Acidophilic microorganisms enhancing geochemical dynamics in an acidic drainage system, Amarillo river in La Rioja, Argentina

The Amarillo River in La Rioja, Argentina, is a natural acidic environment that is influenced by an abandoned mine. The river is characterized by extremely low pH and high concentrations of metals and metalloids. Fe(III)-bearing neoformed precipitated minerals are widespread along the hydrological basin. This work reports the presence of different species of iron-oxidizing bacteria and demonstrates that their action has a significant role in geochemical processes of the Amarillo River, mainly by catalyzing Fe²⁺ oxidation and intensifying the Fe(III)-bearing mineral precipitation. Various iron oxidizers (i.e. Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans, Ferrimicrobium acidophilum, Alicyclobacillus cycloheptanicus) were detected in enrichment cultures at different temperatures. Moreover, this is the first report confirming that Acidithiobacillus ferrivorans is able to grow at 4 °C. Other acidophilic bacteria (i.e., Acidiphilium iwatensii) and fungi (e.g., Fodinomyces uranophilus, Coniochaeta fodinicola, Acidea extrema, Penicillium sp. and Cladosporium pseudocladosporioides) were also detected. In vitro laboratory studies recreating natural Fe(III)-bearing mineral formation showed that mineral precipitation rate was higher than 350 mg L^-1 day^-1 in the presence of microorganisms whereas it was about 15 mg L^-1 day^-1 under abiotic conditions. Jarosite was the only mineral detected in the precipitates generated by microbial action and it was also identified in the Amarillo River bed sediments. Biological Fe²⁺ oxidation rates depend on temperature which range from 8 to 32 mM day^-1 at 4 and 30 °C, respectively. Finally, a conceptual model recognizing the significant microbial role is proposed to gain a better understanding of the biogeochemistry dynamics of the Amarillo River.

Metal biorecovery and bioremediation: Whether or not thermophilic are better than mesophilic microorganisms

Metal mobilization and immobilization catalyzed by microbial action are key processes in environmental biotechnology. Metal mobilization from ores, mining wastes, or solid residues can be used for recovering metals and/or remediating polluted environments; furthermore, immobilization reduces the migration of metals; cleans up effluents plus ground- and surface water; and, moreover, can help to concentrate and recover metals. Usually these processes provide certain advantages over traditional technologies such as more efficient economical and environmentally sustainable results. Since elevated temperatures typically increase chemical kinetics, it could be expected that bioprocesses should also be enhanced by replacing mesophiles with thermophiles or hyperthermophiles. Nevertheless, other issues like process stability, flexibility, and thermophile-versus-mesophile resistance to acidity and/or metal toxicity should be carefully considered. This review critically analyzes and compares thermophilic and mesophilic microbial performances in recent and selected representative examples of metal bioremediation and biorecovery.

Combined strategy for removal of Reactive Black 5 by biomass sorption on Macrocystis pyrifera and zerovalent iron nanoparticles

Reactive Black 5, RB5, has been used as a model azo dye to evaluate the removal efficiency of sorption on Macrocystis pyrifera biomass (Mpyr) and commercial zerovalent iron nanoparticles (nZVI) in individual and combined treatments. The best conditions for the treatment with the isolated materials were first determined, and then, in series and combined treatments were performed under these conditions, achieving removal efficiencies higher than 80% of the initial dye concentration. Strengths and weaknesses of all removal strategies (individual, in series and combined) are analyzed regarding the application on real effluents. Mpyr efficiently adsorbed RB5, but also increased the total organic content by partial dissolution of components of the algal biomass. Removal experiments with commercial nZVI were also efficient but liberated Fe to the solution, and sulfanilic acid was observed after the treatment as a product of RB5 degradation. In contrast, after the Mpyr treatment, no sulfanilic acid was detected, suggesting that sulfanilic acid is efficiently adsorbed by the biomass. The best condition was the integrated use of Mpyr and nZVI, with a remarkable removal efficiency (69-80%) obtained after only 1 h of treatment. Finally, nZVI were successfully immobilized in Mpyr, and the hybrid material was used to remove RB5 in continuous flow experiments at pH 3, obtaining a removal capacity of 39.9 mg RB5 g-1 after a total processed volume of 630 mL of [RB5]0 = 100 mg L-1.

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.

Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina

Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment.

EXAFS and DFT study of the cadmium and lead adsorption on modified silica nanoparticles

Silica nanoparticles of 7 nm diameter were modified with (3-aminopropyl) triethoxysilane (APTES) and characterized by CP-MAS (13)C and (29)Si NMR, FTIR, zeta potential measurements, and thermogravimetry. The particles were shown to sorb successfully divalent lead and cadmium ions from aqueous solution. Lead complexation with these silica nanoparticles was clearly confirmed by EXAFS (Extended X-ray Absorption Fine Structure) with synchrotron light measurements. Predicted Pb-N and Pb-C distances obtained from quantum-chemical calculations are in very good agreement with the EXAFS determinations. The calculations also support the higher APTES affinity for Pb(2+) compared to Cd(2+).

