Genome Similarity Implies that Citrus-Parasitic Burrowing Nematodes do not Represent a Unique Species

Burrowing nematodes from Central America, Dominican Republic, Florida, Guadeloupe, Hawaii, and Puerto Rico were characterized for their ability to parasitize citrus, but citrus parasites were found only in Florida. Sequence tag sites originally amplified from a citrus-parasitic burrowing nematode were polymorphic among 37 burrowing nematode isolates and were not correlated with citrus parasitism, nematode isolate collection site, or amplification of a 2.4-kb sequence tag site (DK#1). Results of a RAPD analysis and characterization of the isozymes phosphoglucose isomerase, lactate dehydrogenase, and malate dehydrogenase indicated that the burrowing nematode isolates were highly similar. Citrus parasitism in Florida appears to be associated with limited changes in the burrowing nematode genome. Findings did not substantiate a previous report that R. citrophilus was present in Hawaii. Overall, these data do not support assignment of sibling species status to burrowing nematodes that differ with respect to citrus parasitism.     

Aggressiveness and Damage Potential of Central American and Caribbean Populations of Radopholus spp. in Banana

Monoxenic cultures of burrowing nematode populations extracted from banana roots from Belize, Guatemala, Honduras, and Costa Rica were established on carrot discs. Cultures of Radopholus spp. were also obtained from Florida, Puerto Rico, Dominican Republic, and Ivory Coast. The aggressiveness (defined as reproductive fitness and root necrosis) of these populations was evaluated by inoculating banana plants (Musa AAA, cv. Grande Naine) with 200 nematodes/plant. Banana plants produced by tissue culture were grown in 0.4-liter styrofoam cups, containing a 1:1 mix of a coarse and a fine sand, at ca. 27 °C and 80% RH. Banana plants were acclimated and allowed to grow for 4 weeks prior to inoculation. Plant height, fresh shoot and root weights, root necrosis, and nematode population densities were determined 8 weeks after inoculation. Burrowing-nematode populations varied in aggressiveness, and their reproductive fitness was generally related to damage reported in the field. Plant height and fresh shoot and root weight did not reflect damage caused by nematodes under our experimental conditions. Necrosis of primary roots was closely related to the reproductive fitness of the nematode populations. Variation in aggressiveness among nematode populations followed a similar trend in the two susceptible hosts tested, Grande Naine and Pisang mas. All nematode populations had a low reproductive factor (Rf ≤2.5) in the resistant host except for the Ivory Coast population which had a moderate reproductive factor (Rf ≤ 5) on Pisang Jari Buaya. This is the first report of a burrowing nematode population parasitizing this important source of resistance to R. similis.     

Molecular and Biochemical Diversity Among Isolates of Radopholus spp. from Different Areas of the World

Eleven isolates of Radopholus similis from various banana-growing areas around the world and one isolate of R. bridgei from turmeric in Indonesia were compared using DNA and isoenzyme analysis. The polymerase chain reaction (PCR) was used to amplify a fragment of ribosomal DNA (rDNA), comprising the two internal transcribed spacers (ITS) and the 5.8S gene. Restriction fragment length polymorphisms (RFLPs) in this rDNA fragment were used to compare the 10 isolates. The analysis of this rDNA region revealed little variation among the isolates tested. However, data also were obtained by random amplified polymorphic DNA (RAPD) analysis of total DNA, and a hierarchical cluster analysis of these data arranged the R. similis isolates into two clusters. The first cluster consisted of isolates from Nigeria, Cameroon, Queensland, and Costa Rica; the second was comprised of isolates from Guinea, Guadeloupe, the Ivory Coast, Uganda, and Sri Lanka. The isolate of R. bridgei from turmeric in Indonesia appeared to be more divergent. This grouping was consistent with that obtained when phosphate glucose isomerase (PGI) isoenzyme patterns were used to compare the R. similis isolates. The results from both RAPD analysis and PGI isoenzyme studies indicate that two gene pools might exist within the R. similis isolates studied. No correlation could be detected between the genomic diversity as determined by RAPD analysis and either geographic distribution of the isolates or differences in their pathogenicity. The results support the hypothesis that R. similis isolates have been spread with banana-planting material.     

