A deep gold mine metagenome as a source of novel esterases.

New sources of enzymes for biotechnological applications are continually being sought for. While diverse microbial ecosysyems have been demonstrated in the deep subsurfaces, deep mines provide easy access to these specialist communities. Therefore, the aim of this study was to assess a deep mine biofilm as a source of novel esterase enzymes. Biofilm was collected from the Beatrix Mine in South Africa, at a depth of 808 m. Assessment of the diversity revealed a group of previously uncultured bacteria and archaea. A metagenome library was screened for esterolytic activity, producing two esterolytic clones: a phospholipase patatin protein and an isochorismatase family protein. The isochorismatase family protein contained the catalytic Asp and Cys but not the Arg, which is considered as important for catalysis. The patatin showed 55% similarity to its closest relative; the patatin family protein from Plesiocystis pacifica. The expressed patatin displayed a preference for the C6 ester and was maximally active at pH 8 and 30°C. This study reported that screening of a relatively small metagenome library from the deep mine biofilm provided two esterolytic clones, which differed from their known counterparts. This indicates that the deep mine ecosystems contain an untapped resource of novel and potentially useful enzymes which may have applications in chemical syntheses

Unconventional lateral gene transfer in extreme thermophilic bacteria.

Conjugation and natural competence are two major mechanisms that explain the acquisition of foreign genes throughout bacterial evolution. In recent decades, several studies in model organisms have revealed in great detail the steps involved in such processes. The findings support the idea that the major basis of these mechanisms is essentially similar in all bacteria. However, recent work has pinpointed the existence of new, evolutionarily different processes underlying lateral gene transfer. In Thermus thermophilus HB27, at least 16 proteins are required for the activity of one of the most efficient natural competence systems known so far. Many of those proteins have no similarities to proteins involved in natural competence in other well-known models. This unusual competence system is conserved, in association with the chromosome, in all other Thermus spp. genomes so far available, it being functional even in strains from isolated environments, such as deep mines. Conjugation is also possible among Thermus spp. Homologues to proteins implicated in conjugation in model bacteria are encoded in the genome of a recently sequenced strain of Thermus thermophilus and shared by other members of the genus. Nevertheless, processive DNA transfer in the absence of a functional natural competence system in strains in which no conjugation homologous genes can be found hints at the existence of an additional and unconventional conjugation mechanism in these bacteria. [Int Microbiol 2011; 14(4):187-199]Spanish Ministry of Science and Innovation. An institutional grant from Ramon Areces Foundation to CBMSO is acknowledgedPeer Reviewe

Unconventional lateral gene transfer in extreme thermophilic bacteria

Conjugation and natural competence are two major mechanisms that explain the acquisition of foreign genes throughout bacterial evolution. In recent decades, several studies in model organisms have revealed in great detail the steps involved in such processes. The findings support the idea that the major basis of these mechanisms is essentially similar in all bacteria. However, recent work has pinpointed the existence of new, evolutionarily different processes underlying lateral gene transfer. In Thermus thermophilus HB27, at least 16 proteins are required for the activity of one of the most efficient natural competence systems known so far. Many of those proteins have no similarities to proteins involved in natural competence in other well-known models. This unusual competence system is conserved, in association with the chromosome, in all other Thermus spp. genomes so far available, it being functional even in strains from isolated environments, such as deep mines. Conjugation is also possible among Thermus spp. Homologues to proteins implicated in conjugation in model bacteria are encoded in the genome of a recently sequenced strain of Thermus thermophilus and shared by other members of the genus. Nevertheless, processive DNA transfer in the absence of a functional natural competence system in strains in which no conjugation homologous genes can be found hints at the existence of an additional and unconventional conjugation mechanism in these bacteria

