Proteome Response of a Metabolically Flexible Anoxygenic Phototroph to Fe(II) Oxidation

Sequence similarity network and protein structure prediction offer insights into the evolution of microbial pathways for ferrous iron oxidation

IMPORTANCE

Microbial Fe(II) oxidation is a crucial process that harnesses and converts the energy available in Fe, contributing significantly to global element cycling. However, there are still many aspects of this process that remain unexplored. In this study, we utilized a combination of comparative genomics, sequence similarity network analysis, and artificial intelligence-driven structure modeling methods to address the lack of structural information on Fe(II) oxidation proteins and offer a comprehensive perspective on the evolution of Fe(II) oxidation pathways. Our findings suggest that several microbial Fe(II) oxidation pathways currently known may have originated within classes Gammaproteobacteria and Betaproteobacteria.

Effects of different carbon sources on methane production and the methanogenic communities in iron rich flooded paddy soil

Various carbon sources as substrates and electron donors can produce methane via different metabolic pathways. In particular, the methane produced by rice cultivation has a severe impact on climate change. However, how Fe³⁺, the most abundant oxide in paddy soil, mediates the methanogenesis of different carbon sources is unknown. In this study, we investigated the effect of four carbon sources with different chain lengths (acetate, glucose, nonanoate, and starch) on CH₄ production and associated methanogens in iron-rich paddy soil over 90 days of anaerobic incubation. We found that glucose and starch were the more preferential substrates for liberating methane compared to acetate, and the rate was also faster. Nonanoate was unable to support methane production. Methanosarcinales and Methanobacteriales were the most predominant methanogenic archaea as shown by 16S rRNA gene sequencing, though their abundance changed over time. Additionally, a significantly higher content of iron-reducing bacteria was observed in the glucose and starch treatments, and it was significantly positively correlated with the copy number of the methanogenic mcrA gene. Together, we confirmed the methanogenic capacity of different carbon sources and their related microorganisms. We also showed that iron oxides play a central role in regulating methane emissions from paddy soils and need more attention to be paid to them.

Bio-imaging with the helium-ion microscope: A review

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

Mechanisms of toxicity by and resistance to ferrous iron in anaerobic systems

Iron is an essential element for nearly all life on Earth, primarily for its value as a redox active cofactor. Iron exists predominantly in two biologically relevant redox states: ferric iron, the oxidized state (Fe³⁺), and ferrous iron, the reduced state (Fe²⁺). Fe²⁺ is well known to facilitate electron transfer reactions that can lead to the generation of reactive oxygen species. Less is known about why iron is toxic to cells in the absence of oxygen, yet this phenomenon is critically important for our understanding of life on early Earth and in iron-rich ecosystems today. In this brief review, we will highlight our current understanding of anaerobic Fe²⁺ toxicity, focusing on molecular mechanistic studies in several model systems.