scholarly journals Evidence of an American Origin for Symbiosis-Related Genes in Rhizobium lusitanum

2011 ◽  
Vol 77 (16) ◽  
pp. 5665-5670 ◽  
Author(s):  
Angel Valverde ◽  
Encarna Velázquez ◽  
Emilio Cervantes ◽  
José M. Igual ◽  
Peter van Berkum
Keyword(s):  
Host Range ◽  
Leucaena Leucocephala ◽  
Sequence Data ◽  
Rapd Analysis ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Nitrogen Fixing ◽  
Chromosomal Dna ◽  
Content Type ◽  
Narrow Host Range

ABSTRACTRandomly amplified polymorphic DNA (RAPD) analysis was used to investigate the diversity of 179 bean isolates recovered from six field sites in the Arcos de Valdevez region of northwestern Portugal. The isolates were divided into 6 groups based on the fingerprint patterns that were obtained. Representatives for each group were selected for sequence analysis of 4 chromosomal DNA regions. Five of the groups were placed withinRhizobium lusitanum, and the other group was placed withinR. tropicitype IIA. Therefore, the collection of Portuguese bean isolates was shown to include the two speciesR. lusitanumandR. tropici. In plant tests, the strains P1-7, P1-1, P1-2, and P1-16 ofR. lusitanumnodulated and formed nitrogen-fixing symbioses both withPhaseolus vulgarisandLeucaena leucocephala. A methyltransferase-encodingnodSgene identical with theR. tropicilocus that confers wide host range was detected in the strain P1-7 as well as 24 others identified asR. lusitanum. A methyltransferase-encodingnodSgene also was detected in the remaining isolates ofR. lusitanum, but in this case the locus was that identified with the narrow-host-rangeR. etli. Representatives of isolates with thenodSofR. etliformed effective nitrogen-fixing symbioses withP. vulgarisand did not nodulateL. leucocephala. From sequence data ofnodS, theR. lusitanumgenes for symbiosis were placed within those of eitherR. tropiciorR. etli. These results would support the suggestion thatR. lusitanumwas the recipient of the genes for symbiosis with beans from bothR. tropiciandR. etli.

scholarly journals Identification of Bacteriophages for Biocontrol of the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae

2014 ◽  
Vol 80 (7) ◽  
pp. 2216-2228 ◽  
Author(s):  
Rebekah A. Frampton ◽  
Corinda Taylor ◽  
Angela V. Holguín Moreno ◽  
Sandra B. Visnovsky ◽  
Nicola K. Petty ◽  
...  
Keyword(s):  
Host Range ◽  
Pseudomonas Syringae ◽  
Management Strategies ◽  
Pulse Field ◽  
Resistant Bacteria ◽  
Bacterial Canker ◽  
Content Type ◽  
Narrow Host Range ◽  
Pulse Field Gel Electrophoresis ◽  
Isolation And Characterization

ABSTRACTPseudomonas syringaepv. actinidiae is a reemerging pathogen which causes bacterial canker of kiwifruit (Actinidiasp.). Since 2008, a global outbreak ofP. syringaepv. actinidiae has occurred, and in 2010 this pathogen was detected in New Zealand. The economic impact and the development of resistance inP. syringaepv. actinidiae and other pathovars against antibiotics and copper sprays have led to a search for alternative management strategies. We isolated 275 phages, 258 of which were active againstP. syringaepv. actinidiae. Extensive host range testing onP. syringaepv. actinidiae, other pseudomonads, and bacteria isolated from kiwifruit orchards showed that most phages have a narrow host range. Twenty-four were analyzed by electron microscopy, pulse-field gel electrophoresis, and restriction digestion. Their suitability for biocontrol was tested by assessing stability and the absence of lysogeny and transduction. A detailed host range was performed, phage-resistant bacteria were isolated, and resistance to other phages was examined. The phages belonged to theCaudoviralesand were analyzed based on morphology and genome size, which showed them to be representatives ofMyoviridae,Podoviridae, andSiphoviridae. Twenty-oneMyoviridaemembers have similar morphologies and genome sizes yet differ in restriction patterns, host range, and resistance, indicating a closely related group. Nine of theseMyoviridaemembers were sequenced, and each was unique. The most closely related sequenced phages were a group infectingPseudomonas aeruginosaand characterized by phages JG004 and PAK_P1. In summary, this study reports the isolation and characterization ofP. syringaepv. actinidiae phages and provides a framework for the intelligent formulation of phage biocontrol agents against kiwifruit bacterial canker.

