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Habitats and environmental variables investigated in a diversity survey on Polynucleobacter bacteria revealed by amplicon sequencing of priB genes

Citation

Hahn, Martin W. (2021), Habitats and environmental variables investigated in a diversity survey on Polynucleobacter bacteria revealed by amplicon sequencing of priB genes, Dryad, Dataset, https://doi.org/10.5061/dryad.hhmgqnkgq

Abstract

Freshwater habitats (ditches, ponds, lakes and rivers) sampled for a biodiversity survey on subcluster PnecC of the genus Polynucleobacter (Bacteria, Proteobacteria, Burkholderiaceae). Subcluster PnecC represents a monophyletic linage within the genus Polynucleobacter and equals a subgenus. The dataset contains data on the geographic location of the habitats and the measured environmental variables. The obtained molecular data and reference sequences of the priB gene and genome sequences of reference strains were deposited in GenBank/EMBL/DDBJ.

Methods

In total, 102 freshwater habitats (Habitat_ID) were sampled. Some of the habitats were sampled two to three times at different dates (usually in different years). Samples 2_Ounas47 and 2_Ounas48 represent the same sample, which was used twice as a technical replicate for the determination of the priB diversity by Illumina sequencing (two Illumina libraries were established). The habitats were classified in three different categories (ditch, Lake_Pond, River). All samples represent surface water samples. Some variables were measured on location, while the absorbance values and the major ion concentrations (mg/L) were measured in the laboratory by using 0.2µm-filtered (on location) samples, which were cooled upon arrival in the laboratory. Major ions concentrations were determined by ion chromatography. No concentrations are given if concentrations of ion species were below the detection limit or outside the calibration range. Geographic coordinates were recorded on location. Altitude (m) and surface area (ha) of the standing water habitats were inferred by using Google Earth. For running waters no surface area data are given. Absorbance values were determined for 0.2µm-filtered water samples by using 1cm cuvettes.

Usage Notes

Besides a few missing data (see below) the data set is complete. A few oxygen and temperature data could not be measured due to problems with the mobile device (presented as n.d., not determined). Empty fields of ion concentrations indicate that the respective ion species was below detection limit or the meassured concentration was outside the callibration range of the ion chromatography instrument. Used abreviations: Temp_C, temperature (°C); Cond_µm_cm, conductivity (µm cm-1); Oxy, oxygen; Abs250, absorbance at 250 nm; Abs365, absorbance at 365 nm; Abs430, absorbance at 430 nm; Abs436, absorbance at 436 nm; NH4, ammonia; K, potassium; Mg, magnesium; Ca, calcium; Cl, chloride; NO2, nitrite; NO3, nitrate; PO4, phosphate; SO4, sulfate. The column headings of the data table are explained in the Read_Me.txt file.

Funding

Austrian Science Fund, Award: 27160-B22