Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms

A cascade of sulfur transferases delivers sulfur to the sulfur-oxidizing heterodisulfide reductase-like complex

A heterodisulfide reductase-like complex (sHdr) and novel lipoate-binding proteins (LbpAs) are central players of a wide-spread pathway of dissimilatory sulfur oxidation. Bioinformatic analysis demonstrate that the cytoplasmic sHdr-LbpA systems are always accompanied by sets of sulfur transferases (DsrE proteins, TusA, and rhodaneses). The exact composition of these sets may vary depending on the organism and sHdr system type. To enable generalizations, we studied model sulfur oxidizers from distant bacterial phyla, that is, Aquificota and Pseudomonadota. DsrE3C of the chemoorganotrophic Alphaproteobacterium Hyphomicrobium denitrificans and DsrE3B from the Gammaproteobacteria Thioalkalivibrio sp. K90mix, an obligate chemolithotroph, and Thiorhodospira sibirica, an obligate photolithotroph, are homotrimers that donate sulfur to TusA. Additionally, the hyphomicrobial rhodanese-like protein Rhd442 exchanges sulfur with both TusA and DsrE3C. The latter is essential for sulfur oxidation in Hm. denitrificans. TusA from Aquifex aeolicus (AqTusA) interacts physiologically with AqDsrE, AqLbpA, and AqsHdr proteins. This is particularly significant as it establishes a direct link between sulfur transferases and the sHdr-LbpA complex that oxidizes sulfane sulfur to sulfite. In vivo, it is unlikely that there is a strict unidirectional transfer between the sulfur-binding enzymes studied. Rather, the sulfur transferases form a network, each with a pool of bound sulfur. Sulfur flux can then be shifted in one direction or the other depending on metabolic requirements. A single pair of sulfur-binding proteins with a preferred transfer direction, such as a DsrE3-type protein towards TusA, may be sufficient to push sulfur into the sink where it is further metabolized or needed.

Fe(III) bioreduction kinetics in anaerobic batch and continuous stirred tank reactors with acidophilic bacteria relevant for bioleaching of limonitic laterites

In the framework of the H2020 project CROCODILE, the recovery of Co from oxidized ores by reductive bioleaching has been studied. The objective was to reduce Fe(III) to Fe(II) to enhance the dissolution of Co from New-Caledonian limonitic laterites, mainly composed of goethite and Mn oxides. This study focused on the Fe(III) bioreduction which is a relevant reaction of this process. In the first step, biomass growth was sustained by aerobic bio-oxidation of elemental sulfur. In the second step, the biomass anaerobically reduced Fe(III) to Fe(II). The last step, which is not in the scope of this study, was the reduction of limonites and the dissolution of metals. This study aimed at assessing the Fe(III) bioreduction rate at 35°C with a microbial consortium composed predominantly of Sulfobacillus (Sb.) species as the iron reducers and Acidithiobacillus (At.) caldus. It evaluated the influence of the biomass concentration on the Fe(III) bioreduction rate and yield, both in batch and continuous mode. The influence of the composition of the growth medium on the bioreduction rate was assessed in continuous mode. A mean Fe(III) bioreduction rate of 1.7 mg·L-1·h-1 was measured in batch mode, i.e., 13 times faster than the abiotic control (0.13 mg·L-1·h-1). An increase in biomass concentrations in the liquid phase from 4 × 108 cells·mL-1 to 3 × 109 cells·mL-1 resulted in an increase of the mean Fe(III) bioreduction rate from 1.7 to 10 mg·L-1·h-1. A test in continuous stirred tank reactors at 35°C resulted in further optimization of the Fe(III) bioreduction rate which reached 20 mg·L-1·h-1. A large excess of nutrients enables to obtain higher kinetics. The determination of this kinetics is essential for the design of a reductive bioleaching process.

Deciphering microbial communities and their unique metabolic repertoire across rock-soil-plant continuum in the Dayoukeng fumarolic geothermal field of the Tatun Volcano Group

High temperature and sulfur concentrations in geothermal sulfur fumaroles host unique microbial ecosystems with niche-specific metabolic diversity and physiological functions. In this study, the microbial communities and their functionalities associated with the Dayoukeng geothermal field and the rock-soil-plant continuum were investigated to underpin the microbial modulation at different distances from the fumaroles source. At the phylum level, Bacteroidota, Planctomycetota, Armatimonadota, and Patescibacteria were abundant in plant samples; Elusimicrobiota and Desulfobacterota were in the rock samples while Nitrospirota, Micrarchaeota, and Deinococcota were dominant in the soil samples. Acidophilic thermophiles were enriched in samples within close proximity to the fumaroles, primarily at a distance of 1 m. The sulfur and iron-oxidizing acidophilic bacterial genera such as Acidothiobacillus and Sulfobacillus were abundant in the rock samples. The thermoacidophilic archaeon Acidianus and acidophilic bacteria Acidiphilium were abundant in the soil samples. Additionally, Thermosporothrix and Acidothermus were found abundant in the plant samples. The results of the functional annotation indicated that dark sulfur oxidation, iron oxidation, and hydrogen oxidation pathways were abundant in the soil samples up to 1 m from the fumaroles, while methanogenic and fermentation pathways were more prevalent in the soil samples located 10 m from the fumaroles. Interestingly, the results of this study indicated a higher microbial richness and abundance of acidophilic communities in the soils and plants compared to the rocks of the DYK fumarolic geothermal field.

Unveiling abundance-dependent metabolic phenotypes of microbial communities

IMPORTANCE

In nature, organisms live in communities and not as isolated species, and their interactions provide a source of resilience to environmental disturbances. Despite their importance in ecology, human health, and industry, understanding how organisms interact in different environments remains an open question. In this work, we provide a novel approach that, only using genomic information, studies the metabolic phenotype exhibited by communities, where the exploration of suboptimal growth flux distributions and the composition of a community allows to unveil its capacity to respond to environmental changes, shedding light of the degrees of metabolic plasticity inherent to the community.

Analysis of Microbial Communities in Membrane Biofilm Reactors Using a High-Density Microarray

Membrane biofilm reactors (MBfRs) have attracted more and more attention in the field of wastewater treatment due to their advantages of high mass transfer efficiency and low-carbon emissions. There are many factors affecting their nitrogen removal abilities, such as operation time, electron donor types, and operation modes. The operation time is directly related to the growth status of microorganisms, so it is very important to understand the effect of different operation times on microbial composition and community succession. In this study, two parallel H₂-based MBfRs were operated, and differences in microbial composition, community succession, and NO₃^--N removal efficiency were investigated on the 30th day and the 60th day of operation. The nitrogen removal efficiency of MBfRs with an operation time of 60 days was higher than that of MBfRs with an operation time of 30 days. Proteobacteria was the dominant phylum in both MBfRs; however, the composition of the microbial community was quite different. At the class level, the community composition of Proteobacteria was similar between the two MBfRs. Alphaproteobacteria was the dominant class in MBfR, and Betaproteobacteria and Gammaproteobacteria were also in high proportion. Combined with the analysis of microbial relative abundance and concentration, the similarity of microbial distribution in the MBfRs was very low on day 30 and day 60, and the phylogenetic relationships of the top 50 dominant universal bacteria and Proteobacteria were different. Although the microbial concentration decreased with the extension of the operation time, the microbial abundance and diversity of specific functional microorganisms increased further. Therefore, the operation time had a significant effect on microbial composition and community succession.

Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica

Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.

Accessing Metals from Low-Grade Ores and the Environmental Impact Considerations: A Review of the Perspectives of Conventional versus Bioleaching Strategies

Mining has advanced primarily through the use of two strategies: pyrometallurgy and hydrometallurgy. Both have been used successfully to extract valuable metals from ore deposits. These strategies, without a doubt, harm the environment. Furthermore, due to decades of excessive mining, there has been a global decline in high-grade ores. This has resulted in a decrease in valuable metal supply, which has prompted a reconsideration of these traditional strategies, as the industry faces the current challenge of accessing the highly sought-after valuable metals from low-grade ores. This review outlines these challenges in detail, provides insights into metal recovery issues, and describes technological advances being made to address the issues associated with dealing with low-grade metals. It also discusses the pragmatic paradigm shift that necessitates the use of biotechnological solutions provided by bioleaching, particularly its environmental friendliness. However, it goes on to criticize the shortcomings of bioleaching while highlighting the potential solutions provided by a bespoke approach that integrates research applications from omics technologies and their applications in the adaptation of bioleaching microorganisms and their interaction with the harsh environments associated with metal ore degradation.

Phylogenetically divergent bacteria consortium from neutral activated sludge showed heightened potential on bioleaching spent lithium-ion batteries

Recycling of spent lithium-ion batteries (LIBs) has become a global issue because of the potential environment risks raised by spent LIBs as well as high valuable metal content remaining in them. Although bioleaching is an environmentally friendly method to recover metals from spent LIBs, the commonly utilized bioleaching bacterial consortia or strains enriched/isolated from acidic environments cannot be applied at large scales owing to their long leaching cycle and poor tolerance to organic compounds. Here, two bioleaching consortia were enriched in 60 days from neutral activated sludge and were identified phylogenetically divergent from the documented bioleaching bacteria. The results showed that the novel consortia shortened the leaching cycle almost by half when compared to the previous reported consortia or strains, of which one consortium dominated by Acidithiobacillus ferrooxidans displayed high bioleaching efficiency on LiMn₂O₄, as 69.46% lithium (Li) and 67.60% manganese (Mn) were leached out in seven days. This consortium was further domesticated using cathodic materials for 100 days and proved consisted of three mixotrophs and two chemoautotrophs, three of which were novel species from the genera Sulfobacillus and Leptospirillum. More genes coding for proteins that utilize organic compounds were annotated in the metagenomic assembled genomes (MAGs) than previously reported. A mutualistic relationship between mixotrophs and chemoautotrophs was suggested to help the consortium surviving under either organic- rich or shortage environments. The results discovered that novel bioleaching bacteria with shorter leaching cycle and higher tolerance to organics could be enriched from non-acidic environments, which showed high potential for the metal recovering from spent LIBs or other organic-rich environments.

Sulfobacillus harzensis sp. nov., an acidophilic bacterium inhabiting mine tailings from a polymetallic mine

A mixotrophic and acidophilic bacterial strain BGR 140^T was isolated from mine tailings in the Harz Mountains near Goslar, Germany. Cells of BGR 140^T were Gram-stain-positive, endospore-forming, motile and rod-shaped. BGR 140^T grew aerobically at 25–55 °C (optimum 45 °C) and at pH 1.5–5.0 (optimum pH 3.0). The results of analysis of the 16S rRNA gene sequences indicated that BGR 140^T was phylogenetically related to different members of the genus Sulfobacillus, and the sequence identities to Sulfobacillus acidophilus DSM 10332^T, Sulfobacillus thermotolerans DSM 17362^T, and Sulfobacillus benefaciens DSM 19468^T were 94.8, 91.8 and 91.6 %, respectively. Its cell wall peptidoglycan is A1γ, composed of meso-diaminopimelic acid. The respiratory quinone is DMK-6. The major polar lipids were determined to be glycolipid, phospholipid and phosphatidylglycerol. The predominant fatty acid is 11-cycloheptanoyl-undecanoate. The genomic DNA G+C content is 58.2 mol%. On the basis of the results of phenotypic and genomic analyses, it is concluded that strain BGR 140^T represents a novel species of the genus Sulfobacillus, for which the name Sulfobacillus harzensis sp. nov. is proposed because of its origin. Its type strain is BGR 140^T (=DSM 109850^T=JCM 39070^T).

Evaluation of temperature, pH and nutrient conditions in bacterial growth and extracellular hydrolytic activities of two Alicyclobacillus spp. strains

Extremophile bacteria have developed the metabolic machinery for living in extreme temperatures, pH, and high-salt content. Two novel bacterium strains Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2, were isolated from crater lake El Chichon in Chiapas, Mexico. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain Alicyclobacillus sp. PA1 and Alicyclobacillus sp. PA2 were closely related to Alicyclobacillus species (98% identity and 94.73% identity, respectively). Both strains were Gram variable, and colonies were circular, smooth and creamy. Electron microscopy showed than Alicyclobacillus sp. PA1 has a daisy-like form and Alicyclobacillus sp. PA2 is a regular rod. Both strains can use diverse carbohydrates and triglycerides as carbon source and they also can use organic and inorganic nitrogen source. But, the two strains can grow without any carbon or nitrogen sources in the culture medium. Temperature, pH and nutrition condition affect bacterial growth. Maximum growth was produced at 65 °C for Alicyclobacillus sp. PA1 (0.732 DO₆₀₀) at pH 3 and Alicyclobacillus sp. PA2 (0.725 DO₆₀₀) at pH 5. Inducible extracellular extremozyme activities were determined for β-galactosidase (Alicyclobacillus sp. PA1: 88.07 ± 0.252 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), cellulose (Alicyclobacillus sp. PA1: 141.20 ± 0.585 U/mg, Alicyclobacillus sp. PA2: 51.57 ± 0.308 U/mg), lipase (Alicyclobacillus sp. PA1: 138.25 ± 0.600 U/mg, Alicyclobacillus sp. PA2: 175.75 ± 1.387 U/mg), xylanase (Alicyclobacillus sp. PA1: 174.72 ± 1.746 U/mg, Alicyclobacillus sp. PA2: 172.69 ± 0.855U/mg), and protease (Alicyclobacillus sp. PA1: 15.12 ± 0.121 U/mg, Alicyclobacillus sp. PA2: 15.33 ± 0.284 U/mg). These results provide new insights on extreme enzymatic production on Alicyclobacillus species.

Temperature and elemental sulfur shape microbial communities in two extremely acidic aquatic volcanic environments

Aquatic environments of volcanic origin provide an exceptional opportunity to study the adaptations of microorganisms to early planet life conditions. Here, we characterized the prokaryotic communities and physicochemical properties of seepage sites at the bottom of the Poas Volcano crater and the Agrio River, two geologically related extremely acidic environments located in Costa Rica. Both locations hold a low pH (1.79-2.20) and have high sulfate and iron concentrations (Fe = 47-206 mg/L, SO₄^2- = 1170-2460 mg/L), but significant differences in their temperature (90.0-95.0 ºC in the seepages at Poas Volcano, 19.1-26.6 ºC in Agrio River) and in the elemental sulfur content. Based on the analysis of 16S rRNA gene sequences, we determined that Sulfobacillus spp. represented more than half of the sequences in Poas Volcano seepage sites, while Agrio River was dominated by Leptospirillum and members of the archaeal order Thermoplasmatales. Both environments share some chemical characteristics and part of their microbiota, however, the temperature and the reduced sulfur are likely the main distinguishing features, ultimately shaping their microbial communities. Our data suggest that in the Poas Volcano-Agrio River system there is a common metabolism but with specialization of species that adapt to the physicochemical conditions of each environment.

