Low genetic but high morphological variation over more than 1000 km coastline refutes omnipresence of cryptic diversity in marine nematodes

A catalogue of the nematode slide collection from the late W.L. Nicholas held at National Research Collections Australia, CSIRO

A catalogue is presented of the nematode slide collection of W.L. Nicholas, which is deposited in the National Research Collections Australia at CSIRO. This is the most extensive slide collection of free-living marine and estuarine nematodes from Australia to date, and consists of 553 putative species, collected across a wide range of Australias eastern and northern regions over the course of nearly 40 years. The collection contains mostly marine and estuarine free-living nematodes collected on coarse substrate in littoral habitats. The most abundant genera were Desmodora, Theristus, and Onyx. Most taxa were found rarely, being recorded only once, and repeated sampling at several sandy beach sites revealed only a small proportion of the fauna on more than one occasion. A significant proportion of the taxa were also found to be widespread, occurring on more than one occasion at more than one location, with Theristus sp., Onyx sp., and Viscosia sp. occurring in the greatest number of localities. The catalogue adds an additional 90 species and 160 genera to the documented fauna of Australian free-living nematodes verifiable by specimens in permanent collections. It thus provides a better framework for studying nematode biodiversity and biogeography in the region.

Two new species of Cyatholaimidae (Nematoda: Chromadorida) from the Southeastern Brazilian coast with emphasis on the pore complex and lateral pore-like structures

Cyatholaimidae is a common and diverse family of mainly marine nematodes, potentially, with a large number of species to be discovered. The taxonomy of the group is marked by a lack of information about the evolutionary history of the characters and of detailed descriptions of morphological structures that may be taxonomically relevant. Two new species of the family are described from a sublittoral region in Southeastern Brazil, emphasizing the importance of the distribution and morphology of pore complex and pore-like structures present on the cuticle. The taxonomic importance of the cuticle ornamentation and spicule shape for the Biarmifer species, as well as the precloacal supplements structures of Pomponema species, are discussed. Biarmifer nesiotes sp. nov. differs from other species of the genus by the presence of eight longitudinal rows of pore complex on the cuticle and by the shape of the copulatory structure. Pomponema longispiculum sp. nov. differs from the most similar species, P. stomachor Wieser, 1954, by the smaller number of turns of the amphidial fovea, the shorter tail and the beginning of the cuticle lateral differentiation (3/4 of the pharynx length vs. end of the pharynx, respectively). We also obtained the SSU rDNA sequence from Pomponema longispiculum sp. nov., which is closely related to Pomponema sp. (MN250093) by about 91%. Updated tabular keys to species identification of each genus (Biarmifer and Pomponema) are included, containing morphometric data, characters related to cuticle ornamentation, and copulatory structures.

Molecular Character of Mylonchulus hawaiiensis and Morphometric Differentiation of Six Mylonchulus (Nematoda; Order: Mononchida; Family: Mylonchulidae) Species Using Multivariate Analysis

Mononchida members are predatory nematodes with the potential to reduce the number of plant-parasitic nematodes in the soil. During a survey on Mononchida in Iran, several populations of Mylonchulus were recovered from various localities. A population of M. hawaiiensis was studied using 18S rDNA. The phylogenetic analysis using Bayesian inference placed the sequenced M. hawiinesis (OP210758) together with other M. hawaiiensis from Japan (AB361438-AB361442) with a 1.00 posterior probability support. In addition, morphological differences between six Mylonchulus (Nematoda; order: Mononchida; Family: Mylonchulidae) populations were investigated in Iran using discriminant analyses (DA), PERMANOVA, and principal coordinate analysis (PCoA). The purpose was to evaluate the efficacy of PCoA and DA in separating the Mylonchulus species, namely M. sigmaturus, M. paitensis, M. lacustris, M. brachyuris, M. kermaninesis, and M. hawaiiensis. To achieve this, 16 morphometric measurements (body length, a, b, c, c′, V, G1, G2, buccal cavity length, buccal cavity width, dorsal tooth apex, dorsal tooth length, neck length, amphid from anterior end, rectum, and tail length) were made on 160 specimens. The analysis of variance showed that all features were significantly different among the species, except a, b, and the amphid position from the anterior end and tail length. The stepwise discriminant analysis revealed that body length, tail length, neck length, and c′ value were the four most discriminating variables useful to distinguish clearly the six species of Mylonchulus. The variables with strong discriminatory power correctly classified 98.87% of individuals from Iran’s sample of known Mylonchulus species. The results provide a morphometric basis for effectively distinguishing Mylonchulus species.

