Biofilm formation and interspecies interactions in mixed cultures of thermo-acidophilic archaea Acidianus spp. and Sulfolobus metallicus

Differential surface modification mechanism of chalcopyrite and pyrite by Thiobacillus ferrooxidans and its response to bioflotation

Mineral processing encounters the challenge of separating chalcopyrite and pyrite, with the conventional high alkali process characterized by issues such as large dosages of reagents, complex procedures, and environmental pollution. This study addresses this challenge by isolating and enriching Thiobacillus ferrooxidans (T·f) from acidic mine drainage, employing it as a biosurfactant. The modification mechanism of T·f was thoroughly analyzed. Fe dissolution through biological oxidation formed a passivation layer (jarosite [KFe3(SO4)2(OH)6], elemental sulfur (S0), and metal sulfides (Cu/Fe-S) on the surface of minerals. Metal oxides, hydroxides, and sulfates were detected on the surface of two minerals, but the difference was that elemental sulfur (S0) and copper sulfide (Cu-S) were detected on the surface of chalcopyrite. elucidating the fundamental reason for the significant difference in surface hydrophobicity between chalcopyrite and pyrite. T·f has been successfully used as a biosurfactant to achieve copper-sulfur separation.

Extremely thermoacidophilic archaea for metal bioleaching: What do their genomes tell Us?

Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.

Sessile Lifestyle Offers Protection against Copper Stress in Saccharolobus solfataricus

Some archaea from the genus Sulfolobus are important for bioleaching of copper, where metal resistant microorganisms are required. Biofilm generation is one of the ways microorganisms cope with some stimuli in nature, including heavy metals. The response to external factors, particularly in the biofilm form of life, is still underexplored in archaea. To explore how model thermoacidophilic archaeon Saccharolobus solfataricus faces copper stress during this lifestyle, changes in biofilms were studied using crystal violet staining, confocal fluorescence microscopy, and qPCR approaches. It was found that biofilm formation reached a maximum at 0.5 mM Cu, before starting to decrease at higher metal concentrations. The morphology of biofilms at 0.5 mM Cu was observed to be different, displaying lower thickness, different sugar patterns, and higher amounts of cells compared to standard growing conditions. Furthermore, copA, which is responsive to intracellular Cu concentration, was downregulated in biofilm cells when compared with planktonic cells exposed to the same metal concentration. The latest results suggests that cells in biofilms are less exposed to Cu than those in planktonic culture. In a PolyP-deficient strain, Cu was not able to induce biofilm formation at 0.5 mM. In summary, the findings reported here suggest that the biofilm form of life confers S. solfataricus advantages to face stress caused by Cu.Biofilm formation remains a relatively unexplored topic in archaeal research. Therefore, this knowledge in model organisms such as S. solfataricus, and how they use it to face stress, could be of great importance to engineer organisms with improved capabilities to be applied in biotechnological processes, such as bioleaching of metals.

Manesh MJ, Sivabalasarma S, Albers SV, Kelly RM. Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin

A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.

Advances in bioleaching of waste lithium batteries under metal ion stress

In modern societies, the accumulation of vast amounts of waste Li-ion batteries (WLIBs) is a grave concern. Bioleaching has great potential for the economic recovery of valuable metals from various electronic wastes. It has been successfully applied in mining on commercial scales. Bioleaching of WLIBs can not only recover valuable metals but also prevent environmental pollution. Many acidophilic microorganisms (APM) have been used in bioleaching of natural ores and urban mines. However, the activities of the growth and metabolism of APM are seriously inhibited by the high concentrations of heavy metal ions released by the bio-solubilization process, which slows down bioleaching over time. Only when the response mechanism of APM to harsh conditions is well understood, effective strategies to address this critical operational hurdle can be obtained. In this review, a multi-scale approach is used to summarize studies on the characteristics of bioleaching processes under metal ion stress. The response mechanisms of bacteria, including the mRNA expression levels of intracellular genes related to heavy metal ion resistance, are also reviewed. Alleviation of metal ion stress via addition of chemicals, such as spermine and glutathione is discussed. Monitoring using electrochemical characteristics of APM biofilms under metal ion stress is explored. In conclusion, effective engineering strategies can be proposed based on a deep understanding of the response mechanisms of APM to metal ion stress, which have been used to improve bioleaching efficiency effectively in lab tests. It is very important to engineer new bioleaching strains with high resistance to metal ions using gene editing and synthetic biotechnology in the near future.

Sticky Bacteria: Understanding the Behavior of a D-Galactose Adapted Consortium of Acidophilic Chemolithotroph Bacteria and Their Attachment on a Concentrate of Polymetallic Mineral

