately 10% of adults have palpable thyroid nodules with the frequency increasing throughout life. The major concern on nodule evaluation is the risk of malignancy (5-10%). Differentiated thyroid carcinoma accounts for 90% of all thyroid malignant neoplasias. Although most patients with cancer have a favorable outcome, some individuals present an aggressive form of the disease and poor prognostic despite recent advances in diagnosis and treatment. Here, a set of clinical guidelines for the evaluation and management of patients with thyroid nodules or differentiated thyroid cancer was developed through consensus by 8 member of the Department of Thyroid, Sociedade Brasileira de Endocrinologia e Metabologia. The participants are from different reference medical centers within Brazil, to reflect different practice patterns. Each committee participant was initially assigned to write a section of the document and to submit it to the chairperson, who revised and assembled the sections into a complete draft document, which was then circulated among all committee members for further revision. All committee members further revised and refined the document. The guidelines were developed based on the expert opinion of the committee participants, as well as on previously published information.

Phenolic composition and antioxidant potential of grain legume seeds: A review.

PubMed

Singh, Balwinder; Singh, Jatinder Pal; Kaur, Amritpal; Singh, Narpinder

2017-11-01

Legumes are a good source of bioactive phenolic compounds which play significant roles in many physiological as well as metabolic processes. Phenolic acids, flavonoids and condensed tannins are the primary phenolic compounds that are present in legume seeds. Majority of the phenolic compounds are present in the legume seed coats. The seed coat of legume seeds primarily contains phenolic acids and flavonoids (mainly catechins and procyanidins). Gallic and protocatechuic acids are common in kidney bean and mung bean. Catechins and procyanidins represent almost 70% of total phenolic compounds in lentils and cranberry beans (seed coat). The antioxidant activity of phenolic compounds is in direct relation with their chemical structures such as number as well as position of the hydroxyl groups. Processing mostly leads to the reduction of phenolic compounds in legumes owing to chemical rearrangements. Phenolic content also decreases due to leaching of water-soluble phenolic compounds into the cooking water. The health benefits of phenolic compounds include acting as anticarcinogenic, anti-thrombotic, anti-ulcer, anti-artherogenic, anti-allergenic, anti-inflammatory, antioxidant, immunemodulating, anti-microbial, cardioprotective and analgesic agents. This review provides comprehensive information of phenolic compounds identified in grain legume seeds along with discussing their antioxidant and health promoting activities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Extrusion cooking: Legume pulses

USDA-ARS?s Scientific Manuscript database

Extrusion is used commercially to produce high value breakfast and snack foods based on cereals such as wheat or corn. However, this processing method is not being commercially used for legume pulses seeds due to the perception that they do not expand well in extrusion. Extrusion cooking of pulses (...

Leguminosae native nodulating bacteria from a gold mine As-contaminated soil: Multi-resistance to trace elements, and possible role in plant growth and mineral nutrition.

PubMed

Rangel, Wesley de M; de Oliveira Longatti, Silvia M; Ferreira, Paulo A A; Bonaldi, Daiane S; Guimarães, Amanda A; Thijs, Sofie; Weyens, Nele; Vangronsveld, Jaco; Moreira, Fatima M S

2017-10-03

Efficient N 2 -fixing Leguminosae nodulating bacteria resistant to As may facilitate plant growth on As-contaminated sites. In order to identify bacteria holding these features, 24 strains were isolated from nodules of the trap species Crotalaria spectabilis (12) and Stizolobium aterrimum (12) growing on an As-contaminated gold mine site. 16S rRNA gene sequencing revealed that most of the strains belonged to the group of α-Proteobacteria, being representatives of the genera Bradyrhizobium, Rhizobium, Inquilinus, Labrys, Bosea, Starkeya, and Methylobacterium. Strains of the first four genera showed symbiotic efficiency with their original host, and demonstrated in vitro specific plant-growth-promoting (PGP) traits (production of organic acids, indole-3-acetic-acid and siderophores, 1-aminocyclopropane-1-carboxylate deaminase activity, and Ca 3 (PO 4 ) 2 solubilization), and increased resistance to As, Zn, and Cd. In addition, these strains and some type and reference rhizobia strains exhibited a wide resistance spectrum to β-lactam antibiotics. Both intrinsic PGP abilities and multi-element resistance of rhizobia are promising for exploiting the symbiosis with different legume plants on trace-element-contaminated soils.

