FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

Garber, Arkadiy I.; Nealson, Kenneth H.; Okamoto, Akimitsu; McAllister, Sean M.; Chan, Clara S.; Barco, Roman A.; Merino, Nancy

doi:10.3389/fmicb.2020.00037

Cited by 262 publications

(260 citation statements)

References 228 publications

(179 reference statements)

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“…These data could imply environmental populations with high level of strain heterogeneity, as described in [68]. In line with this, it is possible that these genes are present on extrachromosomal elements, which were not reconstructed herein and in previous studies, and explaining the reported di culty to retrieve those genes in Fe(II) oxydizers [40]. The presence of a plasmid in the Wolbachia endosymbiont from Culex pipiens mosquitoes was rst identi ed following similar distinct coverage signature as compared to bacterial genes in ovaries metagenomes [69].…”

Section: An Arsenal Of Genes For Host-symbiont Colonization and Intersupporting

confidence: 48%

“…We realized an HMM pro ling on resulting contigs databases using the program 'anvi-run-hmms' and assigned gene functions using the program 'anvi-run-ncbi-cogs' as well as KEGG function with kofamscan [39]. We then used FeGenie to identify canonical iron genes [40].We assigned taxonomy determined by the Genome Taxonomy Database (GTDB) using the anvi-run-scg-taxonomy program. We performed read recruitment analyses with Bowtie v2.3.4 [41].…”

Section: Metagenomic Analysismentioning

confidence: 99%

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Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Cambon‐Bonavita

Aubé

Cueff-Gauchard

et al. 2020

Preprint

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BackgroundMutualistic symbioses between invertebrate animals and chemosynthetic bacteria are at the basis of Life in hydrothermal vent ecosystems. The shrimp Rimicaris exoculata, which dominates animal fauna along the Mid Atlantic Ridge, houses in its cephalothorax a complex bacterial community including Campylobacteria, Gamma- Delta- and some recently discovered iron oxyhydroxides-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane and hydrogen as energy sources. Here, we used a DNA extraction procedure adapted to recalcitrant embedded bacteria and generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic community. We aimed reconstructing symbiotic genomes from specimen collected in three geochemically contrasted vent fields, TAG, Rainbow and Snake Pit to unravel the specificity, variability and adaptation of host-microbes associations.ResultsUsing these data we were able to reconstruct 49 high quality metagenome-assembled genomes (MAGs) from TAG and Rainbow vents fields. Most critically, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (ANI < 77% from the closest relative Ghiorsea bivora isolated from TAG and <88% between each other), suggesting potential novel species. Genes for CBB carbon fixation, iron and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and quorum sensing as well as multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts that co-exist in a single shrimp at both basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further insights into the seemingly functional redundancy between those epibionts revealed important differences. ConclusionThese data highlight microniche partitioning in the Rimicaris holobiont and confirm recent works that show functional diversity enables multiple symbiont strains to coexist in animals from hydrothermal vents.

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Section: An Arsenal Of Genes For Host-symbiont Colonization and Intersupporting

confidence: 48%

Section: Metagenomic Analysismentioning

confidence: 99%

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Cambon‐Bonavita

Aubé

Cueff-Gauchard

et al. 2020

Preprint

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“…Modern metagenomic studies have shown that potential for both sulfate and Fe 3? reduction is spread also beyond the taxa from which isolates exist (Rasigraf et al 2019;Garber et al 2020).…”

Section: Microbial Communities At the Study Sitesmentioning

confidence: 99%

Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary

et al. 2020

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Methane is produced microbially in vast quantities in sediments throughout the world's oceans. However, anaerobic oxidation of methane (AOM) provides a near-quantitative sink for the produced methane and is primarily responsible for preventing methane emissions from the oceans to the atmosphere. AOM is a complex microbial process that involves several different microbial groups and metabolic pathways. The role of different electron acceptors in AOM has been studied for decades, yet large uncertainties remain, especially in terms of understanding the processes in natural settings. This study reports Keywords Baltic sea Á Methanotrophy Á Radiotracer incubation Á High throughput sequencing Á 16S rRNA gene

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“…Genes involved in iron oxidation or reduction were also searched using FeGenie 75 , commit 30174bb, with default settings.…”

Section: Assessment Of Genomic Potential For Photosynthesis Within Thmentioning

confidence: 99%

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

Tsuji

Shaw

Nagashima

et al. 2020

Preprint

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SummaryChlorophyll-based phototrophy is performed using quinone and/or Fe-S type reaction centers1,2. Unlike oxygenic phototrophs, where both reaction center classes are used in tandem as Photosystem II and Photosystem I, anoxygenic phototrophs use only one class of reaction center, termed Type II (RCII) or Type I (RCI) reaction centers, separately for phototrophy3. Here we report the cultivation and characterization of a filamentous anoxygenic phototroph within the Chloroflexota (formerly Chloroflexi4) phylum, provisionally named ‘Candidatus Chlorohelix allophototropha’, that performs phototrophy using a distinct fourth clade of RCI protein, despite placing sister taxonomically to RCII-utilizing Chloroflexota members. ‘Ca. Chx. allophototropha’ contains chlorosomes, uses bacteriochlorophyll c, and encodes the FMO protein like other RCI-utilizing phototrophs in the Chlorobiales and Chloracidobacterales orders5. ‘Ca. Chx. allophototropha’ also encodes the potential for carbon fixation using the Calvin-Benson-Bassham (CBB) cycle, unlike all known RCI-utilizing phototrophs6. The discovery of ‘Ca. Chx. allophototropha’, as the first representative of a novel Chloroflexota order (i.e., ‘Ca. Chloroheliales’), sheds light on longstanding questions about the evolution of photosynthesis, including the origin of chlorosomes among RCII-utilizing Chloroflexota members5,7. The Chloroflexota is now the only phylum outside the Cyanobacteria containing genomic potential for both quinone and Fe-S type reaction centers and can thus serve as an additional system for exploring fundamental questions about the evolution of photosynthesis.

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FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

Cited by 262 publications

References 228 publications

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Niche Partitioning in the Rimicaris Exoculata Holobiont: The Case of the First Symbiotic Zetaproteobacteria

Influence of electron acceptor availability and microbial community structure on sedimentary methane oxidation in a boreal estuary

Anoxygenic phototrophicChloroflexotamember uses a Type I reaction center

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