David Barrie Johnson

Bangor University · School of Biological Sciences

Metals have been used for thousands of years and have had pivotal roles in the development of human civilisation. Both the scale and range of metals that are used in modern and emerging technologies, and industrial and domestic applications have increased vastly in recent years. Harnessing microorganisms to facilitate the extraction and recovery of...

The microbial ecology of acidic mine and sulfide cave ecosystems is well characterised with respect to aquatic communities, typically revealing low taxonomic complexity and dominance by a relatively limited number of cosmopolitan acidophilic bacterial and archaeal taxa. Whilst pH, temperature, and geochemistry are recognised drivers of diversity in...

Ten strains of extremely acidophilic bacteria, isolated from different environments form a distinct monophyletic clade within the phylum Firmicutes. Comparison of complete genomes of the proposed type strains confirm that they comprise two genera (proposed names Sulfoacidibacillus and Ferroacidibacillus), and at least three species (S. ferrooxidans...

Acidophiles are a defined group of extremophilic microorganisms that have distinct physiological features that separate them from the rest of the biosphere. Those that populate biomining operations and environments that are impacted by mining (acid mine drainage waters, etc.) often face additional challenges and stresses, such as elevated concentra...

Sulfate-reducing bacteria (SRB) catalyse the dissimilatory reduction of sulfate to hydrogen sulfide using a wide range of small molecular weight organic compounds, and hydrogen, as electron donors. Here we report the effects of different combinations of small molecular weight alcohols on the performance and bacterial composition of a moderately low...

The draft whole-genome sequence of the extremely acidophilic and novel Firmicutes strain S ⁰ AB is reported. The genome comprises 3.3 Mbp and has a GC content of 43.72%. In total, 3,240 protein-coding genes, 56 tRNA genes, and 11 rRNA genes were predicted.

We report the draft genome sequence of the Firmicute strain Y002, a facultatively anaerobic, acidophilic bacterium that catalyzes the dissimilatory oxidation of iron and sulfur and the reduction of ferric iron. Analysis of the genome (2.9 Mb; G+C content, 46 mol%) provided insights into its ability to grow in extremely acidic geothermal environment...

Limonitic layers of the regolith, which are often stockpiled as waste materials at laterite mines, commonly contain significant concentrations of valuable base metals, such as nickel, cobalt, and manganese. There is currently considerable demand for these transition metals, and this is projected to continue to increase (alongside their commodity va...

A heterogeneous Pd catalyst, biologically-mineralized palladium nanoparticles (bio-Pd), was synthesized using sulfidogenic bacteria which reduced soluble Pd(II) to catalytically-active Pd-nanoparticles (NPs). Heat treatment (processing) of bio-Pd (5 or 20 wt% on the cells) made by Desulfovibrio desulfuricans evolved supported Pd-catalyst comprising...

Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to have evolved from type III systems through the loss of the target-cleaving nuclease and partial deterioration of the large subunit of the effector complex. All known type IV CRISPR-Cas systems are encoded on plasmids, integrative and conjugative elements (...

Packed bed bioreactors were used to remove soluble manganese from a synthetic mine water as the final stage of an integrated bioremediation process. The synthetic mine water had undergone initial processing using a sulfidogenic bioreactor (pH 4.0–5.5) which removed all transition metals present in elevated concentrations (Cu, Ni, Zn and Co) apart f...

Members of the genus Acidithiobacillus, now ranked within the class Acidithiobacillia, are model bacteria for the study of chemolithotrophic energy conversion under extreme conditions. Knowledge of the genomic and taxonomic diversity of Acidithiobacillia is still limited. Here, we present a systematic analysis of nearly 100 genomes from the class s...

Experiments were carried out to examine the oxido-reduction of manganese by extremely acidophilic Acidithiobacillus spp. grown with either elemental sulfur or molecular hydrogen as electron donor. While there was no evidence for manganese (II) oxidation, dissolution of solid phase manganese dioxide was observed in cultures grown aerobically on both...

Hydrogen can serve as an electron donor for chemolithotrophic acidophiles, especially in the deep terrestrial subsurface and geothermal ecosystems. Nevertheless, the current knowledge of hydrogen utilization by mesophilic acidophiles is minimal. A multi-omics analysis was applied on Acidithiobacillus ferrooxidans growing on hydrogen, and a respirat...

