Barrie Johnson | Bangor University (original) (raw)

Papers by Barrie Johnson

Applied and Environmental Microbiology, Jan 15, 2010

Applied sciences, May 10, 2021

Environmental Technology, Jan 23, 2016

Microorganisms, Jul 2, 2020

Applied and Environmental Microbiology, Apr 1, 2018

Frontiers in Microbiology, 2022

Limonitic layers of the regolith, which are often stockpiled as waste materials at laterite mines... more 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 values) during the next few decades, due in the most part to their use in battery and renewable technologies. Limonite bioprocessing is an emerging technology that often uses acidophilic prokaryotes to catalyse the oxidation of zero-valent sulphur coupled to the reduction of Fe (III) and Mn (IV) minerals, resulting in the release of target metals. Chromium-bearing minerals, such as chromite, where the metal is present as Cr (III), are widespread in laterite deposits. However, there are also reports that the more oxidised and more biotoxic form of this metal [Cr (VI)] may be present in some limonites, formed by the oxidation of Cr (III) by ma...

Frontiers in Microbiology, 2012

Frontiers in Bioengineering and Biotechnology

Sulfate-reducing bacteria (SRB) catalyse the dissimilatory reduction of sulfate to hydrogen sulfi... more 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 pH sulfidogenic bioreactor (pH 4.0–5.5) operated at 35°C in continuous flow mode. Ethanol alone and methanol or ethanol used in combination with glycerol were evaluated based on their equivalent amounts of carbon. Although evidenced that methanol was utilised as electron donor to fuel sulfidogenesis at pH 5.5, rates of sulfate reduction/sulfide production were negatively impacted when this alcohol was first introduced to the system, though these rates increased in subsequent phases as a result of adaptation of the microbial community. Further increased dosage of methanol again caused rates of sulfidogenesis to decrease. Methanol addition ...

Microbiology Resource Announcements

The draft whole-genome sequence of the extremely acidophilic and novel Firmicutes strain S 0 AB i... more 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.

The CRISPR Journal, 2021

Type IV CRISPR-Cas are a distinct variety of highly derived CRISPR-Cas systems that appear to hav... more 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 (ICEs), or prophages, and are thought to contribute to competition between these elements, although the mechanistic details of their function remain unknown. There is a clear parallel between the compositions and likely origin of type IV and type I systems recruited by Tn7-like transposons and mediating RNA-guided transposition. We investigated the diversity and evolutionary relationships of type IV systems, with a focus on those in Acidithiobacillia, where this variety of CRISPR is particularly abundant and always found on ICEs. Our analysis revealed remarkable evolutionary plasticity of type IV CRISPR-Cas systems, with adaptation and ancillary genes originating from different ancestral CRISPR-Cas varieties, and extensive gene shuffling within the type IV loci. The adaptation module and the CRISPR array apparently were lost in the type IV ancestor but were subsequently recaptured by type IV systems on several independent occasions. We demonstrate a high level of heterogeneity among the repeats with type IV CRISPR arrays, which far exceed the heterogeneity of any other known CRISPR repeats and suggest a unique adaptation mechanism. The spacers in the type IV arrays, for which protospacers could be identified, match plasmid genes, in particular those encoding the conjugation apparatus components. Both the biochemical mechanism of type IV CRISPR-Cas function and their role in the competition among mobile genetic elements remain to be investigated.

Frontiers in microbiology, 2018

A sulfidogenic bioreactor, operated at low pH (4-5), was set up and used to remove transition met... more 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 immobilized on porous glass beads, and was operated continuously for 462 days, during which time the 2 L bioreactor processed >2,000 L of synthetic mine water. The initial treatment involved removing copper (the most abundant metal present) off-line in a stream of HS-containing gas generated by the bioreactor, which caused the synthetic mine water pH to fall to 2.1. The copper-free water was then amended with glycerol (the principal electron donor), yeast extract and basal salts, and pumped directly into the bioreactor where the other three transition metals were precipitated (also as sulfides), concurrent with increased solution pH. Al...

Minerals, 2014

Mining of metals and coals generates solid and liquid wastes that are potentially hazardous to th... more Mining of metals and coals generates solid and liquid wastes that are potentially hazardous to the environment. Traditional methods to reduce the production of pollutants from mining and to treat impacted water courses are mostly physico-chemical in nature, though passive remediation of mine waters utilizes reactions that are catalysed by microorganisms. This paper reviews recent advances in biotechnologies that have been proposed both to secure reactive mine tailings and to remediate mine waters. Empirical management of tailings ponds to promote the growth of micro-algae that sustain populations of bacteria that essentially reverse the processes involved in the formation of acid mine drainage has been proposed. Elsewhere, targeted biomineralization has been demonstrated to produce solid products that allow metals present in mine waters to be recovered and recycled, rather than to be disposed of in landfill.