Improving the Cathodic Biofilm Growth Capabilities of Kyrpidia spormannii EA-1 by Undirected Mutagenesis

The biotechnological usage of carbon dioxide has become a relevant aim for future processes. Microbial electrosynthesis is a rather new technique to energize biological CO₂ fixation with the advantage to establish a continuous process based on a cathodic biofilm that is supplied with renewable electrical energy as electron and energy source. In this study, the recently characterized cathodic biofilm forming microorganism Kyrpidia spormannii strain EA-1 was used in an adaptive laboratory evolution experiment to enhance its cathodic biofilm growth capabilities. At the end of the experiment, the adapted cathodic population exhibited an up to fourfold higher biofilm accumulation rate, as well as faster substratum coverage and a more uniform biofilm morphology compared to the progenitor strain. Genomic variant analysis revealed a genomically heterogeneous population with genetic variations occurring to various extends throughout the community. Via the conducted analysis we identified possible targets for future genetic engineering with the aim to further optimize cathodic growth. Moreover, the results assist in elucidating the underlying processes that enable cathodic biofilm formation.

Microbial Community Structure Along a Horizontal Oxygen Gradient in a Costa Rican Volcanic Influenced Acid Rock Drainage System

We describe the geochemistry and microbial diversity of a pristine environment that resembles an acid rock drainage (ARD) but it is actually the result of hydrothermal and volcanic influences. We designate this environment, and other comparable sites, as volcanic influenced acid rock drainage (VARD) systems. The metal content and sulfuric acid in this ecosystem stem from the volcanic milieu and not from the product of pyrite oxidation. Based on the analysis of 16S rRNA gene amplicons, we report the microbial community structure in the pristine San Cayetano Costa Rican VARD environment (pH = 2.94-3.06, sulfate ~ 0.87-1.19 g L^-1, iron ~ 35-61 mg L^-1 (waters), and ~ 8-293 g kg^-1 (sediments)). San Cayetano was found to be dominated by microorganisms involved in the geochemical cycling of iron, sulfur, and nitrogen; however, the identity and abundance of the species changed with the oxygen content (0.40-6.06 mg L^-1) along the river course. The hypoxic source of San Cayetano is dominated by a putative anaerobic sulfate-reducing Deltaproteobacterium. Sulfur-oxidizing bacteria such as Acidithiobacillus or Sulfobacillus are found in smaller proportions with respect to typical ARD. In the oxic downstream, we identified aerobic iron-oxidizers (Leptospirillum, Acidithrix, Ferrovum) and heterotrophic bacteria (Burkholderiaceae bacterium, Trichococcus, Acidocella). Thermoplasmatales archaea closely related to environmental phylotypes found in other ARD niches were also observed throughout the entire ecosystem. Overall, our study shows the differences and similarities in the diversity and distribution of the microbial communities between an ARD and a VARD system at the source and along the oxygen gradient that establishes on the course of the river.

Bacterial community evolution along full-scale municipal wastewater treatment processes

Sewage pollution is a major threat to public health because sewage is always accompanied by pathogens. Generally, wastewater treatment plants (WWTP) receive and treat sewage to control pathogenic risks and improve environmental health. This study investigated the changes in the bacterial community over the course of treatment by a WWTP. Illumina MiSeq high-throughput sequencing was performed to characterize the bacterial communities in the WWTP. This study found that potential pathogens in the WWTP, especially the genera Arcobacter and Acinetobacter, were greatly reduced. In addition, high chemical oxygen demand levels provided excessive growth substrates for the genera Hyphomicrobium and Rhodoplanes, the abundance of which could exceed autotrophic bacteria, increasing the ammonium removal. According to the network analysis, the bacterial assemblage was not randomly arranged in the WWTP, and various defined processes led to higher intra-phylum (such as Proteobacteria) coexistence than expected. Moreover, the metabolic functions of bacterial communities significantly improved in the WWTP compared with the influent. Together, the data in this study emphasize the need to understand the bacterial community of WWTPs better. When analyzing the risks of WWTP drainage systems to the environment and human health, these data should be considered.

Effect of inoculum history, growth substrates and yeast extract addition on inhibition of Sulfobacillus thermosulfidooxidans by NaCl

This study reports on the effect of inoculum history, growth substrates, and yeast extract on sodium chloride tolerance of Sulfobacillus thermosulfidooxidans DSM 9293^T. The concentrations of NaCl for complete inhibition of Fe²⁺ oxidation by cells initially grown with ferrous iron sulfate, or tetrathionate, or pyrite as energy sources were 525 mM, 725 mM, and 800 mM, respectively. Noticeably, regardless of NaCl concentrations, oxygen consumption rates of S. thermosulfidooxidans with 20 mM tetrathionate were higher than with 50 mM FeSO₄. NaCl concentrations of higher than 400 mM strongly inhibited the iron respiration of S. thermosulfidooxidans. In contrast, the presence of NaCl was shown to stimulate tetrathionate oxidation. This trend was especially pronounced in NaCl-adapted cells where respiration rates at 200 mM NaCl were threefold of those in the absence of NaCl. In NaCl-adapted cultures greater respiration rates for tetrathionate were observed than in non-NaCl-adapted cultures, especially at concentrations ≥ 200 mM NaCl. At concentrations of ≤ 200 mM NaCl, cell growth and iron oxidation were enhanced with the addition of increasing concentrations of yeast extract. Thus, cell numbers in cultures with 0.05% yeast extract were ∼5 times higher than without yeast extract addition. At NaCl concentration as high as 400 mM, however, iron oxidation rates improved compared to control assays without yeast extract, but there was no clear dependence on yeast extract concentrations. The initial growth of bacteria with and without yeast extract in the presence of different NaCl concentrations was shown to impact leaching of copper from chalcopyrite. Copper dissolution was enhanced in the presence of 200 mM NaCl and absence of yeast extract, while the addition of 0.02% yeast extract was shown to promote copper solubilization in the presence of 500 mM NaCl.

Profiling native aquifer bacteria in a uranium roll-front deposit and their role in biogeochemical cycle dynamics: Insights regarding in situ recovery mining

A uranium-mineralized sandy aquifer, planned for mining by means of uranium in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding uranium roll-front deposits. Since microorganisms play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was on the characterization of bacteria residing in an aquifer surrounding a uranium roll-front deposit that forms part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the native aquifer, including the mineralized orebody, as well as compartments located both upstream (oxidized waters) and downstream (reduced waters) of this area. An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed. In addition, high-throughput sequencing data showed that the bacterial community structure was shaped by the redox gradient and oxygen availability. Several interesting bacteria were identified, including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans), iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may also be involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). Canonical correspondence analysis (CCA) and co-occurrence patterns confirmed strong correlations among the bacterial genera, suggesting either shared/preferred environmental conditions or the performance of similar/complementary functions. As a whole, the bacterial community residing in each aquifer compartment would appear to define an ecologically functional ecosystem, containing suitable microorganisms (e.g. acidophilic bacteria) prone to promote the remediation of the acidified aquifer by natural attenuation. Assessing the composition and structure of the aquifer's native bacteria is a prerequisite for understanding natural attenuation and predicting the role of bacterial input in improving ISR efficiency.