scholarly journals Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

2013 ◽  
Vol 80 (2) ◽  
pp. 446-454 ◽  
Author(s):  
Rosa Isela Santamaría ◽  
Patricia Bustos ◽  
Omar Sepúlveda-Robles ◽  
Luis Lozano ◽  
César Rodríguez ◽  
...  
Keyword(s):  
Host Range ◽  
Restriction Enzymes ◽  
Open Reading Frames ◽  
Rhizobium Etli ◽  
Content Type ◽  
Narrow Host Range ◽  
Bean Plants ◽  
Synthesis And Processing ◽  
A Minor

ABSTRACTIn this work, we isolated and characterized 14 bacteriophages that infectRhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48R. etlistrains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes andin vivocloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ∼45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species.

scholarly journals Molecular Basis of Symbiotic Promiscuity

2000 ◽  
Vol 64 (1) ◽  
pp. 180-201 ◽  
Author(s):  
Xavier Perret ◽  
Christian Staehelin ◽  
William J. Broughton
Keyword(s):  
Host Range ◽  
Molecular Basis ◽  
Soil Bacteria ◽  
Molecular Mechanisms ◽  
Ecological Niches ◽  
Nitrogen Fixing ◽  
Nitrogen Fixing Bacteria ◽  
Nitrogen Input ◽  
Narrow Host Range

SUMMARY Eukaryotes often form symbioses with microorganisms. Among these, associations between plants and nitrogen-fixing bacteria are responsible for the nitrogen input into various ecological niches. Plants of many different families have evolved the capacity to develop root or stem nodules with diverse genera of soil bacteria. Of these, symbioses between legumes and rhizobia (Azorhizobium, Bradyrhizobium, Mesorhizobium, and Rhizobium) are the most important from an agricultural perspective. Nitrogen-fixing nodules arise when symbiotic rhizobia penetrate their hosts in a strictly controlled and coordinated manner. Molecular codes are exchanged between the symbionts in the rhizosphere to select compatible rhizobia from pathogens. Entry into the plant is restricted to bacteria that have the “keys” to a succession of legume “doors”. Some symbionts intimately associate with many different partners (and are thus promiscuous), while others are more selective and have a narrow host range. For historical reasons, narrow host range has been more intensively investigated than promiscuity. In our view, this has given a false impression of specificity in legume-Rhizobium associations. Rather, we suggest that restricted host ranges are limited to specific niches and represent specialization of widespread and more ancestral promiscuous symbioses. Here we analyze the molecular mechanisms governing symbiotic promiscuity in rhizobia and show that it is controlled by a number of molecular keys.

scholarly journals Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches

2015 ◽  
Vol 82 (3) ◽  
pp. 808-815 ◽  
Author(s):  
Pingfeng Yu ◽  
Jacques Mathieu ◽  
Mengyan Li ◽  
Zhaoyi Dai ◽  
Pedro J. J. Alvarez
Keyword(s):  
Host Range ◽  
Pseudomonas Syringae ◽  
Burst Size ◽  
Broad Host Range ◽  
Ecological Significance ◽  
Content Type ◽  
Narrow Host Range ◽  
Isolation Methods ◽  
Culture Independent ◽  
K 12

ABSTRACTMany studies on phage biology are based on isolation methods that may inadvertently select for narrow-host-range phages. Consequently, broad-host-range phages, whose ecological significance is largely unexplored, are consistently overlooked. To enhance research on such polyvalent phages, we developed two sequential multihost isolation methods and tested both culture-dependent and culture-independent phage libraries for broad infectivity. Lytic phages isolated from activated sludge were capable of interspecies or even interorder infectivity without a significant reduction in the efficiency of plating (0.45 to 1.15). Two polyvalent phages (PX1 of thePodoviridaefamily and PEf1 of theSiphoviridaefamily) were characterized in terms of adsorption rate (3.54 × 10−10to 8.53 × 10−10ml/min), latent time (40 to 55 min), and burst size (45 to 99 PFU/cell), using different hosts. These phages were enriched with a nonpathogenic host (Pseudomonas putidaF1 orEscherichia coliK-12) and subsequently used to infect model problematic bacteria. By using a multiplicity of infection of 10 in bacterial challenge tests, >60% lethality was observed forPseudomonas aeruginosarelative to uninfected controls. The corresponding lethality forPseudomonas syringaewas ∼50%. Overall, this work suggests that polyvalent phages may be readily isolated from the environment by using different sequential hosts, and this approach should facilitate the study of their ecological significance as well as enable novel applications.

