Metagenomic analyses uncover the differential effect of azide treatment on bacterial community structure by enriching a specific Cyanobacteria present in a saline-alkaline environmental sample

Int Microbiol. 2020 Aug;23(3):467-474. doi: 10.1007/s10123-020-00119-z. Epub 2020 Jan 14.

Abstract

Treatment of environmental samples under field conditions may require the application of chemical preservatives, although their use sometimes produces changes in the microbial communities. Sodium azide, a commonly used preservative, is known to differentially affect the growth of bacteria. Application of azide and darkness incubation to Isabel soda lake water samples induced changes in the structure of the bacterial community, as assessed by partial 16S rRNA gene pyrosequencing. Untreated water samples (WU) were dominated by gammaproteobacterial sequences accounting for 86%, while in the azide-treated (WA) samples, this group was reduced to 33% abundance, and cyanobacteria-related sequences became dominant with 53%. Shotgun sequencing and genome recruitment analyses pointed to Halomonas campanensis strain LS21 (genome size 4.07 Mbp) and Synechococcus sp. RS9917 (2.58 Mbp) as the higher recruiting genomes from the sequence reads of WA and WU environmental libraries, respectively, covering nearly the complete genomes. Combined treatment of water samples with sodium azide and darkness has proven effective on the selective enrichment of a cyanobacterial group. This approach may allow the complete (or almost-complete) genome sequencing of Cyanobacteria from metagenomic DNA of different origins, and thus increasing the number of the underrepresented cyanobacterial genomes in the databases.

Keywords: 16S rRNA analysis; Amplitag-pyrosequencing; Genome recruitment; Halo-alkalophile bacteria; Halomonas; Synechococcus.

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Cyanobacteria / genetics
  • Cyanobacteria / isolation & purification*
  • DNA, Bacterial
  • Environmental Microbiology
  • Enzyme Inhibitors / adverse effects
  • Genome, Bacterial
  • Lakes / microbiology
  • Metagenomics / methods*
  • Microbiota* / genetics
  • Salinity
  • Sodium Azide / adverse effects*

Substances

  • DNA, Bacterial
  • Enzyme Inhibitors
  • Sodium Azide