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Article ; Online: Novel contributions to the molecular and morphological diversity of freshwater monothalamid foraminifera: Description of six new species.

Siemensma, Ferry / Holzmann, Maria

2023 Volume 90, Page(s) 126014

Abstract: Non-marine monothalamous foraminifera are common in freshwater and soil habitats. They comprise a poorly-known group lacking sufficient information about diversity, morphology, reproduction, distribution and ecology. Based on an integrative morphological ...

Abstract	Non-marine monothalamous foraminifera are common in freshwater and soil habitats. They comprise a poorly-known group lacking sufficient information about diversity, morphology, reproduction, distribution and ecology. Based on an integrative morphological and molecular approach we describe a new family, a new genus and six new species of freshwater monothalamids from different localities in the Netherlands and France. We establish Astroperula as a new genus of organic walled freshwater foraminifera that contains two species, Astroperula dumacki and Astroperula parvipila. Furthermore, two new agglutinated freshwater monothalamids are described and illustrated, Limnogromia leanneae and Lacogromia pawlowskii, one new organic walled, Velamentofex dujardini, and a new naked monothalamid, Haplomyxa retiforma. Additional information is provided about a special form of cell division in Claparedellus lachmannii and L. leanneae, and feeding behavior in cultures of V. dujardini. Morphological observations are added for an unidentified Limnogromia sampled from the Netherlands and two types of Lacogromia sampled from an alpine region in the French Pyrenees and a karst sinkhole in Bosnia and Herzegovina. The present study provides additional insight into the ecology, diversity and occurrence of freshwater monothalamids and emphasizes the fact that a combination of morphological and molecular methods is necessary to clearly distinguish species in this group.
MeSH term(s)	Foraminifera/genetics ; Cell Division ; Ecology ; Fresh Water ; Reproduction
Language	English
Publishing date	2023-08-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2047872-0
ISSN	1618-0429 ; 0932-4739
ISSN (online)	1618-0429
ISSN	0932-4739
DOI	10.1016/j.ejop.2023.126014
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Article ; Online: Shell Colour in Cercozoa; a Simple Trait to Distinguish Thecofilosea from Imbricatea?

Dumack, Kenneth / Siemensma, Ferry

Protist

2020 Volume 171, Issue 2, Page(s) 125718

Abstract: Rigid and persistent shells of microeukaryotes are widely used as bioindicators in ecological and paleontological studies. Drawing conclusions on ecological or evolutionary patterns depends strongly on the right taxonomic assignment of the observed ... ...

Abstract	Rigid and persistent shells of microeukaryotes are widely used as bioindicators in ecological and paleontological studies. Drawing conclusions on ecological or evolutionary patterns depends strongly on the right taxonomic assignment of the observed species, however confusion is common. Especially in filose shelled amoebae it is often unclear whether species belong to the Imbricatea or Thecofilosea when only morphological data are collected. Molecular surveys shed light on their evolutionary relationship; based on these we propose a hypothesis how to differentiate doubtful species even light microscopically.
MeSH term(s)	Animals ; Cercozoa/classification ; Cercozoa/cytology ; Cercozoa/genetics ; Phylogeny ; Pigmentation/physiology ; Species Specificity
Language	English
Publishing date	2020-02-15
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2020.125718
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Article ; Online: First data on testate amoebae associated with the endemic cave bivalve Congeria jalzici Morton & Bilandžija, 2013 with a description of Psammonobiotus dinarica sp. nov

Baković, Najla / Siemensma, Ferry / Puljas, Sanja / Baković, Robert / Ozimec, Roman / Ostojić, Ana / Mesić, Zrinka

Subterranean Biology. 2023 Feb. 21, v. 45 p.53-74

2023

Abstract: AbstractTestate amoebae are phylogenetically a very diverse group of eukaryotic microorganisms. They can be found in marine and freshwater habitats and in soil. Some of these single-celled organisms inhabit both surface and cave habitats, but their ... ...

