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Polar Biology

, Volume 41, Issue 11, pp 2181–2198 | Cite as

Diversity of key genes for carbon and nitrogen fixation in soils from the Sør Rondane Mountains, East Antarctica

  • Guillaume Tahon
  • Bjorn Tytgat
  • Anne Willems
Original Paper
  • 146 Downloads

Abstract

Although Cyanobacteria are generally considered the most important primary producers and diazotrophs in Antarctic terrestrial ecosystems, in several high-altitude Antarctic regions, they were previously reported to be relatively rare in some samples. In view of these observations, we investigated the presence of non-cyanobacterial carbon- and nitrogen-fixing microorganisms in oligotrophic exposed soils without visible cyanobacterial biomass from the Sør Rondane Mountains, East Antarctica. An Illumina amplicon sequencing approach was used to analyze the bacterial community composition and the diversity and abundance of key genes involved in the carbon- and nitrogen-fixation processes. Analysis of the large subunit of type I ribulose-1,5-biphosphate carboxylase/oxygenase genes (cbbL) revealed a large actinobacterial, and alpha-, beta-, and gammaproteobacterial diversity of CbbL type IC, whereas type IA diversity was restricted to Bradyrhizobium sp.-like sequences. Although a large portion of the CbbL sequences grouped with those of cultivated bacteria, some belonged to currently unknown phylotypes. Data of 16S rRNA genes, however, also revealed that samples contained either considerable numbers of Cyanobacteria or Trebouxiophyceae as oxygenic phototrophic primary producers. Dinitrogenase-reductase genes (nifH) most similar to those of Nostocales cyanobacteria were dominantly retrieved from these oligotrophic soils. These findings suggest that diverse microorganisms capable of assimilating carbon dioxide through the Calvin–Benson–Bassham cycle inhabit these extreme terrestrial systems and potentially may contribute to primary production. However, Cyanobacteria, present in greatly varying numbers as assessed by Illumina amplicon sequencing of a 16S rRNA gene fragment, appear to be the most important nitrogen fixers in these habitats.

Keywords

RuBisCO Diazotrophy Sequencing Autotrophy Community analysis Antarctic 

Abbreviations

AA

Amino acid

ONU

Operational nitrogenase unit

ORU

Operational RuBisCO unit

OTU

Operational taxonomic unit

PE

Paired-end

rRNA

Ribosomal RNA

RuBisCO

Ribulose-1,5-biphosphate carboxylase/oxygenase

UT

Utsteinen

Notes

Acknowledgements

This work was supported by the Fund for Scientific Research—Flanders (Project G.0146.12). Additional support was provided by the Belgian Science Policy Office (Project CCAMBIO). The computational resources (Stevin Supercomputer Infrastructure) and services used in this work were provided by the Flemish Supercomputer Center (VSC) funded by Ghent University, the Hercules Foundation, and the Flemish Government—department EWI. This work is a contribution to the State of the Antarctic Ecosystem (AntEco) research program of the Scientific Committee on Antarctic Research (SCAR).

Compliance with Ethical Standards

Conflict of interest

The authors declare there is no conflict of interest.

Supplementary material

300_2018_2353_MOESM1_ESM.docx (23 kb)
Online Resource 1 PCR primers (without adapters) and conditions used for screening different genes. Supplementary material 1 (DOCX 22 kb)
300_2018_2353_MOESM2_ESM.xlsx (66 kb)
Online Resource 2 Composition of ORUs, ONUs and OTUs. Each worksheet is named after the analyzed gene and shows the number of sequences per sample for each ORU (CbbL IAIC), ONU (NifH) or OTU (16S rRNA). For CbbL IAIC, the visual cluster the ORU groups in is listed next to the ORU. Separate ORUs are labelled as “separate”. For the 16S rRNA OTUs, classification is provided next to each OTU. Supplementary material 2 (XLSX 66 kb)
300_2018_2353_MOESM3_ESM.tif (1.3 mb)
Online Resource 3 Graphical comparison between relative abundances of reads and OTUs recovered with different extraction protocols. The comparison is based on the values supplied in Table 5. Bar charts show the relative abundances of reads (top) and OTUs (bottom) recovered with the DNA extraction protocol used by Tytgat et al. (2016) (combination of (Corinaldesi et al. 2005) and (Zwart et al. 1998)) and the extraction method used in the current study (PowerLyzer® PowerSoil® DNA isolation kit). For every sample, the left bar chart shows the relative abundances as obtained by Tytgat et al. (2016), whereas the right bar chart shows those obtained by use of the PowerLyzer® PowerSoil® DNA isolation kit. Phyla with relative abundances of reads or OTUs below 1.00% are grouped together in the < 1% group Supplementary material 3 (TIFF 1350 kb)
300_2018_2353_MOESM4_ESM.jpg (6.9 mb)
Online Resource 4 Maximum likelihood phylogenetic tree (1000 bootstrap replicates) of CbbL IA, IB and IC (bacterial RuBisCO type I). Scale bar indicates 0.1 substitutions per amino acid position. Related type IA and IC were grouped into clusters (displayed as gray triangles) that were named after cultivated bacteria that grouped in the cluster or, in the absence of cultivated members, were given a Utsteinen (UT) cluster number designation. Total branch lengths to the closest and the farthest leaf are used as sides of the triangle. For reference data, accession number and taxon name is listed. Bootstrap values above 70% are shown. CbbM sequences (RuBisCO type II) were used as an outgroup. Supplementary material 4 (JPEG 7040 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Laboratory of Microbiology, Department of Biochemistry and MicrobiologyGhent UniversityGhentBelgium
  2. 2.Laboratory of Protistology and Aquatic Ecology, Department of BiologyGhent UniversityGhentBelgium

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