Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities

Schenk J, Kleinbölting N, Traunspurger W. Comparison of morphological, DNA barcoding, and metabarcoding characterizations of freshwater nematode communities. Ecology and Evolution. 2020;10(6): ece3.6104.Biomonitoring approaches and investigations of many ecological questions require assessments of the biodiversity of a given habitat. Small organisms, ranging from protozoans to metazoans, are of great ecological importance and comprise a major share of the planet's biodiversity but they are extremely difficult to identify, due to their minute body sizes and indistinct structures. Thus, most biodiversity studies that include small organisms draw on several methods for species delimitation, ranging from traditional microscopy to molecular techniques. In this study, we compared the efficiency of these methods by analyzing a community of nematodes. Specifically, we evaluated the performances of traditional morphological identification, single-specimen barcoding (Sanger sequencing), and metabarcoding in the identification of 1500 nematodes from sediment samples. The molecular approaches were based on the analysis of the 28S ribosomal large and 18S small subunits (LSU and SSU). The morphological analysis resulted in the determination of 22 nematode species. Barcoding identified a comparable number of operational taxonomic units (OTUs) based on 28S rDNA (n = 20) and fewer OTUs based on 18S rDNA (n = 12). Metabarcoding identified a higher OTU number but fewer amplicon sequence variants (AVSs) (n = 48 OTUs, n = 17 ASVs for 28S rDNA, and n = 31 OTUs, n = 6 ASVs for 18S rDNA). Between the three approaches (morphology, barcoding, and metabarcoding), only three species (13.6%) were shared. This lack of taxonomic resolution hinders reliable community identifications to the species level. Further database curation will ensure the effective use of molecular species identification

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

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

18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences

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

Description of Tobriloides loofi n. sp. from natal, South Africa (Nematoda: Onchulidae)

Tobriloides loofi n. sp. has a huge cardia, three whorls of cephalic setae and an onchulid structure of the posterior oesophagus, which place it in the rare genus Tobriloides Loof, 1973. It differs mainly from the only other species in this genus, Tobriloides choii Loof, 1973, in its large size, the presence of males in T. loofi and the position of the vulva (midbody in T. loofi and more posterior in T. choii). This is the first description of a member of the genus Tobriloides from South Africa, as well as the first record of a new species within this genus in 16 years. Line drawings, light- and scanning electron micrographs are included in the text, as well as a short discussion of intergenus relationships of Tobriloides

Nematoden als indicator voor de waterkwaliteit

Het beoordelen van de waterkwaliteit is een lastige zaak. Vaak wordt de chemische kwaliteit bepaald, maar eigenlijk willen we weten welke effecten die heeft op de biologische kwaliteit. Veld- en microscopisch onderzoek aan biologische indicatoren is bewerkelijk en bovendien zijn de resultaten niet eenduidig. Met de ontwikkeling van DNA-analysetechnieken is het mogelijk geworden nematoden in de waterbodem snel en accuraat te analyseren. Nematoden zijn kleine aaltjes (lengte 0,3 tot 1,0 mm) die in grote aantallen en met een aanzienlijke diversiteit in de waterbodem aanwezig zijn. De combinatie van hoge dichtheden en grote verscheidenheid maakt de nematodengemeenschap tot potentiële bio-indicator voor de waterkwaliteit. Een pilot liet zien dat DNA-analyse van nematoden in de waterbodem duidelijke signalen van eutrofiëring aangaf en daarmee inzicht gaf in de waterkwaliteit

Effects of drought-induced stress on nematode communities in aquatic and terrestrial habitats of the Nebraska Sandhills

IntroductionGlobal change events (e.g., worsening drought) are increasing environmental stress in a variety of terrestrial and aquatic habitats. The degree to which communities in soils and sediments are driven by temporal environmental changes across multiple habitat types from the same region is not clear.MethodsWe used nematodes, a common bioindicator of soil and sediment health, to determine how community diversity and composition are altered by rising alkalinity across lakes, shorelines, and prairies in the western Nebraska Sandhills. We sampled these three habitats from five lake basins spanning an alkalinity gradient (pH 7–11) across three years (2019, 2020, 2021). During our sampling, the Sandhills experienced a range of drought intensities, with 2019 being a wet year, followed by severe drought in 2020, and abnormally dry/moderate drought in 2021. To determine if diversity and composition of nematodes responded to increased alkalinity and drought-induced stress we used different modelling approaches, including Random Forest and pairwise comparisons.Results and discussionOverall, nematode diversity in lakes was most affected by increasing alkalinity over time, whereas in shorelines and prairies diversity was most reliant on bacterial diversity and potential nematode-nematode interactions. In comparison to shorelines and prairies, community composition in lakes was the least variable and consistently driven by pH and lake water levels. In contrast, compositions in the shorelines and prairies were more variable and explained at varying degrees by pH, year, lake basin, and climate-associated variables. In addition, relative abundance and compositional nature of select copious taxa were highly unpredictable, indicating potential instability in these habitats. Future research is necessary to address the ecologic stability of the Sandhills and determine where conservation efforts are most needed

Description of Caprionchulus diversipapillatus n.gen., n.sp. from Caprivi, Namibia (Nematoda: Onchulinae)

Caprionchulus diversipapillatus n.gen, n.sp. was found in a small fresh-water pond in eastern Caprivi. The new genus differs from all other genera within the subfamily Onchulinae Andrássy, 1963 in the almost barrel- shaped stoma containing a single dorsal tooth, an elongated cardia comprising three vertical rows of four cells each and peculiar supplements consisting of two conspicuous adanal setae and a row of six to eight papilloid supplements, the last four of which are in pairs. The spicule shape is also different from other members of the Onchulinae

Soil Invertebrates (Nematoda, Acari : Oribatei, Collembola) of Codri Forest Reserve (Special Papers in Honor of late Professor Ryozo Yoshii)

We investigated the diversity of soil nematodes and microarthropods in oak, beech, lime-ash, oak-hornbeam, maple-hornbeam and mixed forests of the Codri Reserve. 339 species including 143 species of nematodes, 88 species of oribatei and 108 spe-cies of Collembola were found. Eight new species of nematodes and Collembola were de-scribed

Видове різноманіття вільноіснуючих нематод (nematoda) канівського водосховища

Нематоди – одна з найчисельніших груп організмів водних екосистем. Видове різноманіття вільноіснуючих нематод залежить, в основному, від типу водойми та її розмірів. У великих водосховищах фауна представлена 150–200 видами круглих червів, у мілких водоймах – обмежена 5–15 видами. У найбільших водоймах існує велика кількість ценозів, які формують різноманітні екологічні комплекси нематод. Характеризуючись великою чисельністю (1–2 млн. екз./м2) та швидкістю розмноження, нематоди приймають активну участь у мінералізації органічних речовин, утворюють значні трофічні ресурси для компонентів макробентосу та молоді риб. Крім того, деякі групи нематод досить чутливі до якості водного середовища. До теперішнього часу залишається мало вивченою фауна та екологія вільноіснуючих нематод прісних водойм України та, зокрема, зовсім відсутні дані щодо сучасного видового складу нематод Канівського водосховища – наймолодшого з каскаду дніпровських водосховищ