Publications by authors named "Wen-Feng Chen"

91 Publications

Siccirubricoccus phaeus sp. nov., isolated from oil reservoir water and emended description of the genus Siccirubricoccus.

Antonie Van Leeuwenhoek 2021 Apr 6;114(4):355-364. Epub 2021 Feb 6.

State Key Laboratory of Agrobiotechnology, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, 100193, People's Republic of China.

A Gram-staining-negative, non-motile, aerobic bacterium, designated 1-3, was isolated from oil reservoir water collected from Liaohe oilfield, north-east of China. Growth was observed at 15-40 °C (optimum 37 °C) and pH 6-10 (optimum 7). The strain can grow under nitrogen-limiting condition. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolate was most closely related to Siccirubricoccus deserti SYSU D8009 (96.7%), followed by Paracraurococcus ruber NS89 (95.7%) and Belnapia rosea CPCC 100156 (94.9%). Genome sequencing revealed a genome size of 6.43 Mbp and a G+C content of 71.3 mol%. The average nucleotide identity values and digital DNA-DNA hybridization between 1-3 and the reference strains were all below the cut-off level (95-96% and 70%, respectively) for species delineation. The strain possessed the cytochrome P450 enzyme, which has the potential to degrade oil. The respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (C ω7c/C ω6c, 38.8%), C (25.6%) and C cyclo ω8c (22.5%). The polar lipids of strain 1-3 comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and three unidentified aminolipids. Based on the genotypic and phenotypic characteristics, strain 1-3 represents a novel species of genus Siccirubricoccus, for which the name Siccirubricoccus phaeus sp. nov. is proposed. The type strain of Siccirubricoccus phaeus is 1-3 (= CGMCC 1.16799 = LMG 31398).
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http://dx.doi.org/10.1007/s10482-021-01516-8DOI Listing
April 2021

Erratum to "Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov., isolated from effective nodules of peanut in Southeast China" [Syst. Appl. Microbiol. 42(2019) 126002].

Syst Appl Microbiol 2021 Jan 16;44(1):126172. Epub 2020 Dec 16.

State Key Lab of Agrobiotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

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http://dx.doi.org/10.1016/j.syapm.2020.126172DOI Listing
January 2021

Physiological and symbiotic variation of a long-term evolved Rhizobium strain under alkaline condition.

Syst Appl Microbiol 2020 Sep 23;43(5):126125. Epub 2020 Jul 23.

College of Food Science and Pharmacy, Xinjiang Agricultural University, Urumqi 830052, Xinjiang Uygur Autonomous Region, China.

Physiological variation and adaptation of the long-term evolved rhizobia to alkaline environments where no host plant existence and the stability of their symbiotic properties when they are reinoculated to legume host remain unclear. A highly effective N-fixing Rhizobium yanglingense strain CCBAU 01603 was used as the ancestral strain and was cultured continuously with/without addition of extra alkaline reagent (KOH) in laboratory conditions for approximately 500 generations. Total 60 evolved clones obtained were checked for their adaptation to higher alkaline pH level and inoculated to their host plant Caragana microphylla to evaluate their symbiotic efficiencies. Most of the evolved clones showed increased adaptation to higher alkaline pH but all of them decreased symbiotic efficiencies, resulting in the formation of irregular root nodules with lower nitrogenase activity, production of abnormal bacteroids, and accumulation more starch grains in uninfected nodule cells. Further demonstration of lower symbiotic efficiencies came from the down-regulated expression of genes related to nitrogen fixation in the bacteroids by transcriptome comparison. In addition, genes related to transporters and other diverse functions were up- or down-regulated in the evolved clones in free-living conditions (like yjiS gene) or in symbiotic situations, demonstrating the significant variations in cellular physiology and symbiosis. Our study revealed that the enhancement of alkaline adaptation but loss of symbiotic efficiencies of the evolved clones had happened during the long-term evolution in alkaline environments where no selective pressures from host plant, offering new insight into the molecular mechanism and direction of rhizobial evolution in nature.
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http://dx.doi.org/10.1016/j.syapm.2020.126125DOI Listing
September 2020

Multiple Genes of Symbiotic Plasmid and Chromosome in Type II Peanut Strains Corresponding to the Incompatible Symbiosis With .

Front Microbiol 2020 23;11:1175. Epub 2020 Jun 23.

State Key Laboratory for Agrobiotechnology, Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China.

Rhizobia are capable of establishing compatible symbiosis with their hosts of origin and plants in the cross-nodulation group that the hosts of origin belonged to. However, different from the normal peanut (Type I strains), the Type II strains showed incompatible symbiosis with . Here, we employed transposon mutagenesis to identify the genetic loci related to this incompatibility in Type II strain CCBAU 53363. As results, seven Tn transposon insertion mutants resulted in an increase in nodule number on . By sequencing analysis of the sequence flanking Tn insertion, six mutants were located in the chromosome of CCBAU 53363, respectively encoding acyltransferase (L265) and hypothetical protein (L615)-unique to CCBAU 53363, two hypothetical proteins (L4 and L82), tripartite tricarboxylate transporter substrate binding protein (L373), and sulfur oxidation c-type cytochrome SoxA (L646), while one mutant was in symbiotic plasmid encoding alanine dehydrogenase (L147). Significant differences were observed in L147 gene sequences and the deduced protein 3D structures between the Type II (in symbiotic plasmid) and Type I strains (in chromosome). Conversely, strains in both types shared high homologies in the chromosome genes L373 and L646 and in their protein 3D structures. These data indicated that the symbiotic plasmid gene in Type II strains might have directly affected their symbiosis incompatibility, whereas the chromosome genes might be indirectly involved in this process by regulating the plasmid symbiosis genes. The seven genes may initially explain the complication associated with symbiotic incompatibility.
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http://dx.doi.org/10.3389/fmicb.2020.01175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7324677PMC
June 2020

sp. nov., isolated from a deep well with oil reservoir water.