Biofilm and planktonic microbial communities in highly acidic soil (pH < 3) in the Soos National Nature Reserve, Czech Republic

Biofilm formation is a typical life strategy used by microorganisms populating acidic water systems. The same strategy might be used by microbes in highly acidic soils that are, however, neglected in this regard. In the present study, the microbial community in such highly acidic soil in the Soos National Nature Reserve (Czech Republic) has been investigated using high-throughput DNA sequencing and the organisms associated with biofilm life mode and those preferring planktonic life were distinguished using the biofilm trap technique. Our data show the differences between biofilm and planktonic microbiota fraction, although the majority of the organisms were capable of using both life modes. The by far most abundant prokaryotic genus was Acidiphilium and fungi were identified among the most abundant eukaryotic elements in biofilm formations. On the other hand, small flagellates from diverse taxonomical groups predominated in plankton. The application of cellulose amendment as well as the depth of sampling significantly influenced the composition of the detected microbial community.

Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations

BACKGROUND

Network inference is an important aim of systems biology. It enables the transformation of OMICs datasets into biological knowledge. It consists of reverse engineering gene regulatory networks from OMICs data, such as RNAseq or mass spectrometry-based proteomics data, through computational methods. This approach allows to identify signalling pathways involved in specific biological functions. The ability to infer causality in gene regulatory networks, in addition to correlation, is crucial for several modelling approaches and allows targeted control in biotechnology applications.

METHODS

We performed simulations according to the approximate Bayesian computation method, where the core model consisted of a steady-state simulation algorithm used to study gene regulatory networks in systems for which a limited level of details is available. The simulations outcome was compared to experimentally measured transcriptomics and proteomics data through approximate Bayesian computation.

RESULTS

The structure of small gene regulatory networks responsible for the regulation of biological functions involved in biomining were inferred from multi OMICs data of mixed bacterial cultures. Several causal inter- and intraspecies interactions were inferred between genes coding for proteins involved in the biomining process, such as heavy metal transport, DNA damage, replication and repair, and membrane biogenesis. The method also provided indications for the role of several uncharacterized proteins by the inferred connection in their network context.

CONCLUSIONS

The combination of fast algorithms with high-performance computing allowed the simulation of a multitude of gene regulatory networks and their comparison to experimentally measured OMICs data through approximate Bayesian computation, enabling the probabilistic inference of causality in gene regulatory networks of a multispecies bacterial system involved in biomining without need of single-cell or multiple perturbation experiments. This information can be used to influence biological functions and control specific processes in biotechnology applications.

Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs

The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.

Geomicrobiology of a seawater-influenced active sulfuric acid cave

Fetida Cave is an active sulfuric acid cave influenced by seawater, showing abundant microbial communities that organize themselves under three main different morphologies: water filaments, vermiculations and moonmilk deposits. These biofilms/deposits have different cave distribution, pH, macro- and microelement and mineralogical composition, carbon and nitrogen content. In particular, water filaments and vermiculations had circumneutral and slightly acidic pH, respectively, both had abundant organic carbon and high microbial diversity. They were rich in macro- and microelements, deriving from mineral dissolution, and, in the case of water filaments, from seawater composition. Vermiculations had different color, partly associated with their mineralogy, and unusual minerals probably due to trapping capacities. Moonmilk was composed of gypsum, poor in organic matter, had an extremely low pH (0-1) and low microbial diversity. Based on 16S rRNA gene analysis, the microbial composition of the biofilms/deposits included autotrophic taxa associated with sulfur and nitrogen cycles and biomineralization processes. In particular, water filaments communities were characterized by bacterial taxa involved in sulfur oxidation and reduction in aquatic, aphotic, microaerophilic/anoxic environments (Campylobacterales, Thiotrichales, Arenicellales, Desulfobacterales, Desulforomonadales) and in chemolithotrophy in marine habitats (Oceanospirillales, Chromatiales). Their biodiversity was linked to the morphology of the water filaments and their collection site. Microbial communities within vermiculations were partly related to their color and showed high abundance of unclassified Betaproteobacteria and sulfur-oxidizing Hydrogenophilales (including Sulfuriferula), and Acidiferrobacterales (including Sulfurifustis), sulfur-reducing Desulfurellales, and ammonia-oxidizing Planctomycetes and Nitrospirae. The microbial community associated with gypsum moonmilk showed the strong dominance (>60%) of the archaeal genus Thermoplasma and lower abundance of chemolithotrophic Acidithiobacillus, metal-oxidizing Metallibacterium, Sulfobacillus, and Acidibacillus. This study describes the geomicrobiology of water filaments, vermiculations and gypsum moonmilk from Fetida Cave, providing insights into the microbial taxa that characterize each morphology and contribute to biogeochemical cycles and speleogenesis of this peculiar seawater-influenced sulfuric acid cave.

Metatranscriptomics reveals microbial adaptation and resistance to extreme environment coupling with bioleaching performance

Chalcopyrite bioleaching by 2, 4 and 6 acidophilic strains with the same inoculation density were studied, respectively. The results indicated that the 6-strain community firstly adapted to bioleaching environment, dissolved the chalcopyrite rapidly and maintained an efficient work until late stage. Transcriptome profiles of the 6-strain community at 6th and 30th day during bioleaching process were investigated by RNA-seq. Comparative transcriptomics identified 226 and 737 significantly up-regulated genes at early and late stage, respectively. Gene annotation results revealed that microorganisms adapted to the oligotrophic environment by enhancing cell proliferation, catalytic activation and binding action to maintain their life activities at early stage, and genes related to signal transduction, localization and transporter were highly expressed as an effective response to the stressful late stage. A graphical representation was presented to show how microorganisms adapted and resisted to the extreme environment by their inner functional properties and promoted the bioleaching efficiency.

Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide

Most aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H₂), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H₂ and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H₂ and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H₂ oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.

Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition

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Deep learning has become widely used in different fields of computer science such as face recognition, but also in biology, for example to detect malignant skin cancers based on images.

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Deep learning applied to microscopy images of biofilm colonization patterns accurately characterized its bacterial composition.

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Deep learning applications only rarely outperform human experts in classification tasks. Here however, deep learning reached an accuracy of 90%, therefore clearly outperforming human experts (50% accurate).

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Our method provides an accurate alternative to standard, time-consuming biochemical methods, using visual information only.

Background

Deep neural networks have been successfully applied to diverse fields of computer vision. However, they only outperform human capacities in a few cases.

Methods

The ability of deep neural networks versus human experts to classify microscopy images was tested on biofilm colonization patterns formed on sulfide minerals composed of up to three different bioleaching bacterial species attached to chalcopyrite sample particles.

