Thomas O. Powers
University of Nebraska–Lincoln
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Molecular Ecology Resources | 2009
Dorota L. Porazinska; Robin M. Giblin-Davis; Lina Faller; William G. Farmerie; Natsumi Kanzaki; Krystalynne Morris; Thomas O. Powers; Abraham E. Tucker; Way Sung; W. Kelley Thomas
Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time‐consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving ~400‐bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82% were > 199 bp in length. Among the reads > 199 bp, 86% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.
Molecular Ecology | 2009
Thomas O. Powers; D. A. Neher; Peter Mullin; Alejandro Esquivel; Robin M. Giblin-Davis; Natsumi Kanzaki; S. P. Stock; M. M. Mora; L. Uribe-Lorio
Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum‐likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated ‘species’ richness ranged from 464 to 502 within the four 40 × 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil‐dwelling plant‐parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.
Molecular Ecology | 2010
Dorota L. Porazinska; Robin M. Giblin-Davis; Alejandro Esquivel; Thomas O. Powers; Way Sung; W. Kelley Thomas
The general patterns of increasing biodiversity from the poles to the equator have been well documented for large terrestrial organisms such as plants and vertebrates but are largely unknown for microbiota. In contrast to macrobiota, microbiota have long been assumed to exhibit cosmopolitan, random distributions and a lack of spatial patterns. To evaluate the assumption, we conducted a survey of nematode diversity within the soil, litter and canopy habitats of the humid lowland tropical rainforest of Costa Rica using an ultrasequencing ecometagenetic approach at a species‐equivalent taxonomic level. Our data indicate that both richness and diversity of nematode communities in the tropical rainforests of Costa Rica are high and exceed observed values from temperate ecosystems. The majority of nematode species were unknown to science, providing evidence for the presence of highly endemic (not cosmopolitan) species of still completely undiscovered biodiversity. Most importantly, the greater taxonomic resolution used here allowed us to reveal predictable habitat associations for specific taxa and thus gain insights into their nonrandom distribution patterns.
Current Genetics | 1986
Thomas O. Powers; E. G. Plazzer
SummaryPhysical characterization of the mitochondrial genome derived from the obligate mosquito parasite, Romanomermis culicivorax has generated some surprising physical properties regarding the molecular structure of nematode mitochondrial DNA (mtDNA). Restriction enzyme analysis of this mtDNA has revealed a mitochondrial genome size of approximately 26 kb, the largest metazoan mtDNA reported to date. Isofemale lineages are monomorphic for one of three size variants, differing by 500-1,000 base pairs, present in our original field population. Cloned hybridization probes derived from a single region exhibiting a 600 by size polymorphism share strong homology with several spatially separated sites distributed about the mtDNA. This suggests that the homology is a result of repeated DNA sequence elements contained within this mitochondrial genome that contribute to mtDNA size polymorphism.
Nematology | 2005
Peter Mullin; T. S. Harris; Thomas O. Powers
Phylogenetic reconstructions based on 18S rDNA sequence data indicate that Dorylaimida, comprising the suborders Nygolaimina and Dorylaimina, is a monophyletic lineage, but that there is a deep division within Nygolaimina, giving rise to the possibility that Nygolaimina is paraphyletic. A well-supported clade comprising members of the traditional orders Mermithida and Mononchida (including Bathyodontina) forms the sister taxon to the Dorylaimida. Inferred relationships within this clade indicate that Mermithida shares more recent common ancestry with Mononchina than does Bathyodontina. Vertebrate parasites within Dorylaimia (Dioctophymida and Trichinellida) are reconstructed in a sister-taxon relationship with the Mononchida/Dorylaimida lineage. The enigmatic order Isolaimida (represented by Isolaimium) appears to be ancestral to all other Dorylaimia sampled. Expanded taxon sampling for phylogenetic analyses of the subclass raises new possibilities for the reconstruction of hypothetical character states in the common ancestor of Dorylaimia.