Int J Syst Evol Microbiol 2020 Jul;70(7):4339-4344

Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

A Gram-stain-negative, rod-shaped bacterium, designated XJ4, was isolated from oil-contaminated water, collected from Xinjiang Province, north-west PR China (45° 1' 27″ N, 85° 6' 14″ E). Growth occurred at 20-45 °C (optimum, 30 °C) and pH 6.0-10.0 (optimum, pH 6.0-7.0). Strain XJ4 could tolerate up to 7 % (w/v) NaCl and grow optimally in the absence of NaCl. Phylogenetic analysis based on comparative sequence analysis of 16S rRNA gene sequences indicated that strain XJ4 belonged to the genus , and that was closely related to cai42 (97.2 %), SP32 (97.0 %) and JA296 (97.0 %). The average nucleotide identity values between XJ4 and three type strains were 77.9, 77.6 and 71.9 %, respectively. The DNA G+C content of strain XJ4 was 69.5 mol%. The sole respiratory quinone was Q-10. The major cellular fatty acid was summed feature 8 (Cω7 and/or Cω6), C and 11-methyl Cω7. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, unidentified phospholipids, an unidentified aminolipid and unidentified lipids. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain XJ4 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is XJ4 (=CGMCC 1.13778=LMG 30952).
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http://dx.doi.org/10.1099/ijsem.0.004294DOI Listing
July 2020

Methionine as a methyl donor regulates caste differentiation in the European honey bee (Apis mellifera).

Insect Sci 2020 Apr 10. Epub 2020 Apr 10.

College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong Province, China.

Nutrition contributes to honey bee caste differentiation, but the role of individual nutrients is still unclear. Most essential amino acid contents, except that of methionine (Met), are greater in royal jelly than worker jelly. After ∼3.5 d, the Met content in the latter was slightly greater than in the former. Met is the major raw material used in the synthesis of S-adenosyl-L-methionine, an active methyl donor for DNA methylation, which is an epigenetic driver of caste differentiation. Here, we tested whether Met regulates caste differentiation in honey bees by determining its effects on the caste development of bees receiving four diets: the basic, basic + 0.2% Met, basic + 0.2% Met + 20 mg/kg 5-azacytidine, and basic + 20 mg/kg 5-azacytidine. The presence of Met decreased the adult bee body length and the numbers of ovarioles, indicating that Met may direct the development of female larvae toward worker bees. The upregulated expression of SAMS, Dnmt1, and Dnmt3 caused by Met exposure in 4-d-old larvae indicated that the worker-inductive effects of Met may occur through the promotion of DNA methylation. We investigated the co-effects of Met and glucose on bee development, and found that the effects of an increased glucose level on the number of ovarioles and body length did not strengthen the worker-inductive effects caused by Met. Our results contribute to caste development theory and suggest that Met-as a methyl donor-plays a regulatory, but not decisive, role in caste differentiation.
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http://dx.doi.org/10.1111/1744-7917.12788DOI Listing
April 2020

sp. nov., isolated from a deep well with oil reservoir water.

Int J Syst Evol Microbiol 2020 Apr 10;70(4):2312-2317. Epub 2020 Feb 10.

Key Laboratory of Soil Microbiology, Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

A Gram-stain-negative, non-motile and ovoid bacterial strain, designated 4-2, was isolated from oil-contaminated water which was collected from Xinjiang Province, north-west PR China. The 16S rRNA gene sequence analysis showed that strain 4-2 belonged to the genus . The species with highest similarity to strain 4-2 was YIM 90738 (97.83 %), followed by '' M26 (97.83 %) and SYSUP0003 (97.25 %). The average nucleotide identity values between 4-2 and three type strains were 84.69, 77.88 and 74.07 %, respectively. The genomic DNA G+C content of strain 4-2 was 61.4 mol%. Chemotaxonomical characteristic results showed that the respiratory quinone was ubiquinone Q-10 and the major fatty acids were summed feature 8 (C7 or C6) and C cyclo 8. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid and an unidentified polar lipid. The predominant polyamines were putrescine, cadaverine and spermidine. On the basis of phenotypic, chemotaxonomic and phylogenetic inferences, strain 4-2 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is 4-2 (=CGMCC 1.13669=LMG 30882).
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http://dx.doi.org/10.1099/ijsem.0.004036DOI Listing
April 2020

Genomic and transcriptomic analysis reveal molecular basis of salinity tolerance in a novel strong salt-tolerant rice landrace Changmaogu.

Rice (N Y) 2019 Dec 27;12(1):99. Epub 2019 Dec 27.

Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.

Background: Salt stress is an important factor that limits rice yield. We identified a novel, strongly salt tolerant rice landrace called Changmaogu (CMG) collected from a coastal beach of Zhanjiang, Guangdong Province, China. The salt tolerance of CMG was much better than that of the international recognized salt tolerant rice cultivar Pokkali in the germination and seedling stages.

Results: To understand the molecular basis of salt tolerance in CMG, we performed BSA-seq for two extreme bulks derived from the cross between CMG and a cultivar sensitive to salt, Zhefu802. Transcriptomic sequencing was conducted for CMG at the germination and young seedling stages. Six candidate regions for salt tolerance were mapped on Chromosome 1 by BSA-seq using the extreme populations. Based on the polymorphisms identified between both parents, we detected 32 genes containing nonsynonymous coding single nucleotide polymorphisms (SNPs) and frameshift mutations in the open reading frame (ORF) regions. With transcriptomic sequencing, we detected a large number of differentially expressed genes (DEGs) at the germination and seedling stages under salt stress. KEGG analysis indicated two of 69 DEGs shared at the germination and seedling stages were significantly enriched in the pathway of carotenoid biosynthesis. Of the 169 overlapping DEGs among three sample points at the seedling stage, 13 and six DEGs were clustered into the pathways of ABA signal transduction and carotenoid biosynthesis, respectively. Of the 32 genes carrying sequence variation, only OsPP2C8 (Os01g0656200) was differentially expressed in the young seedling stage under salt stress and also showed sequence polymorphism in the ORFs between CMG and Zhefu802.

Conclusion: OsPP2C8 was identified as the target candidate gene for salinity tolerance in the seedling stage. This provides an important genetic resource for the breeding of novel salt tolerant rice cultivars.
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http://dx.doi.org/10.1186/s12284-019-0360-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934643PMC
December 2019

Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov., isolated from effective nodules of peanut in Southeast China.

