Diversity and phylogenetic relationships within the spiral nematodes of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as inferred from analysis of the D2-D3 expansion segments of 28S rRNA gene sequences
Subbotin S.A.,Plant Pest Diagnostic Center |
Subbotin S.A.,RAS Severtsov Institute of Ecology |
Inserra R.N.,DPI |
Marais M.,ARC Plant Protection Research Institute |
And 6 more authors.
Nematology | Year: 2011
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. © 2011 Brill.
Van Den Berg E.,ARC Plant Protection Research Institute |
Yeates G.W.,P.O. Box 1758 |
Navas-Cortes J.A.,CSIC - Institute for Sustainable Agriculture |
Ploeg A.T.,University of California at Riverside |
And 6 more authors.
Nematology | Year: 2013
Scutellonema spp. are widely distributed across tropical and subtropical regions of the world and are associated with numerous agricultural and horticultural crops. Identification of many Scutellonema species is not always reliable, in part because many species share very similar diagnostic characters. In this study, we provide morphological and molecular characterisation of S. brachyurus from the USA and South Africa, S. bradys from Nigeria and three unidentified species from California, USA, New Zealand and Burkina Faso. Morphological descriptions, measurements, light and scanning electron microscopic photos and drawings are given for S. brachyurus. Females of S. brachyurus from the USA (type A) and South Africa (type B) showed a significant variation in the number of sectors and blocks on the lip annuli, ranging from about 4-12 and from 8-20, respectively. Molecular analysis using the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences revealed two distinct genotypes within S. brachyurus samples: type A (samples from USA, Italy, Korea, Taiwan) and type B (South Africa). Multivariate analyses determined that S. brachyurus from the USA and Taiwan (type A) differed from that from South Africa (type B) mainly in body, tail and DGO lengths, and ratios b′, c′, c and V. Phylogenetic relationships within Scutellonema are given as inferred from the analyses of the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences. PCR-RFLP diagnostic profiles and PCR with species-specific primers are developed for the studied Scutellonema species. © 2013 Koninklijke Brill NV, Leiden.
Yeates G.W.,PO Box 1758 |
Zhao Z.Q.,Landcare Research
New Zealand Entomologist | Year: 2012
Four species of New Zealand Nematoda are considered Nationally Threatened: Three are Nationally Critical (Contracaecum eudyptes (Ascarididae), Longidorus waikouaitii (Longidoridae), Radopholus cavenessi (Pratylenchidae)) and one (Cosmocerca archeyi (Cosmocercidae)) is Nationally Vulnerable. Three species are At Risk, comprising two that are Declining (Aplectana novaezelandiae, Cosmocerca australis (Cosmocercidae)) and one that is Recovering (Hatterianema hollandei (Heterakidae)). A further 136 taxa are Introduced and Naturalised, 10 species are Vagrant, and 509 taxa are Not Threatened. © 2012 The Entomological Society of New Zealand.
Subbotin S.A.,Plant Pest Diagnostic Center |
Subbotin S.A.,RAS A.N. Severtsov Institute of Ecology and Evolution |
Chitambar J.J.,Plant Pest Diagnostic Center |
Chizhov V.N.,RAS A.N. Severtsov Institute of Ecology and Evolution |
And 11 more authors.
Zoological Journal of the Linnean Society | Year: 2014
The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant-parasitic nematodes, collectively known as 'sheath nematodes'. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2-D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR-restriction fragment length polymorphisms (PCR-RFLPs) of the D2-D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2-D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira-Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far. © 2014 The Linnean Society of London.
Schon N.L.,Massey University |
Mackay A.D.,Agresearch Ltd. |
Yeates G.W.,PO Box 1758 |
Minor M.A.,Massey University
Applied Soil Ecology | Year: 2010
The impact on soil invertebrates of changes in the physical environment and feed availability in intensive pastoral systems is difficult to predict given the number of interacting factors. This study explores the influence of a change in defoliation regimes (pastoral fallow, cut and carry, cow grazing), feed type and availability to ruminants (pasture and pasture supplemented with maize) and dairy cow stocking rates (3, 4 and 5 cowsha-1) on the abundance and diversity of soil invertebrates (macrofauna, mesofauna and microfauna). Samples were collected from two depths (0-7.5 and 7.5-15cm) on a well-structured loamy Andosol soil in two seasons (autumn and winter). Treatments allowed an independent assessment of the influence of changes in food sources to the soil food-web from that of physical disturbance from livestock treading.There was a clear distinction in habitable pore space between the fallow and other treatments. The high porosity under fallow (28% under fallow vs. 11-13% under other treatments) appears to be an important factor, increasing faunal abundance and biomass, including macrofaunal predators and Oribatida. Large inputs of litter under fallow benefited epigeic earthworms and resulted in a dominance of bacterial-feeding nematodes (Nematode Channel Ratio 0.97), reflecting the still high quality litter from previous management. Grazed pastures had higher abundances of plant-feeding and plant-associated nematodes as they were stimulated by increased root growth (abundances up to 1.2×106indm-2). While there was little difference in total earthworm abundance between treatments, anecic A. longa became progressively more abundant under higher cow stocking rates as food availability and physical pressure increased (18indm-2 vs. 128indm-2, under 3 and 5 cowsha-1, respectively). Initial earthworm functional diversity is important and we suggest that anecic earthworms can substitute for epigeic earthworms in intensively managed pastoral systems by incorporating litter, as well as being important ecosystem engineers. © 2010 Elsevier B.V.