Effect of Endophytic Fusarium oxysporum on Host Preference of Radopholus similis to Tissue Culture Banana Plants

The burrowing nematode Radopholus similis is one of the major constraints to banana (Musa spp.) production worldwide. Resource-poor farmers can potentially manage R. similis by using naturally occurring banana endophytes, such as nonpathogenic Fusarium oxysporum, that are inoculated into tissue culture banana plantlets. At present, it is unclear at what stage in the R. similis infection process the endophytes are most effective. In this study, the effect of three endophytic F. oxysporum isolates (V5w2, Eny1.31i and Eny7.11o) on R. similis host preference of either endophyte-treated or untreated banana plants was investigated. No differences were observed between the proportion of nematodes attracted to either root segments excised from endophyte-treated or untreated plants, or in experiments using endophyte-treated and untreated tissue culture banana plantlets. These results imply that the early processes of banana plant host recognition by R. similis are not affected by endophyte infection.     

Characterization of native <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> strains by PCR-RAPD based fingerprinting

Seventy isolates of Bacillus thuringiensis were isolated from soil samples collected from cotton fields. These isolates were characterized by randomly amplified poylmorphic DNA (RAPD) markers to determine their genetic diversity pattern based on their source of origin. Different random decamer primers were used for RAPD amplification, which generated a total of 1935 fragments; of these 1865 were polymorphic and 68 monomorphic. The primers OPA03, OPA08, OPD14, OPD19, OPD20, OPE17 and OPD19 produced 100% polymorphic fragments, whereas primers OPC06, OPC20 and OPD17 produced 20, 31 and 17 monomorphic fragments, respectively. When the RAPD banding pattern data was subjected to dendrogram construction, the 70 isolates fell into two separate clusters, cluster I and cluster II, which includes 26 and 44 B. thuringiensis isolates, respectively. These two main clusters were further divided into four subclusters at Eucledian distance of 150 and 80% similarity index. All primers showed amplification and indicated the good diversity of B. thuringiensis isolates. The RAPD pattern showed 4–10 bands per isolate, with MWt in the range of 0.4–3.5 Kb and an average of 193.5 fragments were produced per primer. The primer OPE17 was found to be the most discriminatory as it produced 286 polymorphic bands.     

First record of entomopathogenic nematodes (Steinernematidae and Heterorhabditidae) in Costa Rica

A survey of entomopathogenic nematodes was conducted in the north Pacific (Guanacaste Conservation Area) and southeast Caribbean (Gandoca-Manzanillo Natural Refuge) regions of Costa Rica. Out of a total of 41 soil samples, 5 were positive for entomopathogenic nematodes (20.5%), with 3 (12.3%) containing Steinernema and 2 (8.2%) Heterorhabditis isolates. Morphological and molecular studies were undertaken to characterize these isolates. The Heterorhabditis isolates were identified as Heterorhabditis indica and the three Steinernema isolates were identified as two new undescribed species. H. indica was recovered from a coastal dry forest. Steinernema n. sp. 1 was isolated from a rainforest valley, between volcanoes. Steinernema sp. n. 2 was isolated from sand dunes in the Caribbean Coast (Punta Uva) near the rainforest strip along the coast. Although limited to two geographic regions, this study suggests entomopathogenic nematodes may be diverse and perhaps widely distributed in Costa Rica. A more intensive survey, covering all geographic regions is currently undergoing.     

Host-range Characterization of Two Pratylenchus coffeae Isolates from Brazil

Two isolates of Pratylenchus coffeae were collected from coffee roots (in Marília, São Paulo State, Brazil) and Aglaonema (in Rio de Janeiro City, Rio de Janeiro State, Brazil) and maintained in the laboratory on alfalfa callus. Twenty-four plants were tested in the greenhouse to characterize the host preference of these isolates. The host ranges of the isolates differed from each other and, interestingly, coffee, banana, and citrus were not among the better hosts of either isolate. Rather, sorghum, maize, rice, millet, okra, melon, eggplant, and lettuce were the best hosts of the Marília isolate. Poor hosts included French marigold, Rangpur lime, banana, sesame, peanut, sunflower, cotton, French bean, onion, and small onion. The best hosts of the Rio de Janeiro isolate were sesame, soybean, sorghum, castor oil plant, watermelon, squash, eggplant, and melon; the poorest hosts were French marigold, coffee, Rangpur lime, banana, sunflower, peanut, maize, millet, French bean, cotton, onion, sweet pepper, lettuce, okra, and small onion. These isolates have important molecular and morphological differences, suggesting host preference is linked to these characteristics.     