PLOS ONE | 2012
Dorota L. Porazinska; Robin M. Giblin-Davis; Thomas O. Powers; W. Kelley Thomas
Large scale diversity patterns are well established for terrestrial macrobiota (e.g. plants and vertebrates), but not for microscopic organisms (e.g. nematodes). Due to small size, high abundance, and extensive dispersal, microbiota are assumed to exhibit cosmopolitan distributions with no biogeographical patterns. This assumption has been extrapolated from local spatial scale studies of a few taxonomic groups utilizing morphological approaches. Recent molecularly-based studies, however, suggest something quite opposite. Nematodes are the most abundant metazoans on earth, but their diversity patterns are largely unknown. We conducted a survey of nematode diversity within three vertical strata (soil, litter, and canopy) of rainforests at two contrasting latitudes in the North American meridian (temperate: the Olympic National Forest, WA, U.S.A and tropical: La Selva Biological Station, Costa Rica) using standardized sampling designs and sample processing protocols. To describe nematode diversity, we applied an ecometagenetic approach using 454 pyrosequencing. We observed that: 1) nematode communities were unique without even a single common species between the two rainforests, 2) nematode communities were unique among habitats in both rainforests, 3) total species richness was 300% more in the tropical than in the temperate rainforest, 4) 80% of the species in the temperate rainforest resided in the soil, whereas only 20% in the tropics, 5) more than 90% of identified species were novel. Overall, our data provided no support for cosmopolitanism at both local (habitats) and large (rainforests) spatial scales. In addition, our data indicated that biogeographical patterns typical of macrobiota also exist for microbiota.
Nematology | 2008
J. A. Brito; R. Kaur; Ramazan Cetintas; Jason D. Stanley; M. L. Mendes; Eugene McAvoy; Thomas O. Powers; D. W. Dickson
A total of 327 root samples collected from horticultural and agronomic crops, and weeds associated with these crops in Florida crop production regions, were examined. Isozyme phenotypes, esterase (EST) and malate dehydrogenase (MDH) phenotypes were used to characterise and identify the species of Meloidogyne present in these samples. At least 26 females from each sample were examined using polyacrylamide gel electrophoresis. Sixteen major bands of EST activity were found, corresponding to 12 phenotypes. A species-specific EST phenotype was consistently associated with each of the Meloidogyne spp. identified: Meloidogyne arenaria, M. floridensis, M. graminicola, M. hapla, M. incognita, M. javanica, M. mayaguensis and M. partityla. Two unique EST phenotypes, which have not been described, were found associated with three unidentified nematode populations. Five bands of MDH activity and four phenotypes were also found among the populations. During this study, new host records were determined for M. floridensis and M. mayaguensis, two recently reported Meloidogyne spp. in Florida. Plant species found as new hosts of M. floridensis were Cucumis sativus, Phaseolus sp., Solanum melongena and one weed species, Emilia sonchifolia, and the M. incognita-resistant peach rootstock ‘Flordaguard’. New hosts for M. mayaguensis were Carica papaya, Capsicum annuum var. Longum, and six weed plants, including Eclipta prostrata, Fatoua villosa, Panicum sp., Poinsettia cyathophora, Solanum americanum and also one unidentified weed species belonging to the family Acanthaceae. To our knowledge, Florida is the only geographic area of North America where M. floridensis and M. mayaguensis have been detected.
Nematology | 2011
Sergei A. Subbotin; Renato N. Inserra; M. Marais; Peter Mullin; Thomas O. Powers; Philip A. Roberts; Esther Van den Berg; G. W. Yeates; James G. Baldwin
The spiral nematodes of the genus Helicotylenchus are globally distributed and associated with the root system of diverse groups of plants in cultivated and uncultivated areas. Several species are considered serious parasites of crops. The identification of many Helicotylenchus species is not always reliable, in part because many species share very similar diagnostic characters and high intraspecific variation. To verify species identification of geographically distant populations of Helicotylenchus , we tested monophyly of some classical morphospecies and studied their phylogenetic relationships; specifically, we conducted sequence and phylogenetic analysis of 89 sequences of the D2-D3 expansion segments of 28S rRNA gene sequences from 54 Helicotylenchus isolates, including species identified as H. brevis , H. digonicus , H. dihystera , H. labiodiscinus , H. leiocephalus , H. martini , H. multicinctus , H. platyurus , H. pseudorobustus and H. vulgaris , together with three outgroup taxa. Phylogenetic analysis distinguished nine highly or moderately supported major clades within Helicotylenchus. Using the molecular approach we were able to confirm congruence with morphologicalbased identification of samples of H. dihystera and H. multicinctus . However, sequence and phylogenetic analysis using Bayesian inference and maximum parsimony analysis showed that isolates collected in different countries and morphologically identified as H. pseudorobustus , H. digonicus or H. vulgaris were each representative of several different and, sometimes, unrelated lineages. Further detailed comparative morphometrics and morphological studies will help to elucidate if there is some misidentification or if putative species actually comprise a complex of cryptic species. Molecular analysis also revealed that 14 samples were classified as representatives of 11 unidentified species. Molecular characterisation of known Helicotylenchus species especially, using samples collected from type localities, is needed for future reliable identification of species of this genus.
