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  • 1.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Adedidran, Funmilola
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    A draft transcriptome of a parasite Neocamacolaimus parasiticus (Camacolaimidae, Plectida)2021In: Journal of Nematology, E-ISSN 0022-300X, article id e2021Article in journal (Refereed)
  • 2.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology. Harper Adams University.
    Back, Matthew
    Prior, Thomas
    Karssen, Gerrit
    Lawson, Rebecca
    Adams, Ian
    Sapp, Melanie
    Metabarcoding of soil nematodes: the importance of taxonomiccoverage and availability of reference sequences in choosingsuitable marker(s)2019In: Metabarcoding and Metagenomics, Vol. 3, p. 77-99Article in journal (Refereed)
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  • 3.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Boström, Sven
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Revision of the genus Cobbionema Filipjev, 1922 (Nematoda, Chromadorida, Selachinematidae)2020In: European journal of taxonomy, E-ISSN 2118-9773, Vol. 702, p. 1-34Article in journal (Refereed)
    Abstract [en]

    This paper reports on the genus Cobbionema Filipjev, 1922 in Sweden with the description of four species and a revision of the genus. Cobbionema acrocerca Filipjev, 1922 is relatively small in size, with a tail that has a conical proximal and a digitate distal section. Cobbionema cylindrolaimoides Schuurmans Stekhoven, 1950 is similar to C. acrocerca in most characters except having a larger body size and heavily cuticularized mandibles. Cobbionema brevispicula sp. nov. is characterised by short spicules and a conoid tail. Cobbionema acuminata sp. nov. is characterised by a long two-part spicule, a conical tail and three (one mid dorsal and two ventrosublateral) sharply pointed tines in the anterior chamber of the stoma that are located more anterior than in all the other species. We also present a molecular phylogeny of the family based on the nearly full-length 18S and the D2-D3 expansion segment of the 28S rRNA genes. Maximum Likelihood and Bayesian trees inferred from both genes strongly support a clade that included Cobbionema, Demonema Cobb, 1894 and Halichoanolaimus de Man, 1888 and another clade with Gammanema Cobb, 1920 and Latronema Wieser, 1954 nested together. None of the trees supported the monophyly of the subfamilies Choniolaiminae and Selachinematinae.

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  • 4.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Boström, Sven
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Rik rundmaskfauna i Store Mosse nationalpark hittades med DNA-metastreckkodning2023In: Fauna och flora : populär tidskrift för biologi, ISSN 0014-8903, Vol. 118, no 2, article id 24-33Article in journal (Other (popular science, discussion, etc.))
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  • 5.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Description of a new marine predatory nematode Latronema dyngi sp. nov. (Nematoda, Chromadorida, Selachinematidae) from the west coast of Sweden and an updated phylogeny of Chromadoria2020In: Marine Biodiversity, ISSN 1867-1616, E-ISSN 1867-1624, Vol. 50, no 113, p. 1-11Article in journal (Refereed)
    Abstract [en]

    A new nematode species, Latronema dyngi sp. nov., is described from Skagerrak off the west coast of Sweden with the type locality near Dyngö island. Latronema dyngi sp. nov. is characterized by multispiral amphideal fovea with circular outline, 0.2– 0.3 corresponding body diameters wide in males and 0.1–0.2 corresponding body diameters wide in females, 12 cuticular longitudinal ridges and 18–27 precloacal supplements in males. Latronema dyngi sp. nov. most closely resembles L. orcinum in terms of body length; demanian ratios a, b, c and c′; number of amphid turns in males; and the ratio of spicule length to cloacal body diameter. The two species can be differentiated by the number longitudinal ridges on the cuticle (12 for Latronema dyngi sp. nov. vs 20–22 for L. orcinum) and spicule length (65–78 μm for L. dyngi vs 60 for L. orcinum) and shape (weakly arcuate for L. dyngi sp. nov. vs strongly arcuate for L. orcinum). We also performed a maximum likelihood phylogenetic analysis on over 250 nematodes of the subclass Chromadoria based on their nearly full-length 18S rDNA sequences. In agreement with previous studies, our analysis supported Selachinematidae as a monophyletic group and placed Richtersia Steiner, 1916 within Desmodoridae Filipjev, 1922 or just outside of the main Desmodorida clade with the latter placement not well supported.