Results

A low number of microscopy images per category (<600) was sufficient for highly efficient computational analysis of the biofilm's bacterial composition. The use of deep neural networks reached an accuracy of classification of ∼90% compared to ∼50% for human experts.

Conclusions

Deep neural networks outperform human experts’ capacity in characterizing bacterial biofilm composition involved in the degradation of chalcopyrite. This approach provides an alternative to standard, time-consuming biochemical methods.

Identification of trehalose as a compatible solute in different species of acidophilic bacteria

The major industrial heap bioleaching processes are located in desert regions (mainly Chile and Australia) where fresh water is scarce and the use of resources with low water activity becomes an attractive alternative. However, in spite of the importance of the microbial populations involved in these processes, little is known about their response or adaptation to osmotic stress. In order to investigate the response to osmotic stress in these microorganisms, six species of acidophilic bacteria were grown at elevated osmotic strength in liquid media, and the compatible solutes synthesised were identified using ion chromatography and MALDI-TOF mass spectrometry. Trehalose was identified as one of, or the sole, compatible solute in all species and strains, apart from Acidithiobacillus thiooxidans where glucose and proline levels increased at elevated osmotic potentials. Several other potential compatible solutes were tentatively identified by MALDITOF analysis. The same compatible solutes were produced by these bacteria regardless of the salt used to produce the osmotic stress. The results correlate with data from sequenced genomes which confirm that many chemolithotrophic and heterotrophic acidophiles possess genes for trehalose synthesis. This is the first report to identify and quantify compatible solutes in acidophilic bacteria that have important roles in biomining technologies.

Microbial communities associated with uranium in-situ recovery mining process are related to acid mine drainage assemblages

A large fraction (47%) of the world's uranium is mined by a technique called "In Situ Recovery" (ISR). This mining technique involves the injection of a leaching fluid (acidic or alkaline) into a uranium-bearing aquifer and the pumping of the resulting solution through cation exchange columns for the recovery of dissolved uranium. The present study reports the in-depth alterations brought to autochthonous microbial communities during acidic ISR activities. Water samples were collected from a uranium roll-front deposit that is part of an ISR mine in operation (Tortkuduk, Kazakhstan). Water samples were obtained at a depth of ca 500 m below ground level from several zones of the Uyuk aquifer following the natural redox zonation inherited from the roll front deposit, including the native mineralized orebody and both upstream and downstream adjacent locations. Samples were collected equally from both the entrance and the exit of the uranium concentration plant. Next-generation sequencing data showed that the redox gradient shaped the community structures, within the anaerobic, reduced, and oligotrophic habitats of the native aquifer zones. Acid injection induced drastic changes in the structures of these communities, with a large decrease in both cell numbers and diversity. Communities present in the acidified (pH values < 2) mining areas exhibited similarities to those present in acid mine drainage, with the dominance of Sulfobacillus sp., Leptospirillum sp. and Acidithiobacillus sp., as well as the archaean Ferroplasma sp. Communities located up- and downstream of the mineralized zone under ISR and affected by acidic fluids were blended with additional facultative anaerobic and acidophilic microorganisms. These mixed biomes may be suitable communities for the natural attenuation of ISR mining-affected subsurface through the reduction of metals and sulfate. Assessing the effect of acidification on the microbial community is critical to evaluating the potential for natural attenuation or active bioremediation strategies.

In Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle

The coinage “pan-genome” was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species’ basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species’ core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H₂ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H₂ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.

Taxonomic distribution, structure/function relationship and metabolic context of the two families of sulfide dehydrogenases: SQR and FCSD

Hydrogen sulfide (H₂S) is a versatile molecule with different functions in living organisms: it can work as a metabolite of sulfur and energetic metabolism or as a signaling molecule in higher Eukaryotes. H₂S is also highly toxic since it is able to inhibit heme cooper oxygen reductases, preventing oxidative phosphorylation. Due to the fact that it can both inhibit and feed the respiratory chain, the immediate role of H₂S on energy metabolism crucially relies on its bioavailability, meaning that studying the central players involved in the H₂S homeostasis is key for understanding sulfide metabolism. Two different enzymes with sulfide oxidation activity (sulfide dehydrogenases) are known: flavocytochrome c sulfide dehydrogenase (FCSD), a sulfide:cytochrome c oxidoreductase; and sulfide:quinone oxidoreductase (SQR). In this work we performed a thorough bioinformatic study of SQRs and FCSDs and integrated all published data. We systematized several properties of these proteins: (i) nature of flavin binding, (ii) capping loops and (iii) presence of key amino acid residues. We also propose an update to the SQR classification system and discuss the role of these proteins in sulfur metabolism.

Expression, purification and function of cysteine desulfurase from Sulfobacillus acidophilus TPY isolated from deep-sea hydrothermal vent

The cysteine desulfurase (SufS) gene of Sulfobacillus acidophilus TPY, a Gram-positive bacterium isolated from deep-sea hydrothermal vent, was cloned and over-expressed in E. coli BL21. The recombinant SufS protein was purified by one-step affinity chromatography. The TPY SufS contained a well conserved motif RXGHHCA as found in that of other microorganisms, suggesting that it belonged to group II of cysteine desulfurase family. The recombinant TPY SufS could catalyze the conversion of l-cysteine to l-alanine and produce persulfide, and the enzyme activity was 95 μ/μL of sulfur ion per minute. The growth of E. coli BL21 was promoted by over-expressing TPY SufS in vivo or by directly adding recombinant TPY SufS in the medium (4.3-4.5 × 10⁸ cells/mL vs. 3.2-3.5 × 10⁸ cells/mL). Furthermore, the highest cell density of E. coli BL21 when the TPY SufS was over-expressed was about 3.5 times that of the control groups in the presence of sodium thiosulfate. These results indicate that the SUF system as the only assembly system of iron-sulfur clusters not only has significant roles in survival of S. acidophilus TPY, but also might be important for combating with high content of sulfide.

Responses of zinc recovery to temperature and mineral composition during sphalerite bioleaching process

Temperature and energy resources (e.g., iron, sulfur and organic matter) usually undergo dynamic changes, and play important roles during industrial bioleaching process. Thus, it is essential to investigate their synergistic effects and the changes of their independent effects with simultaneous actions of multi-factors. In this study, we explored the synergistic effects of temperature and original mineral compositions (OMCs, energy resources) on the sphalerite bioleaching process. The microbial community structure was monitored by 16S rRNA gene sequencing technology and showed clear segregation along temperature gradients and Shannon diversity decreased at high temperature. On the contrary, the physicochemical parameters (pH and [Fe³⁺]) in the leachate were significantly affected by the OMCs. Interestingly, the influence of temperature on zinc recovery was greater at relatively simpler OMCs level, whereas the influence of OMCs was stronger at lower temperature. In addition, using [Fe³⁺], pH, relative abundances of dominant OTUs of microbial community and temperature as variable parameters, several models were constructed to predict zinc leaching efficiency, providing a possibility to predict the metal recovery efficiency under temperature change and variable energy resources.