The genus Acidihalobacter has three validated species, Acidihalobacter ferrooxydans , Acidihalobacter prosperus and Acidihalobacter aeolinanus , all of which were isolated from Vulcano island, Italy. They are obligately chemolithotrophic, aerobic, acidophilic and halophilic in nature and use either ferrous iron or reduced sulphur as electron donors...

A novel, obligately anaerobic, acidophilic bacterium (strain I2511), isolated from sediment in an abandoned copper mine, was shown to couple the oxidation of organic electron donors to the reduction of both zero-valent sulfur and ferric iron in acidic media. The isolate was an obligate heterotroph that used a variety of organic compounds as electro...

Reactive pyritic mine tailings can be populated by chemolithotrophic prokaryotes that enhance the solubilities of many metals, though iron-reducing heterotrophic microorganisms can inhibit the environmental risk posed by tailings by promoting processes that are the reverse of those carried out by pyrite-oxidising autotrophic bacteria. A strain (IT2...

Experiments were carried out to test the amenabilities of mineral deposits that contained cobalt deported in arseno-sulfide (cobaltite) and arsenide (skutterudite) minerals, to oxidative bioleaching at mesophilic temperatures and low pH. An ore sample from the Iron Mask deposit (Canada) and a mineral concentrate from a working mine (Bou Azzer, Moro...

The abundance of limonitic laterite ores in tropical and sub-tropical areas represents a large, and mostly unexploited, cobalt resource. Bioprocessing oxidised ores, and also waste materials such as tailings and processing residues, using acidophilic microorganisms to catalyse the reductive dissolution of iron and manganese minerals, is an environm...

Strain MG, isolated from an acidic pond sediment on the island of Milos (Greece), is proposed as a novel species of ferrous iron- and sulfur-oxidizing Acidithiobacillus. Currently, four of the eight validated species of this genus oxidize ferrous iron, and strain MG shares many key characteristics with these four, including the capacities for catal...

Environmental pollution associated with metal-contaminated waters discharging from abandoned mine sites is a global issue. Remediation using passive systems, such as constructed wetlands, has several significant detractions which active treatment systems that harness the abilities of hydrogen sulfide-generating bacteria to immobilize transition met...

Acid mine/rock drainage (AMD/ARD) is generated by the microbially-accelerated oxidative dissolution of sulfide minerals in working and abandoned mine sites, and some natural environments. Iron-oxidizing microorganisms (IOM) regenerate the oxidant Fe3+, while sulfur-oxidizing microorganisms (SOM) contribute to AMD/ARD by generating H2SO4 via the oxi...

The study of extreme acidophiles, broadly defined as microorganisms that grow optimally at pH values below 3, was initiated by the discovery by Waksman and Joffe in the early 1900s of a bacterium that was able to live in the dilute sulfuric acid it generated by oxidizing elemental sulfur. The number of known acidophiles remained relatively small un...

The geothermal Copahue-Caviahue (GCC) system (Argentina) is an extreme acidic environment, dominated by the activity of the Copahue volcano. Environments characterized by low pH values, such as volcanic areas, are of particular interest for the search of acidophilic microorganisms with application in biotechnological processes. In this work, sulfat...

Two laboratory-scale bioreactors, operated in flow-through mode at fixed pH values, were set up to generate sulfuric acid from elemental sulfur at different temperatures using consortia of sulfur-oxidizing acidophilic prokaryotes. One bioreactor, maintained at 30 °C, was dominated by Acidithiobacillus albertensis when operated at pH 1.0 and by Sulf...

The genus Acidithiobacillus currently includes seven species with validly published names, which fall into two major groups, those that can oxidize ferrous iron and those that do not. All seven species can use zero-valent sulfur and reduced sulfur oxy-anions as electron donors, are obligately chemolithotrophic and acidophilic bacteria with pH growt...

Biogas-energy is marginally profitable against the “parasitic” energy demands of processing biomass. Biogas involves microbial fermentation of feedstock hydrolyzate generated enzymatically or thermochemically. The latter also produces 5-hydroxymethyl furfural (5-HMF) which can be catalytically upgraded to 2, 5-dimethyl furan (DMF), a “drop in fuel....

Recent research has demonstrated the applicability of a biotechnological approach for extracting base metals using acidophilic bacteria that catalyze the reductive dissolution of ferric iron oxides from oxidized ores, using elemental sulfur as an electron donor. In Brazil, lateritic deposits are frequently associated with phosphate minerals such as...

