Four years in the Caucasus – observations on the ecology of nivicolous myxomycetes

Schnittler, Martin; Erastova, Daria A.; Shchepin, Oleg N.; Heinrich, Erica C.; Novozhilov, Yu. K.

doi:10.1016/j.funeco.2015.01.003

Cited by 24 publications

(18 citation statements)

References 28 publications

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“…From 1,177 fructifications observed within the transect, 44 morphospecies were determined (Suppl. S5 and Schnittler et al., ). Three of these were bright‐spored myxomycetes and therefore not detectable with the primers used in this study.…”

Section: Resultsmentioning

confidence: 95%

“…The results were compared to the morphospecies inventory from the surveys of the same site (1,177 specimens belonging to 46 morphospecies, see Suppl. S5 and Novozhilov et al., ; Schnittler et al., ). The OTUs were BLASTed against the newly created reference database and the top hit selected, with default settings (BLAST Command Line Applications User Manual, ), when these were not met the OTU was assigned “no match.” Some sequences in the ePCR data set were found to be of fungal origin (see Results and Discussion); therefore, we calculated the binding specificity of the primer pair S3b/S31R to these sequences following default settings in the PrimerProspector pipeline (Walters et al., ).…”

Section: Methodsmentioning

confidence: 97%

“…During four field surveys for fruit bodies of nivicolous myxomycete (an ecological group of species, which emerges from the soil and forms fruit bodies along the edge of melting snowbanks in spring primarily in mountain regions, hence the name “nivicolous”) conducted in spring seasons 2010–2013, an elevational transect was studied between 1,700 and 3,000 m a.s.l. in the Teberda State Biosphere Reserve, northern Caucasus (Novozhilov et al., ; Schnittler, Erastova, Shchepin, Heinrich, & Novozhilov, ). Seven soil samples were collected in 2011 and 2012, by pooling c. 10 g of soil from of the uppermost soil horizon (A0) gathered over an area of c. 2 × 2 m (for location, see corresponding sites for data loggers listed in Schnittler et al., and Suppl.…”

Section: Methodsmentioning

confidence: 99%

“…in the Teberda State Biosphere Reserve, northern Caucasus (Novozhilov et al., ; Schnittler, Erastova, Shchepin, Heinrich, & Novozhilov, ). Seven soil samples were collected in 2011 and 2012, by pooling c. 10 g of soil from of the uppermost soil horizon (A0) gathered over an area of c. 2 × 2 m (for location, see corresponding sites for data loggers listed in Schnittler et al., and Suppl. S5).…”

Section: Methodsmentioning

confidence: 99%

See 3 more Smart Citations

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Dahl

Brejnrod

Unterseher³

et al. 2017

Molecular Ecology Resources

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Unicellular, eukaryotic organisms (protists) play a key role in soil food webs as major predators of microorganisms. However, due to the polyphyletic nature of protists, no single universal barcode can be established for this group, and the structure of many protistean communities remains unresolved. Plasmodial slime moulds (Myxogastria or Myxomycetes) stand out among protists by their formation of fruit bodies, which allow for a morphological species concept. By Sanger sequencing of a large collection of morphospecies, this study presents the largest database to date of dark-spored myxomycetes and evaluate a partial 18S SSU gene marker for species annotation. We identify and discuss the use of an intraspecific sequence similarity threshold of 99.1% for species differentiation (OTU picking) in environmental PCR studies (ePCR) and estimate a hidden diversity of putative species, exceeding those of described morphospecies by 99%. When applying the identified threshold to an ePCR data set (including sequences from both NGS and cloning), we find 64 OTUs of which 21.9% had a direct match (>99.1% similarity) to the database and the remaining had on average 90.2 ± 0.8% similarity to their best match, thus thought to represent undiscovered diversity of dark-spored myxomycetes.

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Section: Resultsmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 97%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Dahl

Brejnrod

Unterseher³

et al. 2017

Molecular Ecology Resources

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“…Their specific habitat along the edge of melting snowbanks was first described in 1908 by Meylan 25 . These myxamoebae thrive and multiply in snow-covered soil 26 , benefiting from the constant temperatures of 0 to 1 °C maintained by the snowpacks 27 . Diversity patterns of fructifications of the ca.…”

Section: Introductionmentioning

confidence: 99%

A four year survey reveals a coherent pattern between occurrence of fruit bodies and soil amoebae populations for nivicolous myxomycetes

Dahl

Shchepin

Schunk

et al. 2018

Sci Rep

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Among soil-inhabiting protists, myxomycetes stand out by their macroscopic fructifications which have allowed studies on their ecology and distribution for more than two hundred years. One of the most distinct ecological guilds in myxomycetes are the nivicolous or “snowbank” myxomycete species, which produce fruit bodies at the edge of melting snowbanks in spring. Relationship between the occurrence of fructifications and myxamoebae remain unknown. In this study we used modern molecular techniques, by direct DNA amplification from soil extracts (NGS metabarcoding) to compare the distribution of soil-inhabiting myxamoebae found in 2016 with fructifications from the same sites collected over the course of four years (2013, 2015–17) along an elevational transect in the northern German Alps. A coherent community composition between fructification and soil myxamoebae, though with species-specific differences in relative abundance, was revealed. Although patterns varied among species, myxamoebae were found at both low and high elevations, whereas fruit bodies were mainly found at higher elevations, likely explained by the presence of a stable and long-lasting snow cover. In addition, a year to year comparison of fructification records support the hypothesis that the abundance of fructifications strongly depends on the onset of snowfall in the previous autumn and the soil temperature regime throughout the winter.

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Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

et al. 2019

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Four years in the Caucasus – observations on the ecology of nivicolous myxomycetes

Cited by 24 publications

References 28 publications

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

Genetic barcoding of dark‐spored myxomycetes (Amoebozoa)—Identification, evaluation and application of a sequence similarity threshold for species differentiation in NGS studies

A four year survey reveals a coherent pattern between occurrence of fruit bodies and soil amoebae populations for nivicolous myxomycetes

Different Degrees of Niche Differentiation for Bacteria, Fungi, and Myxomycetes Within an Elevational Transect in the German Alps

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