Characterization of Pratylenchus penetrans from Ten Geographically Isolated Populations Based on Their Reaction on Potato

Single female cuhures of Pratylenchus penetrans were established from soil and root samples collected from 10 geographically isolated locations in North America. The resultant isolates were used to evaluate nematode egression from and multiplication on roots of potato clones to distinguish intraspecific differences among isolates. The 10 nematode isolates were statistically separated into four groups based on percentage of nematodes that egressed from the P. penetrans-resistant potato done L 118-2. The Cornell (CR), Wisconsin (WI), Long Island (LI), and Adirondack (AD) isolates, selected as representative isolates of each of the four groups, exhibited 53%, 39%, 25%, and 10% egression from L118-2, respectively. Reproduction of these four isolates was measured on three potato cultivars (Russet Burbank, Butte, and Hudson) and two breeding lines (NY85 and L118-2). The LI and AD isolates reproduced well on all five potato clones. The CR isolate reproduced well on Russet Burbank and NY85 but significantly less on Butte, Hudson, and L118-2. Reproduction of the WI isolate was less than the LI and AD isolates but more than the CR isolate on all potato clones tested except Russet Burbank. Reproduction of the WI isolate on Russet Burbank was less than the other three isolates. Based on these results, four distinct intraspecific variants of P. penetrans are proposed: Cornell, Wisconsin, Long Island, and Adirondack.     

Sequence Tag Site and Host Range Assays Demonstrate that Radapholus similis and R. citraphilus are not Reproductively Isolated

Males of citrus-parasitic Radopholus citrophilus (FL1) were mated with non-citrus-parasitic R. similis (FL5) females. Progeny inherited a 2.4-kb sequence tag site (DK#1) and the ability to reproduce in citrus from the paternal parent (FLl); both traits were absent in the maternal line (FL5). The hybrid progeny produced offspring in roots of citrus seedlings over an 8-month period and therefore were considered reproductively viable. Genomic DNA hybridization studies indicated that one or more copies of DK#1 were present in R. citrophilus FL1. It is not likely that DK#1 represents a citrus parasitism gene because it was amplified from some burrowing nematode isolates that did not parasitize citrus and because DK#1 contains no open reading frames. Inability to reliably test individual nematodes for their ability to parasitize citrus was a constraint to obtaining F2 data required for definitive genetic characterization of citrus parasitism in burrowing nematodes, and alternate approaches will be required. Although the physical relationship of DK#1 and the citrus parasitism locus remains undefined, results of controlled mating studies using these parameters as genetic markers enabled us to identify hybrid F₁ progeny. Therefore, R. similis and R. citrophilus are not sibling species since gene flow between the two does not appear to be restricted via geographic isolation (sympatric in Florida) or by genetics.     

Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India

The present investigation was undertaken for the assessment of 12 accessions of Zingiber officinale Rosc. collected from subcontinent of India by RAPD markers. DNA was isolated using CTAB method. Thirteen out of twenty primers screened were informative and produced 275 amplification products, among which 261 products (94.90%) were found to be polymorphic. The percentage polymorphism of all 12 accessions ranged from 88.23% to 100%. Most of the RAPD markers studied showed different levels of genetic polymorphism. The data of 275 RAPD bands were used to generate Jaccard’s similarity coefficients and to construct a dendrogram by means of UPGMA. Results showed that ginger undergoes genetic variation due to a wide range of ecological conditions. This investigation was an understanding of genetic variation within the accessions. It will also provide an important input into determining resourceful management strategies and help to breeders for ginger improvement program.     