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  • 6.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Twenty Years after De Ley and Blaxter—How Far Did We Progress in Understanding the Phylogeny of the Phylum Nematoda?2021In: Animals, E-ISSN 2076-2615, Vol. 11, no 12, p. 3479-3479Article in journal (Refereed)
  • 7.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Roberts, Nickellaus G.
    Adediran, Funmilola
    Smythe, Ashleigh B.
    Kocot, Kevin M.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes2022In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 9, article id 769565Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships within many lineages of the phylum Nematoda remainunresolved, despite numerous morphology-based and molecular analyses. Weperformed several phylogenomic analyses using 286 published genomes andtranscriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina,Rhabditina, and Tylenchina separately, and by analyzing a selection of species fromthe whole phylum Nematoda. The phylogeny of Trichinellida supported the divisionof Trichinella into encapsulated and non-encapsulated species and placed them assister to Trichuris. The Spirurina subtree supported the clades formed by species fromAscaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea.The analysis of Tylenchina supported a clade that included all sampled species fromTylenchomorpha and placed it as sister to clades that included sampled speciesfrom Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis thatpostulates the single origin of the stomatostylet. The Rhabditina subtree placed a cladecomposed of all sampled species from Diplogastridae as sister to a lineage consistingof paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a cladecomposed of sampled species belonging to Strongylida. It also strongly supportedall suborders within Strongylida. In the phylum-wide analysis, a clade composedof all sampled species belonging to Enoplia were consistently placed as sister toDorylaimia + Chromadoria. The topology of the Nematoda backbone was consistentwith previous studies, including polyphyletic placement of sampled representatives ofMonhysterida and Araeolaimida.

  • 8.
    Ahmed, Mohammed
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Slos, Dieter
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Assessing the diversity of nematodes in the Store Mosse National Park (Sweden) using metabarcoding2024In: Metabarcoding and Metagenomics, E-ISSN 2534-9708, Vol. 8, p. 1-8Article in journal (Refereed)
  • 9.
    Balog, Luca Eszter
    et al.
    Eötvös Loránd University, Hungary.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Török, Júlia Katalin
    Eötvös Loránd University, Hungary.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology. Department of Zoology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden.
    Redescription of an insect-associated nematode, Reiterina typica (Stefański, 1922) Sudhaus, 2011 (Rhabditida: Rhabditidae) found in scarab grubs in Hungary2023In: Nematology (Leiden. Print), ISSN 1388-5545, E-ISSN 1568-5411, Vol. 25, no 6, p. 699-712Article in journal (Refereed)
  • 10.
    Bouguerche, Chahinez
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Huston, Daniel C.
    Australian National Insect Collection, National Research Collections Australia, CSIRO, PO Box 1700, Canberra, ACT 2601, Australia.
    Cribb, Thomas H.
    The University of Queensland, School of Biological Sciences, St Lucia, QLD, 4072, Australia.
    Karlsbakk, Egil
    Department of Biological Sciences, University of Bergen, 7803, 5020 Bergen, Norway.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Hidden in the fog: morphological and molecular characterisation of Derogenes varicus sensu stricto (Trematoda, Derogenidae) from Sweden and Norway, and redescription of two poorly known Derogenes species2023In: Parasite, ISSN 1252-607X, E-ISSN 1776-1042, Vol. 30, p. 35-35Article in journal (Refereed)
    Abstract [en]