Composition of legume soaking water and emulsifying properties in gluten-free bread.

PubMed

Huang, San; Liu, Yuling; Zhang, Weihan; Dale, Kylie J; Liu, Silu; Zhu, Jingnan; Serventi, Luca

2018-04-01

Soaking of legumes results in the loss of macronutrients, micronutrients and phytochemicals. Fibre, protein and phytochemicals found in legumes exert emulsifying activity that may improve the structure and texture of gluten-free bread. The legume soaking water of haricot beans, garbanzo chickpeas, whole green lentils, split yellow peas and yellow soybeans were tested in this study for functional properties and use as food ingredients. Composition, physicochemical properties and effect on the quality of gluten-free bread were determined for each legume soaking water. Haricot beans and split yellow peas released the highest amount of solids in the legume soaking water: 1.89 and 2.38 g/100 g, respectively. Insoluble fibre was the main constituent of haricot beans legume soaking water, while water-soluble carbohydrates and protein were the major fraction of split yellow peas. High quantities of phenolics (∼400 µg/g) and saponins (∼3 mg/g) were found in the legume soaking water of haricot beans, whole green lentils and split yellow peas. High emulsifying activity (46 and 50%) was found for the legume soaking water of garbanzo chickpeas and split yellow peas, probably due to their protein content and high ratio of water-soluble carbohydrates to dry matter. Such activity resulted in softer texture of the gluten-free bread. A homogeneous structure of crumb pores was found for split yellow peas, opposing that of whole green lentils. A balance between the contents of yeast nutrients and antinutrients was the likely basis of the different appearances.

Selenium hyperaccumulation by Astragalus (Fabaceae) does not inhibit root nodule symbiosis.

PubMed

Alford, Elan R; Pilon-Smits, Elizabeth A H; Fakra, Sirine C; Paschke, Mark W

2012-12-01

A survey of the root-nodule symbiosis in Astragalus and its interaction with selenium (Se) has not been conducted before. Such studies can provide insight into how edaphic conditions modify symbiotic interactions and influence partner coevolution. In this paper plant-organ Se concentration ([Se]) was investigated to assess potential Se exposure to endophytes. • Selenium distribution and molecular speciation of root nodules from Se-hyperaccumulators Astragalus bisulcatus, A. praelongus, and A. racemosus was determined by Se K-edge x-ray absorption spectroscopy. A series of greenhouse experiments were conducted to characterize the response of root-nodule symbiosis in Se-hyperaccumulators and nonhyperaccumulators. • Nodules in three Se-hyperaccumulators (Astragalus crotalariae, A. praelongus, and A. preussii) are reported for the first time. Leaves, flowers, and fruits from Se-hyperaccumulators were routinely above the hyperaccumulator threshold (1,000 µg Se g(-1) DW), but root samples rarely contained that amount, and nodules never exceeded 110 µg Se g(-1) DW. Nodules from A. bisulcatus, A. praelongus, and A. racemosus had Se throughout, with a majority stored in C-Se-C form. Finally, an evaluation of nodulation in Se-hyperaccumulators and nonhyperaccumulators indicated that there was no nodulation inhibition because of plant Se tolerance. Rather, we found that in Se-hyperaccumulators higher levels of Se treatment (up to 100 µM Se) corresponded with higher nodule counts, indicating a potential role for dinitrogen fixation in Se-hyperaccumulation. The effect was not found in nonhyperaccumulators. • As the evolution of Se hyperaccumulation in Astragalus developed, root-nodule symbiosis may have played an integral role.

Automatic lung nodule classification with radiomics approach

NASA Astrophysics Data System (ADS)