Potential of Foliar,Dip, and Injection Applications of Avermectins for Control of Plant-Parasitic Nematodes

Studies were conducted to determine the potential of two avermectin compounds, abamectin and emamectin benzoate, for controlling plant-parasitic nematodes when applied by three methods: foliar spray, root dip, and pseudostem injection. Experiments were conducted against Meloidogyne incognita on tomato, M. javanica on banana, and Radopholus similis on banana. Foliar applications of both avermectins to banana and tomato were not effective for controlling any of the nematodes evaluated. Root dips of banana and tomato were moderately effective for controlling M. incognita on tomato and R. similis on banana. Injections (1 ml) of avermectins into banana pseudostems were effective for controlling M. javanica and R similis, and were comparable to control achieved with a conventional chemical nematicide, fenamiphos. Injections of 125 to 2,000 μg/plant effectively controlled one or both nematodes on banana; abamectin was more effective than emamectin benzoate for controlling nematodes.     

Differentiation of Two New York Isolates of Pratylenchus penetrans Based on Their Reaction on Potato

The behavior of two isolates of Pratylenchus penetrans on six potato clones was assessed to test the hypothesis that these nematode isolates from New York were different. Four potato cultivars (Superior, Russet Burbank, Butte, and Hudson) and two breeding lines (NY85 and L118-2) were inoculated with nematode isolates designated Cornell (CR) and Long Island (LI). Population increase and egression of nematodes from roots were used to distinguish resistance and susceptibility of the potato clones. Based on numbers of eggs, juveniles, and adults in their roots 30 days after inoculation, potato clones Butte, Hudson, and L118-2 were designated resistant to the CR isolate and susceptible to the LI isolate. More eggs were found in the roots of all plants inoculated with the LI isolate than with the CR isolate. The clones NY85 and L118-2 were inoculated with the CR and LI isolates in a 2 x 2 factorial experiment to assess differences in nematode egression. Egression was measured, beginning 3 days after inoculation, for 12 days. The rates of egression were similar for the four treatments and fit linear regression models, but differences were detected in numbers of egressed nematodes. More nematodes of the CR isolate than the LI isolate egressed from L118-2. Differences in egression of females was particularly significant and can be used as an alternative or supplement to reproduction tests to assess resistance in potato to P. penetrans and to distinguish variation in virulence.     

Effect of Crotalaria juncea Amendment on Nematode Communities in Soil with Different Agricultural Histories

Effect of sunn hemp (Crotalaria juncea) hay amendment on nematode community structure in the soil surrounding roots of yellow squash (Cucurbita pepo) infected with root-knot nematodes was examined in two greenhouse experiments. Soils were from field plots treated long-term (LT) with yard-waste compost or no yard-waste compost in LT experiment, and from a short-term (ST) agricultural site in ST experiment. Soils collected were either amended or not amended with C. juncea hay. Nematode communities were examined 2 months after squash was inoculated with Meloidogyne incognita. Amendment increased (P < 0.05) omnivorous nematodes in both experiments but increased only bacterivorous nematodes in ST experiment (P < 0.05), where the soil had relatively low organic matter (<2%). This effect of C. juncea amendment did not occur in LT experiment, in which bacterivores were already abundant. Fungivorous nematodes were not increased by C. juncea amendment in either experiment, but predatory nematodes were increased when present. Although most nematode faunal indices, including enrichment index, structure index, and channel index, were not affected by C. juncea amendment, structure index values were affected by previous soil organic matter content. Results illustrate the importance of considering soil history (organic matter, nutrient level, free-living nematode number) in anticipating changes following amendment with C. juncea hay.     

