Plant-Parasitic Nematodes Are Potential Pathogens of Miscanthus × giganteus and Panicum virgatum Used for Biofuels

Influence of the Environment and Vegetable Cropping Systems on Plant-Parasitic Nematode Communities in Southern Georgia

Plant-parasitic nematodes (PPN) limit yields of vegetable production in the United States. During the spring and fall cropping seasons of 2018, 436 fields in bare ground and plastic bed cropping systems were randomly sampled from 29 counties in southern Georgia. The incidence (%), mean relative abundance, and maximum relative abundance (nematodes per 100 cm³ of soil) of the 10 different PPN genera detected in 32 vegetable crops in bare ground and plastic bed cropping systems include Meloidogyne spp. (67.3%; mean, 292; maximum, 14,144), Nanidorus spp. (49.4%; mean, 6; maximum, 136), Mesocriconema spp. (39.6%; mean, 17; maximum, 340), Helicotylenchus spp. (31.6%; mean, 20; maximum, 1152), Pratylenchus spp. (20.1%; mean, 2; maximum, 398), Rotylenchulus spp. (5.9%; mean, 1; maximum, 116), Hoplolaimus spp. (12.6%; mean, 1; maximum, 78), Heterodera spp. (2.3%; mean, <1; maximum, 60), Tylenchorhynchus spp. (0.9%; mean, <1; maximum, 12), and Xiphinema spp. (0.2%; mean, <1; maximum, 2). A nonmetric multidimensional scaling analysis indicated that most environmental and geological factors (i.e., longitude, precipitation, soil moisture, sand and silt content, and soil electrical conductivity) had no apparent relationship with nematode counts, except for latitude, soil pH, and temperature. The multirank permutation procedure followed by indicator species analysis and nonparametric Kruskal-Wallis analysis of variance indicated that Meloidogyne spp. are the predominant PPN associated with plastic beds in the south region sampled. The south region consisted mainly of commercial fields that rotated multiple vegetables crops through the same plastic beds. All other PPNs were associated with bare ground beds in the north region that are commonly rotated with row crops. This study validates that Meloidogyne spp. are the most important PPN in vegetable fields of southern Georgia and suggests that cropping systems have a greater effect on PPN population dynamics than the environment.

First record of the ectoparasitic nematode Amplimerlinius macrurus (Nematoda: Tylenchida) on the perennial grass Miscanthus × giganteus (Angiosperms: Poaceae) in Ukraine

The growing interest in biomass production of Miscanthus × giganteus (M × g) (Poaceae) on agricultural and marginal lands has prompted researches to identify plant pathogens and diseases affecting this crop which has a great potential for production of biofuels and different bioproducts. A soil survey of nematodes in the M × g rhizosphere and a report on the collection of the plant-parasitic nematode Amplimerlinius macrurus (Belonolaimidae) were accomplished in two locations in Ukraine. It is known that this family of nematodes can reduce the root system and biomass of Poaceae family plants. Both molecular and morphological characters were used to identify the nematodes; measurements and photomicrographs of the species were presented. This is the first documentation and description of A. macrurus in Ukraine to the best of our knowledge. Further investigation is underway to confirm the pathogenicity of this species on perennial grasses plantations.

Breeding Targets to Improve Biomass Quality in Miscanthus

Lignocellulosic crops are attractive bioresources for energy and chemicals production within a sustainable, carbon circular society. Miscanthus is one of the perennial grasses that exhibits great potential as a dedicated feedstock for conversion to biobased products in integrated biorefineries. The current biorefinery strategies are primarily focused on polysaccharide valorization and require severe pretreatments to overcome the lignin barrier. The need for such pretreatments represents an economic burden and impacts the overall sustainability of the biorefinery. Hence, increasing its efficiency has been a topic of great interest. Inversely, though pretreatment will remain an essential step, there is room to reduce its severity by optimizing the biomass composition rendering it more exploitable. Extensive studies have examined the miscanthus cell wall structures in great detail, and pinpointed those components that affect biomass digestibility under various pretreatments. Although lignin content has been identified as the most important factor limiting cell wall deconstruction, the effect of polysaccharides and interaction between the different constituents play an important role as well. The natural variation that is available within different miscanthus species and increased understanding of biosynthetic cell wall pathways have specified the potential to create novel accessions with improved digestibility through breeding or genetic modification. This review discusses the contribution of the main cell wall components on biomass degradation in relation to hydrothermal, dilute acid and alkaline pretreatments. Furthermore, traits worth advancing through breeding will be discussed in light of past, present and future breeding efforts.