Syst Appl Microbiol 2019 Sep 19;42(5):126002. Epub 2019 Jul 19.

State Key Lab of Agrobiotechnology, Ministry of Agriculture Key Lab of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

Nine slow-growing rhizobia isolated from effective nodules on peanut (Arachis hypogaea) were characterized to clarify the taxonomic status using a polyphasic approach. They were assigned to the genus Bradyrhizobium on the basis of 16S rRNA sequences. MLSA of concatenated glnII-recA-dnaK genes classified them into three species represented by CCBAU 53390, CCBAU 51670 and CCBAU 51778, which presented the closest similarity to B. guangxiense CCBAU 53363, B. guangdongense CCBAU 51649 and B. manausense BR 3351, B. vignae 7-2 and B. forestalis INPA 54B, respectively. The dDDH (digital DNA-DNA hybridization) and ANI (Average Nucleotide Identity) between the genomes of the three representative strains and type strains for the closest Bradyrhizobium species were less than 42.1% and 91.98%, respectively, below the threshold of species circumscription. Effective nodules could be induced on peanut and Lablab purpureus by all representative strains, while Vigna radiata formed effective nodules only with CCBAU 53390 and CCBAU 51778. Phenotypic characteristics including sole carbon sources and growth features supported the phylogenetic results. Based on the genotypic and phenotypic features, strains CCBAU 53390, CCBAU 51670 and CCBAU 51778 are designated the type strains of three novel species, for which the names Bradyrhizobium nanningense sp. nov., Bradyrhizobium guangzhouense sp. nov. and Bradyrhizobium zhanjiangense sp. nov. are proposed, respectively.
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http://dx.doi.org/10.1016/j.syapm.2019.126002DOI Listing
September 2019

Water-Soluble Humic Materials Regulate Quorum Sensing in Through a Novel Repressor of .

Front Microbiol 2018 21;9:3194. Epub 2018 Dec 21.

State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbial, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, China.

Quorum sensing (QS) plays an important role in the growth, nodulation, and nitrogen fixation of rhizobia. In this study, we show that water-soluble humic materials (WSHM) repress the expression of the QS related genes , and in This decreased the production of -acetyl homoserine lactones (AHL) and exopolysaccharides (EPS), and ultimately increased cell density. We also identified a novel regulator, SMc03890 (renamed QsrR), which binds directly to the promoter. Deletion of increased expression. WSHM repressed the expression of by augmenting the interaction between QsrR and the promoter; this was determined by a bacterial-one-hybrid assay. These effects of WSHM on the QS system in may be the underlying mechanism by which WSHM increase the symbiotic nitrogen fixation of inoculated with . This study provides the first evidence that humic acids regulate the QS of rhizobia and suggests that WSHM could be used as fertilizers to improve the efficiency of symbiotic nitrogen fixation.
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http://dx.doi.org/10.3389/fmicb.2018.03194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309736PMC
December 2018

The experimental study of shunt-decompression arterialized vein flap.

Cancer Cell Int 2018 27;18:148. Epub 2018 Sep 27.

Department of Hand Surgery, Shenzhen Baoan Shajing People's Hospital, No. 3 Shajing St. Bao'an District, Shenzhen, 518104 Guangdong People's Republic of China.

Background: Arterialized vein flap is a kind of unphysiological flap. Unphysiological reconstruction of blood circulation leads to higher load than that supported by physiological flap and is the culprit of flap swelling, blood stasis, skin blistering, and necrosis after flap grafting. To resolve the multiple disadvantages of traditional flap grafting, by introducing the principles of fluid mechanics, shunt-decompression surgery is prepared to decline the circulation preload and improve the prognosis of arterialized vein flap grafting.

Methods: By introducing the principles of fluid mechanics, we established the model of shunt-decompression arterialized vein flap, which satisfied the common properties of general fluid that the interface pressure between object and fluid is reduced when the velocity of fluid is increased and vice versa-the effect of Bernoulli. Under this rule, we anastomose the arterialized vein to the branch of main artery of recipient region or make end-to-side anastomosis, which can maintain the blood flow of main artery, decrease the perfusion of flap, and preserve the decompressive effect of main artery to branches. From March, 2016 to September, 2016, we performed animal experiments on ten male bama mini pigs with average weight of 28 ± 2.35 kg. Superior epigastric artery of pig was used for feeding artery to arterialize the superficial epigastric veins. The total area of flap is 8 cm × 6 cm. End-to-side anastomosis and end-to-end anastomosis were established in experimental group and control group, respectively. Doppler speckle perfusion imaging apparatus was used to monitor the alterations of flap perfusion, blood flow of flap, tissue swelling and survival of flaps.

Results: The average flap perfusion (PU) at 1 week after surgery is 83.62 ± 3.14 in experimental group and 98.14 ± 6.54 in control group, respectively (P < 0.05), indicating the significant reduction of flap blood perfusion in experimental group as compared with control group. As to the survival of flaps, 7 flaps completely survived, 3 showed partial necrosis, and no one was found as complete necrosis in experimental group, while only 3 flaps survived, and 4 flaps and 3 flaps showed partial necrosis and complete necrosis in control group, respectively (P < 0.05).

Conclusion: Based on the physiological features of arterialized vein flap and its problems in clinical application, we improved the anastomosis strategy of flap grafting and obtained excellent experimental outcomes, which provides an insight for the clinical application of arterialized vein flaps.
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http://dx.doi.org/10.1186/s12935-018-0622-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161395PMC
September 2018

Sphingomonas oleivorans sp. nov., isolated from oil-contaminated soil.

Int J Syst Evol Microbiol 2018 Dec 25;68(12):3720-3725. Epub 2018 Sep 25.