Plant Disease | 2014
A. Ramírez-Suárez; L. Rosas-Hernández; S. Alcasio-Rangel; Thomas O. Powers
In early April 2012, a sampling of watermelon crop Citrullus lanatus (Thunb.) Matsum & Nakai, 1916 cv. Sunsugar took place as part of the National System of Epidemiological Phytosanitary Surveillance (SINAVEF-MEX). This sampling was conducted at Riachuelos locality, Tecolutla, Veracruz, located at the geographic coordinates: 20.42008° N and 96.9627° W, within 50 meters of the Gulf of Mexico. Plants showed yellowing, stunting, and high levels of infection expressed by extensive galling on the roots. These symptoms were reproduced in the greenhouse on watermelon cv. Sunsugar. Egg masses were extracted to obtain juveniles (J2). Female necks and perineal patterns were mounted as well as males and J2 to take measurements of selected morphometric characters. To determine the nematode identity based on a morphological species concept, the following characters were considered. Females: stylet length, DGO and perineal pattern; males: stylet length; J2: body, stylet, tail, and hyaline tail terminus length. The morphometric analysis showed that those values corresponded to the original description of the root-knot nematode Meloidogyne enterolobii Yang & Eisenback, 1983 (=M. mayaguensis Rammah & Hirschmann, 1988) (1,2,3,4). For confirmation of this finding, a molecular diagnosis was performed using markers located in rDNA and mtDNA by PCR amplification and DNA sequencing. The rDNA region analyzed was the expansion segments D2-D3 of the 28S gene (primers D2A and D3B). This produced an amplified product of 780 bp. With regard to mtDNA, an amplification of the marker located between the genes COII/16S (primers C2F3 and 1108) resulted in a fragment of 705 bp that is specific for M. enterolobii (1). Sequences of the amplified products were compared with sequences from GenBank (NCBI). The sequences of both markers exhibited 99 and 100% identity with sequences corresponding to M. enterolobii isolates from Florida, Puerto Rico, and China. Maximum likelihood phylogenetic trees of rDNA and mtDNA sequences demonstrated that the Mexican isolate of M. enterolobii grouped among other isolates exclusive of other Meloidogyne species. The detection of this nematode in Veracruz, Mexico, expands the previously known worldwide distribution. It represents a serious threat due to the high level of aggressiveness shown in watermelon, which was so severe that growers had to change to a different crop. To our knowledge, this is the first report of the root-knot nematode M. enterolobii infecting watermelon cv. Sunsugar in Veracruz, Mexico. References: (1) J. Brito et al. J. Nematol. 36:232, 2004. (2) G. Karssen et al. ZooKeys 181:67, 2012. (3) A. Rammah and H. Hirshmann. J. Nematol. 20:58, 1988. (4) B. Yang and J. Eisenback. J. Nematol. 15:381, 1983.
Communications in Soil Science and Plant Analysis | 2008
R. B. Mendoza; Thomas G. Franti; John W. Doran; Thomas O. Powers; C. W. Zanner
Abstract: Soil quality indicators and nematode abundance were characterized in a loessial soil under long‐term conservation tillage to evaluate the effects of no‐till, double‐disk, chisel, and moldboard plow treatments. Indicators included soil electrical conductivity (EC), soil texture, soil organic matter (SOM), and total particulate organic matter (tPOM). Nematode abundance was positively correlated with EC, silt content, and total POM and negatively correlated with clay content. Clay content was the main source of variation among soil quality indicators and was negatively correlated with nematode abundance and most indicators. The gain in SOM in the no‐till system amounted to 10887 kg over the 24 years or 454 kg ha−1 year−1, about half of this difference (45%) resulting from soil erosion in plowed soils. The balance of gain in SOM with no till (249 kg ha−1 year−1) was due to SOM sequestration with no till. No‐till management reduced soil erosion, increased SOM, and enhanced soil physical characteristics.