A commercial process for bioreactor leaching of a nickel concentrate by-product of talc mining has been described previously. It was developed and operated (2016-2018) at about 45-46 degrees C. Further features of bioleaching that concentrate have now been investigated in laboratory-scale reactors with continuous feeds of up to 10% (w/v) solids and an emphasis on temperatures at and a few degrees above that of the commercial process. The sulfur-oxidizing At. caldus was more abundant than the sulfide mineral-oxidizing S. thermosulfidooxidans and Atm. siderophilum at 48 degrees C but was essentially lost with a 3 degrees C temperature rise, simultaneously with a rise in pH and in iron precipitation from solution, without adversely affecting nickel leaching. The relative abundance among bacteria was similar between two reactors operated in series but there was more than a fourfold increase in the relative abundance of the ferrous-iron oxidizing, heterotrophic archaeon Ac. cupricumulans in the secondary reactor, most likely in response to an increase in the acidity as the sulfide concentrate oxidation proceeded.

CO2 is a major nutrient for autotrophic, mineral sulfide-oxidizing bacteria. The uptake and fixation of this carbon source is therefore critical for industrial mineral sulfide bioprocessing. The CO2 concentration influenced growth of five iron- or sulfur-oxidizing acidophiles to different extents. Those less affected by a growth-limiting CO2 concentration included Acidithiobacillus ferrooxidans and Acidithiomicrobium ferrooxidans. Acidithiobacillus ferrooxidans showed efficient uptake of 14CO2 from its concentration in air when previously grown under air while the maximum rate of CO2 uptake by cells previously grown under an enhanced CO2 concentration was only approached when the CO2 was increased to 0.1% v/v in air. In contrast, growth of Sulfobacillus thermosulfidooxidans was more adversely affected by limiting CO2 under air and the CO2 uptake rate was the same in cells grown with limiting or excess CO2. At. ferrooxidans also appeared to fix accumulated CO2 more efficiently than S. thermosulfidooxidans and RT-qPCR confirmed that adaptation of At. ferrooxidans to growth under limiting CO2 included production of form 1A ribulose bis-phosphate carboxylase in place of the form 1Aq enzyme which was predominant during growth under an enhanced CO2 concentration.

A novel thermoacidophilic archeaon, strain J1T (=DSM 112778T,=JCM 34702T), was isolated from a hot pool in a volcanic area of Java, Indonesia. Cells of the strain were irregular, motile cocci of 1.0-1.2 µm diameter. Aerobic, organoheterotrophic growth with casamino acids was observed at an optimum temperature of 70 °C in a range of 55-78 °C and at an optimum pH of 3 in a range of 1.5 to 5. Various organic compounds were utilized, including a greater variety of sugars than has been reported for growth of other species of the genus. Chemolithoautotrophic growth was observed with reduced sulphur compounds, including mineral sulphides. Ferric iron was reduced during anaerobic growth with elemental sulphur. Cellular lipids were calditoglycerocaldarchaeol and caldarchaeol with some derivates. The organism contained the respiratory quinone caldariellaquinone. On the basis of phylogenetic and chemotaxonomic comparison with its closest relatives, it was concluded that strain J1T represents a novel species, for which the name Metallosphaera javensis is proposed. Low DNA-DNA relatedness values (16S rRNA gene <98.4%, average nucleotide identity (ANI) <80.1%) distinguished J1T from other species of the genus Metallosphaera and the DNA G+C content of 47.3% is the highest among the known species of the genus.

Ferrous iron- and sulfur-oxidizing Acidihalobacter species and similar so far unclassified bacteria have been isolated from the islands of Vulcano (Italy) and Milos (Greece), specifically from where seawater was acidified at sulfide-rich geothermal sites. Acidithiobacillus species which tolerated concentrations of chloride that inhibit most Acidithiobacillus spp. were also isolated from sites on both islands: these were At. thiooxidans strains and an unclassified species, Acidithiobacillus sp. strain V1. The potential of salt-tolerant acidophiles for industrial application in promoting copper extraction from mineral sulfides where chloride is naturally present at concentrations which would inhibit most acidophiles, or where seawater rather than fresh water is available, appears to be limited by the sensitivity of ferrous-iron oxidizing Acidihalobacter spp. to copper. However, tolerance of copper and chloride shown by At. thiooxidans strain A7 suggests it could oxidize sulfur and benefit acid leaching if ferric iron or copper was provided as the primary oxidant of sulfide ores.

