Identification of sulfate‐reducing magnetotactic bacteria via a group‐specific 16S rDNA primer and correlative fluorescence and electron microscopy: Strategy for culture‐independent study

Abstract

Magnetotactic bacteria (MTB) biomineralize intracellular magnetic nanocrystals and swim along geomagnetic field lines. While few axenic MTB cultures exist, living cells can be separated magnetically from natural environments for analysis. The bacterial universal 27F/1492R primer pair has been used widely to amplify nearly full-length 16S rRNA genes and to provide phylogenetic portraits of MTB communities. However, incomplete coverage and amplification biases inevitably prevent detection of some phylogenetically specific or non-abundant MTB. Here, we propose a new formulation of the upstream 390F primer that we combined with the downstream 1492R primer to specifically amplify 1100-bp 16S rRNA gene sequences of sulfate-reducing MTB in freshwater sediments from Lake Weiyanghu, Xi'an, northwestern China. With correlative fluorescence in situ hybridization and scanning/transmission electron microscopy, three novel MTB strains (WYHR-2, WYHR-3 and WYHR-4) from the Desulfobacterota phylum were identified phylogenetically and structurally at the single-cell level. Strain WYHR-2 produces bullet-shaped magnetosome magnetite, while the other two strains produce both cubic/prismatic greigite and bullet-shaped magnetite. Our results expand knowledge of bacterial diversity and magnetosome biomineralization of sulfate-reducing MTB. We also propose a general strategy for identifying and characterizing uncultured MTB from natural environments.

Key gene networks that control magnetosome biomineralization in magnetotactic bacteria

“…Diverse living MTB were collected magnetically from laboratory microcosms of water and sediment from lakes or salt ponds using homemade magnetic separation apparatus (Fig. 1a–c and Supplementary Table S1 ) [ 29 , 30 ]. Molecular analysis of 16S rRNA gene sequences indicates that five MTB strains (tentatively named YQV-1, WYHS-4, YQC-5, YQR-1 and YQC-9) from the magnetic collections are novel species because they share low sequence identity (<97%) with known bacterial sequences (Fig.…”

Glacial‐Interglacial Circulation and Climatic Changes in the South Indian Ocean (Kerguelen Plateau Region) Recorded by Detrital and Biogenic Magnetic Minerals

“…Indeed, this promoted an increase of the SO upwelling strength that enhanced the transport of more organic matter, sulfate, and other nutrients. Nutrient availability and relatively warm environments promoted MTB blooms, which may have particularly stimulated proliferation of dissimilatory sulfate‐reducing MTB (Li et al., 2022, 2021) that are well known to produce straight bullet‐shaped magnetite magnetosomes (Li, Menguy, Roberts, et al., 2020; Pósfai et al., 2013). In contrast, due to the northward migration of the APF during the glacial periods, the SO upwelling position could have not impacted the KP region, which resulted in a local nutrient deficiency and limited MTB proliferation (Civel‐Mazens et al., 2021; Thöle et al., 2019).…”

Three Fe(III)-reducing and nitrogen-fixing bacteria, Anaeromyxobacter terrae sp. nov., Anaeromyxobacter oryzisoli sp. nov. and Anaeromyxobacter soli sp. nov., isolated from paddy soil

“…The genomic DNA of SG22 T , SG63 T and SG29 T was extracted using the TIANamp Bacterial DNA kit (TIANGEN). The amplification and sequencing of the 16S rRNA gene were conducted using universal bacterial primers 27F (5′-AGAGTTTGATCMTGGCTCAG-3′) and 1492R (5′-TACGGYTACCTTGTTACGACTT-3′) as described previously [18]. Thermal cycling conditions were as follows: 95 °C for 5 min, followed by 30 cycles of 95 °C for 30 s, 55 °C for 60 s and 72 °C for 30 s. The 16S rRNA gene sequence similarity was calculated by comparing them with sequences in the NCBI GenBank database and the EzBioCloud platform [19].…”