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Limnofila
Scientific classification
Domain:	Eukaryota
Clade:	Diaphoretickes
Clade:	SAR
Phylum:	Cercozoa
Class:	Granofilosea
Order:	Limnofilida Cavalier-Smith & Bass, 2009
Family:	Limnofilidae Cavalier-Smith & Bass, 2009
Genus:	Limnofila Cavalier-Smith & Bass, 2009
Type species
Limnofila borokensis Cavalier-Smith & Bass, 2009
Species
L. anglica L. borokensis L. longa L. oxoniensis L. mylnikovi

Limnofila (from Greek limnos 'marsh' and fila 'threads') is a genus of heterotrophic protists that live in freshwater habitats and feed on bacteria. They are also present in the soil ecosystem, where they play an important role as predators of bacteria. They are classified as a single family Limnofilidae and order Limnofilida.

Characteristics

Limnofilida is phylogenetically defined as the largest clade that includes Limnofila, its only current member, but excludes Massisteria, which belongs to order Leucodictyida. It excludes the phylogenetically distant marine Nanofila which is morphologically similar but with unbranched filopodia. They are small freshwater heterotrophic protists with very slender, branching granular filopodia (or granulopodia), adhered to the substrate during feeding. Their trophic (feeding) phase is a small globular cell. They can present flagella, but are generally not visible under a light microscope.

The cellular ultrastructure of two species of Limnofilida has been studied (L. borokensis and L. mylnikovi). They present flat mitochondrial cristae and complex concentric-structured extrusomes. Their filopodia (filose, or thread-like, pseudopodia) are supported by bundles of 2–6 microtubules. Unlike Heliomonadida, they have no prominent centrosome.

Ecology

Limnofilida are bacterivorous eukaryotes, they feed on bacteria through phagocytosis. As such, they are important soil predators of microbes and belong to a diverse ecological community of soil protists. Although they are described as a freshwater group, they are present in soil microbial communities. They appear as a minority of cercozoan environmental DNA sequences or OTUs in temperate agricultural fields of Germany (1.3%). They also compose a similar minority of the cercozoan OTUs found in two separate forest soils of Norway and the Czech Republic (2%), but are present in a consistent manner across all levels: leaf litter, pure soil, rhizosphere, and in association with plant roots.

Systematics

Origin and etymology

The genus Limnofila was created in 2009 by protistologists Thomas Cavalier-Smith and David Bass, through a research article published in the journal Protist. It was described to encompass several naked amoebae with granular filose pseudopodia (or filopodia) that did not belong in phylogenetic analyses to either Endomyxa or Foraminifera. On the basis of phylogenetic analyses based on 18S rRNA genes, they were assigned to a clade of Cercozoa known as Granofilosea, which was newly described in the same article. In particular, the genus was assigned to a monotypic order Limnofilida and family Limnofilidae. Limnofilida was defined as the most inclusive clade containing Limnofila but excluding Massisteria, which belongs to Leucodictyida. The name Limnofila comes from Greek limnos 'marsh' and fila 'threads', to emphasise both their exclusively freshwater habitat and their exceedingly thin thread-like filopodia.

Molecular phylogeny

Limnofila, and Limnofilida as a whole, are the earliest diverging clade within Granofilosea, followed by Leucodictyida, Cryptofilida and Desmothoracida. Granofilosea is, in turn, the sister group of Monadofilosa, which contains the remaining filose cercozoan amoebae. Below is a simplified cladogram of Granofilosea from a 2011 phylogenetic analysis based on 18S rRNA genes, where the clades of environmental DNA are not shown.

Species

There are 5 species of Limnofila, all described in the same 2009 paper where the genus was first described. Two species, L. anglica and L. longa, were isolated from a freshwater lake known as Priest Pot in Cumbria, England. One species, L. oxoniensis, was isolated from garden soil in Oxford. The remaining two species, L. borokensis and L. mylnikovi, were isolated from samples collected in waste treatment plants of Borok, Yaroslavskaya oblast, Russia, and were originally misidentified as Gymnophrys cometa.

1. Limnofila anglica — Cumbria, England.
2. Limnofila borokensis — Borok, Russia.
3. Limnofila longa — Cumbria, England.
4. Limnofila oxoniensis — Oxford, England.
5. Limnofila mylnikovi — Borok, Russia (unsequenced).

References

1. ^ Bass D, Chao EE, Nikolaev S, Yabuki A, Ishida K, Berney C, Pakzad U, Wylezich C, Cavalier-Smith T (2009). "Phylogeny of novel naked Filose and Reticulose Cercozoa: Granofilosea cl. n. and Proteomyxidea revised". Protist. 160 (1): 75–109. doi:10.1016/j.protis.2008.07.002. PMID 18952499.
2. ^ Degrune, Florine; Dumack, Kenneth; Fiore-Donno, Anna Maria; Bonkowski, Michael; Sosa-Hernández, Moisés A.; Schloter, Michael; Kautz, Timo; Fischer, Doreen; Rillig, Matthias C. (April 2019). "Distinct communities of Cercozoa at different soil depths in a temperate agricultural field". FEMS Microbiology Ecology. 95 (4): fiz041. doi:10.1093/femsec/fiz041.
3. Fiore-Donno, Anna Maria; Human, Zander R.; Štursová, Martina; Mundra, Sunil; Morgado, Luis; Kauserud, Håvard; Baldrian, Petr; Bonkowski, Michael (2022). "Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition". Soil Biology and Biochemistry. 168: 108628. doi:10.1016/j.soilbio.2022.108628. hdl:10852/101716.
4. Howe AT, Bass D, Scoble JM, Lewis R, Vickerman K, Arndt H, Cavalier-Smith T (2011). "Novel Cultured Protists Identify Deep-branching Environmental DNA Clades of Cercozoa: New Genera Tremula, Micrometopion, Minimassisteria, Nudifila, Peregrinia". Protist. 162 (2): 332–372. doi:10.1016/j.protis.2010.10.002. ISSN 1434-4610.
5. Calabuig I (2016), Priest Pot species list, Cumbria, Britain, Department of Biology, University of Copenhagen, doi:10.15468/lih6qc, retrieved 2023-09-22
6. Nikolaev, S.I.; et al. (2003). "Gymnophrys cometa and Lecythium sp. are Core Cercozoa: Evolutionary Implications" (PDF). Acta Protozoologica. 42: 183–190. Archived from the original (PDF) on 2009-06-17.

• Taxa described in 2009
• Rhizaria genera