First Report of Stubby-Root Nematode, Paratrichodorus minor, on Onion in Georgia, U.S.A

Onions ( Allium cepa L.) are the leading vegetable crop in Georgia accounting for 13.7% of total state vegetable production ( Wolfe and Stubbs, 2017 ). In November 2017, two samples each of onion (var. Candy Ann) seedlings and soil were received from the University of Georgia Cooperative Extension office in Tattnall County, GA. The samples were collected from a nursery fumigated with metam sodium and used for sweet onion transplant production. Symptoms of the damaged plants included stunted growth both in the root system and foliage, tip die-back of the leaves ( Fig. 1A,B ), and slight swelling at the tip of roots. Vermiform life stages from the soil samples were extracted using centrifugal-flotation technique ( Jenkins, 1964 ). On an average, 67 stubby-root nematodes per 100 cm 3 of soil were obtained. Additional two soil samples were collected from the nursery in December 2017 to confirm the presence of the nematode. On an average, 1 and 75 nematodes per 100 cm 3 of soil were recovered from areas with healthy and infested plants, respectively. Because the male individuals were not found in the soil samples, females were used for species identification. Morphological and molecular analyses of females ( Fig. 2A-C ) identified the species as Paratrichodorus minor (Colbran) Siddiqi; ( Decraemer, 1995 ). Nematode body shape was "cigar-shaped" with dorsally curved "onchiostyle" stylet Females had an oval-shaped vagina, vulva a transverse slit, and lateral body pores were absent. The measurements of females ( n = 20) included: body length 671.1 (570.1-785.3) µm; body width 32.5 (27.8-37.0) µm; onchiostyle 32.5 (31.1-34.8) µm; anterior end to esophagus-intestinal valve 117.6 (101.2-128.5) µm; a 21.5 (15.3-28.1) µm; b 5.2 (4.9-6.3) µm; V 52.9% (48.1-55.4%) µm; and vagina length 8.7 (7.8-10.7) µm. To confirm the identity of P. minor, DNA was extracted from single females ( n = 3) using Extract-N-Amp ™ Tissue PCR Kit (Sigma-Alredich Inc., St. Louis, MO). The partial 18S rRNA, the D2-D3 expansion segments of 28S rRNA, and ITS1 rDNA were amplified using primer pairs 360F (5' CTACCACATCCAAGGAAGGC 3')/932R (5' TATCTGATCGCTGTCGAACC 3'), D2A (5' ACAAGTACCGTGAGGGAAAGTTG 3')/D3B (5' TCGGAAGGAACCAGCTACTA 3'), and BL18 (5' CCCGTCGCTACTACCGATT 3')/5818 (5' ACGARCCGAGTGATCCAC 3'), respectively ( Riga et al., 2007 ; Duarte et al., 2010 ; Ye et al., 2015 ; Shaver et al., 2016 ). The obtained PCR fragments were purified using QIAquick Gel Extraction Kit (Qiagen Inc., Santa Clara, CA, USA), sequenced and deposited in the GenBank databases (18S rRNA: MG856931; 28S rRNA: MG856933; ITS1 rDNA: MH464152). The 18S rRNA, 28S D2-D3, and ITS1 rDNA sequences shared 99% similarity (100% coverage) with GenBank accessions of P. minor from California, Arkansas, and China (18S rRNA: JN123365; 28S D2-D3: JN123395; ITS1 rDNA: GU645811). In a pathogenicity test, five sweet onion seeds var. Pirate were planted (one per pot) in 11.5-cm-diameter polyethylene pots containing 1,000 cm 3 of equal parts of pasteurized field soil and sand, and then inoculated with 1,000 fresh P. minor . Plants were grown for 9 wk in a greenhouse at 25 ± 2°C prior to extraction of nematodes from soil. Plant roots were abbreviated and final population density of P. minor was 2,856 ± 104 per pot (285 nematodes/100 cm 3 of soil) confirming the nematode parasitism on onion. To our knowledge, this is the first report of P. minor parasitizing onion in Georgia. Stubby-root nematode ( Paratrichodorus sp.) has already been reported on corn, St. Augustine grass, and switchgrass in Georgia ( Heald and Perry, 1969 ; Davis and Timper, 2000 ; Mekete et al., 2011 ). In the U.S.A, P. minor is known to occur on diverse crops in most of the states ( Decraemer, 1995 ; CABI/EPPO, 2002 ). A survey of vegetable-producing areas in Georgia is currently under investigation to determine the distribution of this economically important nematode species. Figure 1Damage symptoms caused by stubby-root nematode Paratrichodorus minor on sweet onion in Georgia. A large area of stunted and chlorotic plant foliage (A); Infested seedlings with abbreviated roots and necrotic leaf tips (B). Figure 2Light microscopy micrographs showing morphological characters of stubby-root nematode, Paratrichodorus minor. Entire body (A), anterior end (B), and posterior region (C) of female nematode.