Ma, Jingchen; Wang, Qian; Ren, Yacheng; Hu, Haibo; Zhao, Jun

2016-03-01

Lung cancer is the first killer among the cancer deaths. Malignant lung nodules have extremely high mortality while some of the benign nodules don't need any treatment .Thus, the accuracy of diagnosis between benign or malignant nodules diagnosis is necessary. Notably, although currently additional invasive biopsy or second CT scan in 3 months later may help radiologists to make judgments, easier diagnosis approaches are imminently needed. In this paper, we propose a novel CAD method to distinguish the benign and malignant lung cancer from CT images directly, which can not only improve the efficiency of rumor diagnosis but also greatly decrease the pain and risk of patients in biopsy collecting process. Briefly, according to the state-of-the-art radiomics approach, 583 features were used at the first step for measurement of nodules' intensity, shape, heterogeneity and information in multi-frequencies. Further, with Random Forest method, we distinguish the benign nodules from malignant nodules by analyzing all these features. Notably, our proposed scheme was tested on all 79 CT scans with diagnosis data available in The Cancer Imaging Archive (TCIA) which contain 127 nodules and each nodule is annotated by at least one of four radiologists participating in the project. Satisfactorily, this method achieved 82.7% accuracy in classification of malignant primary lung nodules and benign nodules. We believe it would bring much value for routine lung cancer diagnosis in CT imaging and provide improvement in decision-support with much lower cost.

Deep learning aided decision support for pulmonary nodules diagnosing: a review.

PubMed

Yang, Yixin; Feng, Xiaoyi; Chi, Wenhao; Li, Zhengyang; Duan, Wenzhe; Liu, Haiping; Liang, Wenhua; Wang, Wei; Chen, Ping; He, Jianxing; Liu, Bo

2018-04-01

Deep learning techniques have recently emerged as promising decision supporting approaches to automatically analyze medical images for different clinical diagnosing purposes. Diagnosing of pulmonary nodules by using computer-assisted diagnosing has received considerable theoretical, computational, and empirical research work, and considerable methods have been developed for detection and classification of pulmonary nodules on different formats of images including chest radiographs, computed tomography (CT), and positron emission tomography in the past five decades. The recent remarkable and significant progress in deep learning for pulmonary nodules achieved in both academia and the industry has demonstrated that deep learning techniques seem to be promising alternative decision support schemes to effectively tackle the central issues in pulmonary nodules diagnosing, including feature extraction, nodule detection, false-positive reduction, and benign-malignant classification for the huge volume of chest scan data. The main goal of this investigation is to provide a comprehensive state-of-the-art review of the deep learning aided decision support for pulmonary nodules diagnosing. As far as the authors know, this is the first time that a review is devoted exclusively to deep learning techniques for pulmonary nodules diagnosing.

Deep learning aided decision support for pulmonary nodules diagnosing: a review

PubMed Central

Yang, Yixin; Feng, Xiaoyi; Chi, Wenhao; Li, Zhengyang; Duan, Wenzhe; Liu, Haiping; Liang, Wenhua; Wang, Wei; Chen, Ping

2018-01-01

Deep learning techniques have recently emerged as promising decision supporting approaches to automatically analyze medical images for different clinical diagnosing purposes. Diagnosing of pulmonary nodules by using computer-assisted diagnosing has received considerable theoretical, computational, and empirical research work, and considerable methods have been developed for detection and classification of pulmonary nodules on different formats of images including chest radiographs, computed tomography (CT), and positron emission tomography in the past five decades. The recent remarkable and significant progress in deep learning for pulmonary nodules achieved in both academia and the industry has demonstrated that deep learning techniques seem to be promising alternative decision support schemes to effectively tackle the central issues in pulmonary nodules diagnosing, including feature extraction, nodule detection, false-positive reduction, and benign-malignant classification for the huge volume of chest scan data. The main goal of this investigation is to provide a comprehensive state-of-the-art review of the deep learning aided decision support for pulmonary nodules diagnosing. As far as the authors know, this is the first time that a review is devoted exclusively to deep learning techniques for pulmonary nodules diagnosing. PMID:29780633

Probability of cancer in pulmonary nodules detected on first screening CT.

PubMed

McWilliams, Annette; Tammemagi, Martin C; Mayo, John R; Roberts, Heidi; Liu, Geoffrey; Soghrati, Kam; Yasufuku, Kazuhiro; Martel, Simon; Laberge, Francis; Gingras, Michel; Atkar-Khattra, Sukhinder; Berg, Christine D; Evans, Ken; Finley, Richard; Yee, John; English, John; Nasute, Paola; Goffin, John; Puksa, Serge; Stewart, Lori; Tsai, Scott; Johnston, Michael R; Manos, Daria; Nicholas, Garth; Goss, Glenwood D; Seely, Jean M; Amjadi, Kayvan; Tremblay, Alain; Burrowes, Paul; MacEachern, Paul; Bhatia, Rick; Tsao, Ming-Sound; Lam, Stephen

