Contrasting microbial communities drive iron cycling across global biomes

Abstract

The global iron (Fe) cycle governs important aspects of biosphere function by defining Fe availability thus supporting productivity of terrestrial and ocean ecosystems. However, the link between soil microbiome function to global patterns in terrestrial iron cycling remains poorly investigated. Here, we developed a novel database termed IRon cycle Annotation (IRcyc-A) targeted at discovering and annotating Fe cycle genes within omics data that we validated against known localized patterns of iron cycling. We leveraged this new tool to analyse the Fe cycle of over 220 publicly available soil metagenomes and metatranscriptomes encompassing a wide range of biomes on Earth. We show that the greatest abundance of Fe(III)-reduction and Fe(II)-oxidation genes were attributed to Acidobacteriota and were most abundant in the microbiomes of peatlands and iron sulfide soils, respectively. This is consistent with the high levels of dissolved Fe recorded in rivers draining such areas. In contrast, genes encoding the biosynthesis of siderophores deployed in iron sequestration in response to Fe deficiency peaked in agroecosystems with the majority assigned to Actinomycetota. Siderophore synthesis genes were negatively correlated with Fe(III)-reduction and Fe(II)-oxidation genes, supporting the view of divergent communities under low and high iron availability. Our findings highlight how iron availability shapes terrestrial microbial communities and how microbial processes can in turn contribute to global patterns in terrestrial Fe and C cycling.

Iron Chelation in Soil: Scalable Biotechnology for Accelerating Carbon Dioxide Removal by Enhanced Rock Weathering

“…After initial in-house removal of adapter and index sequences, the cleaned sequencing R1 reads from each metagenome and metatranscriptome were uploaded to the Galaxy Europe server ( ) 44 in FASTQ format and were then converted to FASTA. Each metagenome was functionally annotated against the IRcyc-A protein database 45 using Diamond 46 in its blastx mode (running parameters: E -value cutoff = 0.001, max number of hits = 1, BLAST tabular output containing query length in base pairs and subject length in amino acids) similar to previously utilized methods for Fe cycling gene annotation. 43 IRcyc-A 45 is a curated protein database for the detection and functional annotation of iron cycling genes and whole-microbiome taxonomy (based on the universal single copy gene rpoA ( 47 ) encoding the DNA-directed RNA polymerase α subunit) within omics designed to limit false-positive hits by filtering them off through matching to SwissProt 48 protein sequences (general filter) and gene families paralogous to the iron cycle gene orthologues (specific filter).…”