Aquatic nematodes from Ethiopia III

Six species of the genus Eumonhystera, one of which is new to science, are described from bottom samples of Lake Tana and two associated rivers, River Abbay and R. Gelda, Ethiopia. E. geraerti n.sp. can be identified by being the only species in the genus that combines very posteriorly positioned vulva [V% = 68.2 ± 0.7 (67.3–69.3)] with very anteriorly positioned amphids (Amph-ABE/LRW = 0.8). The other five species encountered, E. dispar (Bastian, 1865) Andrássy, 1981, E. filiformis (Bastian, 1865) Andrássy, 1981, E. pseudobulbosa (von Daday, 1896) Andrássy, 1981, E. mwerazii (Meyl, 1957) Andrássy, 1981, and E. vulgaris (de Man, 1880), Andrássy, 1981, are described in detail. The identities of some of the already described populations of E. dispar, E. filiformis and E. vulgaris are questioned and clearer and better ways of defining each of these three species are suggested. A peritrophic-like membrane on the outer side of the brush-border of the intestine of E. mwerazii, a species reported here for the first time out of its type locality, is reported. Also, scanning electronmicrographs of sectioned and entire specimens of E. mwerazii are presented. All species are reported from Ethiopia for the first time.     

Defining operational taxonomic units using DNA barcode data

The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.     

Aquatic nematodes from Ethiopia VII

Three species of Rhabdolaimus de Man, 1880 and two (of which one is new to science) of Udonchus Cobb, 1913 are described from sediment samples of two lakes, two rivers and a hot spring, Ethiopia. Udonchus merhatibebi n.sp. is characterized by a distinctly truncate lip region and small cardia surrounded by gland cells that he on the anterior intestine at 45 °. The presence of twelve rugae in the cheilostome in the genus Udonchus is reported here for the first time. As a result, the family Rhabdolaimidae has been moved from suborder Leptolaimina to the superfamily Microlaimoidea in the suborder Chromadorina. The family Rhabdolaimidae is also subdivided into the subfamilies Rhabdolaiminae Chitwood, 1951 and Undonchinae n. subfam.. Scanning electronmicroscopic pictures of the five species viz. R. aquaticus de Man, 1880, R. cf. minor Cobb, 1914, R. terrestris de Man, 1880, U. merhatibebi n.sp. and U. tenuicaudatus Cobb, 1913 are also given.Abbreviations ABE = anterior body end - ABW = anal body width - Amph = amphid - Amph W = amphidial fovea width - CBW = corresponding body width - GL = gonad length - G1L = anterior gonad length - G2L = posterior gonad length - L = length - LM = light microscope - LRW = lip region width - MBW = maximum body width - n = number of specimens - NR = nerve ring from the anterior end - Ph L = pharyngeal length (neck length) - RL = rectal length - SEM = scanning electron microscope - V-A = distance from vulva to anus - W = width     

Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae

Background

Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity.

Results

We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99 % sequence identity in rDNA sequence and orthology across 85.6 % of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8 %) were present in Serratia while 33 (84.6 %) and 35 (89 %) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively.

Conclusion

The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result – killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1697-8) contains supplementary material, which is available to authorized users.     

Thalassomonhystera traesti n.sp., Eumonhystera andrassyi and three Monhystrella species (Monhysteridae: Nematoda) from Li River, China

A new Thalassomonhystera species, i.e. T. traesti n.sp., and a new subspecies, Monhystrella lepidura chinensis n. subsp., together with Eumonhystera andrassyi (Biró, 1969) Andrássy, 1981, Monhystrella macrura (de Man, 1880) Andrássy, 1981 and Monhystrella iranica Schiemer, 1965 are described from Li River at Guiling, China. Thalassomonhystera traesti n.sp. is characterised by a combination of the following characters: expanded lip region, large and anteriorly situated amphids, prominent inner labial sensilla, and slender spicules and tube-like gubernaculum in males. Monhystrella lepidura chinensis n. subsp. belongs to Monhystrella lepidura (Andrássy, 1963) Andrássy, 1968 but differs from the three hitherto described subspecies in its possession of a pharynx that posteriorly expands into a double bulb. Monhystrella macrura, M. iranica and Eumonhystera andrassyiare reported here for the first time from China.     