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 catalyzing the oxidative dissolution of pyrite and for anaerobic growth via ferric iron respiration. Strain MG also grows aerobically on hydrogen and anaerobically on hydrogen coupled to ferric iron reduction. While the 16S rRNA genes of the iron-oxidizing Acidi-thiobacillus species (and strain MG) are located in a distinct phylogenetic clade and are closely related (98-99% 16S rRNA gene identity), genomic relatedness indexes (ANI/dDDH) revealed strong genomic divergence between strain MG and all sequenced type strains of the taxon, and placed MG as the first cultured representative of an ancestral phylotype of iron oxidizing acidithiobacilli. Strain MG is proposed as a novel species, Acidithiobacillus ferrianus sp. nov. The type strain is MG(T) (= DSM 107098(T) = JCM 33084(T)). Similar strains have been found as isolates or indicated by cloned 16S rRNA genes from several mineral sulfide mine sites.

The mineral sulfide-oxidising Acidithiobacillus ferrooxidans has been extensively studied over many years but some fundamental aspects of its metabolism remain uncertain, particularly with regard to its anaerobic oxidation of sulfur. This label-free, liquid chromatography-electron spray ionisation-mass spectrometry-based proteomic analysis estimated relative protein abundance during aerobic and anaerobic growth of At. ferrooxidans. One of its two bc1 complexes, that encoded by the petII operon, was strongly implicated in anaerobic ferric iron-coupled sulfur oxidation, probably in conjunction with two cytochromes. These two cytochromes are homologs of the Cyc2 and Cyc1 proteins that are involved in ferrous iron oxidation. The previously undetected cytochromes apparently associated with anaerobic growth in At. ferrooxidans appear to be absent in many other ferrous iron-oxidising acidophiles that can also reduce ferric iron, which suggests a diversity in the ferric-iron-coupled sulfur oxidation pathways. For aerobic growth of At. ferrooxidans, this analysis was consistent with the generally accepted mechanism for its oxidation of ferrous iron. Unexpectedly, proteins encoded by the petI operon were not abundant and generally not detected in the proteomic analyses of cells grown aerobically on sulfur, although there was some expression of genes of the petI and petII operons in these cells.

The influence of temperature on bioleaching of a copper-silver concentrate of a black shale-ore was observed at 30, 48 and 76 degrees C. Post-leach residues' weights and copper contents decreased with increase in leaching temperature while the iron contents increased through more iron precipitation. A designed, incremental increase in the concentration of copper in solution resulted in Sulfobacillus thermosulfidooxidans replacing a species of Acidithiomicrobium as the dominant iron-and mineral sulfide-oxidizing strain in the mixed culture used at 48 degrees C. The temperature of bioleaching influenced the hydrometallurgical extraction of silver from post-leach residues. Thiosulfate was most effective with a high temperature bioleach residue while ferric chloride and copper/ammonium/thiosulfate was most effective with a low temperature bioleach residue. (C) 2016 Elsevier Ltd. All rights reserved.

The ferrous iron- and sulfur-oxidizing Acidithiomicrobium was the dominant iron-oxidizing bacterium in a mixed culture of moderate thermophiles in a bioreactor with a high concentration of nickel in solution (20 g l(-1)) and a continuous feed of nickel concentrate. This is the first demonstration specifically indicating that this bacterium could be used for industrial processing of a base metal sulfide concentrate. However, its sensitivity to copper determined that it was replaced by Sulfobacillus thermosulfidooxidans in the mixed culture when the feed was a nickel-copper concentrate. The extraction of copper from the nickel-copper concentrate by moderate thermophiles, despite fine grinding of the feed, was relatively poor (50% at 49 degrees C) compared to that achieved with high temperature archaea (92% at 77 degrees C) in single, continuous reactors with 5% w/v concentrate feeds and residence times of 2.7 and 2.5 days respectively. (C) 2016 Elsevier Ltd. All rights reserved.