Bacterial, Archaeal, and Eukaryotic Diversity across Distinct Microhabitats in an Acid Mine Drainage

Acid mine drainages are characterized by their low pH and the presence of dissolved toxic metallic species. Microorganisms survive in different microhabitats within the ecosystem, namely water, sediments, and biofilms. In this report, we surveyed the microbial diversity within all domains of life in the different microhabitats at Los Rueldos abandoned mercury underground mine (NW Spain), and predicted bacterial function based on community composition. Sediment samples contained higher proportions of soil bacteria (AD3, Acidobacteria), as well as Crenarchaeota and Methanomassiliicoccaceae archaea. Oxic and hypoxic biofilm samples were enriched in bacterial iron oxidizers from the genus Leptospirillum, order Acidithiobacillales, class Betaproteobacteria, and archaea from the class Thermoplasmata. Water samples were enriched in Cyanobacteria and Thermoplasmata archaea at a 3–98% of the sunlight influence, whilst Betaproteobacteria, Thermoplasmata archaea, and Micrarchaea dominated in acid water collected in total darkness. Stalactites hanging from the Fe-rich mine ceiling were dominated by the neutrophilic iron oxidizer Gallionella and other lineages that were absent in the rest of the microhabitats (e.g., Chlorobi, Chloroflexi). Eukaryotes were detected in biofilms and open-air water samples, and belonged mainly to clades SAR (Alveolata and Stramenopiles), and Opisthokonta (Fungi). Oxic and hypoxic biofilms displayed higher proportions of ciliates (Gonostomum, Oxytricha), whereas water samples were enriched in fungi (Paramicrosporidium and unknown microbial Helotiales). Predicted function through bacterial community composition suggested adaptive evolutive convergence of function in heterogeneous communities. Our study showcases a broad description of the microbial diversity across different microhabitats in the same environment and expands the knowledge on the diversity of microbial eukaryotes in AMD habitats.

Comparative Genomics Unravels the Functional Roles of Co-occurring Acidophilic Bacteria in Bioleaching Heaps

The spatial-temporal distribution of populations in various econiches is thought to be potentially related to individual differences in the utilization of nutrients or other resources, but their functional roles in the microbial communities remain elusive. We compared differentiation in gene repertoire and metabolic profiles, with a focus on the potential functional traits of three commonly recognized members (Acidithiobacillus caldus, Leptospirillum ferriphilum, and Sulfobacillus thermosulfidooxidans) in bioleaching heaps. Comparative genomics revealed that intra-species divergence might be driven by horizontal gene transfer. These co-occurring bacteria shared a few homologous genes, which significantly suggested the genomic differences between these organisms. Notably, relatively more genes assigned to the Clusters of Orthologous Groups category [G] (carbohydrate transport and metabolism) were identified in Sulfobacillus thermosulfidooxidans compared to the two other species, which probably indicated their mixotrophic capabilities that assimilate both organic and inorganic forms of carbon. Further inspection revealed distinctive metabolic capabilities involving carbon assimilation, nitrogen uptake, and iron-sulfur cycling, providing robust evidence for functional differences with respect to nutrient utilization. Therefore, we proposed that the mutual compensation of functionalities among these co-occurring organisms might provide a selective advantage for efficiently utilizing the limited resources in their habitats. Furthermore, it might be favorable to chemoautotrophs' lifestyles to form mutualistic interactions with these heterotrophic and/or mixotrophic acidophiles, whereby the latter could degrade organic compounds to effectively detoxify the environments. Collectively, the findings shed light on the genetic traits and potential metabolic activities of these organisms, and enable us to make some inferences about genomic and functional differences that might allow them to co-exist.

Microbial community dynamics in Inferno Crater Lake, a thermally fluctuating geothermal spring

Understanding how microbial communities respond and adjust to ecosystem perturbation is often difficult to interpret due to multiple and often simultaneous variations in observed conditions. In this research, we investigated the microbial community dynamics of Inferno Crater Lake, an acidic geothermal spring in New Zealand with a unique thermal cycle that varies between 30 and 80 °C over a period of 40-60 days. Using a combination of next-generation sequencing, geochemical analysis and quantitative PCR we found that the microbial community composition was predominantly chemolithotrophic and strongly associated with the thermal cycle. At temperatures >65 °C, the microbial community was dominated almost exclusively by sulphur-oxidising archaea (Sulfolobus-like spp.). By contrast, at mesophilic temperatures the community structure was more mixed, comprising both archaea and bacteria but dominated primarily by chemolithotrophic sulphur and hydrogen oxidisers. Multivariate analysis of physicochemical data confirmed that temperature was the only significant variable associated with community turnover. This research contributes to our understanding of microbial community dynamics in variable environments, using a naturally alternating system as a model and extends our limited knowledge of acidophile ecology in geothermal habitats.

In-depth characterization of bacterial and archaeal communities present in the abandoned Kettara pyrrhotite mine tailings (Morocco)

In Morocco, pollution caused by closed mines continues to be a serious threat to the environment, like the generation of acid mine drainage. Mine drainage is produced by environmental and microbial oxidation of sulfur minerals originating from mine wastes. The fundamental role of microbial communities is well known, like implication of Fe-oxidizing and to a lesser extent S-oxidizing microorganism in bioleaching. However, the structure of the microbial communities varies a lot from one site to another, like diversity depends on many factors such as mineralogy, concentration of metals and metalloids or pH, etc. In this study, prokaryotic communities in the pyrrhotite-rich tailings of Kettara mine were characterized using the Illumina sequencing. In-depth phylogenetic analysis revealed a total of 12 phyla of bacteria and 1 phyla of Archaea. The majority of sequences belonged to the phylum of Proteobacteria and Firmicutes with a predominance of Bacillus, Pseudomonas or Corynebacterium genera. Many microbial populations are implicated in the iron, sulfur and arsenic cycles, like Acidiferrobacter, Leptospirillum, or Alicyclobacillus in Fe; Acidiferrobacter and Sulfobacillus in S; and Bacillus or Pseudomonas in As. This is one of the first description of prokaryotic communities in pyrrhotite-rich mine tailings using high-throughput sequencing.

Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss

Recent phylogenomic analysis has suggested that three strains isolated from different copper mine tailings around the world were taxonomically affiliated with Sulfobacillusthermosulfidooxidans Here, we present a detailed investigation of their genomic features, particularly with respect to metabolic potentials and stress tolerance mechanisms. Comprehensive analysis of the Sulfobacillus genomes identified a core set of essential genes with specialized biological functions in the survival of acidophiles in their habitats, despite differences in their metabolic pathways. The Sulfobacillus strains also showed evidence for stress management, thereby enabling them to efficiently respond to harsh environments. Further analysis of metabolic profiles provided novel insights into the presence of genomic streamlining, highlighting the importance of gene loss as a main mechanism that potentially contributes to cellular economization. Another important evolutionary force, especially in larger genomes, is gene acquisition via horizontal gene transfer (HGT), which might play a crucial role in the recruitment of novel functionalities. Also, a successful integration of genes acquired from archaeal donors appears to be an effective way of enhancing the adaptive capacity to cope with environmental changes. Taken together, the findings of this study significantly expand the spectrum of HGT and genome reduction in shaping the evolutionary history of Sulfobacillus strains.IMPORTANCE Horizontal gene transfer (HGT) and gene loss are recognized as major driving forces that contribute to the adaptive evolution of microbial genomes, although their relative importance remains elusive. The findings of this study suggest that highly frequent gene turnovers within microorganisms via HGT were necessary to incur additional novel functionalities to increase the capacity of acidophiles to adapt to changing environments. Evidence also reveals a fascinating phenomenon of potential cross-kingdom HGT. Furthermore, genome streamlining may be a critical force in driving the evolution of microbial genomes. Taken together, this study provides insights into the importance of both HGT and gene loss in the evolution and diversification of bacterial genomes.