Abstract	AbstractTestate amoebae are phylogenetically a very diverse group of eukaryotic microorganisms. They can be found in marine and freshwater habitats and in soil. Some of these single-celled organisms inhabit both surface and cave habitats, but their diversity in caves has barely been explored. Recent studies in the Dinaric region imply that testate amoebae in caves show a high diversity. The aim of this study was to identify the alpha diversity of testate amoebae in the Lika region (Dinaric karst, Croatia) and to compare the habitats of different caves based on testate amoebae assemblages. In eight caves we found more than 40 testate amoebae taxa, including a new testate amoeba species, Psammonobiotus dinarica sp. nov. The greatest diversity of testate amoebae was found in Markov ponor (27 taxa). The Bray-Curtis Similarity Index showed that testate amoebae assemblages in caves inhabited by the endemic and endangered cave bivalve Congeria jalzici (Markov ponor, Dankov ponor and Dražice ponor) differ from caves not inhabited by this species. This differentiation is attributed to the impact of the sinking Lika river, which occasionally completely submerges these caves, creating specific habitats for eukaryotic microorganisms. This study contributes to our understanding of the diversity, biogeography and ecology of testate amoebae in caves, as well as providing further insight into the conditions that sustain populations of C. jalzici.
Keywords	Bivalvia ; biogeography ; freshwater ; karsts ; phylogeny ; rivers ; soil ; species diversity ; Croatia ; cave flooding ; cave heterogeneity ; cave protists ; Centropyxis ; Difflugia ; hygropetric ; Markov ponor ; Microchlamyspatella ; psammobiotic testate amoebae ; sinkholes ; unicellular cave organisms
Language	English
Dates of publication	2023-0221
Size	p. 53-74.
Publishing place	Pensoft Publishers
Document type	Article ; Online
ZDB-ID	2633922-5
ISSN	1314-2615 ; 1768-1448
ISSN (online)	1314-2615
ISSN	1768-1448
DOI	10.3897/subtbiol.45.97105
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Transfer of the thecate amoebae Lecythium spinosum and Pamphagus armatus to Rhizaspis (Thecofilosea, Cercozoa, Rhizaria).

Dumack, Kenneth / Siemensma, Ferry / Clauß, Steffen

European journal of protistology

2021 Volume 83, Page(s) 125843

Abstract: Thecofilosea is a class in Cercozoa (Rhizaria) comprising mainly freshwater-inhabiting algivores. Recently, numerous isolates of thecofilosean amoebae have been cultured and were characterized by an integrated morphological and molecular approach. The ... ...

Abstract	Thecofilosea is a class in Cercozoa (Rhizaria) comprising mainly freshwater-inhabiting algivores. Recently, numerous isolates of thecofilosean amoebae have been cultured and were characterized by an integrated morphological and molecular approach. The captivating spine-bearing taxa in Thecofilosea were not yet molecularly characterized due to being very rare. There are only two known spine-bearing species, Pamphagus armatus and Lecythium spinosum, which were synonymized by Penard in 1902. Due to a morphological difference of those taxa, we discuss here that we disagree with this taxonomical act. We further isolated single cells of Pamphagus armatus directly from their habitat and successfully sequenced their SSU rDNA, which we subjected to phylogenetic analyses. We show that Pamphagus armatus branches within the Rhizaspididae (Tectofilosida, Thecofilosea). Accordingly, we transfer Pamphagus armatus and the assumingly closely related species Lecythium spinosum to Rhizaspis.
MeSH term(s)	Amoeba/genetics ; Cercozoa ; DNA, Ribosomal/genetics ; Phylogeny ; Rhizaria/genetics
Chemical Substances	DNA, Ribosomal
Language	English
Publishing date	2021-09-28
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2047872-0
ISSN	1618-0429 ; 0932-4739
ISSN (online)	1618-0429
ISSN	0932-4739
DOI	10.1016/j.ejop.2021.125843
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Article ; Online: It's time to consider the Arcellinida shell as a weapon.

Dumack, Kenneth / Lara, Enrique / Duckert, Clément / Ermolaeva, Elizaveta / Siemensma, Ferry / Singer, David / Krashevska, Valentyna / Lamentowicz, Mariusz / Mitchell, Edward A D

European journal of protistology

2024 Volume 92, Page(s) 126051

Abstract: The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. ... ...