scholarly journals NET N MINERALISATION IN COCONUT/NITROGEN FIXING TREE BASED SYSTEM

CORD ◽  
1997 ◽  
Vol 13 (01) ◽  
pp. 34
Author(s):  
N.A Tennakoon ◽  
M. de S, Liyanage
Keyword(s):  
Incubation Period ◽  
Leucaena Leucocephala ◽  
Gliricidia Sepium ◽  
The Other ◽  
Acacia Auriculiformis ◽  
Calliandra Calothyrsus ◽  
N Availability ◽  
N Mineralisation ◽  
Nitrogen Fixing ◽  
Field Incubation

To study the net N mineralisation rates of coconut/NFT plantations, a field incubation technique was carried out. In this study, four types of NFT i.e. Acacia auriculiformis, Calliandra calothyrsus, Gliricidia sepium, Leucaena leucocephala and coconut monocropping were selected. Forty plastic tubes were inserted into the soil, to a depth of 15 cm at a distance of 2 m and l m away from coconut palm, for field incubation period of 2 weeks. Similarly another set of forty tubes were inserted for a 4 week field incubation period, after removing the previous set of tubes. Fresh soll samples (same depth) were also taken close to the inserted tubes on the day on which tubes were inserted for the estimation of initial N concentrations in the soil. Mineralised N concentrations were extracted by 2 M KCl and the net N mineralisation rates were calculated.   Net N mineralisation was significantly higher (P= 0.001) 4 weeks after field incubation peniod than 2 weeks and also, the significant higher (P= 0.001) net N mineralisation was shown 2 m away from coconut than l m away from coconut. The highest net N mineralisation (4.9 ‑ 15.5 kgha-1) was found in Gliricidia site than in the other NFT sites, followed by Leucaena > Calliandra > Acacia. The lowest net N mineralisation (1.2 ‑ 2.2 kgha-1) was recorded in the coconut monocrop, either 2 weeks or 4 weeks incubation period. This study clearly indicated that growing NFTs with coconut enhances N availability in coconut lands and Gliricidia being the most promismig.

scholarly journals Bacteriophage PBC1 and Its Endolysin as an Antimicrobial Agent against Bacillus cereus

2015 ◽  
Vol 81 (7) ◽  
pp. 2274-2283 ◽  
Author(s):  
Minsuk Kong ◽  
Sangryeol Ryu
Keyword(s):  
Bacillus Cereus ◽  
Host Range ◽  
Catalytic Domain ◽  
Food Poisoning ◽  
Genome Comparison ◽  
Lytic Enzymes ◽  
Content Type ◽  
Virulent Phage ◽  
Narrow Host Range ◽  
Bacillus Clarkii

ABSTRACTBacillus cereusis an opportunistic human pathogen responsible for food poisoning and other, nongastrointestinal infections. Due to the emergence of multidrug-resistantB. cereusstrains, the demand for alternative therapeutic options is increasing. To address these problems, we isolated and characterized aSiphoviridaevirulent phage, PBC1, and its lytic enzymes. PBC1 showed a very narrow host range, infecting only 1 of 22B. cereusstrains. Phylogenetic analysis based on the major capsid protein revealed that PBC1 is more closely related to theBacillus clarkiiphage BCJA1c and phages of lactic acid bacteria than to the phages infectingB. cereus. Whole-genome comparison showed that the late-gene region, including the terminase gene, structural genes, and holin gene of PBC1, is similar to that fromB. cereustemperate phage 250, whereas their endolysins are different. Compared to the extreme host specificity of PBC1, its endolysin, LysPBC1, showed a much broader lytic spectrum, albeit limited to the genusBacillus. The catalytic domain of LysPBC1 when expressed alone also showedBacillus-specific lytic activity, which was lower against theB. cereusgroup but higher against theBacillus subtilisgroup than the full-length protein. Taken together, these results suggest that the virulent phage PBC1 is a useful component of a phage cocktail to controlB. cereus, even with its exceptionally narrow host range, as it can kill a strain ofB. cereusthat is not killed by other phages, and that LysPBC1 is an alternative biocontrol agent againstB. cereus.

