Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

Pérez‐Rodríguez, Ileana; Rawls, Matthew; Coykendall, D. Katharine; Foustoukos, Dionysis I.

doi:10.1099/ijsem.0.000798

Cited by 25 publications

(10 citation statements)

References 42 publications

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“…Thus, the samples from river and BHB02, which have a greater IRB diversity, exhibited increased activity of Fe(III) reduction in enrichment cultures. Deferrisoma spp., which have been previously observed in shallow-water or deep-sea hydrothermal vents (Pérez-Rodríguez et al 2016;Slobodkina et al 2012), had the highest relative IRB abundance in riverine sediments' enrichment cultures (YR1 and YR2). Ethanol is an important intermediate metabolite of acetate and can also be used as an electron donor for IRB.…”

Section: Discussionsupporting

confidence: 50%

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary

Zhang

Liu

Zheng

et al. 2019

Mar Life Sci Technol

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Rivers are the primary contributors of iron and other elements to the global oceans. Iron-reducing bacteria play an important biogeochemical role in coupling the iron and carbon redox cycles. However, the extent of changes in community structures and iron-reduction activities of iron-reducing bacteria in riverine and coastal marine sediments remains unclear. This study presents information on the spatial patterns and relative abundance of iron-reducing bacteria in sediments of the Yellow River estuary and the adjacent Bohai Sea. High-throughput sequencing of bacterial 16S rRNA found that the highest relative abundances and diversities were from the estuary (Yellow River-Bohai Sea mixing zone). Pseudomonas, Thiobacillus, Geobacter, Rhodoferax, and Clostridium were the most abundant putative iron-reducing bacteria genera in the sediments of the Yellow River. Vibrio, Shewanella, and Thiobacillus were the most abundant in the sediments of the Bohai Sea. The putative iron-reducing bacterial community was positively correlated with the concentrations of total nitrogen and ammonium in coastal marine sediments, and was significantly correlated with the concentration of nitrate in river sediments. The riverine sediments, with a more diverse iron-reducing bacterial community, exhibited increased activity of Fe(III) reduction in enrichment cultures. The estuary-wide high abundance of putative iron-reducing bacteria suggests that the effect of river-sea interaction on bacterial distribution patterns is high. The results of this study will help the understanding of the biogeochemical cycling of iron in riverine and coastal marine environments. Keywords Iron-reducing bacteria • River • Coastal sea • River-sea interaction Edited by Chengchao Chen.

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Section: Discussionsupporting

confidence: 50%

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary

Zhang

Liu

Zheng

et al. 2019

Mar Life Sci Technol

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“…While not observed in D. camini , a related Deferrisoma sp. has previously demonstrated this capability (Pérez-Rodríguez et al, 2016 ).…”

Section: Resultsmentioning

confidence: 92%

“…Deferrisoma spp. are known to be FeRB (Slobodkina et al, 2012 ; Pérez-Rodríguez et al, 2016 ), and although the exact mechanism for Fe(III) reduction has not been described in this organism, the published genome for D. camini S3R1 encodes a homolog of the Geobacter- like pcc -porin (IMG gene ID 2517273319) and accompanying c -cyts that were predicted in the EET system model (Shi et al, 2016 ). Although the c- cyts in D. camini were predicted to be only periplasmic, extracellular c- cyts were detected elsewhere in the genomes.…”

Section: Resultsmentioning

confidence: 99%

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs

Fortney

Converse

et al. 2018

Front. Microbiol.