I.a'mi.a. N.L. fem. n. Iamia arbitrary name formed from the acronym of the Institute of Applied Microbiology at the University of Tokyo, which has made significant contributions to microbiology. Actinobacteria / Acidimicrobiia / Acidimicrobiales / Iamiaceae / Iamia Gram‐stain‐positive rods . Aerobic. Oxidase‐ and catalase‐positive. Mesophilic. The predominant menaquinone is MK‐9(H 6 ). The major whole‐cell fatty acids are C 17:0 , C 17:1 ω8 c , C 15:0 , and C 16:0 . Isolated from the epidermis of a sea cucumber and grown on marine agar. DNA G + C content ( mol %): 74. Type species : Iamia majanohamensis Kurahashi, Fukunaga, Sakiyama, Harayama and Yokota 2009, 871 VP .

•Microbial reduction of ferric iron was coupled to anaerobic sulfur oxidation.•Anoxic conditions enhanced removal of iron from a polysulfide ore environment.•The microbial activity was demonstrated from 30 to 75°C.•At 70°C, anoxic/aerated phase alternation increased base metal leaching yields.

A.ci.di.mi.cro.bi'i.a. N.L. neut. n. Acidimicrobium type genus of the type order; suff. ‐ ia ending to denote a class; N.L. pl. neut. n. Acidimicrobiia the Acidimicrobiales class. Actinobacteria / Acidimicrobiia

Analysis of phylogenomic metrics of a recently released draft genome sequence of the halotolerant, acidophile 'Thiobacillus prosperus' DSM 5130 indicates that it is not a member of the genus Thiobacillus within the class Betaproteobacteria as originally proposed. Based on data from 16S rRNA gene phylogeny, and analyses of multiprotein phylogeny and average nucleotide identity (ANI), we show that it belongs to a new genus within the family Ectothiorhodospiraceae, for which we propose the name Acidihalobacter gen. nov. In accordance, it is proposed that 'Thiobacillus prosperus' DSM 5130 be named Acidihalobacter prosperus gen. nov., sp. nov. DSM 5130(T) (=JCM 30709(T)) and that it becomes the type strain of the type species of this genus.

Mineral sulfide concentrate oxidation by thermoacidophilic archaea was reported in the 1970s with a culture which was described as “possibly related to Sulfolobus” but which contained the species later named as Acidianus brierleyi. In the following two decades, the mineral sulfide-oxidizing capacity of Sulfolobus metallicus became the subject of many studies partly because it appeared to tolerate higher concentrations of copper and solids in bioreactors than those tolerated by the strains of Acidianus and Metallosphaera that were available. However, some bioreactor pilot plant developments followed with mixed cultures dominated by A. brierleyi at 70°C. At higher temperatures, pilot and industrial demonstration plants used mixed cultures dominated by poorly characterized novel species. Most of these novel species will require classification in novel genera to reflect their phylogenetic separation from previously named thermoacidophilic archaea.

A polymetallic sulfide ore from which several metals are commercially extracted has a high pyrrhotite content that results in elevated temperatures in the ore leaching heaps. Laboratory ore columns were inoculated with moderately thermophilic bacteria and thermophilic archaea to assess the influence of microbial activity on leaching of metals from the ore at 47°C and 68°C. The populations of moderately thermophilic bacteria that became established on the ore were dominated by acidophilic Actinobacteria. Excessive precipitation of oxidized iron compounds in the presence of microbial activity hindered extensive leaching from small-scale ore columns (0.7kg ore). Copper extraction was generally delayed in comparison to that of the other target metals (principally nickel and zinc) when ore column effluent solutions remained above about pH 2.5.