2013-09-05

Major issues in the implementation of screening for lung cancer by means of low-dose computed tomography (CT) are the definition of a positive result and the management of lung nodules detected on the scans. We conducted a population-based prospective study to determine factors predicting the probability that lung nodules detected on the first screening low-dose CT scans are malignant or will be found to be malignant on follow-up. We analyzed data from two cohorts of participants undergoing low-dose CT screening. The development data set included participants in the Pan-Canadian Early Detection of Lung Cancer Study (PanCan). The validation data set included participants involved in chemoprevention trials at the British Columbia Cancer Agency (BCCA), sponsored by the U.S. National Cancer Institute. The final outcomes of all nodules of any size that were detected on baseline low-dose CT scans were tracked. Parsimonious and fuller multivariable logistic-regression models were prepared to estimate the probability of lung cancer. In the PanCan data set, 1871 persons had 7008 nodules, of which 102 were malignant, and in the BCCA data set, 1090 persons had 5021 nodules, of which 42 were malignant. Among persons with nodules, the rates of cancer in the two data sets were 5.5% and 3.7%, respectively. Predictors of cancer in the model included older age, female sex, family history of lung cancer, emphysema, larger nodule size, location of the nodule in the upper lobe, part-solid nodule type, lower nodule count, and spiculation. Our final parsimonious and full models showed excellent discrimination and calibration, with areas under the receiver-operating-characteristic curve of more than 0.90, even for nodules that were 10 mm or smaller in the validation set. Predictive tools based on patient and nodule characteristics can be used to accurately estimate the probability that lung nodules detected on baseline screening low-dose CT scans are malignant. (Funded by the Terry Fox

Hyperfunctioning thyroid nodules in children.

PubMed

Abe, K; Konno, M; Sato, T; Matsuura, N

1980-10-01

We studied two cases of hyperfunctioning thyroid nodules in children. A 9-year-old girl and an 11-year-old girl had thyroid masses in otherwise nonpalpable thyroid glands. Scintiscan showed hyperfunctioning thyroid nodules. The former patient had elevated values for T4 and T3, and plasma thyrotropin (TSH) level failed to respond to stimulation with thyrotropin releasing hormone (TRH), whereas the latter patient had normal values for T4, and T3 and plasma TSH response to TRH was normal. After the surgical removal of nodules, scintiscan exhibited radioactivity in the contralateral lobe of the thyroid gland in the former and in the ectopic thyroid tissue in the latter. Results of microscopic examinations of thyroid nodules were consistent with adenomatous goiter.

Weightlifter's Nodule: A New Variant of Athlete's Nodule.

PubMed

Goldberg, Jamie; Campanelli, Carmen; Lee, Jason B

2015-01-01

A 17-year-old high school football player presented to our dermatology clinic complaining of two asymptomatic lumps on the upper part of his back. The first lump was noticed on the right side of the upper aspect of his back following a weightlifting session. The second lump appeared on the left side of the upper part of his back several weeks later. The patient's personal and family medical history was unremarkable. Physical examination revealed an ill-defined, firm, mobile subcutaneous nodule measuring approximately 3 cm on the right upper part of the back and a similar but smaller nodule on the left upper portion of the back (Figure 1). The location of the lesions corresponded to the areas of maximal pressure produced by a squat bar that he uses frequently during weightlifting (Figure 2). Histologic analysis of the right lesion revealed a markedly expanded dermis caused by a striking increase in the number of collagen bundles that were relatively normal in thickness, accompanied by a subtle increase in the number of fibroblasts (Figure 3). In some foci, fibroplasia along with increased deposition of mucin further contributed to the expansion of the dermis (Figure 3). Although the process spanned the entire dermis, it was more pronounced in the deep reticular dermis, particularly near the subcutis as collagen bundles were arranged in a more haphazard array in this region. Verhoeff-Van Gieson stain revealed diminished and fragmented elastic fibers within some of the involved areas. This reactive fibrosis can be seen in athlete's nodules as a result of repetitive blunt pressure. We proposed a diagnosis of weightlifter's nodule to further classify these lesions and the patient was instructed to discontinue associated weightlifting activities.

Diagnosis of hyperfunctional thyroid nodules: impact of US-elastography.