1​Key Laboratory of Soil Microbiology , Ministry of Agriculture, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

Strain FW-11 was isolated from oil-contaminated soil from Panjin in Liaoning, China. It was a Gram-stain-negative, aerobic and rod-shaped bacterium. The strain was confirmed to be a member of the genus Sphingomonas based on phylogenetic inference and phenotypic characteristics. The best growth of strain FW-11 occurred at 30 °C and pH 6.0-7.0. The strain was non-spore-forming, catalase-negative and oxidase-negative. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The cell-wall peptidoglycan of strain FW-11 included alanine, glycine, glutamic acid, aspartic acid and meso-diaminopimelate. The predominant isoprenoid quinones were ubiquinone Q-10 (93.2 %) and Q-9 (6.8 %). The fatty acid profile (>5 %) included C18 : 1ω6c (43.1 %), C16 : 0 (14.6 %), C17 : 1ω6c (14.0 %) and C14 : 0 2-OH (11.1 %). The most similar neighbours of FW-11 were Sphingomonas fennica K101 (97.4 %) and Sphingomonas haloaromaticamans A175 (97.0 %). The average nucleotide identity relatedness values between strain FW-11 and the two type strains (S. fennica K101 and S. haloaromaticamans A175) were 73.2 and 75.3 %, respectively. The genome size of FW-11 was 3.8 Mbp, comprising 3735 predicted genes with a DNA G+C content of 64.0 mol%. Based on phenotypic, chemotaxonomic and phylogenetic data, strain FW-11 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas oleivorans sp. nov. is proposed. The type strain is FW-11 (=LMG 29274=HAMBI 3659).
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http://dx.doi.org/10.1099/ijsem.0.003014DOI Listing
December 2018

Symbiotic characteristics of Bradyrhizobium diazoefficiens USDA 110 mutants associated with shrubby sophora (Sophora flavescens) and soybean (Glycine max).

Microbiol Res 2018 Sep 21;214:19-27. Epub 2018 May 21.

State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China. Electronic address:

Site-specific insertion plasmid pVO155 was used to knockout the genes involved in the alternation of host range of strain Bradyrhizobium diazoefficiens USDA 110 from its original determinate-nodule-forming host soybean (Glycine max), to promiscuous and indeterminate-nodule-forming shrubby legume sophora (Sophora flavescens). Symbiotic phenotypes of these mutants inoculated to these two legumes, were compared to those infected by wild-type strain USDA 110. Six genes of the total fourteen Tn5 transposon mutated genes were broken using the pVO155 plasmid. Both Tn5 and pVO155-inserted mutants could nodulate S. flavescens with different morphologies of low-efficient indeterminate nodules. One to several rod or irregular bacteroids, containing different contents of poly-β-hydroxybutyrate or polyphosphate were found within the symbiosomes in nodulated cells of S. flavescens infected by the pVO155-inserted mutants. Moreover, none of bacteroids were observed in the pseudonodules of S. flavescens, infected by wild-type strain USDA 110. These mutants had the nodulation ability with soybean but the symbiotic efficiency reduced to diverse extents. These findings enlighten the complicated interactions between rhizobia and legumes, i. e., mutation of genes involved in metabolic pathways, transporters, chemotaxis and mobility could alter the rhizobial entry and development of the bacteroid inside the nodules of a new host legume.
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http://dx.doi.org/10.1016/j.micres.2018.05.012DOI Listing
September 2018

Evidence for Phosphate Starvation of Rhizobia without Terminal Differentiation in Legume Nodules.

Mol Plant Microbe Interact 2018 10 20;31(10):1060-1068. Epub 2018 Aug 20.

State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, Rhizobium Research Center, and College of Biological Sciences, China Agricultural University, 100193, Beijing, China.

Phosphate homeostasis is tightly modulated in all organisms, including bacteria, which harbor both high- and low-affinity transporters acting under conditions of fluctuating phosphate levels. It was thought that nitrogen-fixing rhizobia, named bacteroids, inhabiting root nodules of legumes are not phosphate limited. Here, we show that the high-affinity phosphate transporter PstSCAB, rather than the low-affinity phosphate transporter Pit, is essential for effective nitrogen fixation of Sinorhizobium fredii in soybean nodules. Symbiotic and growth defects of the pst mutant can be effectively restored by knocking out PhoB, the transcriptional repressor of pit. The pst homologs of representative rhizobia were actively transcribed in bacteroids without terminal differentiation in nodules of diverse legumes (soybean, pigeonpea, cowpea, common bean, and Sophora flavescens) but exhibited a basal expression level in terminally differentiated bacteroids (alfalfa, pea, and peanut). Rhizobium leguminosarum bv. viciae Rlv3841 undergoes characteristic nonterminal and terminal differentiations in nodules of S. flavescens and pea, respectively. The pst mutant of Rlv3841 showed impaired adaptation to the nodule environment of S. flavescens but was indistinguishable from the wild-type strain in pea nodules. Taken together, root nodule rhizobia can be either phosphate limited or nonlimited regarding the rhizobial differentiation fate, which is a host-dependent feature.
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http://dx.doi.org/10.1094/MPMI-02-18-0031-RDOI Listing
October 2018

Evolutionarily Conserved , T1SS, and Hydrogenase System in Rhizobia of and .

Front Microbiol 2017 20;8:2282. Epub 2017 Nov 20.

State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing, China.

species are the main microsymbionts associated with the medicinal or sand-fixation plants and (AC) in temperate regions of China, while all the strains isolated from each of these plants could nodulate both of them. However, strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with . Therefore, the common features shared by these symbiotic rhizobia in genera of and still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two ( CCBAU01550, CCBAU45272) and five representative strains ( CCBAU01583, CCBAU01570, CCBAU01502, CCBAU01399, and CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including , T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including , T1SS as the possible main determinants; and , hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.
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http://dx.doi.org/10.3389/fmicb.2017.02282DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702008PMC
November 2017

Nonspecific Symbiosis Between Sophora flavescens and Different Rhizobia.

Mol Plant Microbe Interact 2018 Feb 27;31(2):224-232. Epub 2017 Nov 27.