A Ferredoxin- and F420H2-Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea

Heterodisulfide reductases (Hdr) of the HdrABC class are ancient enzymes and a component of the anaerobic core belonging to the prokaryotic common ancestor. The ancient origin is consistent with the widespread occurrence of genes encoding putative HdrABC homologs in metabolically diverse prokaryotes predicting diverse physiological functions; however, only one HdrABC has been characterized and that was from a narrow metabolic group of obligate CO₂-reducing methanogenic anaerobes (methanogens) from the domain Archaea. Here we report the biochemical characterization of an HdrABC homolog (HdrA2B2C2) from the acetate-utilizing methanogen Methanosarcina acetivorans with unusual properties structurally and functionally distinct from the only other HdrABC characterized. Homologs of the HdrA2B2C2 archetype are present in phylogenetically and metabolically diverse species from the domains Bacteria and Archaea. The expression of the individual HdrA2, HdrB2, and HdrB2C2 enzymes in Escherichia coli, and reconstitution of an active HdrA2B2C2 complex, revealed an intersubunit electron transport pathway dependent on ferredoxin or coenzyme F₄₂₀ (F₄₂₀H₂) as an electron donor. Remarkably, HdrA2B2C2 couples the previously unknown endergonic oxidation of F₄₂₀H₂ and reduction of ferredoxin with the exergonic oxidation of F₄₂₀H₂ and reduction of the heterodisulfide of coenzyme M and coenzyme B (CoMS-SCoB). The unique electron bifurcation predicts a role for HdrA2B2C2 in Fe(III)-dependent anaerobic methane oxidation (ANME) by M. acetivorans and uncultured species from ANME environments. HdrA2B2C2, ubiquitous in acetotrophic methanogens, was shown to participate in electron transfer during acetotrophic growth of M. acetivorans and proposed to be essential for growth in the environment when acetate is limiting.

Discovery of the archetype HdrA2B2C2 heterodisulfide reductase with categorically unique properties extends the understanding of this ancient family beyond CO₂-reducing methanogens to include diverse prokaryotes from the domains Bacteria and Archaea. The unprecedented coenzyme F₄₂₀-dependent electron bifurcation, an emerging fundamental principle of energy conservation, predicts a role for HdrA2B2C2 in diverse metabolisms, including anaerobic CH₄-oxidizing pathways. The results document an electron transport role for HdrA2B2C2 in acetate-utilizing methanogens responsible for at least two-thirds of the methane produced in Earth’s biosphere. The previously unavailable heterologous production of individual subunits and the reconstitution of HdrA2B2C2 with activity have provided an understanding of intersubunit electron transfer in the HdrABC class and a platform for investigating the principles of electron bifurcation.

Gene Turnover Contributes to the Evolutionary Adaptation of Acidithiobacillus caldus: Insights from Comparative Genomics

Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geographic origins as well as in ecological preferences. Based on phylogenomic analysis, we clustered the six A. caldus strains isolated from various ecological niches into two groups: group 1 strains with smaller genomes and group 2 strains with larger genomes. We found no obvious intraspecific divergence with respect to predicted genes that are related to central metabolism and stress management strategies between these two groups. Although numerous highly homogeneous genes were observed, high genetic diversity was also detected. Preliminary inspection provided a first glimpse of the potential correlation between intraspecific diversity at the genome level and environmental variation, especially geochemical conditions. Evolutionary genetic analyses further showed evidence that the difference in environmental conditions might be a crucial factor to drive the divergent evolution of A. caldus species. We identified a diverse pool of mobile genetic elements including insertion sequences and genomic islands, which suggests a high frequency of genetic exchange in these harsh habitats. Comprehensive analysis revealed that gene gains and losses were both dominant evolutionary forces that directed the genomic diversification of A. caldus species. For instance, horizontal gene transfer and gene duplication events in group 2 strains might contribute to an increase in microbial DNA content and novel functions. Moreover, genomes undergo extensive changes in group 1 strains such as removal of potential non-functional DNA, which results in the formation of compact and streamlined genomes. Taken together, the findings presented herein show highly frequent gene turnover of A. caldus species that inhabit extremely acidic environments, and shed new light on the contribution of gene turnover to the evolutionary adaptation of acidophiles.

Sulfur Metabolism Pathways in Sulfobacillus acidophilus TPY, A Gram-Positive Moderate Thermoacidophile from a Hydrothermal Vent

Sulfobacillus acidophilus TPY, isolated from a hydrothermal vent in the Pacific Ocean, is a moderately thermoacidophilic Gram-positive bacterium that can oxidize ferrous iron or sulfur compounds to obtain energy. In this study, comparative transcriptomic analyses of S. acidophilus TPY were performed under different redox conditions. Based on these results, pathways involved in sulfur metabolism were proposed. Additional evidence was obtained by analyzing mRNA abundance of selected genes involved in the sulfur metabolism of sulfur oxygenase reductase (SOR)-overexpressed S. acidophilus TPY recombinant under different redox conditions. Comparative transcriptomic analyses of S. acidophilus TPY cultured in the presence of ferrous sulfate (FeSO4) or elemental sulfur (S0) were employed to detect differentially transcribed genes and operons involved in sulfur metabolism. The mRNA abundances of genes involved in sulfur metabolism decreased in cultures containing elemental sulfur, as opposed to cultures in which FeSO4 was present where an increase in the expression of sulfur metabolism genes, particularly sulfite reductase (SiR) involved in the dissimilatory sulfate reduction, was observed. SOR, whose mRNA abundance increased in S0 culture, may play an important role in the initial sulfur oxidation. In order to confirm the pathways, SOR overexpression in S. acidophilus TPY and subsequent mRNA abundance analysis of sulfur metabolism-related genes were carried out. Conjugation-based transformation of pTrc99A derived plasmid from heterotrophic E. coli to facultative autotrophic S. acidophilus TPY was developed in this study. Transconjugation between E. coli and S. acidophilus was performed on modified solid 2:2 medium at pH 4.8 and 37°C for 72 h. The SOR-overexpressed recombinant S. acidophilus TPY-SOR had a [Formula: see text]-accumulation increase, higher oxidation/ reduction potentials (ORPs) and lower pH compared with the wild type strain in the late growth stage of S0 culture condition. The transcript level of sor gene in the recombinant strain increased in both S0 and FeSO4 culture conditions, which influenced the transcription of other genes in the proposed sulfur metabolism pathways. Overall, these results expand our understanding of sulfur metabolism within the Sulfobacillus genus and provide a successful gene-manipulation method.