Frontiers in microbiology, 2017

The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and an... more 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. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within ...

Advances in microbial physiology, 2009

Acidophilic micro-organisms are those (mostly prokaryotes) that grow optimally at pH <3 (extre... more Acidophilic micro-organisms are those (mostly prokaryotes) that grow optimally at pH <3 (extreme acidophiles) or at pH 3-5 (moderate acidophiles). Although once considered to comprise relatively few species of bacteria and archaea, the biodiversity of extreme acidophiles is now recognized as being extensive, both in terms of their physiologies and phylogenetic affiliations. Chemolithotrophy (the ability to use inorganic chemicals as electron donors) is widespread among extreme acidophiles, as ferrous iron and sulfur represent two major available energy sources in many natural and man-made extremely acidic environments. Dissimilatory reduction of iron and sulfur (as a consequence of their use as electron acceptors in oxygen-limited and anoxic environments) are also a major biogeochemical processes in low-pH environments. Acidophiles display considerable diversity in how they assimilate carbon; some are obligate autotrophs, others obligate heterotrophs, while a large number use eit...

Advanced Materials Research, 2007

... Twelve mineral concentrates and one polymetallic ore were subjected to bioleaching by a heter... more ... Twelve mineral concentrates and one polymetallic ore were subjected to bioleaching by a heterogeneous mixed culture of moderately thermophilic ... g/t silver); (iii) copper-nickel (two concentrates); (iv) single concentrates of enargite; zinc (sphalerite) and lead (galena) and a ...

Hydrometallurgy, 2003

The microbiology of water draining two abandoned mines in the UK and of a pilot-scale-constructed... more The microbiology of water draining two abandoned mines in the UK and of a pilot-scale-constructed wetland site at one of the mine sites has been studied. The oxidation of ferrous iron in the acid mine drainage (AMD) of both mines is controlled by indigenous microbes and oxygen concentration, and is limited by the availability of nutrients, especially phosphate. A group of isolates that catalyse the oxidation of ferrous iron at pH >3 (''moderate acidophiles'') were obtained from these samples; these outnumbered the more familiar extremely acidophilic iron oxidisers such as Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans. As in the feed AMD, moderate acidophiles outnumbered the more familiar extremely acidophilic iron-oxidising microbes in the surface water and sediment samples of the aerobic wetlands. Novel heterotrophic microorganisms were also isolated from the wetlands. Phylogenetic analysis based on 16S rRNA gene sequence showed that the moderately acidophilic iron oxidisers are unrelated to other more extremely acidophilic iron oxidisers, and revealed that the most dominant heterotrophic microorganisms include a novel Acidobacterium species and Propionibacterium acnes. These results suggest an important role for previously unknown moderately acidophilic iron-oxidising bacteria in the bioremediation of acidic mine drainage waters.

Hydrometallurgy, 2008

The primary copper sulfide mineral chalcopyrite (CuFeS2) is recalcitrant to both chemical and bio... more The primary copper sulfide mineral chalcopyrite (CuFeS2) is recalcitrant to both chemical and biological leaching, due to the supposed passivation of the mineral surface by sulfur and/or ferric iron compounds. Previous work has shown that addition of soluble silver can ...

FEMS Microbiology Reviews, 1993

Bacterial dissimilatory reduction of iron and sulphur in extremely acidic environments is describ... more Bacterial dissimilatory reduction of iron and sulphur in extremely acidic environments is described. Evidence for reduction at two disused mine sites is presented, within stratified 'acid streamers' growths and in sediments from an acid mine drainage stream. A high proportion (approx. 40%) of mesophilic heterotrophic acidophiles were found to be capable of reducing ferric iron (soluble and insoluble forms) under microaerophilic and anoxic conditions. Mixed cultures of Thiobacillus ferrooxidans and Acidiphilium-like isolate SJH displayed cycling of iron in shake flask and fermenter cultures. Oxido-reduction of iron in mixed cultures was determined by oxygen concentration and availability of organic substrates. Some moderately thermophilic iron-oxidising bacteria were also shown to be capable of reducing ferric iron under conditions of limiting oxygen when grown in glycerol/yeast extract or elemental sulphur media. Cycling of iron was observed in pure cultures of these acidophiles. Sulphate-reducing bacteria isolated from acid streamers could be grown in acidified glycerol/yeast extract media (as low as pH 2.9), but not in media used conventionally for their laboratory culture. An endospore-forming, non-motile rod resembling Desulfotomaculum has been isolated. This bacterium has a wide pH spectrum, and appears to be acid-tolerant rather than acidophilic.