Abstract	The shells of testate amoebae are morphologically diverse and persistent in the environment. Accordingly, the examination of the morphology and composition of shells became a standard tool in ecological, palaeoecological, and evolutionary studies. However, so far the function of the shell remains poorly understood and, although based on limited evidence, the shell was considered as a defense mechanism. Based on recent evidence, we propose that the shell of arcellinid testate amoebae is a crucial component facilitating the amoebae's attack of large prey. Accordingly, the shell is not purely protective, but must be considered also as a weapon. This change in perspective opens up numerous new avenues in protistology and will lead to a substantial change in ecological, palaeoecological, and evolutionary research.
MeSH term(s)	Phylogeny ; Lobosea ; Amoeba ; Biological Evolution
Language	English
Publishing date	2024-01-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2047872-0
ISSN	1618-0429 ; 0932-4739
ISSN (online)	1618-0429
ISSN	0932-4739
DOI	10.1016/j.ejop.2024.126051
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Article ; Online: SSU rDNA Phylogeny Indicates the Scale-lacking Trivalvulariida ord. nov. as a Sister Group to the Euglyphida (Cercozoa, Rhizaria).

Siemensma, Ferry / Dumack, Kenneth

Protist

2019 Volume 171, Issue 1, Page(s) 125701

Abstract: The testate amoeba Leptogromia operculata was described by Valkanov in 1970 from marine waters. We re-discovered this species in brackish water along the North Sea in the Netherlands. Based on detailed comparison of morphology and SSU rDNA phylogeny we ... ...

Abstract	The testate amoeba Leptogromia operculata was described by Valkanov in 1970 from marine waters. We re-discovered this species in brackish water along the North Sea in the Netherlands. Based on detailed comparison of morphology and SSU rDNA phylogeny we conclude that this species represents a sister clade to the Euglyphida (Imbricatea, Cercozoa). We further describe a similar species Trivalvularis immunda gen. nov., sp. nov. from freshwater in France and the Netherlands on basis of morphological data. Trivalvularis and Leptogromia share a unique oral apparatus with three valves that can close the aperture of the shell. Due to this unique morphological character and the phylogenetic analysis of L. operculata we place both species in a new family Trivalvulariidae in the new order Trivalvulariida.
MeSH term(s)	Cercozoa/classification ; Cercozoa/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Netherlands ; Phylogeny ; Saline Waters ; Species Specificity
Chemical Substances	DNA, Protozoan ; DNA, Ribosomal
Language	English
Publishing date	2019-11-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2019.125701
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Article ; Online: The Dancing Star: Reinvestigation of Artodiscus saltans (Variosea, Amoebozoa) Penard 1890.

Ntakou, Efthymia / Siemensma, Ferry / Bonkowski, Michael / Dumack, Kenneth

Protist

2019 Volume 170, Issue 4, Page(s) 349–357

Abstract: Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of ... ...

Abstract	Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of four European countries. We subjected three cells of one strain from Germany to molecular analyses and, interestingly, obtained six different rDNA sequences. Phylogenetic analyses of these SSU rDNA sequences revealed that A. saltans branches close to the amoebozoan Multicilia marina (Variosea, Amoebozoa).
MeSH term(s)	Amoebozoa/classification ; Amoebozoa/genetics ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Europe ; Germany ; Phylogeny ; Species Specificity
Chemical Substances	DNA, Protozoan ; DNA, Ribosomal
Language	English
Publishing date	2019-06-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2019.06.002
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Article: The Dancing Star: Reinvestigation of Artodiscus saltans (Variosea, Amoebozoa) Penard 1890

Ntakou, Efthymia / Bonkowski, Michael / Dumack, Kenneth / Siemensma, Ferry

Protist. 2019 Aug., v. 170, no. 4

2019

Abstract	Artodiscus saltans, first described by Penard (1890), has a unique morphology. Without genetic data it could not yet been reliably placed into a wider taxonomical context. We present morphological data for A. saltans from different aquatic habitats of four European countries. We subjected three cells of one strain from Germany to molecular analyses and, interestingly, obtained six different rDNA sequences. Phylogenetic analyses of these SSU rDNA sequences revealed that A. saltans branches close to the amoebozoan Multicilia marina (Variosea, Amoebozoa).
Keywords	aquatic habitat ; nucleotide sequences ; phylogeny ; ribosomal DNA ; Variosea ; Germany
Language	English
Dates of publication	2019-08
Size	p. 349-357.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2019.06.002
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Article ; Online: Expansion of the cytochrome C oxidase subunit I database and description of four new lobose testate amoebae species (Amoebozoa; Arcellinida).