Phylum Nematoda: trends in species descriptions, the documentation of diversity, systematics, and the species concept

This paper summarizes the trends in nematode species description and systematics emerging from a comparison of the latest comprehensive classification and census of Phylum Nematoda (Hodda 2022a, b) with earlier classifications (listed in Hodda 2007).   It also offers some general observations on trends in nematode systematics emerging from the review of the voluminous literature used to produce the classification.   The trends in nematodes can be compared with developments in the systematics of other organisms to shed light on many of the general issues confronting systematists now and into the future.  

Meloidogyne graminicola-A Threat to Rice Production: Review Update on Distribution, Biology, Identification, and Management

Simple Summary

New risks to plant health are constantly emerging. Such is the case of the rice root knot nematode Meloidogyne graminicola, adapted to flooded conditions and representing a risk to all types of rice agro-systems. It has been recently detected in Italy and added to the European and Mediterranean Plant Protection Organization (EPPO) Alert List. The presence of this nematode in Europe poses a threat to rice production, as there is a high probability to spread, due to trade activities and climate changes. In view of its importance, an extensive updated review was carried out.

Abstract

Rice (Oryza sativa L.) is one of the main cultivated crops worldwide and represents a staple food for more than half of the world population. Root-knot nematodes (RKNs), Meloidogyne spp., and particularly M. graminicola, are serious pests of rice, being, probably, the most economically important plant-parasitic nematode in this crop. M. graminicola is an obligate sedentary endoparasite adapted to flooded conditions. Until recently, M. graminicola was present mainly in irrigated rice fields in Asia, parts of the Americas, and South Africa. However, in July 2016, it was found in northern Italy in the Piedmont region and in May 2018 in the Lombardy region in the province of Pavia. Following the first detection in the EPPO region, this pest was included in the EPPO Alert List as its wide host range and ability to survive during long periods in environments with low oxygen content, represent a threat for rice production in the European Union. Considering the impact of this nematode on agriculture, a literature review focusing on M. graminicola distribution, biology, identification, and management was conducted.

Incidence of the Rice Root-Knot Nematode, Meloidogyne graminicola, in Guangxi, China

Root-knot nematodes (Meloidogyne spp.) are the most destructive group of plant-parasitic nematodes. Plants infected by Meloidogyne spp. develop above-ground symptoms, stunting, yellowing, nutrient deficiencies, and gall formations with typical hook-shaped root tips. Infected plants experience yield losses. During 2018-2019 survey, leaf chlorosis rice plants were found in 206 fields of 67 counties in Guangxi, China, around 30 days after transplanting. Galls and hooked tips on the roots and pear-shaped females were observed. About 32.04% of fields were infested with the nematode. The nematodes were identified as Meloidogyne graminicola base on morphological and molecular analysis. To the best of our knowledge, this is the first report of M. graminicola on rice plants in Guangxi, China. The results of this study urge the discovery of resistant cultivars and the development of management strategies.

The identification of sympatric cryptic free-living nematode species in the Antarctic intertidal

The diversity of free-living nematodes in the beaches of two Antarctic islands, King George and Deception islands was investigated. We used morphological and molecular (LSU, and two fragments of SSU sequences) approaches to evaluate 236 nematodes. Specimens were assigned to at least genera using morphology and were assessed for the presence of cryptic speciation. The following genera were identified: Halomonhystera, Litoditis, Enoploides, Chromadorita, Theristus, Oncholaimus, Viscosia, Gammanema, Bathylaimus, Choanolaimus, and Paracanthonchus; along with specimens from the families Anticomidae and Linhomoeidae. Cryptic speciation was identified within the genera Halomonhystera and Litoditis. All of the cryptic species identified live sympatrically. The two cryptic species of Halomonhystera exhibited no significant morphological differences. However, Litoditis species 2 was significantly larger than Litoditis species 1. The utility of molecular data in confirming the identifications of some of the morphologically more challenging families of nematodes was demonstrated. In terms of which molecular sequences to use for the identification of free-living nematodes, the SSU sequences were more variable than the LSU sequences, and thus provided more resolution in the identification of cryptic speciation. Finally, despite the considerable amount of time and effort required to put together genetic and morphological data, the resulting advance in our understanding of diversity and ecology of free-living marine nematodes, makes that effort worthwhile.