Redox transformations of sulfur, involving dissimilatory and assimilatory oxidation and reduction reactions, occurs in water bodies and terrestrial environments worldwide, leading to dynamic cycling of this element throughout the biosphere. In cases where zero-valent (elemental) sulfur, sulfate and other oxidized forms are used as electron acceptor...

[Figure presented] Acidithiobacillus ferrooxidans is by far the most widely studied of all extremely acidophilic prokaryotes. While it is found in many types of natural low-pH environments in a variety of geoclimatic contexts, it has been more widely cited in anthropogenic (mostly mine-impacted) environments. It is responsible for accelerating the...

The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response...

A sulfidogenic bioreactor, operated at low pH (4–5), was set up and used to remove transition metals (copper, nickel, cobalt, and zinc) from a synthetic mine water, based on the chemistry of a moderately acidic (pH 5) drainage stream at an operating copper mine in Brazil. The module was constructed as an upflow biofilm reactor, with microorganisms...

The current global demand in terms of both the amounts and range of metals for industrial and domestic use greatly exceeds that at any previous time in human history. Recycling is inadequate to meet these needs and therefore mining primary metal ores will continue to be a major industry in the foreseeable future. The question of how metal mining ca...

The ability of acidophilic bacteria to grow in the presence of elevated concentrations of cationic transition metals, though varying between species, has long been recognized to be far greater than that of most neutrophiles. Conversely, their sensitivity to both inorganic and organic anions, with the notable exception of sulfate, has generally been...

Pregnant leach solutions (PLS) resulting from (bio)leaching of copper ores are characterized by low pH, high concentrations of Fe (III), Cu, Zn and often significant amounts of Ni and Co. In order to make the metals available for further processing they require selective recovery form the acidic, multi-metal solution. Commonly, copper and other bas...

Deep in situ biomining (DISB) offers the potential for exploiting metal-rich ore bodies that are currently difficult or non-economic to access, with far less environmental impact than current deep or opencast mining practices. DISB is being developed within the EU Horizon 2020 project “BIOMOre” which targets a calcareous sedimentary copper ore, kup...

Leptospirillum ferriphilum and Acidithiobacillus caldus are both thermotolerant acidophilic bacteria that frequently co-exist in natural and man-made environments, such as biomining sites. Both are aerobic chemolithotrophs; L. ferriphilum is known only to use ferrous iron as electron donor, while A. caldus can use zero-valent and reduced sulfur, an...

Extremely acidic environments have global distribution and can have natural or, increasingly, anthropogenic origins. Extreme acidophiles grow optimally at pH 3 or less, have multiple strategies for tolerating stresses that accompany high levels of acidity and are scattered in all three domains of the tree of life. Metagenomic studies have expanded...

The type strain of the mineral-oxidizing acidophilic bacterium Acidithiobacillus ferridurans was grown in liquid medium containing elevated concentrations of sodium chloride with hydrogen as electron donor. While it became more tolerant to chloride, after about 1 year, the salt-stressed acidophile was found to have lost its ability to oxidize iron,...

Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genom...

A sustainable, environmentally-benign and cost effective biotechnology for extracting and recovering base metals from deep-buried base metal deposits (“deep in situ biomining”) is being developed within the EU Horizon 2020 project “BioMOre”. This involves: (i) opening flow channels within the ore body; (ii) acid leaching to dissolve acid-labile min...

“Deep in situ biomining”, widely considered to be a potentially environmentally-benign and cost effective biotechnology for extracting and recovering base metals from deep-buried base metal deposits, is being developed within the EU Horizon 2020 project “BioMOre”. Data are presented from non-aerated column experiments in which a saline, calcareous...

The major objective of the EU Horizon 2020 project “BioMOre” is the technical realization of indirect in situ leaching of Kupferschiefer sandstone and black shale ore by a ferric iron lixiviant generated by a mixed culture of autotrophic, acidophilic, iron-oxidizing bacteria and archaea in a ferric iron-generating bioreactor (FIGB). These organisms...

Two different species of acidophilic micro-algae were grown in axenic culture, biomass harvested and injected into a low pH sulfate-reducing bioreactor, to act as a substrate for biosulfidogenesis. The hydrogen sulfide generated was used to precipitate copper in an off-line vessel, and the bioreactor pH was maintained by automated addition of a pH...