Genetic variability within isolates of Colletotrichum lindemuthianum belonging to race 65 from the state of Minas Gerais, Brazil

Colletotrichum lindemuthianum, the causal agent of anthracnose in the common bean (Phaseolus vulgaris), presents a wide genetic and pathogenic variability that gives rise to complications in the development of resistant bean cultivars. The aim of this study was to identify the variability within race 65 of C. lindemuthianum, the race most commonly encountered in Brazil, through randomly amplified polymorphic DNA (RAPD) and anastomosis analyses. Thirteen isolates of race 65, collected in different years and from various host cultivars located in diverse areas of the state of Minas Gerais, Brazil, were investigated. Twenty-four RAPD primers were employed and 83 polymorphic bands amplified. Genetic similarities were estimated from the Sorensen-Dice coefficient and ranged from 0.54 to 0.82. The dendrogram obtained by cluster analysis classified the isolates into 11 separate groups. For the purposes of the analysis of anastomosis, isolates were considered to be compatible when the fusion of hyphae from different isolates could be observed. The proportion of compatible reactions for each isolate was estimated and similarity estimates, based on the Russel & Rao coefficient, ranged from 0.28 to 0.85. Isolates were classified into 11 anastomosis groups, 10 of which were formed by only one isolate. Although isolates LV61, LV73 and LV58 were classified in the same anastomosis group, they were genetically distinct according to RAPD analysis. Results from both RAPD and anastomosis analyses revealed great variability within C. lindemuthianum race 65.     

Phylogeography of Pinus subsection Australes in the Caribbean Basin

Background and Aims

Four species of Pinus subsection Australes occur in the Caribbean Basin: P. caribaea, P. cubensis, P. maestrensis and P. occidentalis. This study analyses the phylogeography of these species to assess possible colonization events from Central America to the islands and subsequent population expansions during glacial periods driven by both drier climate and larger emerged land areas.

Methods

Allele size data were obtained for plastid microsatellites for 314 individuals from 24 populations, covering the distribution range of subsection Australes in the Caribbean Basin.

Key Results

In total, 113 plastid haplotypes were identified. The highest genetic diversity was found in populations of P. caribaea. Overall, Caribbean Basin populations fit the isolation by distance model. Significant phylogeographical structure was found (R_ST = 0·671 > permuted R_ST = 0·101; P < 0·0001). The haplotype network and a Bayesian analysis of population structure (BAPS) indicated different Central American origins for P. caribaea var. bahamensis and P. caribaea var. caribaea plastids, with Central America populations in northern and south-eastern groups. Sudden expansion times for BAPS clusters were close to three glacial maxima.

Conclusions

Central America contains ancestral plastid haplotypes. Population expansion has played a major role in the distribution of genetic diversity in P. caribaea var. hondurensis. Two colonization events gave rise to the P. caribaea var. bahamensis and P. caribaea var. caribaea lineages. Plastid variation in the eastern species (P. cubensis, P. maestrensis and P. occidentalis) evolved independently from that in P. caribaea var. caribaea. Incomplete lineage sorting between P. cubensis and P. maestrensis is apparent. Inferred expansion times for P. caribaea var. bahamensis and for the eastern lineages correspond to glacial maxima, whereas those for P. caribaea var. hondurensis correspond to the beginning of the temperature decrease that led to Marine Isotope Stage 8.     

Persistence of Four Heterorhabditis spp. Isolates in Soil: Role of Lipid Reserves

Infective juveniles of four Heterorhabditis isolates (H. bacteriophora HI, H. megidis UK211 and HF85, and H. downesi M245) were stored in moist (pF 1.7) and dry (pF 3.3) loam soil at 20°C for up to 141 days. Survival, assessed by the number of nematodes extracted by centrifugal flotation, declined over time, reaching fewer than 18% alive by day 141 for all but one treatment (H. bacteriophora HI in dry soil). The infectivity of nematodes in soil for Tenebrio molitor also declined over time, roughly in accordance with the decline in numbers of nematodes. Energy reserves of extracted nematodes were assessed by image analysis densitometry. There were differences among isolates both in survival and in the depletion of reserves, and there was a significant correlation between these two parameters, suggesting that the extent to which energy reserves are depleted affects survival or that a common factor influences both. However, significant nematode mortality occurred while levels of reserves remained high, and the maximum reduction in utilizable body content for any treatment was 51%, well above starvation level. Therefore, the decline in numbers of living nematodes and the reduced nematode infectivity in soil cannot directly result from starvation of the nematodes. Survival and infectivity declined more rapidly in moist than in dry soil; one isolate, H. downesi M245, was less affected by soil moisture content than the other three isolates.     