1 State Key Laboratory of Agrobiotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China.

We explored the genetic basis of the promiscuous symbiosis of Sophora flavescens with diverse rhizobia. To determine the impact of Nod factors (NFs) on the symbiosis of S. flavescens, nodulation-related gene mutants of representative rhizobial strains were generated. Strains with mutations in common nodulation genes (nodC, nodM, and nodE) failed to nodulate S. flavescens, indicating that the promiscuous nodulation of this plant is strictly dependent on the basic NF structure. Mutations of the NF decoration genes nodH, nodS, nodZ, and noeI did not affect the nodulation of S. flavescens, but these mutations affected the nitrogen-fixation efficiency of nodules. Wild-type Bradyrhizobium diazoefficiens USDA110 cannot nodulate S. flavescens, but we obtained 14 Tn5 mutants of B. diazoefficiens that nodulated S. flavescens. This suggested that the mutations had disrupted a negative regulator that prevents nodulation of S. flavescens, leading to nonspecific nodulation. For Ensifer fredii CCBAU 45436 mutants, the minimal NF structure was sufficient for nodulation of soybean and S. flavescens. In summary, the mechanism of promiscuous symbiosis of S. flavescens with rhizobia might be related to its nonspecific recognition of NF structures, and the host specificity of rhizobia may also be controlled by currently unknown nodulation-related genes.
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http://dx.doi.org/10.1094/MPMI-05-17-0117-RDOI Listing
February 2018

Agrobacterium salinitolerans sp. nov., a saline-alkaline-tolerant bacterium isolated from root nodule of Sesbania cannabina.

Int J Syst Evol Microbiol 2017 Jun 20;67(6):1906-1911. Epub 2017 Jun 20.

Key Laboratory of Coastal Biology and Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, PR China.

Two Gram-staining-negative, aerobic bacteria (YIC 5082T and YIC4104) isolated from root nodules of Sesbania cannabina grown in a high-salt and alkaline environment were identified as a group in the genus Agrobacterium because they shared 100 and 99.7 % sequence similarities of 16S rRNA and recA+atpD genes, respectively. These two strains showed 99.2/100 % and 93.9/95.4 % 16S rRNA and recA+atpD gene sequence similarities to Agrobacterium radiobacter LMG140T and Agrobacterium. pusense NRCPB10T, respectively. The average nucleotide identities (ANI) of genome sequences were 89.95 % or lower between YIC 5082T and the species of the genus Agrobacterium examined. Moreover, these two test strains formed a unique nifH lineage deeply separated from other rhizobia. Although the nodC gene was not detected in YIC 5082T and YIC4104, they could form effective root nodules on S. cannabina plants. The main cellular fatty acids in YIC 5082T were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, summed feature 2 (C12 : 0 aldehyde/unknown equivalent chain length 10.9525) and C16 : 0. The DNA G+C content of YIC 5082T was 59.3 mol%. The failure to utilize d-sorbitol as a carbon source distinguished YIC 5082T from the type strains of related species. YIC 5082T could grow in presence of 5.0 % (w/v) NaCl and at a pH of up to 10.0. Based on results regarding the genetic and phenotypic properties of YIC 5082T and YIC4104 the name Agrobacterium salinitolerans sp. nov. is proposed and YIC 5082T (=HAMBI 3646T=LMG 29287T) is designed as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.001885DOI Listing
June 2017

Agrobacterium deltaense sp. nov., an endophytic bacteria isolated from nodule of Sesbania cannabina.

Arch Microbiol 2017 Sep 6;199(7):1003-1009. Epub 2017 Apr 6.

Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, People's Republic of China.

A Gram-negative, non-spore-forming, aerobic rods, strain YIC4121, was isolated from root nodule of Sesbania cannabina grown in Dongying (Yellow River Delta), Shandong Province, PR China. Based on phylogenetic analysis of 16 S rRNA gene sequences, strain YIC4121 was assigned to the genus Agrobacterium with 99.7, 99.3, 99.0, 98.8 and 98.7% sequence similarities to Agrobacterium radiobacter LMG140, A. pusense NRCPB10, A. arsenijevicii KFB 330, A. nepotum 39/7 and A. larrymoorei ATCC51759. Analysis of the concatenated housekeeping genes (recA-atpD-glnII), showed lower sequence similarities (≤94.6%) between strain YIC4121 and other recognized Agrobacterium species. Strain YIC4121 shared whole-genome average nucleotide identities (ANI) 87.94, 91.27 and 77.42%, with A. pusense NRCPB10, A. radiobacter LMG140 and A. larrymoorei ATCC51759. The predominant cellular fatty acids were C cyclo ω8c, summed feature 2 (C aldehyde/unknown 10.9525), summed feature 8 (C ω7c/C ω6c), C 3 OH and C. The G + C content of strain YIC4121 was 59.80 mol%. Tween 80, lactulose, citric acid, α-ketoglutaric acid, glycyl-L-glutamic acid and 2, 3-butanediol could not be utilized as carbon source, distinguishing strain YIC4121 from the other related species. Based on the distinctly genetic and phenotypic dissimilarity, a novel species Agrobacterium deltaense sp. nov. is proposed with YIC4121 (=HAMBI 3654 = LMG 29283) as the type strain.
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http://dx.doi.org/10.1007/s00203-017-1367-0DOI Listing
September 2017

Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max).

Syst Appl Microbiol 2017 Apr 2;40(3):144-149. Epub 2017 Feb 2.

State Key Laboratory of Agro-Biotechnology; College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology; Beijing 100193, PR China. Electronic address:

Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167 and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167 could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167 contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167 from other type strains of the related species. The genome size of CCBAU 251167 was 6.2Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167 (=ACCC 19939=LMG 29645) as type strain.
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http://dx.doi.org/10.1016/j.syapm.2017.01.002DOI Listing
April 2017

Competition between rhizobia under different environmental conditions affects the nodulation of a legume.

Syst Appl Microbiol 2017 Mar 27;40(2):114-119. Epub 2016 Dec 27.

State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobium Research Center, China Agricultural University, Beijing 100193, China.