Unconventional lateral gene transfer in extreme thermophilic bacteria

Conjugation and natural competence are two major mechanisms that explain the acquisition of foreign genes throughout bacterial evolution. In recent decades, several studies in model organisms have revealed in great detail the steps involved in such processes. The findings support the idea that the major basis of these mechanisms is essentially similar in all bacteria. However, recent work has pinpointed the existence of new, evolutionarily different processes underlying lateral gene transfer. In Thermus thermophilus HB27, at least 16 proteins are required for the activity of one of the most efficient natural competence systems known so far. Many of those proteins have no similarities to proteins involved in natural competence in other well-known models. This unusual competence system is conserved, in association with the chromosome, in all other Thermus spp. genomes so far available, it being functional even in strains from isolated environments, such as deep mines. Conjugation is also possible among Thermus spp. Homologues to proteins implicated in conjugation in model bacteria are encoded in the genome of a recently sequenced strain of Thermus thermophilus and shared by other members of the genus. Nevertheless, processive DNA transfer in the absence of a functional natural competence system in strains in which no conjugation homologous genes can be found hints at the existence of an additional and unconventional conjugation mechanism in these bacteriaThis work was supported by grant BIO2010-18875 from the Spanish Ministry of Science and Innovation. An institutional grant from Ramón Areces Foundation to CBMSO is acknowledged. CEC holds a Juan de la Cierva postdoctoral contract from the Spanish Ministry of Science and Innovation. CB and LA are founded by FPI and JAE fellowships from the Ministry of Education and the Spanish National Research Council (CSIC), respectivel

Enhancement of biogas production via co-digestion of wastewater treatment sewage sludge and brewery spent grain : physicochemical characterization and microbial community

The present study intends to evaluate a synergy towards enhanced biogas production by co-digesting municipal sewage sludge (SS) with brewery spent grain (BSG). To execute this, physicochemical and metagenomics analysis was conducted on the sewage sludge substrate. The automatic methane potential test system II (AMPTS II) biochemical methane potential (BMP) batch setup was operated at 35 ± 5 ◦C, pH range of 6.5–7.5 for 30 days’ digestion time on AMPTS II and 150 days on semi-continuous setup, where the organic loading rate (OLR) was guided by pH and the volatile fatty acids to total alkalinity (VFA/TA) ratio. Metagenomics analysis revealed that Proteobacteria was the most abundant phyla, consisting of hydrolytic and fermentative bacteria. The archaea community of hydrogenotrophic methanogen genus was enriched by methanogens. The highest BMP was obtained with co-digestion of SS and BSG, and 9.65 g/kg of VS. This not only increased biogas production by 104% but also accelerated the biodegradation of organic matters. However, a significant reduction in the biogas yield, from 10.23 NL/day to 2.02 NL/day, was observed in a semi-continuous process. As such, it can be concluded that different species in different types of sludge can synergistically enhance the production of biogas. However, the operating conditions should be optimized and monitored at all times. The anaerobic co-digestion of SS and BSG might be considered as a cost-effective solution that could contribute to the energy self-efficiency of wastewater treatment works (WWTWs) and sustainable waste management. It is recommended to upscale co-digestion of the feed for the pilot biogas plant. This will also go a long way in curtailing and minimizing the impacts of sludge disposal in the environment.https://www.mdpi.com/journal/sustainabilitydm2022Chemical Engineerin

Internet access constrains science development and training at South African universities

The original publication is available at http://www.sajs.co.za/As a group of young scientists whose future careers depend increasingly on access to Internet resources, we are extremely concerned by the apparent lack of understanding of the stranglehold that current approaches to Internet pricing are placing on the development of science in South Africa.Lette

Biomineralization and Bioaccumulation of Europium by a Thermophilic Metal Resistant Bacterium

Rare earth metals are widely used in the production of many modern technologies. However, there is concern that supply cannot meet the growing demand in the near future. The extraction from low-grade sources such as geothermal fluids could contribute to address the increasing demand for these compounds. Here we investigated the interaction and eventual bioaccumulation of europium (Eu) by a thermophilic bacterium, Thermus scotoductus SA-01. We demonstrated that this bacterial strain can survive in high levels (up to 1 mM) of Eu, which is hundred times higher than typical concentrations found in the environment. Furthermore, Eu seems to stimulate the growth of T. scotoductus SA-01 at low (0.01–0.1 mM) concentrations. We also found, using TEM-EDX analysis, that the bacterium can accumulate Eu both intracellularly and extracellularly. FT-IR results confirmed that carbonyl and carboxyl groups were involved in the biosorption of Eu. Infrared and HR-XPS analysis demonstrated that Eu can be biomineralized by T. scotoductus SA-01 as Eu2(CO3)3. This suggests that T. scotoductus SA-01 can potentially be used for the biorecovery of rare earth metals from geothermal fluids

Complex Effects of Cytochrome P450 Monooxygenase on Purple Membrane and Bacterioruberin Production in an Extremely Halophilic Archaeon: Genetic, Phenotypic, and Transcriptomic Analyses