Development of a Damage Function Model for Pratylenchus penetrans on Corn

The lesion nematode Pratylenchus penetrans is a common pest of corn in the north-central United States. There are relatively few studies documenting the impact of Pratylenchus spp. on grain yield even though they are recognized as pests of corn and the target of commercial seed treatments. We adapted a component error modeling approach to develop a damage function for P. penetrans that included the influence of year and site in the yield loss relationship. Field data from six site-years was used to derive panel data consisting of all pairwise comparisons of the difference in nematode population densities and the associated proportional yield difference. Fourteen regression models of the relationship between proportional yield loss and the difference in nematode density were developed from soil and root assays at different corn growth stages. Seven models were significant: four models based on nematode population densities in soil (initial and final samples) and three based on nematode densities in seminal roots (corn growth stages V1 to V2 and V6) and adventitious roots (corn growth stage R1 to R2). The model we consider to be the most important, that based on the initial soil assay, estimated the yield loss caused by each nematode to be 0.0142%. The grand mean of the 118 plots we sampled implied a yield loss of 3.79%. The random effects of year and field did not contribute significantly to any of the models but were close to significance for some, suggesting a benefit from larger data sets. Experimental error was the largest component of the variance for all of the models; therefore, the damage function is more useful for demonstrating impact of P. penetrans rather than for accurately predicting yield loss at the field level. All of the fields in our study were an irrigated loamy sand soil, with grain yields above the county average; therefore, it is possible that our damage function is conservative. The value of soil sampling has been questioned for P. penetrans and this study shows it to be equal to if not better than root assays for predicting yield.

Multi-Year Pathogen Survey of Biofuel Switchgrass Breeding Plots Reveals High Prevalence of Infections by Panicum mosaic virus and Its Satellite Virus

Switchgrass (Panicum virgatum) cultivars are currently under development as lignocellulosic feedstock. Here we present a survey of three established switchgrass experimental nurseries in Nebraska in which we identified Panicum mosaic virus (PMV) as the most prevalent virus. In 2012, 72% of 139 symptomatic plants tested positive for PMV. Of the PMV-positive samples, 19% were coinfected with its satellite virus (SPMV). Less than 14% of all sampled plants in 2012 were positive for four additional viruses known to infect switchgrass. In 2013, randomized sampling of switchgrass individuals from the same 2012 breeding plots revealed that infection by PMV or PMV+SPMV was both more prevalent and associated with more severe symptoms in the cultivar Summer, and experimental lines with Summer parentage, than populations derived from the cultivar Kanlow. A 3-year analysis, from 2012 to 2014, showed that previously uninfected switchgrass plants acquire PMV or PMV+SPMV between harvest cycles. In contrast, some plants apparently did not maintain PMV infections at detectable levels from year-to-year. These findings suggest that PMV and SPMV should be considered important pathogens of switchgrass and serious potential threats to biofuel crop production efficiency.