Explore the vast range of titles available.

A pure culture of the complete nitrifier Nitrospira inopinata shows a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers and genomic potential for alternative metabolisms, probably reflecting an important role in nitrification in oligotrophic environments. Nutrient-starved nitrification Nitrospira inopinata was the first bacterium identified that is capable of catalysing complete ammonia oxidization (referred to as comammox). Holger Daims and colleagues now report a pure culture of this organism, which enabled a characterization of its physiology. The authors find that N. inopinata has a high affinity for ammonia, a low maximum rate of ammonia oxidation, a high growth yield compared to canonical nitrifiers, and the genomic potential for alternative metabolisms. The team compare the nitrification kinetics of N. inopinata to that of four ammonia-oxidizing archaea. The results suggest that N. inopinata is likely to have an important role in nitrification, especially in oligotrophic environments. Nitrification, the oxidation of ammonia (NH 3 ) via nitrite (NO 2 − ) to nitrate (NO 3 − ), is a key process of the biogeochemical nitrogen cycle. For decades, ammonia and nitrite oxidation were thought to be separately catalysed by ammonia-oxidizing bacteria (AOB) and archaea (AOA), and by nitrite-oxidizing bacteria (NOB). The recent discovery of complete ammonia oxidizers (comammox) in the NOB genus Nitrospira 1 , 2 , which alone convert ammonia to nitrate, raised questions about the ecological niches in which comammox Nitrospira successfully compete with canonical nitrifiers. Here we isolate a pure culture of a comammox bacterium, Nitrospira inopinata , and show that it is adapted to slow growth in oligotrophic and dynamic habitats on the basis of a high affinity for ammonia, low maximum rate of ammonia oxidation, high growth yield compared to canonical nitrifiers, and genomic potential for alternative metabolisms. The nitrification kinetics of four AOA from soil and hot springs were determined for comparison. Their surprisingly poor substrate affinities and lower growth yields reveal that, in contrast to earlier assumptions, AOA are not necessarily the most competitive ammonia oxidizers present in strongly oligotrophic environments and that N. inopinata has the highest substrate affinity of all analysed ammonia oxidizer isolates except the marine AOA Nitrosopumilus maritimus SCM1 (ref. 3 ). These results suggest a role for comammox organisms in nitrification under oligotrophic and dynamic conditions.

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira , a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira -contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities. Until now, the oxidation steps necessary for complete nitrification have always been observed to occur in two separate microorganisms in a cross-feeding interaction; here, together with the study by van Kessel et al ., Daims et al . report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as “comammox” (for complete ammonia oxidation). Time to rethink nitrification Two groups this week report the enrichment and characterization of Nitrospira species that encode all of the enzymes necessary to catalyse complete nitrification, a phenotype referred to as 'comammox' (for complete ammonia oxidation). Until now, this two-step reaction was thought to involve two organisms in a cross-feeding interaction. Phylogenetic analyses suggest that comammox Nitrospira are present in a number of diverse environments, so these findings have the potential to fundamentally change our view of the nitrogen cycle and open a new frontier in nitrification research.

The ferrous iron oxidation by mixed culture of moderately thermophilic microorganisms (Sulfobacillus thermosulfidooxidans Sh 10-1 and Acidiplasma MBA-1) was investigated in continuous experiments in three packed-bed reactors connected in series at temperature 55°C, and a pH of 1.0. Two solutions were used in the experiments. The first one contained (g L-1) 59 Fe2+, the second one contained (g L-1) 59 Fe2+, 16 Fe3+, 2 Cu2+, 2 Zn2+. The hydraulic retention time was 120 hours. Iron oxidation rates in the experiment with the first solution were 0.5, 0.35, and 0.2 g L-1 h-1 in first, second and third reactor, respectively. The oxidation rates in the experiment with the second solution were 0.3, 0.2, and 0.185 g L-1 h-1 in first, second and third reactor, respectively. Iron oxidation efficiencies in the experiments with the first and second solutions were 77% and 47%. Stable continuous iron oxidation at high temperature was successfully demonstrated, but further investigations are required for improving the rate and efficiencies of oxidation.