Ribeiro, Giulia M / Useros, Fernando / Dumack, Kenneth / González-Miguéns, Rubén / Siemensma, Ferry / Porfírio-Sousa, Alfredo L / Soler-Zamora, Carmen / Pedro Barbosa Alcino, João / Lahr, Daniel J G / Lara, Enrique

European journal of protistology

2023 Volume 91, Page(s) 126013

Abstract: Arcellinida is ascending in importance in protistology, but description of their diversity still presents multiple challenges. Furthermore, applicable tools for surveillance of these organisms are still in developing stages. Importantly, a good database ... ...

Abstract	Arcellinida is ascending in importance in protistology, but description of their diversity still presents multiple challenges. Furthermore, applicable tools for surveillance of these organisms are still in developing stages. Importantly, a good database that sets a correspondence between molecular barcodes and species morphology is lacking. Cytochrome oxidase (COI) has been suggested as the most relevant marker for species discrimination in Arcellinida. However, some major groups of Arcellinida are still lacking a COI sequence. Here we expand the database of COI marker sequences for Arcellinids, using single-cell PCR, transcriptomics, and database scavenging. In the present work, we added 24 new Arcellinida COI sequences to the database, covering all unsampled infra- and suborders. Additionally, we added six new SSUrRNA sequences and described four new species using morphological, morphometrical, and molecular evidence: Heleopera steppica, Centropyxis blatta, Arcella uspiensis, and Cylindrifflugia periurbana. This new database will provide a new starting point to address new research questions from shell evolution, biogeography, and systematics of arcellinids.
MeSH term(s)	Amoeba ; Electron Transport Complex IV/genetics ; Phylogeny ; Amoebozoa ; Lobosea
Chemical Substances	Electron Transport Complex IV (EC 1.9.3.1)
Language	English
Publishing date	2023-08-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2047872-0
ISSN	1618-0429 ; 0932-4739
ISSN (online)	1618-0429
ISSN	0932-4739
DOI	10.1016/j.ejop.2023.126013
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Article ; Online: Rediscovery of the Testate Amoeba Genus Penardeugenia (Thaumatomonadida, Imbricatea).

Dumack, Kenneth / Siemensma, Ferry / Bonkowski, Michael

Protist

2017 Volume 169, Issue 1, Page(s) 29–42

Abstract: The genus Penardeugenia DEFLANDRE 1958 accommodates a single species which was described as Pamphagus bathybioticus PENARD 1904. Although this species seems to be well characterized in its description, it has never been recorded again. Despite its ... ...

Abstract	The genus Penardeugenia DEFLANDRE 1958 accommodates a single species which was described as Pamphagus bathybioticus PENARD 1904. Although this species seems to be well characterized in its description, it has never been recorded again. Despite its possession of silica scales, it was assigned to the scale-lacking Chlamydophryidae (Thecofilosea, Cercozoa). We here present morphological data of three isolates. One of them was successfully cultured and enabled the amplification of its SSU rDNA sequence. Molecular analyses revealed the evolutionary origin of Penardeugenia in the scale-bearing flagellate class Thaumatomonadida, which is backed up by morphological similarities of their scales. We consider Penardeugenia to represent a closely related genus to Thaumatomastix, which apparently lost its ability to form flagella. We describe two new species from Germany, P. huelsmannii and P. hausmannii.
MeSH term(s)	Cercozoa/classification ; Cercozoa/genetics ; Cercozoa/growth & development ; Cercozoa/isolation & purification ; DNA, Protozoan/genetics ; DNA, Ribosomal/genetics ; Evolution, Molecular ; Germany ; Phylogeny
Chemical Substances	DNA, Protozoan ; DNA, Ribosomal
Language	English
Publishing date	2017-12-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2017.12.002
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