Wardle D.A.,Swedish University of Agricultural Sciences |
Jonsson M.,Umeå University |
Kalela-Brundin M.,Museum of Forestry |
Lagerstrom A.,Swedish University of Agricultural Sciences |
And 3 more authors.
Ecology | Year: 2012
Despite the likely importance of inter-year dynamics of plant production and consumer biota for driving community- and ecosystem-level processes, very few studies have explored how and why these dynamics vary across contrasting ecosystems. We utilized a well-characterized system of 30 lake islands in the boreal forest zone of northern Sweden across which soil fertility and productivity vary considerably, with larger islands being more fertile and productive than smaller ones. In this system we assessed the inter-year dynamics of several measures of plant production and the soil microbial community (primary consumers in the decomposer food web) for each of nine years, and soil microfaunal groups (secondary and tertiary consumers) for each of six of those years. We found that, for measures of plant production and each of the three consumer trophic levels, inter-year dynamics were strongly affected by island size. Further, many variables were strongly affected by island size (and thus bottom-up regulation by soil fertility and resources) in some years, but not in other years, most likely due to inter-year variation in climatic conditions. For each of the plant and microbial variables for which we had nine years of data, we also determined the inter-year coefficient of variation (CV), an inverse measure of stability. We found that CVs of some measures of plant productivity were greater on large islands, whereas those of other measures were greater on smaller islands; CVs of microbial variables were unresponsive to island size. We also found that the effects of island size on the temporal dynamics of some variables were related to inter-year variability of macroclimatic variables. As such, our results show that the inter-year dynamics of both plant productivity and decomposer biota across each of three trophic levels, as well as the inter-year stability of plant productivity, differ greatly across contrasting ecosystems, with potentially important but largely overlooked implications for community and ecosystem processes. © 2012 by the Ecological Society of America.
St.John M.G.,Landcare Research |
Bellingham P.J.,Landcare Research |
Walker L.R.,University of Nevada, Las Vegas |
Orwin K.H.,Lancaster University |
And 5 more authors.
Journal of Ecology | Year: 2012
1. Many ecosystems are gaining some species and losing others, leading to large shifts in community composition. Plants that support nitrogen (N)-fixing symbionts (hereafter N-fixers) are major ecosystem drivers but human-induced environmental changes can lead to their loss; the impacts of this loss have seldom been studied. In New Zealand, the gain of some invasive herbivorous mammals leads to the loss of N-fixing shrubs that are pioneers during primary succession. 2. We studied primary successional surfaces caused by river floods and landslides in a remote valley in New Zealand's South Island. We set up and maintained a removal experiment over 10 years, with N-fixing Carmichaelia odorata (hereafter Carmichaelia) either left intact or removed to represent the effects that invasive herbivorous mammals could cause under high densities. 3. Above-ground effects of 10 years of Carmichaelia removal included a 7-fold reduction of woody plant biomass, but had no effect on the shorter non-woody vegetation. Foliar N concentrations of two woody species were also reduced. Carmichaelia removal reduced local or α-diversity but enhanced β-diversity of the remaining vegetation at the functional group but not the species level. 4. Below-ground effects of 10 years of Carmichaelia removal included large reductions in soil carbon (C) and N levels, and biomass or abundance of several groups of soil biota occupying three consumer trophic levels as well as the root-, bacterial- and fungal-based energy channels. Invertebrate bacterial consumers were more adversely affected than were fungal consumers. Carmichaelia loss reduced α-diversity of some below-ground groups, while β-diversity was unresponsive or enhanced. 5. Synthesis. Our results reveal that loss of a single functionally distinct plant species, such as occurs through herbivore invasion, can cause substantial effects both above-ground and below-ground. This may affect the trajectory of the ecosystem over successional time, especially in primary seres that otherwise have very low soil carbon (C) and nitrogen (N) reservoirs. More generally, our results support the view that the simultaneous gains of some organisms (e.g. invasive herbivorous mammals) and resultant losses of others (e.g. palatable N-fixing plants) are a major element of human-induced global change that may be transforming many communities and ecosystems world-wide. Our results reveal that loss of a single functionally distinct plant species, such as occurs through herbivore invasion, can cause substantial effects both above-ground and below-ground. This may affect the trajectory of the ecosystem over successional time, especially in primary seres that otherwise have very low soil carbon (C) and nitrogen (N) reservoirs. More generally, our results support the view that the simultaneous gains of some organisms (e.g. invasive herbivorous mammals) and resultant losses of others (e.g. palatable N-fixing plants) is a major element of human-induced global change that may be transforming many communities and ecosystems worldwide. © 2012 British Ecological Society.