    Derogenes varicus (Müller, 1784) is widely reported as a trematode with exceptionally low host specificity and a wide, bipolar distribution. However, several recent studies have suggested that D. varicus represents a species complex and based on molecular evidence, four genetic lineages (labeled as “DV1–4”) have been designated within the D. varicus species complex. This possibility requires improved (ideally molecular) characterisation of specimens from the type-host (Salmo salar) and type-locality (off Denmark). During examination of trematode parasites of fish from Scandinavian and Arctic waters (Sweden and Norway), we found specimens of D. varicus in the stomach of Merlangius merlangus off the coast of Sweden, and in Gadus morhua off the coast of Sweden and Norway; we compared them to D. varicus from the type-host, the Atlantic salmon Salmo salar from Norway, to verify their conspecificity. Newly generated sequences (28S rDNA, ITS2 and cox1) of Scandinavian and Arctic specimens consistent with D. varicus all formed a single clade, DV1. 28S sequences of D. varicus from S. salar from Norway, i.e., close to the Danish type locality, clustered within the DV1 clade along with sequences of D. varicus from various hosts including Limanda limanda, G. morhua and Myoxocephalus scorpius from the White Sea and the Barents Sea (Russia), without any host-related structuring. We thus consider that the lineage DV1 represents D. varicus sensu stricto. Additionally, specimens from M. merlangus had a similar morphology and anatomy to those of D. varicus from L. limanda, G. morhua and M. scorpius from T. Odhner’s collection, supporting the presence of a single species in the DV1 lineage designated herein as D. varicus sensu stricto. We redescribe D. varicus sensu stricto, add new morphological characters and provide morphometric data. We infer that D. varicus types DV2–4 all relate to separate species. We also revise type-specimens of Derogenes minor Looss, 1901 from the A. Looss collection in the Swedish Museum of Natural History and provide redescriptions of it and of the type-species of the genus, Derogenes ruber Lühe, 1900. In light of their morphological distinctiveness relative to D. varicus sensu stricto, we reinstate D. parvus Szidat, 1950 and D. fuhrmanni Mola, 1912.

  • 11. Gharbi, Kamilia
    et al.
    Bouguerche, Chahinez
    Swedish Museum of Natural History, Department of Zoology.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Pérez-Ponce de León, Gerardo
    Tazerouti, Fadila
    Redescription and Molecular Characterisation of Derogenes ruber Lühe, 1900 (Hemiuroidea: Derogenidae) from Chelidonichthys lastoviza (Scorpaeniformes: Triglidae) in the Western Mediterranean2024In: Acta Parasitologica, ISSN 1230-2821, E-ISSN 1896-1851, Vol. 69, no 309, p. 309-323Article in journal (Refereed)
    Abstract [en]

    Purpose: Derogenes ruber Lühe, 1900, the type-species of the genus Derogenes Lühe, 1900, is a poorly known derogenid digenean. The original description of this species was not illustrated and aspects of the morphology of the parasite from the type-host remain scarce. Available records of this species were brief and/or lacked illustrations and were based on morphology alone. Additionally, molecular data for Derogenes spp. are warranted to untangle species complexes as they provide a better assessment of interspecifc genetic divergence.

    Methods: Derogenes ruber is redescribed based on newly collected specimens from the gall bladder of its type-host Chelidonichthys lastoviza (Bonnaterre, 1788) collected in the Western Mediterranean of the Algerian coast during 2017–2019 and molecular data are provided using a partial fragment of the nuclear 28S ribosomal RNA gene (28S rRNA), the internal transcribed spacer 2 (ITS2) and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene.

    Results: We herein provide a detailed illustrated redescription and morphometric data of D. ruber from its type-host C. lastoviza. We report a new geographical record (of Algeria) for it. Derogenes ruber is also genetically characterised for the frst time. Species/lineages of Derogenes were recovered in fve strongly supported reciprocally monophyletic clades: (i) D. ruber from C. lastoviza of Algeria; (ii) D. lacustris from Galaxias maculatus (Jenyns) of Argentina; (iii) Lineage “D. varicus DV1” (D. varicus sensu stricto) from fsh hosts in the White and Barents seas and the North Sea; (iv) Lineage “D. varicus DV2” from mollusc hosts in the White Sea; and (v) Lineage “D. varicus DV3” from Eumicrotremus fedorovi Mandrytsa. in the Pacifc Ocean. Hence, comparison of the newly generated sequences with other available data for Derogenes species supports the distinction of D. ruber confrming its taxonomic status and helping assess interspecifc variation. Comparison of D. ruber with the closely related species Derogenes latus revealed overlaps in morphometric data and the validity of the latter species is questioned. Conclusion The combination of morphological and molecular data provided for D. ruber provides a frm foundation for further investigations of Derogenes spp. Although we do describe herein material of D. ruber from the type-host, given that the occurrence of a single Derogenes species in various hosts has been challenged by molecular data, and both D. lacustris and D. varicus sensu stricto had been genetically proven to occur in various hosts, D. ruber and D. latus may be indeed synonymous. Additional sequencing efort on Derogenes spp. will strengthen systematic comparative studies and evolutionary relationships within the Derogenidae in general.