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Iron (Fe) redox-based metabolisms likely supported life on early Earth and may support life on other Fe-rich rocky planets such as Mars. Modern systems that support active Fe redox cycling such as Chocolate Pots (CP) hot springs provide insight into how life could have functioned in such environments. Previous research demonstrated that Fe- and Si-rich and slightly acidic to circumneutral-pH springs at CP host active dissimilatory Fe(III) reducing microorganisms. However, the abundance and distribution of Fe(III)-reducing communities at CP is not well-understood, especially as they exist in situ. In addition, the potential for direct Fe(II) oxidation by lithotrophs in CP springs is understudied, in particular when compared to indirect oxidation promoted by oxygen producing Cyanobacteria. Here, a culture-independent approach, including 16S rRNA gene amplicon and shotgun metagenomic sequencing, was used to determine the distribution of putative Fe cycling microorganisms in vent fluids and sediment cores collected along the outflow channel of CP. Metagenome-assembled genomes (MAGs) of organisms native to sediment and planktonic microbial communities were screened for extracellular electron transfer (EET) systems putatively involved in Fe redox cycling and for CO2 fixation pathways. Abundant MAGs containing putative EET systems were identified as part of the sediment community at locations where Fe(III) reduction activity has previously been documented. MAGs encoding both putative EET systems and CO2 fixation pathways, inferred to be FeOB, were also present, but were less abundant components of the communities. These results suggest that the majority of the Fe(III) oxides that support in situ Fe(III) reduction are derived from abiotic oxidation. This study provides new insights into the interplay between Fe redox cycling and CO2 fixation in sustaining chemotrophic communities in CP with attendant implications for other neutral-pH hot springs.

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“…The final pH of the medium was pH 6.3–6.5. Strain EPR-M T was isolated by seven consecutive series of dilutions at 40 °C and confirmed as a pure culture by microscopy observations, 16S rRNA gene analysis (as described in [28]) and, ultimately, by sequencing EPR-M T ’s full genome [29]. Strain HR-1, grown here in the same medium conditions as strain EPR-M T , was previously isolated from an Fe mat at Lō'ihi Seamount [30].…”

Section: Full-textmentioning

confidence: 99%

Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter

Pérez‐Rodríguez

Choi

Abuyen

et al. 2021

International Journal of Systematic and Evolutionary Microbiology

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A novel mesophilic, anaerobic, mixotrophic bacterium, with designated strains EPR-MT and HR-1, was isolated from a semi-extinct hydrothermal vent at the East Pacific Rise and from an Fe-mat at Lō'ihi Seamount, respectively. The cells were Gram-negative, pleomorphic rods of about 2.0 µm in length and 0.5 µm in width. Strain EPR-MT grew between 25 and 45 °C (optimum, 37.5–40 °C), 10 and 50 g l−1 NaCl (optimum, 15–20 g l−1) and pH 5.5 and 8.6 (optimum, pH 6.4). Strain HR-1 grew between 20 and 45 °C (optimum, 37.5–40 °C), 10 and 50 g l−1 NaCl (optimum, 15–25 g l−1) and pH 5.5 and 8.6 (optimum, pH 6.4). Shortest generation times with H2 as the primary electron donor, CO2 as the carbon source and ferric citrate as terminal electron acceptor were 6.7 and 5.5 h for EPR-MT and HR-1, respectively. Fe(OH)3, MnO2, AsO4 3-, SO4 2-, SeO4 2-, S2O3 2-, S0 and NO3 - were also used as terminal electron acceptors. Acetate, yeast extract, formate, lactate, tryptone and Casamino acids also served as both electron donors and carbon sources. G+C content of the genomic DNA was 59.4 mol% for strain EPR-MT and 59.2 mol% for strain HR-1. Phylogenetic and phylogenomic analyses indicated that both strains were closely related to each other and to Geothermobacter ehrlichii , within the class δ- Proteobacteria (now within the class Desulfuromonadia ). Based on phylogenetic and phylogenomic analyses in addition to physiological and biochemical characteristics, both strains were found to represent a novel species within the genus Geothermobacter , for which the name Geothermobacter hydrogeniphilus sp. nov. is proposed. Geothermobacter hydrogeniphilus is represented by type strain EPR-MT (=JCM 32109T=KCTC 15831T=ATCC TSD-173T) and strain HR-1 (=JCM 32110=KCTC 15832).

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Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea

Cited by 25 publications

References 42 publications

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary

The differentiation of iron-reducing bacterial community and iron-reduction activity between riverine and marine sediments in the Yellow River estuary

Investigating the Composition and Metabolic Potential of Microbial Communities in Chocolate Pots Hot Springs

Geothermobacter hydrogeniphilus sp. nov., a mesophilic, iron(III)-reducing bacterium from seafloor/subseafloor environments in the Pacific Ocean, and emended description of the genus Geothermobacter

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