Isozyme and RAPD variation among and within hemp dogbane (Apocynum cannabinum) populations

Weed Science ◽  
1998 ◽  
Vol 46 (4) ◽  
pp. 408-413 ◽  
Author(s):  
Corey V. Ransom ◽  
David S. Douches ◽  
James J. Kells
Keyword(s):  
Genetic Variation ◽  
Genetic Distance ◽  
Phenotypic Variation ◽  
Population Genetic ◽  
Rapd Analysis ◽  
Analysis Data ◽  
The Other ◽  
Randomly Amplified Polymorphic Dna ◽  
Population Genetic Analysis ◽  
Two Populations

Clonal individuals from 16 hemp dogbane populations with phenotypic variation were analyzed using isozyme and randomly amplified polymorphic DNA (RAPD) analysis. Plants originated from populations in Michigan and Illinois. Three knownApocynumspecies, spreading dogbane, hemp dogbane, and prairie dogbane, were evaluated. Genetic distance among populations was more pronounced with isozyme analysis compared to RAPD analysis. The combined isozyme and RAPD analysis data separated spreading dogbane from all other plants analyzed. Genetic variation was present among the 16 hemp dogbane populations, but was less than expected based on the phenotypic variation present among the collections. The short genetic distance between the 16 hemp dogbane collections and the threeApocynumspecies suggests that variation among populations of hemp dogbane may be from outcrossing with other closely relatedApocynumspecies. Isozyme and RAPD analyses were also conducted on plants from two populations in Michigan to determine the level of genetic variation among plants within the same population. Genetic analysis revealed that one population was entirely clonal, while the other population was a mixture of clonal and segregating plants.

scholarly journals Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity

2012 ◽  
Vol 78 (24) ◽  
pp. 8666-8675 ◽  
Author(s):  
Kitiya Vongkamjan ◽  
Andrea Moreno Switt ◽  
Henk C. den Bakker ◽  
Esther D. Fortes ◽  
Martin Wiedmann
Keyword(s):  
Host Range ◽  
Dairy Farm ◽  
Dairy Farms ◽  
Genomic Diversity ◽  
Broad Host Range ◽  
Content Type ◽  
Narrow Host Range ◽  
Food Borne ◽  
Size Diversity ◽  
Range Characterization

ABSTRACTSince the food-borne pathogenListeria monocytogenesis common in dairy farm environments, it is likely that phages infecting this bacterium (“listeriaphages”) are abundant on dairy farms. To better understand the ecology and diversity of listeriaphages on dairy farms and to develop a diverse phage collection for further studies, silage samples collected on two dairy farms were screened forL. monocytogenesand listeriaphages. While only 4.5% of silage samples tested positive forL. monocytogenes, 47.8% of samples were positive for listeriaphages, containing up to >1.5 × 104PFU/g. Host range characterization of the 114 phage isolates obtained, with a reference set of 13L. monocytogenesstrains representing the nine major serotypes and four lineages, revealed considerable host range diversity; phage isolates were classified into nine lysis groups. While one serotype 3c strain was not lysed by any phage isolates, serotype 4 strains were highly susceptible to phages and were lysed by 63.2 to 88.6% of phages tested. Overall, 12.3% of phage isolates showed a narrow host range (lysing 1 to 5 strains), while 28.9% of phages represented broad host range (lysing ≥11 strains). Genome sizes of the phage isolates were estimated to range from approximately 26 to 140 kb. The extensive host range and genomic diversity of phages observed here suggest an important role of phages in the ecology ofL. monocytogeneson dairy farms. In addition, the phage collection developed here has the potential to facilitate further development of phage-based biocontrol strategies (e.g., in silage) and other phage-based tools.

scholarly journals Cooccurrence of Broad- and Narrow-Host-Range Viruses Infecting the Bloom-Forming Toxic Cyanobacterium Microcystis aeruginosa

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Daichi Morimoto ◽  
Kento Tominaga ◽  
Yosuke Nishimura ◽  
Naohiro Yoshida ◽  
Shigeko Kimura ◽  
...  
Keyword(s):  
Host Range ◽  
Microcystis Aeruginosa ◽  
Current Knowledge ◽  
Broad Host Range ◽  
Antiviral Defense ◽  
Content Type ◽  
Narrow Host Range ◽  
Toxic Cyanobacterium ◽  
Antiviral Responses ◽  
Group Ii