Microorganisms living in acidic environments associated with various types of mining wastes can be used for bioremediation of acid mine drainage (AMD) and related waste streams. We studied microbial diversity of the acidic sediments of a leachate puddle at the basement of a waste rock pile from gold mining in abandoned gold deposit in Martiga (Kemerovo region, West Siberia, Russia). The enrichments were established from four sediment samples with a pH ranging from 2.29 to 6.16. The enrichments cultures were set up at aerobic and anaerobic conditions. Pure cultures of bacteria involved in iron and sulfur oxidation were isolated. The isolated iron- and sulfur-oxidizing cultures were affiliated with Acidithiobacillus and Acidocella genera as was revealed by 16S rRNA gene sequencing. Strains of Desulfosporosinus-like spore-forming bacteria were isolated under anaerobic conditions. The pure culture isolates physiological and biochemical characterization is underway, which will provide new knowledge of AMD formation and natural processes of metal attenuation. The strains can also be prospective agents for use in bioleaching and bioremediation processes.

Refractory sulfide ores are ubiquitous resources of gold around the world. It was demonstrated that biooxidation pretreatment of refractory whole ores could be conducted in heaps. The effectiveness of column biooxidation of off-balance gold ores from Bakyrchik and Bolshevik deposits (northeast Kazakhstan) containing pyrite and arsenopyrite was examined in the laboratory. Bakyrchick ore contained 1.5% of pyrite, 3% of arsenopyrite and 4.5 g/t of gold. Bolshevik ore contained 1% of pyrite, 1% of arsenopyrite and 10.7 g/t of gold. The recovery rates of gold from the Bakyrchik and Bolshevik ores by direct cyanidation were 4.5% and 8.2%, respectively. Representative samples of each ore were processed in air-lift percolators. A bioleaching experiment was performed in duplicate. The enrichment culture was obtained from the pyrite flotation wastes and used as an inoculum. Bioleaching was conducted for 60 days at ambient temperature (20-25°C). The recovery rates of gold from the bioleaching residues of Bakyrchik and Bolshevik ores by cyanidation were 21.0% and 48.5%, respectively. The results obtained in the present work may be used to estimate perspectives of heap bio-oxidation for the recovery of gold from these sulfide ores.

Using molecular genetic methods, 10 species wereidentified in the community of neutrophilic microorganisms isolated from thebioreactor during the process of biooxidation of gold-arsenicpyrrhotite-bearing sulfide ore flotation concentrate. The microbial communitywas composed of chemolithotrophs oxidizing elemental sulfur and its reducedcompounds and chemoorganotrophs. The predominant S0-oxidizingchemolithotrophic strain and 3 strains of chemoorganotrophs were isolated inpure cultures. Phylogenetic identification of the pure cultures revealed thechemolithotrophic microorganism to belong to Thermithiobacillus tepidarius,while organotrophic microorganisms were identified as Parapedobacter sp.,Nocardioides nitrophenolicus, and Nocardioides sp. Themorphological and physiological characteristics of Thermithiobacillustepidarius and Nocardioides nitrophenolicus, the culturespredominant in the community of neutrophilic microorganisms, were studied.Active growth of T. tepidarius occurs within a temperature range of38–48°C at the optimal pH value of 7.0–7.5. The maximal specific growth rate ofT. tepidarius on sulfur and on solid residue which remains after theprocess of bioleaching/biooxidation of sulfide ore flotation concentrate (biooxidationresidue) was 0.13 and 0.135 h-1, respectively. The average maximalrate of S0 oxidation in the biooxidation residue was 0.107 g S0oxidizedper g S0initial h-1. The ability of Nocardioidesnitrophenolicus to destruct thiocyanate was shown.