Halophilic archaea are known to produce a diverse array of pigments for phototrophy and photoprotection. The aim of this paper was to determine the role of a Halobacterium gene encoding the predicted cytochrome P450 monooxygenase (CYP174A1) in pigment synthesis through a combined genetic, phenotypic, and transcriptomic approach. We report on the observed phenotype changes [increased bacterioruberin levels and the loss of purple membrane (PM)] between the Halobacterium salinarum R1 and its CYP174A1-deletion mutant. In addition, we report on the whole-genome DNA microarray analysis, which supports the phenotype of PM loss. This work expands our understanding of the bop-gene regulon, and its relation to carotenoid biosynthesis, and sheds light on our broader understanding of the role (s) of CYP174A1 in archaeal pigment synthesis. To date, this is the first study in which the physiological role of any cytochrome P450 monooxygenase (CYP450) in extremely halophilic archaea has been reported

Evaluating the effects of pH and temperature on sulphate-reducing bacteria and modelling of their effects in stirred bioreactors

DATA AVAILABILITY STATEMENT : Data used and presented in this study can be made available upon requests to the corresponding authors.Sulphate (SO4) abundance in the earth’s crust contributes largely to industrial wastewater contamination lowering the pH, which exuberates the dissolution of metals forming acidic drainages. Biological sulphate reduction as a remediation process can be affected by factors such as pH, temperature and high sulphide concentrations. In this study, sulphate-reducing bacterial community enriched from mine wastewaters was applied in semi-automated bioreactors to assess the effects of these factors on microbial sulphate reduction capacities. Low pH (3.5) and temperature (10°C) were observed to promote the toxicity of sulphur-reduced species on the consortium while mesophilic temperature (25°C) and near neutral pH (6.2) were observed to induce optimum SO4 reduction attaining a maximum of 95% SO4 reduction. Obtained SO4 reduction dynamics data was then applied in formulating a unique non-competitive inhibition equation that models biogeochemical events during SO4 reduction under varied pH and temperature conditions and predicts the efficacy of a bioremediation system.http://www.tandfonline.com/journals/tcsb21am2024Chemical EngineeringSDG-12:Responsible consumption and productio

Environmental and Geochemical characterization of alkaline mine wastes from Phalaborwa (Palabora) Complex, South Africa

A detailed characterization of alkaline tailing ponds and waste rock dumps from Phalaborwa Igneous Complex (PIC) South Africa, has been accomplished. The study goes beyond the environmental characterization of mining wastes, offering the first insight towards the recycling of the wastes as alkaline reagent to neutralize acid industrial wastewater. To achieve these aims, tailings and waste rocks were characterized using a combination of conventional, novel and modified Acid Rock Drainage (ARD) prediction methodologies, as well as South African leachate tests, sequential extractions and pseudo-total digestions. The scarcity of Fe-sulphide minerals and the abundance of alkaline minerals indicated that PIC wastes are not ARD producers. The highest neutralization potential was found in the carbonatite rocks and East tailing samples (range between 289 and 801 kg CaCO3 eq/t). According to the National Environmental Management Waste Act (59/2008) of South Africa, tailing ponds and waste rock dumps from PIC classify as non-hazardous (Type 3 waste). The sequential extractions showed that the different fractions from most of the samples would mostly release sulphate and non-toxic elements, such as Ca, Mg, Na and K, which might be a concern if leached in high concentration. In addition, relatively high concentrations of radionuclides, such as U and Th (average of 6.7 and 36.3 mg/kg, respectively) are present in the non-labile fraction of PIC wastes, while the leachable concentrations were always below 0.006 mg/L. Among PIC wastes, East tailing would be the best option as alkaline reagent to neutralize acid wastewater because of its high neutralization potential and non-harmful leachate composition. In general, this study exposes the shortcomings in mine waste characterization, particularly for alkaline mine wastes, and introduces the assessment of potential revalorization as a novel practice in mine waste characterization that, if extended as a regular practice, would facilitate a circular economy approach to the mining industry with its consequent economic and environmental benefits.This work was supported by the Department of Science and Technology (South Africa) through the ERAMIN project of the Horizon2020 (AMDREY-PCIN2015-242-256). It was also partially financed by: UNESCO (UNESCO-IUGS-IGCP-Project 682), Ministerio de Ciencia e Innovacin project MOS, Spain (grant number CGL2016-79204-R), CORFO and Codelco (project CORFO-16PTECME-66524), project CONICYT/PIA AFB180004 and Science Foundation Ireland (grant number 18/IF/6347). Special thanks are due to the staff of Palabora Mining Company and Foskor for their assistance during the sampling. The authors would like to thank the reviewers for their thoughtful comments and efforts towards improving the manuscriptDepartamento de Geologí