Pregnant leach solutions (PLS) resulting from bioleaching of copper concentrate from Kupferschiefer are characterized by low pH and high concentrations of Fe, Cu, Zn as well as significant amounts of Ni and Co. In order to recover the valuable metals for further processing, chemical methods and a novel biological-induced technique that promotes sel...

Lateritic deposits containing rare earth elements (REE) are important resources in Brazil, where monazite is the main REE-bearing mineral and is frequently associated with iron hydroxy-oxides and quartz. In order to recover valuable metals such as REE and uranium, experiments were carried out under reductive mineral dissolution using Acidithiobacil...

The iron-oxidizing species Acidithiobacillus ferrivorans is one of few acidophiles able to oxidize ferrous iron and reduced inorganic sulfur compounds at low temperatures (<10°C). To complete the genome of At. ferrivorans strain CF27, new sequences were generated, and an update assembly and functional annotation were undertaken, followed by a compa...

Trehalose biosynthesis in Acidithiobacillus ferrivorans CF27.(A) Various pathways for trehalose biosynthesis in At. ferrivorans CF27. Functional description of proteins are: TreS, trehalose synthase; GlgX, glycogen debranching protein; TreZ, malto-oligosyltrehalose trehalohydrolase; TreY, malto-oligosyltrehalose synthase. The trehalose operon is sh...

(A) Synteny of chemotaxis and flagellar biosynthesis genes between Acidithiobacillus species. The upper 3anel shows the cluster of genes involved in chemotaxis and flagellar biosynthesis in At. ferrivorans CF27 (see Supplementary Table S5 for AFERRI_v2_numbers) while the lower panel shows these clusters in the other Acidithiobacillus genomes. In be...

Venn diagram of orthologous groups (OG) from seven Acidithiobacillus genomes. The strain names are: CF27, At. ferrivorans CF27; SS3, At. ferrivorans SS3; ATCC 23270, At. ferrooxidans ATCC 23270T; ATCC 53993, At. ferrooxidans ATCC 53993; ATCC 19377, At. thiooxidans ATCC 19377T; SM1, At. caldus SM-1; and ATCC 51756, At. caldus ATCC 51756T. OGs are di...

Transition metal and arsenic resistance mechanisms in Acidithiobacillus spp.. Organization of cus (A), corA (B), mer (C) and ars (D) operons in At. ferrivorans CF27 (see Supplementary Table S5 for AFERRI_v2_numbers) and other Acidithiobacillus genomes. The strain names are: CF27, At. ferrivorans CF27; SS3, At. ferrivorans SS3; ATCC 23270, At. ferro...

Biomining of base and precious metal-containing sulfidic ores and concentrates is an important global biotechnology. Currently, mineral bio-processing is carried out in dumps, heaps and stirred tanks located on the land surface. An alternative approach, “deep in situ biomining”, would solubilise target metals from fractured ore bodies buried deep (...

Four novel strains of Acidobacteria were isolated from water samples taken from pit lakes at two abandoned metal mines in the Iberian Pyrite Belt mining district, south-west Spain. Three of the isolates belong to the genus Acidicapsa (MCF9(T), MCF10(T), and MCF14) and one of them to the genus Granulicella (MCF40(T)). All isolates are moderately aci...

Dissimilatory reduction of sulfate, mediated by various species of sulfate-reducing bacteria (SRB) and a few characterized species of archaea, can be used to remediate acid mine drainage (AMD). Hydrogen sulfide (H2S/HS⁻) generated by SRB removes toxic metals from AMD as sulfide biominerals. For this, SRB are usually housed in separate reactor vesse...

Experiments were carried out to examine redox transformations of copper and chromium by acidophilic bacteria (Acidithiobacillus, Leptospirillum, and Acidiphilium), and also of iron (III) reduction by Acidithiobacillus spp. under aerobic conditions. Reduction of iron (III) was found with all five species of Acidithiobacillus tested, grown aerobicall...

The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Pre...

Demand for cobalt is increasing worldwide, primarily as a result of its use in rechargeable batteries, super-alloys, and the chemicals industry. Extraction and recovery of cobalt from primary ores and waste materials using (novel) bioprocessing approaches has been suggested to have significant potential as a means to secure the supply of this criti...