Nematodes are the most abundant and diverse animals on the planet but lack representation in biodiversity research. This presents a problem for studying nematode diversity, particularly when molecular tools (i.e., barcoding and metabarcoding) rely on well-populated and curated reference databases, which are absent for nematodes. To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. As part of the curation process, taxonomic strings were standardized to contain a fixed number of taxonomic ranks relevant to nematology and updated for the most recent accepted nematode classifications. In addition, apparent erroneous sequences were removed. To test the efficacy and accuracy of 18S-NemaBase, we compared it to an older but also curated SILVA v111 and the newest SILVA v138 by assigning taxonomies and analyzing the diversity of a nematode dataset from the Western Nebraska Sandhills. We showed that 18S-NemaBase provided more accurate taxonomic assignments and diversity assessments than either version of SILVA, with a much easier workflow and no need for manual corrections. Additionally, observed diversity further improved when 18S-NemaBase was supplemented with reference sequences from nematodes present in the study site. Although the 18S-NemaBase is a step in the right direction, a concerted effort to increase the number of high-quality, accessible, full-length nematode reference sequences is more important now than ever.
Meloidogyne incognita (southern root-knot nematode, SRKN) is a major pest in tomato (Solanum lycopersicum) production in the Southeastern United States. Management has relied on fumigant and carbamate non-fumigant nematicides. New non-fumigant nematicides, such as fluopyram, are available and field evaluation of new nematicides is needed. The objectives of this research were to assess the efficacy of new (fluopyram) and established (oxamyl) nonfumigant nematicides as well as fumigation (1,3-dichloropropene) for (1) SRKN management, and (2) impacts on total soil abundances of non-target, free-living nematodes in field tests in Florida. Fumigation with 1,3-D consistently managed SRKN and, in two of three trials, increased yield relative to untreated. Oxamyl and fluopyram also had efficacy in managing SRKN, but were inconsistent from year to year. Oxamyl provided better root galling control than fluopyram in one of two trials, but otherwise those nematicides provided similar SRKN management and yield response. Supplementing 1,3-D fumigation with fluopyram did not improve SRKN management or yield relative to fumigation alone. Fumigation consistently reduced free-living nematode abundances relative to untreated. Oxamyl and fluopyram were more inconsistent, but always reduced total free-living nematode abundances when effective against SRKN. In summary, while non-fumigant nematicides provided some management of SRKN, fumigation continued to be the most consistent option. All nematicides had deleterious effects on free-living nematodes.
Sting nematode is acutely damaging to a wide range of crops and is relatively common in sandy soils in the southeastern United States. Sweetpotato is an important crop in this region, and its production may be expanding to localities where sting nematode is an important pest. Despite this, the relationship between sweetpotato and sting nematode is not well-defined. Therefore, the objectives of this study were to assess (1) the relative host status of sweetpotato for sting nematode and (2) damage potential of sting nematode on sweetpotato in repeated greenhouse experiments. A known sting nematode host (field corn), a known poor host (sunn hemp), and sweetpotato cultivars susceptible (‘Beauregard’) and resistant (‘Covington’) to southern root-knot nematode were challenged with sting nematode. In both trials, field corn supported greater final soil sting nematode abundances than sunn hemp or either sweetpotato cultivar. Based on the average reproductive factor, field corn was confirmed as a susceptible host, whereas sunn hemp and sweetpotato were poor hosts. Sting nematode did not impair the growth of any crop, suggesting greenhouse conditions were not conducive to damage since field corn sustains damage in field conditions. These results suggest that sunn hemp and sweetpotato could be useful rotation crops for managing sting nematode, but future work is needed to assess sting nematode pathogenicity on these crops under field conditions.
Introduction. The root-lesion nematodes, Pratylenchus spp., have a wide host range and reduce the yield of different crops. Information on the diversity of Pratylenchus species is scarce in Costa Rica. Objective. To identify the Pratylenchus species associated with 12 crops based on the D3 region of the 28S rDNA gene. Materials and methods. During 2013 to 2015, root samples were collected in Alajuela, Cartago, Guanacaste, Heredia, and San José in crops of rice (Oryza sativa), black pepper (Piper nigrum), sugarcane (Saccharum officinarum), aster (Aster sp.), coffee (Coffea arabica), banana (Musa paradisiaca), lily (Lilium sp.), gypsophila (Gypsophila sp.), onion (Allium cepa), potato (Solanum tuberosum), strawberry (Fragaria x ananassa), and leather-leaf fern (Rumohra adiantiformis). The D3 region of the 28S rDNA gene from each population was amplified and sequenced. A GenBank Blast Search was performed for each sequence. The phylogenetic relationships were established by Bayesian Inference. Results. Blast Search indicated the presence of P. pseudocoffeae in aster, P. brachyurus in black pepper, P. crenatus in onion and potato, P. hippeastri and P. gutierrezi in sugarcane and coffee, respectively. Pratylenchus bolivianus in leather-leaf fern and potato, P. penetrans in onion, strawberry, gypsophila, and lily, P. zeae in rice and sugarcane, while P. speijeri in banana. The phylogenetic analysis corroborated the Pratylenchus species identity with exceptions of sequences from 1) banana, grouped to P. coffeae complex group, 2) sugar cane, grouped to P. hippeastri complex group 3) onion and potato were related with P. crenatus, in an independent group, and 4) leather-leaf fern and potato were grouped with P. bolivianus with low resolution. Conclusions. Nine genetic groups of Pratylenchus were found, some of those should be verified with other molecular markers to get a conclusive identification.
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