Mutualistic symbiosis and nitrogen fixation of legume rhizobia play a key role in ecological environments. Although many different rhizobial species can form nodules with a specific legume, there is often a dominant microsymbiont, which has the highest nodule occupancy rates, and they are often known as the "most favorable rhizobia". Shifts in the most favorable rhizobia for a legume in different geographical regions or soil types are not well understood. Therefore, in order to explore the shift model, an experiment was designed using successive inoculations of rhizobia on one legume. The plants were grown in either sterile vermiculite or a sandy soil. Results showed that, depending on the environment, a legume could select its preferential rhizobial partner in order to establish symbiosis. For perennial legumes, nodulation is a continuous and sequential process. In this study, when the most favorable rhizobial strain was available to infect the plant first, it was dominant in the nodules, regardless of the existence of other rhizobial strains in the rhizosphere. Other rhizobial strains had an opportunity to establish symbiosis with the plant when the most favorable rhizobial strain was not present in the rhizosphere. Nodule occupancy rates of the most favorable rhizobial strain depended on the competitiveness of other rhizobial strains in the rhizosphere and the environmental adaptability of the favorable rhizobial strain (in this case, to mild vermiculite or hostile sandy soil). To produce high nodulation and efficient nitrogen fixation, the most favorable rhizobial strain should be selected and inoculated into the rhizosphere of legume plants under optimum environmental conditions.
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http://dx.doi.org/10.1016/j.syapm.2016.12.003DOI Listing
March 2017

Cultivable endophytic bacteria from heavy metal(loid)-tolerant plants.

Arch Microbiol 2016 Dec 11;198(10):941-956. Epub 2016 Jun 11.

Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340, Ciudad de México, Mexico.

To evaluate the interactions among endophytes, plants and heavy metal/arsenic contamination, root endophytic bacteria of Prosopis laevigata (Humb and Bonpl. ex Willd) and Sphaeralcea angustifolia grown in a heavy metal(loid)-contaminated zone in San Luis Potosi, Mexico, were isolated and characterized. Greater abundance and species richness were found in Prosopis than in Sphaeralcea and in the nutrient Pb-Zn-rich hill than in the poor nutrient and As-Cu-rich mine tailing. The 25 species identified among the 60 isolates formed three groups in the correspondence analysis, relating to Prosopis/hill (11 species), Prosopis/mine tailing (4 species) and Sphaeralcea/hill (4 species), with six species ungrouped. Most of the isolates showed high or extremely high resistance to arsenic, such as ≥100 mM for As(V) and ≥20 mM for As(III), in mineral medium. These results demonstrated that the abundance and community composition of root endophytic bacteria were strongly affected by the concentration and type of the heavy metals and metalloids (arsenic), as well as the plant species.
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http://dx.doi.org/10.1007/s00203-016-1252-2DOI Listing
December 2016

Rhizobium hidalgonense sp. nov., a nodule endophytic bacterium of Phaseolus vulgaris in acid soil.

Arch Microbiol 2017 Jan 24;199(1):97-104. Epub 2016 Aug 24.

Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, People's Republic of China.

One Gram-negative, aerobic, motile, rod-shaped bacterium, designated as FH14, was isolated from nodules of Phaseolus vulgaris grown in Hidalgo State of Mexico. Results based upon 16S rRNA gene (≥99.8 % similarities to known species), concatenated sequence (recA, atpD and glnII) analysis of three housekeeping genes (≤93.4 % similarities to known species) and average nucleotide identity (ANI) values of genome sequence (ranged from 87.6 to 90.0 % to related species) indicated the distinct position of strain FH14 within the genus Rhizobium. In analyses of symbiotic genes, only nitrogen fixation gene nifH was amplified that had nucleotide sequence identical to those of the bean-nodulating strains in R. phaseoli and R. vallis, while nodulation gene nodC gene was not amplified. The failure of nodulation to its original host P. vulgaris and other legumes evidenced the loss of its nodulation capability. Strain FH14 contained summed feature 8 (C ω6c/C ω7c, 59.96 %), C (10.6 %) and summed feature 2 (C aldehyde/unknown 10.928, 10.24 %) as the major components of cellular fatty acids. Failure to utilize alaninamide, and utilizing L-alanine, L-asparagine and γ-amino butyric acid as carbon source, distinguished the strain FH14 from the type strains for the related species. The genome size and DNA G+C content of FH14 were 6.94 Mbp and 60.8 mol %, respectively. Based on those results, a novel specie in Rhizobium, named Rhizobium hidalgonense sp. nov., was proposed, with FH14 (=HAMBI 3636 = LMG 29288) as the type strain.
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http://dx.doi.org/10.1007/s00203-016-1281-xDOI Listing
January 2017

Ensifer glycinis sp. nov., a rhizobial species associated with species of the genus Glycine.

Int J Syst Evol Microbiol 2016 Sep 28;66(8):2910-2916. Epub 2016 Apr 28.

State Key Laboratory of Agro-Biotechnology, College of Biological Sciences and Rhizobium Research Center, China Agricultural University; MOA Key Laboratory of Soil Microbiology, Beijing 100193, PR China.

Rhizobial strains from root nodules of Astragalus mongholicus and soybean (Glycine max) were characterized phylogenetically as members of the genus Ensifer (formerly named Sinorhizobium), based on 16S rRNA gene sequence comparisons. Results based upon concatenated sequence analysis of three housekeeping genes (recA, atpD and glnII, ≤ 93.8 % similarities to known species) and average nucleotide identity (ANI) values of whole genome sequence comparisons (ranging from 89.6 % to 83.4 % to Ensifer fredii and Ensifer saheli, respectively) indicated the distinct positions of these novel strains within the genus Ensifer. Phylogeny of symbiotic genes (nodC and nifH) of three novel strains clustered them with rhizobial species Ensifer fredii and Ensifer sojae, both isolated from nodules of Glycine max. Cross-nodulation tests showed that the representative strain CCBAU 23380T could form root nodules with nitrogen fixation capability on Glycine soja, Albizia julibrissin, Vigna unguiculata and Cajanus cajan, but failed to nodulate Astragalus mongholicus, its original host legume. Strain CCBAU 23380T formed inefficient nodules on G. max, and it did not contain 18 : 0, 18 : 1ω7c 11-methyl or summed feature 1 fatty acids, which differed from other related strains. Failure to utilize malonic acid as a carbon source distinguished strain CCBAU 23380T from the type strains of related species. The genome size of CCBAU 23380T was 6.0 Mbp, comprising 5624 predicted genes with DNA G+C content of 62.4 mol%. Based on the results above, a novel species, Ensifer glycinis sp. nov., is proposed, with CCBAU 23380T (=LMG 29231T =HAMBI 3645T) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.001120DOI Listing
September 2016

Genetic diversity and distribution of rhizobia associated with the medicinal legumes Astragalus spp. and Hedysarum polybotrys in agricultural soils.

