Genomic potential for photoferrotrophy in a seasonally anoxic Boreal Shield lake

AbstractPhotoferrotrophy, the light-induced oxidation of ferrous iron, is thought to have contributed to primary production within Earth’s early anoxic oceans yet is presumed to be of little modern environmental relevance. Here we use genome-resolved metagenomics and enrichment cultivation to explore the potential for photoferrotrophy in the anoxic water columns of globally abundant Boreal Shield lakes. We recovered four high-completeness and low-contamination draft genome bins assigned to the class Chlorobia (formerly phylum Chlorobi) from environmental metagenome data and enriched two novel sulfide-oxidizing species, also from the Chlorobia. The sequenced genomes of both enriched species, including the novel “Candidatus Chlorobium canadense”, encoded the cyc2 candidate gene marker for iron oxidation, suggesting the potential for photoferrotrophic growth. Surprisingly, one of the environmental genome bins encoded cyc2 and lacked sulfur oxidation gene pathways altogether. Despite the presence of cyc2 in the corresponding draft genome, we were unable to induce photoferrotrophy in “Ca. Chlorobium canadense”, suggesting that yet-unexplored mechanisms regulate expression of sulfide and ferrous iron oxidation gene systems, or that previously unrecognized functions for this outer membrane cytochrome exist. Doubling the known diversity of Chlorobia-associated cyc2 genes, metagenome data showed that putative photoferrotrophic populations occurred in one lake but that only sulfide-oxidizing populations were present in a neighboring lake, implying that strong ecological or geochemical controls govern the favourability of photoferrotrophy in aquatic environments. These results indicate that anoxygenic photoautotrophs in Boreal Shield lakes could have unexplored metabolic diversity that is controlled by ecological and biogeochemical drivers pertinent to understanding Earth’s early microbial communities.

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Two-Component Systems in the Regulation of Sulfur and Ferrous Iron Oxidation in Acidophilic Bacteria

10.5772/intechopen.96553 ◽

2021 ◽

Author(s):

Lifeng Li ◽

Zhaobao Wang

Keyword(s):

Ferrous Iron ◽

Response Regulator ◽

Iron Oxidation ◽

Regulatory System ◽

Sulfur Oxidation ◽

Acidophilic Bacteria ◽

Ferrous Iron Oxidation ◽

Two Component ◽

Two Component Systems ◽

External Stimuli

The two-component system (TCS) is a regulatory system composed of a sensor histidine kinase (HK) and a cytoplasmic response regulator (RR), which participates in the bacterial adaptation to external stimuli. Sulfur oxidation and ferrous iron oxidation are basic energy metabolism systems for chemoautotrophic acidophilic bacteria in acid mine environments. Understanding how these bacteria perceive and respond to complex environmental stimuli offers insights into oxidization mechanisms and the potential for improved applications. In this chapter, we summarized the TCSs involved in the regulation of sulfur and ferrous iron metabolic pathways in these acidophilic bacteria. In particular, we examined the role and molecular mechanism of these TCSs in the regulation of iron and sulfur oxidation in Acidithiobacillus spp.. Moreover, research perspectives on TCSs in acidophilic bacteria are discussed in this section.

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Dispersion of sulfur enables sulfur oxidation before iron oxidation in Acidithiobacillus ferrooxidans: A valuable formulation for the genetic engineering toolbox

10.22541/au.161486164.44901503/v1 ◽

2021 ◽

Author(s):

Yuta Inaba ◽

Timothy Kernan ◽

Alan West ◽

Scott Banta

Keyword(s):

Acidithiobacillus Ferrooxidans ◽

Ferrous Iron ◽

Iron Reduction ◽

Fluorescent Protein ◽

Energy Content ◽

Iron Oxidation ◽

Sulfur Oxidation ◽

Surface Hydrophobicity ◽

Substrate Utilization Pattern ◽

Ferrous Iron Oxidation

Acidithiobacillus ferrooxidans are acidophilic chemolithoautotrophs that are commonly reported to exhibit diauxic population growth behavior where ferrous iron is oxidized before elemental sulfur when both are available, despite the higher energy content of sulfur. We have discovered sulfur dispersion formulations that enables sulfur oxidation before ferrous iron oxidation. The oxidation of dispersed sulfur can lower the culture pH within days below the range where aerobic ferrous iron oxidation can occur so that ferric iron reduction occurs which had previously been reported over extended incubation periods with untreated sulfur. Therefore, we demonstrate that this substrate utilization pattern is strongly dependent on the cell loading in relation to sulfur concentration, sulfur surface hydrophobicity, and the pH of the culture. Our dispersed sulfur formulation, lig-sulfur, can be used to support the rapid antibiotic selection of plasmid-transformed cells, which is not possible in liquid cultures where ferrous iron is the main source of energy for these acidophiles. Furthermore, we find that media containing lig-sulfur supports higher production of green fluorescent protein (GFP) compared to media containing ferrous iron. The use of dispersed sulfur is a valuable new tool for the development of engineered A. ferrooxidans strains and it provides a new method to control iron and sulfur oxidation behaviors.