Counting Nematodes with a Microplate Reader

The feasibility of counting plant-parasitic nematodes in aqueous suspensions by measuring light transmittance through aqueous suspensions with an ELISA microplate reader was explored. Absorbance readings for eggs or vermiform stages of three species were linearly related (R² > 0.99) to concentrations between 0 and 10,000 nematodes/ml. Coefficients of variation ranged from 12-23%, depending on the species and developmental stage used. The method, therefore, was at least as accurate as direct counts of nematodes in aliquots on a microscope and more than 100 times as fast. The method should have direct application in research programs on plant resistance to nematodes, nematode population dynamics, and nematode behavior.     

Characterization of M. tuberculosis strains from west African patients by spoligotyping

Analysis of Mycobacterium tuberculosis strains was carried out using isolates collected from 69 Senegalese and 20 Ivory Coast tuberculosis patients. These 89 isolates were typed by means of the spoligotyping technique, showing clusterized populations of bacterial strains. In the Senegalese patients, 35 genetic profiles were observed with 10 clusters of spoligotypes from 44 isolates. Among Ivory Coast patients, 11 spoligotypes were found for 20 isolates. A particular cluster of isolates was evident both in Senegalese (10) and Ivory Coast (11) patients. These results show the existence of polymorphism of the direct repeat region for African M. tuberculosis strains. However they suggest that additionnal markers are needed for accurate epidemiological studies in areas that are highly endemic for tuberculosis.     

Genetic diversity of <Emphasis Type="Italic">Macrophomina phaseolina</Emphasis> isolates from certain agro-climatic regions of India by using RAPD markers

Genetic diversity analysis of Macrophomina phaseolina isolates obtained from different host range and diverse geographical locations in India was carried out using RAPD fingerprinting. Of the thirteen 10-mer random primers used, primer OPB-08 gave the maximum polymorphism and the UPGMA clustering could separate 50 isolates in to ten groups at more than 65% similarity level. The ten clusters correlated well with the geographical locations with exceptions for isolates obtained from Eastern and Western Ghats. There was a segregation of isolates from these two geographical locations in to two clusters thus, distributing 10 genotypes in to eight geographical locations. All the isolates M. phaseolina irrespective of their host and geographical origin, exhibited two representative monomorphic bands at 250 bp and 1 kb, presence of these bands suggests that isolates might have evolved from a common ancestor but due to geographical isolation fallowed by natural selection and genetic drift might have segregated in to subpopulations. Genetic similarity in the pathogenic population reflects the dispersal of single lineage in all locations in India.     

Diversity of Meloidogyne spp. on Musa in Martinique,Guadeloupe, and French Guiana

Ninety-six isolates of Meloidogyne species collected from banana fields from Martinique, Guadeloupe, and French Guiana, were examined using esterase (Est) and malate dehydrogenase (Mdh) phenotypes. Adult females identified as M. arenaria, M. incognita, M. javanica, M. cruciani, M. hispanica, and Meloidogyne sp. showed species-specific phenotypes only for the esterase enzymes. Intraspecific variability among isolates of M. arenaria, M. incognita, and M. javanica was detected using Est and Mdh. Perineal patterns were used as a complementary tool together with enzyme characterization and were essential for checking the morphological consistency of the identification. The major species of M. arenaria and M. incognita were detected at 61.9% and 34.3% of the total number of isolates, respectively, and the other minor species at 3.8%. The mixed Meloidogyne species were detected in 45.1% of the samples. Genetic analysis was conducted using RAPD markers, which alone or in combination provided reliable polymorphisms both between and within species. RAPD analysis of the data resulted in clustering of species and isolates congruent with esterase phenotype characterization. The intraspecific variability in M. incognita and in M. arenaria represented 14.9% and 61.6% of the amplified polymorphic fragments, respectively. This high level of variation in M. arenaria isolates may indicate multiple origins for populations classified as M. arenaria or more than one species inside the same group, but more detailed morphological and DNA studies will be necessary to test this hypothesis.