  • 12.
    Ikoy, Israel
    et al.
    University of Limerick.
    Egeter, Bastian
    Universidade do Porto.
    Chaves, Cátia
    Universidade do Porto.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Fowler, Andrew
    University of Limerick.
    Schmalenberger, Achim
    University of Limerick.
    Responses of soil microbiota and nematodes to application of organic and inorganic fertilizers in grassland columns2020In: Biology and Fertility of Soils, ISSN 0178-2762, E-ISSN 1432-0789, Vol. 56, p. 647-662Article in journal (Refereed)
    Abstract [en]

    Enhancing the role of the soil microbiota in plant phosphorus (P) and sulfur (S) supply through application of organic fertilizer could reduce dependencies on non-sustainable synthetic fertilizers. To compare the effects of organic/inorganic fertilizers on the soil microbiota, soil columns with Lolium perenne (ryegrass) were set up in a greenhouse and amended with an inorganic fertilizer, cattle slurry (organic), or urea (P- and S-free control). Ryegrass rhizosphere of the slurry treatment had significantly higher abundances of bacterial feeding nematodes, mycorrhizal colonization, cultivable heterotrophic bacteria, phosphonate- and sulfonate-utilizing bacteria, arylsulfatase activity, available P, and Variovorax asfA gene copies compared to the inorganic and urea treatments. Phosphomonoesterase activities, and gene abundances involved in organic P and S transformations (phoD, phoC, Burkholderia, and Polaromonas asfA) were similar in all treatments. Grass dry matter yield and shoot uptake of N, P, and S were significantly higher in the inorganic treatment compared to the urea and slurry treatments. Community compositions differed significantly between the three fertilizer treatments and included the bacterial, alkaline phosphomonoesterase- producing bacterial, fungal, AM fungal, and nematode communities. Bacteriodetes were found in higher relative abundance in the organic treatment, while Acidobacteria were more abundant in the urea and inorganic fertilizer treatments. These com- munity shifts correlated significantly with grass dry matter yield, uptake of N, P, and S, mycorrhizal colonization, enzyme activities, abundances of bacteria, and bacterial feeding nematodes. We concluded that organic fertilization promoted soil microbes and nematodes which have the potential to support sustainable plant growth, provided that the overall nutrient requirements are met.

  • 13. Ikoyi, Israel
    et al.
    Egeter, Bastian
    Chaves, Cátia
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Fowler, Andrew
    Schmalenberger, Achim
    Responses of soil microbiota and nematodes to application of organic and inorganic fertilizers in grassland columns2020In: Biology and Fertility of Soils, ISSN 0178-2762, E-ISSN 1432-0789, Vol. 56, p. 647-662Article in journal (Refereed)
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  • 14.
    Sandberg, Henrik
    et al.
    Stockholms universitet.
    Isabell-Shen, Dandan
    Stockholms universitet.
    Broman, Elias
    Stockholms universitet.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Nascimento, Francisco
    Stockholms universitet.
    NEMOte BARCODing: Förbättrad miljöövervakning av Östersjöns bentiska ekosystem2024Report (Other academic)
    Abstract [sv]

    Förändringar av ekosystem och hot mot biologisk mångfald, samt de på denna mångfald vilande ekosystemtjänsterna, har skapat ett behov av mer robusta och kostnadseffektiva miljöövervakningsmetoder. Projektet NEMOte BARCODing har undersökt om de frilevande nematoderna kan hjälpa oss att fylla detta behov. Metastreckkodning (metabarcoding på engelska), en av de moderna DNA-metoderna, har möjliggjort att meiofauna-organismer som nematoder effektiv kan provtas. Nematoderna är en av de mest mångfaldshaltiga organismgrupperna i världen, och de har visat sig vara bra indikatorer på ekosystems hälsa och förändringar i miljön. I Östersjön, där traditionellt enbart större organismer, makrofauna, har använts, kan nematoderna tillföra värdefull information. Då antal makrofauna-arter i Östersjön är lågt har bedömningar av ekosystemhälsa baserat på makrofauna mindre upp­lösning än bedömningar baserat på de mer mångfaldiga och abundanta nematod-samhället. 