PubMed

Ruhlmann, M; Stebner, V; Görges, R; Farahati, J; Simon, D; Bockisch, A; Rosenbaum-Krumme, S; Nagarajah, J

2014-01-01

Several studies described the ultrasound based real-time elastography (USE) having a high sensitivity, specificity and negative predictive value in the diagnosis of suspicious thyroid nodules. Recently published studies called these results into question. Until now the usefulness of USE in the diagnosis of scintigraphically hyperfunctional thyroid nodules is not examined. This study included 135 hyperfunctional thyroid nodules of 102 consecutive patients. The following attributes of the nodules were analyzed: stiffness with the USE using scores of Rago or Asteria and ultrasound criteria using TIRADS. 94 of the examined thyroid nodules (70%) were rated as hard (suspicious for malignancy) and 41 nodules (30%) as soft (not suspicious) with a specificity of 30%. The scoring systems of Rago and Asteria showed no significant difference. Applying the TIRADS criteria 44 nodules (33%) have a higher risk for malignancy (33 nodules TIRADS 4a, 11 nodules TIRADS 4b). Combining USE and TIRADS 32 nodules (24%) are categorized as suspicious (intersection of hard nodules that are categorized as TIRADS 4a or 4b). Ultrasound based real-time elastography cannot identify scintigraphically hyperfunctional thyroid nodules as benign nodules reliably. Its accuracy in the assessment of at least "hot" thyroid nodules is to be questioned.

Standard-, Reduced-, and No-Dose Thin-Section Radiologic Examinations: Comparison of Capability for Nodule Detection and Nodule Type Assessment in Patients Suspected of Having Pulmonary Nodules.

PubMed

Ohno, Yoshiharu; Koyama, Hisanobu; Yoshikawa, Takeshi; Kishida, Yuji; Seki, Shinichiro; Takenaka, Daisuke; Yui, Masao; Miyazaki, Mitsue; Sugimura, Kazuro

2017-08-01

Purpose To compare the capability of pulmonary thin-section magnetic resonance (MR) imaging with ultrashort echo time (UTE) with that of standard- and reduced-dose thin-section computed tomography (CT) in nodule detection and evaluation of nodule type. Materials and Methods The institutional review board approved this study, and written informed consent was obtained from each patient. Standard- and reduced-dose chest CT (60 and 250 mA) and MR imaging with UTE were used to examine 52 patients; 29 were men (mean age, 66.4 years ± 7.3 [standard deviation]; age range, 48-79 years) and 23 were women (mean age, 64.8 years ± 10.1; age range, 42-83 years). Probability of nodule presence was assessed for all methods with a five-point visual scoring system. All nodules were then classified as missed, ground-glass, part-solid, or solid nodules. To compare nodule detection capability of the three methods, consensus for performances was rated by using jackknife free-response receiver operating characteristic analysis, and κ analysis was used to compare intermethod agreement for nodule type classification. Results There was no significant difference (F = 0.70, P = .59) in figure of merit between methods (standard-dose CT, 0.86; reduced-dose CT, 0.84; MR imaging with UTE, 0.86). There was no significant difference in sensitivity between methods (standard-dose CT vs reduced-dose CT, P = .50; standard-dose CT vs MR imaging with UTE, P = .50; reduced-dose CT vs MR imaging with UTE, P >.99). Intermethod agreement was excellent (standard-dose CT vs reduced-dose CT, κ = 0.98, P < .001; standard-dose CT vs MR imaging with UTE, κ = 0.98, P < .001; reduced-dose CT vs MR imaging with UTE, κ = 0.99, P < .001). Conclusion Pulmonary thin-section MR imaging with UTE was useful in nodule detection and evaluation of nodule type, and it is considered at least as efficacious as standard- or reduced-dose thin-section CT. © RSNA, 2017 Online supplemental material is available for this article.

African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils

PubMed Central

Puozaa, Doris K.; Dakora, Felix D.