Genomic and metagenomic challenges and opportunities for bioleaching: a mini-review

High-throughput genomic technologies are accelerating progress in understanding the diversity of microbial life in many environments. Here we highlight advances in genomics and metagenomics of microorganisms from bioleaching heaps and related acidic mining environments. Bioleaching heaps used for copper recovery provide significant opportunities to study the processes and mechanisms underlying microbial successions and the influence of community composition on ecosystem functioning. Obtaining quantitative and process-level knowledge of these dynamics is pivotal for understanding how microorganisms contribute to the solubilization of copper for industrial recovery. Advances in DNA sequencing technology provide unprecedented opportunities to obtain information about the genomes of bioleaching microorganisms, allowing predictive models of metabolic potential and ecosystem-level interactions to be constructed. These approaches are enabling predictive phenotyping of organisms many of which are recalcitrant to genetic approaches or are unculturable. This mini-review describes current bioleaching genomic and metagenomic projects and addresses the use of genome information to: (i) build metabolic models; (ii) predict microbial interactions; (iii) estimate genetic diversity; and (iv) study microbial evolution. Key challenges and perspectives of bioleaching genomics/metagenomics are addressed.

Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum"

Acid mine drainage (AMD), associated with active and abandoned mining sites, is a habitat for acidophilic microorganisms that gain energy from the oxidation of reduced sulfur compounds and ferrous iron and that thrive at pH below 4. Members of the recently proposed genus “Ferrovum” are the first acidophilic iron oxidizers to be described within the Betaproteobacteria. Although they have been detected as typical community members in AMD habitats worldwide, knowledge of their phylogenetic and metabolic diversity is scarce. Genomics approaches appear to be most promising in addressing this lacuna since isolation and cultivation of “Ferrovum” has proven to be extremely difficult and has so far only been successful for the designated type strain “Ferrovum myxofaciens” P3G. In this study, the genomes of two novel strains of “Ferrovum” (PN-J185 and Z-31) derived from water samples of a mine water treatment plant were sequenced. These genomes were compared with those of “Ferrovum” sp. JA12 that also originated from the mine water treatment plant, and of the type strain (P3G). Phylogenomic scrutiny suggests that the four strains represent three “Ferrovum” species that cluster in two groups (1 and 2). Comprehensive analysis of their predicted metabolic pathways revealed that these groups harbor characteristic metabolic profiles, notably with respect to motility, chemotaxis, nitrogen metabolism, biofilm formation and their potential strategies to cope with the acidic environment. For example, while the “F. myxofaciens” strains (group 1) appear to be motile and diazotrophic, the non-motile group 2 strains have the predicted potential to use a greater variety of fixed nitrogen sources. Furthermore, analysis of their genome synteny provides first insights into their genome evolution, suggesting that horizontal gene transfer and genome reduction in the group 2 strains by loss of genes encoding complete metabolic pathways or physiological features contributed to the observed diversification.

Insights from the docked DoxDA Model with Thiosulphate

Redox reaction of inorganic sulphur compound is very essential to maintain a global sulphur cycle. Certain experimental evidences suggest that gamma-proteobacterial Acidothiobacillus thiooxidans; lacking the sulphur-oxidizing (sox) operon, has an alternative thiosulphate oxidation pathway. Dox operon having essentially participating proteins; DoxD and DoxA serves as the central players for this alternative pathway of thiosulphate oxidation. So, to identify their role in thiosulphate oxidation process, functional 3D model of DoxD and DoxA protein's independently functioning conserved domains were built after the contentment of necessary stereochemical features. After formation of the best suited DoxDA protein-complex, DoxDA was MD simulated in several steps and finally through MD simulation run utilizing GROMACS. Even after running beyond 20ns, 18ns simulated protein complex was the most stable and was selected for further study. Residual binding mode conferred mainly two ionic and twelve Hbonded interactions in DoxDA. Astonishingly, Asp167 and Arg18 from DoxA and DoxD, respectively was observed to hold a pivotal role in 6 H-bonds accompanied by a separate ionic interaction. Interestingly, four residues from DoxD; Trp32, Met33, Lys36 and Asn140 strengthened the DoxD-thiosulphate interaction. Interaction energy (deltaG = (-) 222.016kcal/mol) and net solvent accessibility calculations depicts spontaneous and fervent residual participation in DoxDA, which is essential for thiosulphate interaction and further sulphur oxidation. Conformational flexibility in DoxD with increased coil percentage benefits DoxD and makes its susceptible for the interaction with thiosulphate even after spontaneous interaction with DoxA. Therefore, this study serves as an insight at computational basis for sulphur oxidation even in organisms lacking sox operon.

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.

Sulfur Oxygenase Reductase (Sor) in the Moderately Thermoacidophilic Leaching Bacteria: Studies in Sulfobacillus thermosulfidooxidans and Acidithiobacillus caldus

The sulfur oxygenase reductase (Sor) catalyzes the oxygen dependent disproportionation of elemental sulfur, producing sulfite, thiosulfate and sulfide. Being considered an “archaeal like” enzyme, it is also encoded in the genomes of some acidophilic leaching bacteria such as Acidithiobacillus caldus, Acidithiobacillus thiooxidans, Acidithiobacillus ferrivorans and Sulfobacillus thermosulfidooxidans, among others. We measured Sor activity in crude extracts from Sb. thermosulfidooxidans DSM 9293^T. The optimum temperature for its oxygenase activity was achieved at 75 °C, confirming the “thermophilic” nature of this enzyme. Additionally, a search for genes probably involved in sulfur metabolism in the genome sequence of Sb. thermosulfidooxidans DSM 9293^T was done. Interestingly, no sox genes were found. Two sor genes, a complete heterodisulfidereductase (hdr) gene cluster, three tetrathionate hydrolase (tth) genes, three sulfide quinonereductase (sqr), as well as the doxD component of a thiosulfate quinonereductase (tqo) were found. Seven At. caldus strains were tested for Sor activity, which was not detected in any of them. We provide evidence that an earlier reported Sor activity from At. caldus S1 and S2 strains most likely was due to the presence of a Sulfobacillus contaminant.

Omics on bioleaching: current and future impacts

Bioleaching corresponds to the microbial-catalyzed process of conversion of insoluble metals into soluble forms. As an applied biotechnology globally used, it represents an extremely interesting field of research where omics techniques can be applied in terms of knowledge development, but moreover in terms of process design, control, and optimization. In this mini-review, the current state of genomics, proteomics, and metabolomics of bioleaching and the major impacts of these analytical methods at industrial scale are highlighted. In summary, genomics has been essential in the determination of the biodiversity of leaching processes and for development of conceptual and functional metabolic models. Proteomic impacts are mostly related to microbe-mineral interaction analysis, including copper resistance and biofilm formation. Early steps of metabolomics in the field of bioleaching have shown a significant potential for the use of metabolites as industrial biomarkers. Development directions are given in order to enhance the future impacts of the omics in biohydrometallurgy.

High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T)

Flavihumibacter solisilvae 3-3(T) (= KACC 17917(T) = JCM 19891(T)) represents a type strain of the genus Flavihumibacter within the family Chitinophagaceae. This strain can use various sole carbon sources, making it applicable in industry and bioremediation. In this study, the draft genomic information of F. solisilvae 3-3(T) is described. F. solisilvae 3-3(T) owns a genome size of 5.41 Mbp, 47 % GC content and a total of 4,698 genes, including 4,215 protein coding genes, 439 pseudo genes and 44 RNA encoding genes. Analysis of its genome reveals high correlation between the genotypes and the phenotypes.

Microbial diversity and metabolic networks in acid mine drainage habitats

Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.