    Det finns dock hinder för DNA-streckkodning ska för att övervaka nematoder i Östersjön: 1. Bristande täckning av nematod-arter i nuvarande referensdatabaser. 2. Bristande kunskap om streckkodningsmetoders förmåga att kvantifiera nematod-samhället och återspegla samhällskompositionen i miljöerna som provtas. Och 3. Bristen på verktyg för att bedöma ekosystemhälsa och ekologiska status från data över nematod-samhället. NEMOte BARCODing har bidragit till att överkomma dessa brister och därigenom till att möjliggöra miljöövervakning av Östersjöns nematoder. 

    I Arbetspaktet 1 förbättrade NEMOte BARCODing existerande referensdatabaser genom att ladda upp referenssekvenser av 18S och 28S rRNA-markörgenerna för 110 av Östersjöns nematod-arter. I Arbetspaket 2 utvärderades sekvenseringsmetoders lämplighet för miljöövervakning. 18S-streckkodning med TAReuk primerparen fungerade bäst av de testade metoderna, gav en god bild av nematod-samhället, och rekommenderas därav för nematod-övervakning i Östersjön. I Arbetspaket 3 har NEMOte BARCODing utvecklat ett verktyg för statusklassning med nematod-data, Nematod-BQI (BQInem), med utgångspunkt i det BQI som används inom svensk miljöövervakning. Andra potentiella verktyg för nematod-övervakning utforskades även och en karta ritades för Nematod-BQI:s framtida utvecklingen, med potentiell inkludering av fler meiofauna-grupper som ett alternativ. 

    Slutligen så förslogs ett pilotprogram för streckkodningsbaserad nematod-övervakning, med rekommenderade metoder, provtagningsupplägg och status klassningsverktyg (BQInem). De frilevande nematoderna kan säga oss mycket om ekosystemens hälsa och arbetet inom NEMOte BARCODing har förhoppningsvis bidragit till att denna information förmedlas.

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  • 15. Westerman, Rickard
    et al.
    Ahmed, Mohammed
    Swedish Museum of Natural History, Department of Zoology.
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Gammarinema scyllae sp. n. and Monhystrium mangrovi sp. n. (Nematoda: Monhysteridae) from land crabs from New Caledonia2022In: Systematic Parasitology, ISSN 0165-5752, E-ISSN 1573-5192, Vol. 99, no 1, p. 83-101Article in journal (Refereed)
    Abstract [en]

    Two new species of nematodes associated with crabs are described from New Caledonia. Gam-marinema scyllae sp. n. from the gill chambers of Scylla serrata (Forsskal) is characterised by 3–4 mmlong body, small outer labial and cephalic sensilla, distinct ocelli, short straight spicules and sub-cylin-drical tail. Monhystrium mangrovi sp. n. from the gill chambers and body cavity of mangrove crab Neosar-matium sp. is characterised by 1–1.4 mm long body; outer labial sensilla longer than cephalic sensilla,amphid located at level with posterior stoma chamber,denticles in posterior stoma chamber and five pairs ofgenital papilla on tail. Phylogenetic relationships oftwo new species and other nematodes from the familyMonhysteridae are analysed based on 18S and partial28S rDNA sequences.

  • 16. Westerman, Rickard
    et al.
    de Moura Neves, Bárbara
    Ahmed, Mohammed
    Holovachov, Oleksandr
    Swedish Museum of Natural History, Department of Zoology.
    Aborjinia corallicola sp. n., a new nematode species (Nematoda: Marimermithidae) associated with the bamboo coral Acanella arbuscula (Johnson)2021In: Systematic Parasitology, ISSN 0165-5752, E-ISSN 1573-5192, Vol. 98, p. 559-579Article in journal (Refereed)
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