Intracellular silicification by early-branching magnetotactic bacteria

Abstract

Biosilicification—the formation of biological structures composed of silica—has a wide distribution among eukaryotes; it plays a major role in global biogeochemical cycles, and has driven the decline of dissolved silicon in the oceans through geological time. While it has long been thought that eukaryotes are the only organisms appreciably affecting the biogeochemical cycling of Si, the recent discoveries of silica transporter genes and marked silicon accumulation in bacteria suggest that prokaryotes may play an underappreciated role in the Si cycle, particularly in ancient times. Here, we report a previously unidentified magnetotactic bacterium that forms intracellular, amorphous silica globules. This bacterium, phylogenetically affiliated with the phylum Nitrospirota, belongs to a deep-branching group of magnetotactic bacteria that also forms intracellular magnetite magnetosomes and sulfur inclusions. This contribution reveals intracellularly controlled silicification within prokaryotes and suggests a previously unrecognized influence on the biogeochemical Si cycle that was operational during early Earth history.

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

“…We then cut WYHR‐4 cells along their long axes with a focused ion beam scanning electron microscope (FIB‐SEM) system (Gu et al, 2020; Li et al, 2022b). The cells hybridized by both the EUB338 and species‐specific WYHR4‐901 probes were first detected by correlative FISH‐SEM observations (Figure 8) and were then sliced and viewed with the FIB‐SEM system.…”

“…It is relatively straightforward to directly link each 16S rRNA genotype with an MTB phenotype through routine sample preparation procedures and use of conventional FM, SEM and TEM instruments. Together with analysing full‐length 16S rRNA gene sequences, the correlative FISH‐SEM/TEM approach is being used increasingly to identify novel MTB strains in China (Li et al, 2019; Li et al, 2020b; Li et al, 2022b; Liu et al, 2021a; Liu et al, 2021b; Liu et al, 2022; Zhang et al, 2017), France (Monteil et al, 2021; Qian et al, 2019; Qian et al, 2020) and Russia (Koziaeva et al, 2019; Koziaeva et al, 2020). Our results confirm that combining the group‐specific primer pair 390F/1492R and the correlative FISH‐SEM/TEM approach is efficient for recognizing MTB from the Desulfobacterota phylum even in low abundances.…”

“…Our results confirm that combining the group‐specific primer pair 390F/1492R and the correlative FISH‐SEM/TEM approach is efficient for recognizing MTB from the Desulfobacterota phylum even in low abundances. Once novel MTB are identified phylogenetically and structurally, structural, chemical and crystallographic features of magnetic particles can be investigated systematically at the single‐cell level and down to the atomic scale, and the implications for biogeochemistry and palaeomagnetism can be assessed in detail (Lefèvre et al, 2012; Li et al, 2020b; Li et al, 2020c; Li et al, 2021; Li et al, 2022b; Monteil et al, 2021). For instance, dissimilatory sulfate reduction by sulfate‐reducing bacteria plays a significant role in mediating redox conditions and biogeochemical processes for subsurface systems because they generally couple oxidation of reduced organic or inorganic compounds to the reduction of sulfate or other oxidized sulfur compounds, producing sulfide as a metabolic product (Jørgensen, 2021).…”

“…With the assistance of magneto‐aerotaxis/chemotaxis, MTB can efficiently shuttle up toward oxic/microaerobic regions and down toward anaerobic regions in the water column or within sediments (Bazylinski & Trubitsyn, 2019; Li et al, 2020a; Lower & Bazylinski, 2013). Overall, they are an important microbial group that drives biogeochemical cycling of C, N, P, S, Si and Fe within the oxic–anoxic transition zone (OATZ) in aquatic environments (Bidaud et al, 2022; Li et al, 2021; Li et al, 2022b; Monteil et al, 2021; Schulz‐Vogt et al, 2019). For geologists, the fossil remains of MTB (called magnetofossils) preserved in ancient sediments or rocks (i) record ideal magnetic signals for reconstructing paleomagnetic and paleoenvironmental information and (ii) provide reliable biomarkers for indicating the presence of ancient MTB and their related paleoecology (Amor et al, 2020; Chang et al, 2018; Kopp & Kirschvink, 2008; Larrasoaña et al, 2014; Li et al, 2020b; Li et al, 2020c; Yamazaki & Kawahata, 1998).…”

Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage

“…Compared to original binning software, automated methods with multiple binning methods, such as MAGO, MetaWRAP or DAS Tool, combine the strengths of a flexible set of established binning algorithms to generate more or better bins 32 – 34 . MetaWRAP is a widely used tool for the metagenome binning of both environmental 35 – 41 and host-associated 42 – 44 samples, and it can obtain the largest number of high-quality draft genomes in tested datasets with relatively less computational requirements 33 , 45 . Additionally, MAGO used DAS Tool for bin refinement, and MetaWRAP outperformed DAS Tool for datasets of varied complexity 33 .…”