Morphological, Morphometric, and Molecular Characterization of Intraspecific Variations within Indian Populations of Meloidogyne graminicola

Fourteen populations of Meloidogyne graminicola were collected from different agroecological regions of India. Morphological and morphometrical comparisons were made for various nematode life stages. Three populations (Hisar, New Delhi, and Samastipur) were different from typical M. graminicola on the basis of the length of eggs; J2 length, a-value, hyaline tail portion; male length, distance up to excretory pore, spicule and gubernaculum lengths; female length and width, stylet length, distance up to excretory pore, EPST (distance of excretory pore from anterior end / stylet length [females]) ratio, and vulval length. Morphological and morphometrical comparison with closely related species M. graminis, M. oryzae, M. salasi, M. triticoryzae, and M. lini clustered these populations into two groups: Anand, Bhubaneswar, Hyderabad, Jammu, Jorhat, Kalyani, Kanpur, Ludhiana, Mandya, Palampur, Vellayani grouped with M. graminicola, M. triticoryzae and M. salasi; whereas, Hisar, New Delhi, Samastipur grouped with M. oryzae and M. graminis. Molecular phylogenetic analysis using internal transcribed spacer (ITS) suggested that in spite of morphological differences, these populations belonged to M. graminicola.

Population genetic structure in Sabatieria (Nematoda) reveals intermediary gene flow and admixture between distant cold seeps from the Mediterranean Sea

BACKGROUND

There is a general lack of information on the dispersal and genetic structuring for populations of small-sized deep-water taxa, including free-living nematodes which inhabit and dominate the seafloor sediments. This is also true for unique and scattered deep-sea habitats such as cold seeps. Given the limited dispersal capacity of marine nematodes, genetic differentiation between such geographically isolated habitat patches is expected to be high. Against this background, we examined genetic variation in both mitochondrial (COI) and nuclear (18S and 28S ribosomal) DNA markers of 333 individuals of the genus Sabatieria, abundantly present in reduced cold-seep sediments. Samples originated from four Eastern Mediterranean cold seeps, separated by hundreds of kilometers, and one seep in the Southeast Atlantic.

RESULTS

Individuals from the Mediterranean and Atlantic were divided into two separate but closely-related species clades. Within the Eastern Mediterranean, all specimens belonged to a single species, but with a strong population genetic structure (ΦST = 0.149). The haplotype network of COI contained 19 haplotypes with the most abundant haplotype (52% of the specimens) shared between all four seeps. The number of private haplotypes was high (15), but the number of mutations between haplotypes was low (1-8). These results indicate intermediary gene flow among the Mediterranean Sabatieria populations with no evidence of long-term barriers to gene flow.

CONCLUSIONS

The presence of shared haplotypes and multiple admixture events indicate that Sabatieria populations from disjunct cold seeps are not completely isolated, with gene flow most likely facilitated through water current transportation of individuals and/or eggs. Genetic structure and molecular diversity indices are comparable to those of epiphytic shallow-water marine nematodes, while no evidence of sympatric cryptic species was found for the cold-seep Sabatieria.

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments

Background

Dispersal ability, population genetic structure and species divergence in marine nematodes are still poorly understood, especially in remote areas such as the Southern Ocean. We investigated genetic differentiation of species and populations of the free-living endobenthic nematode genera Sabatieria and Desmodora using nuclear 18S rDNA, internal transcribed spacer (ITS) rDNA, and mitochondrial cytochrome oxidase I (COI) gene sequences. Specimens were collected at continental shelf depths (200–500 m) near the Antarctic Peninsula, Scotia Arc and eastern side of the Weddell Sea. The two nematode genera co-occurred at all sampled locations, but with different vertical distribution in the sediment. A combination of phylogenetic (GMYC, Bayesian Inference, Maximum Likelihood) and population genetic (AMOVA) analyses were used for species delimitation and assessment of gene flow between sampling locations.

Results

Sequence analyses resulted in the delimitation of four divergent species lineages in Sabatieria, two of which could not be discriminated morphologically and most likely constitute cryptic species. Two species were recognised in Desmodora, one of which showed large intraspecific morphological variation. Both genera comprised species that were restricted to one side of the Weddell Sea and species that were widely spread across it. Population genetic structuring was highly significant and more pronounced in the deeper sediment-dwelling Sabatieria species, which are generally less prone to resuspension and passive dispersal in the water column than surface Desmodora species.

Conclusions

Our results indicate that gene flow is restricted at large geographic distance in the Southern Ocean, which casts doubt on the efficiency of the Weddell gyre and Antarctic Circumpolar Current in facilitating circum-Antarctic nematode species distributions. We also show that genetic structuring and cryptic speciation can be very different in nematode species isolated from the same geographic area, but with different habitat preferences (surface versus deeper sediment layers).

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0968-1) contains supplementary material, which is available to authorized users.