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Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways

Microbiology ◽

10.1099/mic.0.044537-0 ◽

2011 ◽

Vol 157 (1) ◽

pp. 111-122 ◽

Cited By ~ 79

Author(s):

Agnès Amouric ◽

Céline Brochier-Armanet ◽

D. Barrie Johnson ◽

Violaine Bonnefoy ◽

Kevin B. Hallberg

Keyword(s):

Ferrous Iron ◽

Iron Oxidation ◽

Sulfur Oxidation ◽

Public And Private ◽

Phenotypic Differences ◽

Ferrous Iron Oxidation ◽

Sulfur Oxidizing ◽

Multiple Species ◽

High Degree ◽

Private Collections

Autotrophic acidophilic iron- and sulfur-oxidizing bacteria of the genus Acidithiobacillus constitute a heterogeneous taxon encompassing a high degree of diversity at the phylogenetic and genetic levels, though currently only two species are recognized (Acidithiobacillus ferrooxidans and Acidithiobacillus ferrivorans). One of the major functional disparities concerns the biochemical mechanisms of iron and sulfur oxidation, with discrepancies reported in the literature concerning the genes and proteins involved in these processes. These include two types of high-potential iron–sulfur proteins (HiPIPs): (i) Iro, which has been described as the iron oxidase; and (ii) Hip, which has been proposed to be involved in the electron transfer between sulfur compounds and oxygen. In addition, two rusticyanins have been described: (i) rusticyanin A, encoded by the rusA gene and belonging to the well-characterized rus operon, which plays a central role in the iron respiratory chain; and (ii) rusticyanin B, a protein to which no function has yet been ascribed. Data from a multilocus sequence analysis of 21 strains of Fe(II)-oxidizing acidithiobacilli obtained from public and private collections using five phylogenetic markers showed that these strains could be divided into four monophyletic groups. These divisions correlated not only with levels of genomic DNA hybridization and phenotypic differences among the strains, but also with the types of rusticyanin and HiPIPs that they harbour. Taken together, the data indicate that Fe(II)-oxidizing acidithiobacilli comprise at least four distinct taxa, all of which are able to oxidize both ferrous iron and sulfur, and suggest that different iron oxidation pathways have evolved in these closely related bacteria.

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Ferrous iron oxidation in moderately thermophilic acidophile Sulfobacillus sibiricus N1T

Canadian Journal of Microbiology ◽

10.1139/w10-063 ◽

2010 ◽

Vol 56 (10) ◽

pp. 803-808 ◽

Cited By ~ 10

Author(s):

Tatiana Y. Dinarieva ◽

Anna E. Zhuravleva ◽

Oksana A. Pavlenko ◽

Iraida A. Tsaplina ◽

Alexander I. Netrusov

Keyword(s):

Ferrous Iron ◽

High Performance ◽

Iron Oxidation ◽

Early Exponential Phase ◽

Moderately Thermophilic ◽

Terminal Oxidases ◽

Cytochrome Bo ◽

Ferrous Iron Oxidation ◽

Transport Chain ◽

Membrane Bound

The iron-oxidizing system of a moderately thermophilic, extremely acidophilic, gram-positive mixotroph, Sulfobacillus sibiricus N1T, was studied by spectroscopic, high-performance liquid chromatography and inhibitory analyses. Hemes B, A, and O were detected in membranes of S. sibiricus N1T. It is proposed that the electron transport chain from Fe2+ to O2 is terminated by 2 physiological oxidases: aa3-type cytochrome, which dominates in the early-exponential phase of growth, and bo3-type cytochrome, whose role in iron oxidation becomes more prominent upon growth of the culture. Both oxidases were sensitive to cyanide and azide. Cytochrome aa3 was more sensitive to cyanide and azide, with Ki values of 4.1 and 2.5 µmol·L–1, respectively, compared with Ki values for cytochrome bo3, which were 9.5 µmol·L–1 for cyanide and 7.0 µmol·L–1 for azide. This is the first evidence for the participation of a bo3-type oxidase in ferrous iron oxidation. The respiratory chain of the mixotroph contains, in addition to the 2 terminal oxidases, a membrane-bound cytochrome b573.

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A kinetic model of ferrous iron oxidation by Acidithiobacillus ferrooxidans in a batch culture

Chemical Industry and Chemical Engineering Quarterly ◽

10.2298/ciceq0502059s ◽

2005 ◽

Vol 11 (2) ◽

pp. 59-62 ◽

Cited By ~ 5

Author(s):

Dragisa Savic ◽

Miodrag Lazic ◽

Vlada Veljkovic ◽

Miroslav Vrvic

Keyword(s):

Kinetic Model ◽

Acidithiobacillus Ferrooxidans ◽

Ferrous Iron ◽

Bubble Column ◽

Iron Oxidation ◽

Yield Coefficient ◽

Transfer Rates ◽

Ferrous Iron Oxidation ◽

Menten Kinetic ◽

Kinetics Of

The batch oxidation kinetics of ferrous iron by Acidithiobacillus ferrooxidans were examined at different oxygen transfer rates and pH in an aerated stirred tank and a bubble column. The microbial growth, oxygen consumption rate and ferrous and ferric iron were monitored during the biooxidation. A kinetic model was established on the basis of the Michaelis-Menten kinetic equation for bacterial growth and the constants estimated from experimental data (maximum specific growth rate 0.069 h-1, saturation constant 2.9 g/dm3, and biomass yield coefficient based on ferrous iron 0.003 gd.w./gFe). Values calculated from the model agreed well with the experimental ones regardless of the bioreactor type and pH conditions.

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