Aims To develop a method to detect bacteria from environmental samples that are able to metabolize lignin. Methods and Results A previously developed UVvis assay method for lignin degradation activity has been developed for use as a spray assay on agar plates. Nine mesophilic strains were isolated using this method from woodland soil incubated in enrichment cultures containing wheat straw lignocellulose: four Microbacterium isolates, two Micrococcus isolates, Rhodococcus erythropolis (all Actinobacteria) and two Ochrobactrum isolates (Alphaproteobacteria). Three thermotolerant isolates were isolated from the same screening method applied at 45 degrees C to samples of composted wheat straw from solid-state fermentation: Thermobifida fusca and two isolates related to uncharacterized species of Rhizobiales and Sphingobacterium (Bacteroidetes), the latter strain showing tenfold higher lignin degradation activity than other isolates. The isolated strains were able to depolymerize samples of size-fractionated high molecular weight and low molecular weight Kraft lignin, and produced low molecular weight metabolites oxalic acid and protocatechuic acid from incubations containing wheat straw lignocellulose. Conclusions A new method for the isolation of bacteria able to metabolize lignin has been developed, which has been used to identify 12 bacterial isolates from environmental sources. The majority of isolates cluster into the Actinobacteria and the Alphaproteobacteria. Significance and Impact of the Study Lignin-degrading bacterial strains could be used to convert lignin-containing feedstocks into renewable chemicals and to identify new bacterial lignin-degrading enzymes.

The concentrations of ferrous iron in ore column effluents and the pH of the effluents during the leaching of a copper sulfide ore were followed as an indication of the activity of the microbial populations that were established in the ore columns. The impact of this activity and the release of copper were influenced by addition of ferric iron to the irrigation solution, by imposed anoxic conditions and, particularly at higher temperatures, by precipitation of oxidised iron compounds. Moderately thermophilic, acidophilic actinobacteria appeared to dominate the microbial population at 47–57°C with a transition to ferrous iron oxidation by thermophilic archaea as the temperature was increased above 60°C.

Some novel actinobacteria from geothermal environments were shown to grow autotrophically with sulfur as an energy source. These bacteria have not been formally named and are referred to here as “ Acidithiomicrobium ” species, as the first of the acidophilic actinobacteria observed to grow on sulfur. They are related to Acidimicrobium ferrooxidans with which they share a capacity for ferrous iron oxidation. Ribulose bisphosphate carboxylase/oxygenase (RuBisCO) is active in CO 2 fixation by Acidimicrobium ferrooxidans , which appears to have acquired its RuBisCO-encoding genes from the proteobacterium Acidithiobacillus ferrooxidans or its ancestor. This lateral transfer of RuBisCO genes between a proteobacterium and an actinobacterium would add to those noted previously among proteobacteria, between proteobacteria and cyanobacteria and between proteobacteria and plastids. “ Acidithiomicrobium ” has RuBisCO-encoding genes which are most closely related to those of Acidimicrobium ferrooxidans and Acidithiobacillus ferrooxidans , and has additional RuBisCO genes of a different lineage. 16S rRNA gene sequences from “ Acidithiomicrobium ” species dominated clone banks of the genes extracted from mixed cultures of moderate thermophiles growing on copper sulfide and polymetallic sulfide ores in ore leaching columns.

Pyrite oxidation was observed in a mixed culture of salt-tolerant, thermotolerant, acidophilic bacteria from warm, acidic, coastal sediments of the island of Milos (Greece). Analysis of 16S rRNA gene sequences cloned from DNA extracted from the mixed culture indicated two species which were related to Thiobacillus prosperus. One of the sequences was found previously in warm, sediment samples from the island of Vulcano (Italy). Iron solubilization from pyrite by the Milos culture at 47°C was most rapid in the presence of NaCl at 30g l−1. A novel species was isolated from the mixed culture and grew in pure culture on pyrite with 50g l−1 NaCl, but iron solubilization was most rapid at just below 50°C with 20g l−1 NaCl. Establishment of activity of the halotolerant, thermotolerant bacteria in copper sulfide ore leaching columns was more difficult than with related bacteria growing at lower temperatures.

Thermotolerant “Thiobacillus prosperus”-like bacteria were enriched from warm, acidic sediments of the island of Milos in the Aegean Sea. Analysis of 16S rRNA gene sequences indicated at least two thermotolerant species, with at least one of them present in similar niches at Vulcano, Italy. Iron solubilization in a pyrite-enrichment culture at 47°C was most rapid in the presence of NaCl at 30 g.l 1. One of the novel species (strain M7) grew in pure culture on pyrite with NaCl at 50 g.l-1, but iron solubilization was most rapid with 20 g NaCl.l 1 at just below 50°C.