ABSTRACT Viruses play important roles in regulating the abundance and composition of bacterial populations in aquatic ecosystems. The bloom-forming toxic cyanobacterium Microcystis aeruginosa is predicted to interact with diverse cyanoviruses, resulting in Microcystis population diversification. However, current knowledge of the genomes from these viruses and their infection programs is limited to those of Microcystis virus Ma-LMM01. Here, we performed a time series sampling at a small pond in Japan during a Microcystis bloom and then investigated the genomic information and transcriptional dynamics of Microcystis-interacting viruses using metagenomic and metatranscriptomic approaches. We identified 15 viral genomic fragments classified into three groups, groups I (including Ma-LMM01), II (high abundance and transcriptional activity), and III (new lineages). According to the phylogenetic distribution of Microcystis strains possessing spacers against each viral group, the group II-original viruses interacted with all three phylogenetically distinct Microcystis population types (phylotypes), whereas the groups I and III-original viruses interacted with only one or two phylotypes, indicating the cooccurrence of broad- (group II) and narrow (groups I and III)-host-range viruses in the bloom. These viral fragments showed the highest transcriptional levels during daytime regardless of their genomic differences. Interestingly, M. aeruginosa expressed antiviral defense genes in the environment, unlike what was seen with an Ma-LMM01 infection in a previous culture experiment. Given that broad-host-range viruses often induce antiviral responses within alternative hosts, our findings suggest that such antiviral responses might inhibit viral multiplication, mainly that of broad-host-range viruses like those in group II. IMPORTANCE The bloom-forming toxic cyanobacterium Microcystis aeruginosa is thought to have diversified its population through the interactions between host and viruses in antiviral defense systems. However, current knowledge of viral genomes and infection programs is limited to those of Microcystis virus Ma-LMM01, which was a narrow host range in which it can escape from the highly abundant host defense systems. Our metagenomic approaches unveiled the cooccurrence of narrow- and broad-host-range Microcystis viruses, which included fifteen viral genomic fragments from Microcystis blooms that were classified into three groups. Interestingly, Microcystis antiviral defense genes were expressed against viral infection in the environment, unlike what was seen in a culture experiment with Ma-LMM01. Given that viruses with a broad host range often induce antiviral responses within alternative hosts, our findings suggest that antiviral responses inhibit viral reproduction, especially that of broad-range viruses like those in group II. This paper augments our understanding of the interactions between M. aeruginosa and its viruses and fills an important knowledge gap.

scholarly journals Independent Evolution with the Gene Flux Originating from Multiple Xanthomonas Species Explains Genomic Heterogeneity in Xanthomonas perforans

2019 ◽  
Vol 85 (20) ◽  
Author(s):  
E. A. Newberry ◽  
R. Bhandari ◽  
G. V. Minsavage ◽  
S. Timilsina ◽  
M. O. Jibrin ◽  
...  
Keyword(s):  
United States ◽  
Homologous Recombination ◽  
Host Range ◽  
Transcription Activation ◽  
The Other ◽  
Phylogenetic Groups ◽  
Southeast United States ◽  
Content Type ◽  
Xanthomonas Perforans ◽  
Pepper Plants

ABSTRACT Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria for that of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of 2 decades, including a shift in race and diversification into three phylogenetic groups driven by genome-wide homologous-recombination events derived from X. euvesicatoria. In our sampling of Xanthomonas strains associated with bacterial spot disease in Alabama, we were readily able to isolate X. perforans from symptomatic pepper plants grown in several Alabama counties, indicating a recent shift in the host range of the pathogen. To investigate the diversity of these pepper-pathogenic strains and their relation to populations associated with tomatoes grown in the southeast United States, we sequenced the genomes of eight X. perforans strains isolated from tomatoes and peppers grown in Alabama and compared them with previously published genome data available from GenBank. Surprisingly, reconstruction of the X. perforans core genome revealed the presence of two novel genetic groups in Alabama that each harbored a different transcription activation-like effector (TALE). While one TALE, AvrHah1, was associated with an emergent lineage pathogenic to both tomato and pepper, the other was identified as a new class within the AvrBs3 family, here designated PthXp1, and was associated with enhanced symptom development on tomato. Examination of patterns of homologous recombination across the larger X. euvesicatoria species complex revealed a dynamic pattern of gene flow, with multiple donors of Xanthomonas spp. associated with diverse hosts of isolation. IMPORTANCE Bacterial leaf spot of tomato and pepper is an endemic plant disease with a global distribution. In this study, we investigated the evolutionary processes leading to the emergence of novel X. perforans lineages identified in Alabama. While one lineage was isolated from symptomatic tomato and pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, here designated PthXp1. Functional analysis of PthXp1 indicated that it does not induce Bs4-mediated resistance in tomato and contributes to virulence, providing an adaptive advantage to strains on tomato. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts that results in the emergence of novel pathogen lineages and associated phenotypes, including host range.

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