Aquatic nematodes from Ethiopia II

Eight species of the genus Monhystrella, six of which are new to science, are described from bottom samples collected from three lakes, two rivers and a hot spring in Ethiopia. Monhystrella hoogewijsi n. sp. is identified by a distinctive bulge on the lip region, position of the amphids, offset and well developed single pharyngeal terminal bulb, tail shorter than vulva-anus distance, tail elongate-conoid for two-thirds of its length, and by the shape and size of the spinneret outlet; M. jacobsi n. sp. by its slender body, distinctively offset and distended lip region, indistinct and weakly expanding single terminal pharyngeal bulb, and shape and size of the tail and spinneret outlet; M. arsiensis n. sp. by its single terminal pharyngeal bulb, position of amphids, shape and length of tail and spinneret outlet; M. woitorum n. sp. by its hemispherical lip region, double terminal pharyngeal bulb, shape and length of the spinneret outlet, and shape and length of tail; M. ethiopica n. sp. by its bipartite stoma, size of amphid in relation to corresponding body width, filiform tail and shape and length of spinneret outlet. M. atteae n. sp. differs from all known Monhystrella species in having an inflated cap-like lip region and fine crystalloid bodies. M. macrura (de Man, 1880) Andrássy, 1981 and M. lepidura altherri (Juget, 1969) Jacobs, 1987 are reported from Ethiopia for the first time. Crystalloid bodies in the genus Monhystrella is reported here for the first time. Also the presence of a hyaline coelomocyte next to the germinal zone of the reproductive system is reported for the first time in the genus here in all eight species. The structures used in the taxonomy of the genus are reviewed.     

Global diversity of nematodes (Nematoda) in freshwater

Despite free-living nematodes being present in all types of limnetic habitats including unfavorable conditions that exclude many other meiobenthic invertebrates, they received less attention than marine and terrestrial forms. Two-fifths of the nematode families, one-fifth of the nearly 1800 genera and only 7% of the about 27,000 nominal species are recorded from freshwater habitats. The Dorylaimia are the most successful in freshwater habitats with nearly two-thirds of all known freshwater nematodes belonging to this subclass. Members of the subclass Enoplia are principally marine though include some exclusively freshwater taxa with extreme endemism. The subclass Chromadoria includes half of the freshwater nematode families and members of the Monhysterida and Plectida are among the most widely reported freshwater nematodes. Studies on freshwater nematodes show extreme regional bias; those from the southern hemisphere are extremely underrepresented, especially compared to European freshwater bodies. The majority of records are from a single biogeographic region. Discussion on nematode endemism is largely premature since apart from Lake Baikal, the nematofauna of ancient lakes as centers of speciation is limited and recent discoveries show high nematode abundance and diversity in cryptic freshwater bodies, underground calcrete formations and stromatolite pools potentially with a high number of new taxa. Guest editors: E.V. Balian, C. Lèvêque, H. Segers & K. Martens Freshwater Animal Diversity Assessment     

Molecular barcodes for soil nematode identification

Using a molecular barcode, derived from single-specimen polymerase chain reaction (PCR) and sequencing of the 5' segment of the small subunit ribosomal RNA (SSU) gene, we have developed a molecular operational taxonomic unit (MOTU) scheme for soil nematodes. Individual specimens were considered to belong to the same MOTU when the sequenced segment of 450 bases was > 99.5% identical. A Scottish upland Agrostis-Festuca grassland soil was sampled, using both culture-based and random selection methods. One hundred and sixty-six cultured isolates were sequenced, and clustered into five MOTU. From 74 randomly sampled individuals across the study site, 19 MOTU were defined. A subsequent sample of 18 individuals from a single subplot contained eight MOTU, four of which were unique to the single subplot sample. Interestingly, seven of these MOTU were not present in the culture-independent sampling. Overall, a total of 23 MOTU were defined from only 240 sequences. Many MOTU could readily be assigned to classical, morphologically defined taxonomic units using a database of SSU sequences from named nematode species. The MOTU technique allows a rapid assessment of nematode taxon diversity in soils. Correlation with a database of sequences from known species offers a route to application of the technique in ecological surveys addressing biological as well as genetic diversity.