Syst Appl Microbiol 2016 Mar 13;39(2):141-9. Epub 2016 Feb 13.

State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China.

With the increasing cultivation of medicinal legumes in agricultural fields, the rhizobia associated with these plants are facing new stresses, mainly from fertilization and irrigation. In this study, investigations on the nodulation of three cultivated medicinal legumes, Astragalus mongholicus, Astragalus membranaceus and Hedysarum polybotrys were performed. Bacterial isolates from root nodules of these legumes were subjected to genetic diversity and multilocus sequence analyses. In addition, the distribution of nodule bacteria related to soil factors and host plants was studied. A total 367 bacterial isolates were obtained and 13 genospecies were identified. The predominant microsymbionts were identified as Mesorhizobium septentrionale, Mesorhizobium temperatum, Mesorhizobium tianshanense, Mesorhizobium ciceri and Mesorhizobium muleiense. M. septentrionale was found in most root nodules especially from legumes grown in the barren soils (with low available nitrogen and low organic carbon contents), while M. temperatum was predominant in nodules where the plants were grown in the nitrogen-rich fields. A. mongholicus tended to be associated with M. septentrionale, M. temperatum and M. ciceri in different soils, while A. membranaceus and H. polybotrys tended to be associated with M. tianshanense and M. septentrionale, respectively. This study showed that soil fertility may be the main determinant for the distribution of rhizobia associated with these cultured legume plants.
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http://dx.doi.org/10.1016/j.syapm.2016.01.004DOI Listing
March 2016

sp. nov., an arsenic-resistant endophytic actinobacterium associated with grown on high-arsenic-polluted mine tailing.

Int J Syst Evol Microbiol 2016 Feb 8;66(2):1027-1033. Epub 2015 Dec 8.

State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

A Gram-stain-positive, aerobic, non-motile, coccoid, arsenic-resistant actinobacterial strain, designated CM1E1, was isolated from the lateral root tissue of grown on a mine tailing in San Luis Potosi, Mexico. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CM1E1 was clustered closely with species of the genus and showed the highest sequence similarity of 98.7 % to TA68. The DNA G+C content of strain CM1E1 was 74.5 mol% (). The major fatty acids were anteiso-C, anteiso-C and iso-C. The peptidoglycan of the cell wall contained lysine and alanine. The major respiratory quinones were MK-7(H) and MK-8(H). On the basis of the phenotypic characterization, phylogenetic relationships and chemotaxonomic analyses, strain CM1E1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is CM1E1 ( = CCBAU 101092 = HAMBI 3625 = LMG 28671).
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http://dx.doi.org/10.1099/ijsem.0.000830DOI Listing
February 2016

Drosophila Nipped-B Mutants Model Cornelia de Lange Syndrome in Growth and Behavior.

PLoS Genet 2015 Nov 6;11(11):e1005655. Epub 2015 Nov 6.

Edward A Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, Saint Louis, Missouri, United States of America.

Individuals with Cornelia de Lange Syndrome (CdLS) display diverse developmental deficits, including slow growth, multiple limb and organ abnormalities, and intellectual disabilities. Severely-affected individuals most often have dominant loss-of-function mutations in the Nipped-B-Like (NIPBL) gene, and milder cases often have missense or in-frame deletion mutations in genes encoding subunits of the cohesin complex. Cohesin mediates sister chromatid cohesion to facilitate accurate chromosome segregation, and NIPBL is required for cohesin to bind to chromosomes. Individuals with CdLS, however, do not display overt cohesion or segregation defects. Rather, studies in human cells and model organisms indicate that modest decreases in NIPBL and cohesin activity alter the transcription of many genes that regulate growth and development. Sister chromatid cohesion factors, including the Nipped-B ortholog of NIPBL, are also critical for gene expression and development in Drosophila melanogaster. Here we describe how a modest reduction in Nipped-B activity alters growth and neurological function in Drosophila. These studies reveal that Nipped-B heterozygous mutant Drosophila show reduced growth, learning, and memory, and altered circadian rhythms. Importantly, the growth deficits are not caused by changes in systemic growth controls, but reductions in cell number and size attributable in part to reduced expression of myc (diminutive) and other growth control genes. The learning, memory and circadian deficits are accompanied by morphological abnormalities in brain structure. These studies confirm that Drosophila Nipped-B mutants provide a useful model for understanding CdLS, and provide new insights into the origins of birth defects.
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http://dx.doi.org/10.1371/journal.pgen.1005655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636142PMC
November 2015

Rhizobium acidisoli sp. nov., isolated from root nodules of Phaseolus vulgaris in acid soils.

Int J Syst Evol Microbiol 2016 01 2;66(1):398-406. Epub 2015 Nov 2.

State Key Laboratory of Agrobiotechnology and College of Biological Sciences, China Agricultural University, Beijing 100193, PR China.

Two Gram-negative, aerobic, non-motile, rod-shaped bacterial strains, FH13T and FH23, representing a novel group of Rhizobium isolated from root nodules of Phaseolus vulgaris in Mexico, were studied by a polyphasic analysis. Phylogeny of 16S rRNA gene sequences revealed them to be members of the genus Rhizobium related most closely to 'Rhizobium anhuiense' CCBAU 23252 (99.7 % similarity), Rhizobium leguminosarum USDA 2370T (98.6 %), and Rhizobium sophorae CCBAU 03386T and others ( ≤ 98.3 %). In sequence analyses of the housekeeping genes recA, glnII and atpD, both strains formed a subclade distinct from all defined species of the genus Rhizobium at sequence similarities of 82.3-94.0 %, demonstrating that they represented a novel genomic species in the genus Rhizobium. Mean levels of DNA-DNA relatedness between the reference strain FH13T and the type strains of related species varied between 13.0 ± 2.0 and 52.1 ± 1.2 %. The DNA G+C content of strain FH13T was 63.5 mol% (Tm). The major cellular fatty acids were 16 : 0, 17 : 0 anteiso, 18 : 0, summed feature 2 (12 : 0 aldehyde/unknown 10.928) and summed feature 8 (18 : 1ω7c). The fatty acid 17 : 1ω5c was unique for this strain. Some phenotypic features, such as failure to utilize adonitol, l-arabinose, d-fructose and d-fucose, and ability to utilize d-galacturonic acid and itaconic acid as carbon source, could also be used to distinguish strain FH13T from the type strains of related species. Based upon these results, a novel species, Rhizobium acidisoli sp. nov., is proposed, with FH13T ( = CCBAU 101094T = HAMBI 3626T = LMG 28672T) as the type strain.
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http://dx.doi.org/10.1099/ijsem.0.000732DOI Listing
January 2016