2017-01-01

Flavonoids secreted by legumes play a major role as signal molecules for attracting compatible rhizobia. The aim of this study was to assess and understand the diversity of microsymbionts nodulating Bambara groundnut (Vigna subterranea L. Verdc.) landraces of different seedcoat colours using restriction fragment length polymorphism and phylogenetic analysis. Seedcoat pigmentation of landraces had effect on the diversity of microsymbionts of Bambara groundnut. Even when planted together in one hole, nodulating bradyrhizobia clustered differently. For example, 16S rDNA-RFLP typing of rhizobial samples TUTVSBLM.I, TUTVSCRM.I and TUTVSRDM.I originating respectively from Black, Cream and Red landraces that were co-planted in the same hole at Manga in the Sudano-sahelian savanna, as well as TUTVSCRK.I and TUTVSRDK.I respectively from Cream and Red landraces co-planted at Kpalisogu in the Guinea savanna, revealed different 16S rDNA- RFLP types. Phylogenetic analysis of 16S rDNA, glnII, recA and atpD sequences showed that Vigna subterranea was nodulated specifically by a diverse group of Bradyrhizobium species (e.g. Bradyrhizobium vignae, and a novel group of Bradyrhizobium spp.) in soils from Ghana and South Africa. The recA gene phylogeny showed incongruency with the other housekeeping genes, indicating the possibility of lateral gene transfer and/or recombination events. The grouping of isolates according to symbiotic gene (nifH and nodD) phylogenies revealed inter- and intra-specific symbiotic plasmid transfer and different evolutionary history. The results also showed that a cropping history and physico-chemical environment of soils increased bradyrhizobial diversity in Ghana and South Africa. PMID:28945783

Lung Nodule Detection via Deep Reinforcement Learning.

PubMed

Ali, Issa; Hart, Gregory R; Gunabushanam, Gowthaman; Liang, Ying; Muhammad, Wazir; Nartowt, Bradley; Kane, Michael; Ma, Xiaomei; Deng, Jun

2018-01-01

Lung cancer is the most common cause of cancer-related death globally. As a preventive measure, the United States Preventive Services Task Force (USPSTF) recommends annual screening of high risk individuals with low-dose computed tomography (CT). The resulting volume of CT scans from millions of people will pose a significant challenge for radiologists to interpret. To fill this gap, computer-aided detection (CAD) algorithms may prove to be the most promising solution. A crucial first step in the analysis of lung cancer screening results using CAD is the detection of pulmonary nodules, which may represent early-stage lung cancer. The objective of this work is to develop and validate a reinforcement learning model based on deep artificial neural networks for early detection of lung nodules in thoracic CT images. Inspired by the AlphaGo system, our deep learning algorithm takes a raw CT image as input and views it as a collection of states, and output a classification of whether a nodule is present or not. The dataset used to train our model is the LIDC/IDRI database hosted by the lung nodule analysis (LUNA) challenge. In total, there are 888 CT scans with annotations based on agreement from at least three out of four radiologists. As a result, there are 590 individuals having one or more nodules, and 298 having none. Our training results yielded an overall accuracy of 99.1% [sensitivity 99.2%, specificity 99.1%, positive predictive value (PPV) 99.1%, negative predictive value (NPV) 99.2%]. In our test, the results yielded an overall accuracy of 64.4% (sensitivity 58.9%, specificity 55.3%, PPV 54.2%, and NPV 60.0%). These early results show promise in solving the major issue of false positives in CT screening of lung nodules, and may help to save unnecessary follow-up tests and expenditures.

Lung Nodule Detection via Deep Reinforcement Learning

PubMed Central

Ali, Issa; Hart, Gregory R.; Gunabushanam, Gowthaman; Liang, Ying; Muhammad, Wazir; Nartowt, Bradley; Kane, Michael; Ma, Xiaomei; Deng, Jun

2018-01-01

Lung cancer is the most common cause of cancer-related death globally. As a preventive measure, the United States Preventive Services Task Force (USPSTF) recommends annual screening of high risk individuals with low-dose computed tomography (CT). The resulting volume of CT scans from millions of people will pose a significant challenge for radiologists to interpret. To fill this gap, computer-aided detection (CAD) algorithms may prove to be the most promising solution. A crucial first step in the analysis of lung cancer screening results using CAD is the detection of pulmonary nodules, which may represent early-stage lung cancer. The objective of this work is to develop and validate a reinforcement learning model based on deep artificial neural networks for early detection of lung nodules in thoracic CT images. Inspired by the AlphaGo system, our deep learning algorithm takes a raw CT image as input and views it as a collection of states, and output a classification of whether a nodule is present or not. The dataset used to train our model is the LIDC/IDRI database hosted by the lung nodule analysis (LUNA) challenge. In total, there are 888 CT scans with annotations based on agreement from at least three out of four radiologists. As a result, there are 590 individuals having one or more nodules, and 298 having none. Our training results yielded an overall accuracy of 99.1% [sensitivity 99.2%, specificity 99.1%, positive predictive value (PPV) 99.1%, negative predictive value (NPV) 99.2%]. In our test, the results yielded an overall accuracy of 64.4% (sensitivity 58.9%, specificity 55.3%, PPV 54.2%, and NPV 60.0%). These early results show promise in solving the major issue of false positives in CT screening of lung nodules, and may help to save unnecessary follow-up tests and expenditures. PMID:29713615