Thermophiles in the genomic era: Biodiversity, science, and applications

Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era.

Physiologic versatility and growth flexibility as the main characteristics of a novel thermoacidophilic Acidianus strain isolated from Copahue geothermal area in Argentina

A novel thermoacidophilic archaeal strain has been isolated from three geothermal acidic hot springs in Copahue, Argentina. One of the most striking characteristic of ALE1 isolate is its metabolic versatility. It grows on sulphur, tetrathionate, iron (II) and sucrose under aerobic conditions, but it can also develop under anaerobic conditions using iron (III) or sulphur as electron acceptors and sulphur or hydrogen as electron donors autotrophically. A temperature of 75 °C and a pH between 2.5 and 3.0 are strain ALE1 optimal growth conditions, but it is able to oxidise iron (II) even at pH 1.0. Cells are irregular cocci surrounded by a regularly arrayed glycoprotein layer (S-layer). Phylogenetic analysis shows that strain ALE1 belongs to the family Sulfolobaceae in the class Thermoprotei, within the phylum Crenarchaeota. Based on 16S rRNA gene sequence similarity on NCBI database, ALE1 does not have closely related relatives, neither in culture nor uncultured, which is more surprising. Its closest related species are strains of Acidianus hospitalis (91 % of sequence similarity), Acidianus infernus (90 %), Acidianus ambivalens (90 %) and Acidianus manzanensis (90 %). Its DNA base composition of 34.5 % mol C + G is higher than that reported for other Acidianus species. Considering physiological and phylogenetic characteristics of strain ALE1, we considered it to represent a novel species of the genus Acidianus (candidatus "Acidianus copahuensis"). The aim of this study is to physiologically characterise this novel archaea in order to understand its role in iron and sulphur geochemical cycles in the Copahue geothermal area and to evaluate its potential applications in bioleaching and biooxidation.

Study of the heavy metal phytoextraction capacity of two forage species growing in an hydroponic environment

Sorghum and alfalfa are two important forage crops. We studied their capacity for accumulating heavy metals in hydroponic experiments. Cadmium, nickel (as divalent cations) and chromium (trivalent and hexavalent) were added individually to the nutrient solution in a range of concentrations from 1 to 80 mg/l. Cr(III) was complexed with EDTA to increase its bioavailability. In alfalfa the increases in the concentration of Cr(III) and Cr(VI) favoured translocation of the metals to the upper parts of the plants, while with Ni(II) the level of translocated metal remained almost unchanged. In sorghum, both Cr(VI) and Ni(II) produced similar results to those in alfalfa, but increases in the concentrations of Cd(II) and Cr(III) in the solution lead to a higher accumulation of the metal at the root level. The concentrations referred to the dry biomass of alfalfa were 500 mg/kg (aerial parts) and 1500 mg/kg (roots) of Cr(III), simultaneously enhancing plant growth. Sorghum captured 500 and 1100 mg/kg (in aerial parts) and 300 and 2000 mg/kg (in roots) for Ni(II) and Cd(II) respectively, without significant damage to its biomass. The results show that alfalfa and sorghum can not only grow in the presence of high heavy metal concentration but also capture and translocate them to the aerial parts; because of these results special attention should be given to these crop plants for their possible use in phytoremediation of large contaminated areas but especially to avoid the possible introduction of the metals accumulated in aerial parts into the food chain when those plants grow in contaminated areas.

Dynamics of microbial community during bioremediation of phenanthrene and chromium(VI)-contaminated soil microcosms

The combined effect of phenanthrene and Cr(VI) on soil microbial activity, community composition and on the efficiency of bioremediation processes has been studied. Biometer flask systems and soil microcosm systems contaminated with 2,000 mg of phenanthrene per kg of dry soil and different Cr(VI) concentrations were investigated. Temperature, soil moisture and oxygen availability were controlled to support bioremediation. Cr(VI) inhibited the phenanthrene mineralization (CO(2) production) and cultivable PAH degrading bacteria at levels of 500-2,600 mg kg(-1). In the bioremediation experiments in soil microcosms the degradation of phenanthrene, the dehydrogenase activity and the increase in PAH degrading bacteria counts were retarded by the presence of Cr(VI) at all studied concentrations (25, 50 and 100 mg kg(-1)). These negative effects did not show a correlation with Cr(VI) concentration. Whereas the presence of Cr(VI) had a negative effect on the phenanthrene elimination rate, co-contamination with phenanthrene reduced the residual Cr(VI) concentration in the water exchangeable Cr(VI) fraction (WEF) in comparison with the soil microcosm contaminated only with Cr(VI). Clear differences were found between the denaturing gradient gel electrophoresis (DGGE) patterns of each soil microcosm, showing that the presence of different Cr(VI) concentrations did modulate the community response to phenanthrene and caused perdurable changes in the structure of the microbial soil community.