Identification and Classification of Rhizobia by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry.

J Proteomics Bioinform 2015;8:98-107. Epub 2015 May 31.

Department of Molecular Biosciences and Bioengineering, University of Hawaii at Manoa, Honolulu, HI 96822, USA.

Mass spectrometry (MS) has been widely used for specific, sensitive and rapid analysis of proteins and has shown a high potential for bacterial identification and characterization. Type strains of four species of rhizobia and DH5α were employed as reference bacteria to optimize various parameters for identification and classification of species of rhizobia by matrix-assisted laser desorption/ionization time-of-flight MS (MALDI TOF MS). The parameters optimized included culture medium states (liquid or solid), bacterial growth phases, colony storage temperature and duration, and protein data processing to enhance the bacterial identification resolution, accuracy and reliability. The medium state had little effects on the mass spectra of protein profiles. A suitable sampling time was between the exponential phase and the stationary phase. Consistent protein mass spectral profiles were observed for colonies pre-grown for 14 days and rhizobia for 21 days at 4°C or 21°C. A dendrogram of 75 rhizobial strains of 4 genera was constructed based on MALDI TOF mass spectra and the topological patterns agreed well with those in the 16S rDNA phylogenetic tree. The potential of developing a mass spectral database for all rhizobia species was assessed with blind samples. The entire process from sample preparation to accurate identification and classification of species required approximately one hour.
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http://dx.doi.org/10.4172/jpb.1000357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616259PMC
May 2015

Brevibacterium metallicus sp. nov., an endophytic bacterium isolated from roots of Prosopis laegivata grown at the edge of a mine tailing in Mexico.

Arch Microbiol 2015 Dec 1;197(10):1151-8. Epub 2015 Oct 1.

Departamento de Microbiología, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, México, D. F., 11340, Mexico.

A Gram-positive, aerobic, nonmotile strain, NM2E3(T) was identified as Brevibacterium based on the 16S rRNA gene sequence analysis and had the highest similarities to Brevibacterium jeotgali SJ5-8(T) (97.3 %). This novel bacterium was isolated from root tissue of Prosopis laegivata grown at the edge of a mine tailing in San Luis Potosí, Mexico. Its cells were non-spore-forming rods, showing catalase and oxidase activities and were able to grow in LB medium added with 40 mM Cu(2+), 72 mM As(5+) and various other toxic elements. Anteiso-C15:0 (41.6 %), anteiso-C17:0 (30 %) and iso-C15:0 (9.5 %) were the major fatty acids. MK-8(H2) (88.4 %) and MK-7(H2) (11.6 %) were the major menaquinones. The DNA G + C content of the strain NM2E3(T) was 70.8 mol % (Tm). DNA-DNA hybridization showed that the strain NM2E3(T) had 39.8, 21.7 and 20.3 % relatedness with B. yomogidense JCM 17779(T), B. jeotgali JCM 18571(T) and B. salitolerans TRM 45(T), respectively. Based on the phenotypic and genotypic analyses, the strain NM2E3(T) (=CCBAU 101093(T) = HAMBI 3627(T) = LMG 8673(T)) is reported as a novel species of the genus Brevibacterium, for which the name Brevibacterium metallicus sp. nov., is proposed.
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http://dx.doi.org/10.1007/s00203-015-1156-6DOI Listing
December 2015

Rhizobial Diversity and Nodulation Characteristics of the Extremely Promiscuous Legume Sophora flavescens.

Mol Plant Microbe Interact 2015 Dec 3;28(12):1338-52. Epub 2015 Dec 3.

1 State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China;

In present study, we report our extensive survey on the diversity and biogeography of rhizobia associated with Sophora flavescens, a sophocarpidine (matrine)-containing medicinal legume. We additionally investigated the cross nodulation, infection pattern, light and electron microscopies of root nodule sections of S. flavescens infected by various rhizobia. Seventeen genospecies of rhizobia belonging to five genera with seven types of symbiotic nodC genes were found to nodulate S. flavescens in natural soils. In the cross-nodulation tests, most representative rhizobia in class α-Proteobacteria, whose host plants belong to different cross-nodulation groups, form effective indeterminate nodules, while representative rhizobia in class β-Proteobacteria form ineffective nodules on S. flavescens. Highly host-specific biovars of Rhizobium leguminosarum (bv. trifolii and bv. viciae) and Rhizobium etli bv. phaseoli could establish symbioses with S. flavescens, providing further evidence that S. flavescens is an extremely promiscuous legume and it does not have strict selectivity on either the symbiotic genes or the species-determining housekeeping genes of rhizobia. Root-hair infection is found as the pattern that rhizobia have gained entry into the curled root hairs. Electron microscopies of ultra-thin sections of S. flavescens root nodules formed by different rhizobia show that the bacteroids are regular or irregular rod shape and nonswollen types. Some bacteroids contain poly-β-hydroxybutyrate (PHB), while others do not, indicating the synthesis of PHB in bacteroids is rhizobia-dependent. The extremely promiscuous symbiosis between S. flavescens and different rhizobia provide us a basis for future studies aimed at understanding the molecular interactions of rhizobia and legumes.
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http://dx.doi.org/10.1094/MPMI-06-15-0141-RDOI Listing
December 2015