Molecular phylogeny and evolution of alcohol dehydrogenase (Adh) genes in legumes

PubMed Central

Fukuda, Tatsuya; Yokoyama, Jun; Nakamura, Toru; Song, In-Ja; Ito, Takuro; Ochiai, Toshinori; Kanno, Akira; Kameya, Toshiaki; Maki, Masayuki

2005-01-01

Background Nuclear genes determine the vast range of phenotypes that are responsible for the adaptive abilities of organisms in nature. Nevertheless, the evolutionary processes that generate the structures and functions of nuclear genes are only now be coming understood. The aim of our study is to isolate the alcohol dehydrogenase (Adh) genes in two distantly related legumes, and use these sequences to examine the molecular evolutionary history of this nuclear gene. Results We isolated the expressed Adh genes from two species of legumes, Sophora flavescens Ait. and Wisteria floribunda DC., by a RT-PCR based approach and found a new Adh locus in addition to homologues of the Adh genes found previously in legumes. To examine the evolution of these genes, we compared the species and gene trees and found gene duplication of the Adh loci in the legumes occurred as an ancient event. Conclusion This is the first report revealing that some legume species have at least two Adh gene loci belonging to separate clades. Phylogenetic analyses suggest that these genes resulted from relatively ancient duplication events. PMID:15836788

Hierarchically Aligning 10 Legume Genomes Establishes a Family-Level Genomics Platform.

PubMed

Wang, Jinpeng; Sun, Pengchuan; Li, Yuxian; Liu, Yinzhe; Yu, Jigao; Ma, Xuelian; Sun, Sangrong; Yang, Nanshan; Xia, Ruiyan; Lei, Tianyu; Liu, Xiaojian; Jiao, Beibei; Xing, Yue; Ge, Weina; Wang, Li; Wang, Zhenyi; Song, Xiaoming; Yuan, Min; Guo, Di; Zhang, Lan; Zhang, Jiaqi; Jin, Dianchuan; Chen, Wei; Pan, Yuxin; Liu, Tao; Jin, Ling; Sun, Jinshuai; Yu, Jiaxiang; Cheng, Rui; Duan, Xueqian; Shen, Shaoqi; Qin, Jun; Zhang, Meng-Chen; Paterson, Andrew H; Wang, Xiyin

2017-05-01

Mainly due to their economic importance, genomes of 10 legumes, including soybean ( Glycine max ), wild peanut ( Arachis duranensis and Arachis ipaensis ), and barrel medic ( Medicago truncatula ), have been sequenced. However, a family-level comparative genomics analysis has been unavailable. With grape ( Vitis vinifera ) and selected legume genomes as outgroups, we managed to perform a hierarchical and event-related alignment of these genomes and deconvoluted layers of homologous regions produced by ancestral polyploidizations or speciations. Consequently, we illustrated genomic fractionation characterized by widespread gene losses after the polyploidizations. Notably, high similarity in gene retention between recently duplicated chromosomes in soybean supported the likely autopolyploidy nature of its tetraploid ancestor. Moreover, although most gene losses were nearly random, largely but not fully described by geometric distribution, we showed that polyploidization contributed divergently to the copy number variation of important gene families. Besides, we showed significantly divergent evolutionary levels among legumes and, by performing synonymous nucleotide substitutions at synonymous sites correction, redated major evolutionary events during their expansion. This effort laid a solid foundation for further genomics exploration in the legume research community and beyond. We describe only a tiny fraction of legume comparative genomics analysis that we performed; more information was stored in the newly constructed Legume Comparative Genomics Research Platform (www.legumegrp.org). © 2017 American Society of Plant Biologists. All Rights Reserved.