Various strategies to accelerate the formation of biofilms on minerals have been studied, and one of them is the use of D-galactose as an inducer of EPS production in planktonic cells of biooxidant bacteria. With the aim to evaluate the influence on the attachment and the effect over the solubilization of a polymetallic mineral concentrate, the behavior of a microbial consortium formed by Acidithiobacillus thiooxidans DSM 14887T and Leptospirillum ferrooxidans DSM 2705T previously induced with D-galactose for the early formation of EPS was studied. These microorganisms were previously adapted to 0.15 and 0.25% of D-galactose, respectively; afterward, different proportions of both strains were put in contact with the particle surface of a concentrate of polymetallic mineral. Also, to evaluate the affinity of each bacterium to the mineral, attachment tests were carried out with one of these species acting as a pre-colonizer. The same consortia were used to evaluate the solubilization of the polymetallic mineral. The results obtained show that the induction by D-galactose increases the microbial attachment percentage to the mineral by at least 10% with respect to the control of non-adapted consortia. On the other hand, the tests carried out with pre-colonization show that the order of inoculation also affects the microbial attachment percentage. From the different proportions tested, it was determined that the use of a consortium with a proportion of 50% of each species previously adapted to D-galactose and inoculated simultaneously, present a microbial attachment percentage to the mineral greater than 95% and better solubilization of a polymetallic mineral, reaching values of 9.7 and 11.7mgL-1 h-1 of Fe3+ and SO4 2-, respectively. Therefore, the use of D-galactose in small concentrations as inducer of EPS in acidophilic cells and the selection of an adequate strategy of inoculation can be beneficial to improve biooxidation since it would allow this process to develop in a shorter time by achieving a greater number of attached cells in a shorter time accelerating the solubilization of a sulfide mineral. Graphical AbstractEPS production using D-galactose as inducer and its influence in the attachment of consortia formed by differents proportions of A. thiooxidans and L. ferrooxidans inoculated at the same time and when one of them acting as a pre-colonizer.

A Unique Gene Module in Thermococcales Archaea Centered on a Hypervariable Protein Containing Immunoglobulin Domains

Molecular mechanisms involved in biological conflicts and self vs nonself recognition in archaea remain poorly characterized. We apply phylogenomic analysis to identify a hypervariable gene module that is widespread among Thermococcales. These loci consist of an upstream gene coding for a large protein containing several immunoglobulin (Ig) domains and unique combinations of downstream genes, some of which also contain Ig domains. In the large Ig domain containing protein, the C-terminal Ig domain sequence is hypervariable, apparently, as a result of recombination between genes from different Thermococcales. To reflect the hypervariability, we denote this gene module VARTIG (VARiable Thermococcales IG). The overall organization of the VARTIG modules is similar to the organization of Polymorphic Toxin Systems (PTS). Archaeal genomes outside Thermococcales encode a variety of Ig domain proteins, but no counterparts to VARTIG and no Ig domains with comparable levels of variability. The specific functions of VARTIG remain unknown but the identified features of this system imply three testable hypotheses: (i) involvement in inter-microbial conflicts analogous to PTS, (ii) role in innate immunity analogous to the vertebrate complement system, and (iii) function in self vs nonself discrimination analogous to the vertebrate Major Histocompatibility Complex. The latter two hypotheses seem to be of particular interest given the apparent analogy to the vertebrate immunity.

RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite

Biooxidation of gold-bearing refractory mineral ores such as arsenopyrite (FeAsS) in stirred tanks produces solutions containing highly toxic arsenic concentrations. In this study, ferrous iron and inorganic sulfur-oxidizing Acidithiobacillus strain IBUN Ppt12 most similar to Acidithiobacillus ferrianus and inorganic sulfur compound oxidizing Acidithiobacillus sp. IBUNS3 were grown in co-culture during biooxidation of refractory FeAsS. Total RNA was extracted and sequenced from the planktonic cells to reveal genes with different transcript counts involved in the response to FeAsS containing medium. The co-culture's response to arsenic release during biooxidation included the ars operon genes that were independently regulated according to the arsenopyrite concentration. Additionally, increased mRNA transcript counts were identified for transmembrane ion transport proteins, stress response mechanisms, accumulation of inorganic polyphosphates, urea catabolic processes, and tryptophan biosynthesis. Acidithiobacillus spp. RNA transcripts also included those encoding the Rus and PetI proteins involved in ferrous iron oxidation and gene clusters annotated as encoding inorganic sulfur compound metabolism enzymes. Finally, mRNA counts of genes related to DNA methylation, management of oxidative stress, chemotaxis, and motility during biooxidation were decreased compared to cells growing without mineral. The results provide insights into the adaptation of Acidithiobacillus spp. to growth during biooxidation of arsenic-bearing sulfides.

Importance of Initial Interfacial Steps during Chalcopyrite Bioleaching by a Thermoacidophilic Archaeon

Studies of thermophilic microorganisms have shown that they have a considerable biotechnological potential due to their optimum growth and metabolism at high temperatures. Thermophilic archaea have unique characteristics with important biotechnological applications; many of these species could be used in bioleaching processes to recover valuable metals from mineral ores. Particularly, bioleaching at high temperatures using thermoacidophilic microorganisms can greatly improve metal solubilization from refractory mineral species such as chalcopyrite (CuFeS₂), one of the most abundant and widespread copper-bearing minerals. Interfacial processes such as early cell adhesion, biofilm development, and the formation of passive layers on the mineral surface play important roles in the initial steps of bioleaching processes. The present work focused on the investigation of different bioleaching conditions using the thermoacidophilic archaeon Acidianus copahuensis DSM 29038 to elucidate which steps are pivotal during the chalcopyrite bioleaching. Fluorescent in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM) were used to visualize the microorganism–mineral interaction. Results showed that up to 85% of copper recovery from chalcopyrite could be achieved using A. copahuensis. Improvements in these yields are intimately related to an early contact between cells and the mineral surface. On the other hand, surface coverage by inactivated cells as well as precipitates significantly reduced copper recoveries.

Interactions Between Cells of Sulfobacillus thermosulfidooxidans and Leptospirillum ferriphilum During Pyrite Bioleaching

Sulfobacillus and Leptospirillum occur frequently in leaching systems. Here we investigated the effects of cells of L. ferriphilum on biofilm formation and leaching performance by S. thermosulfidooxidans. The effects were caused by the presence of L. ferriphilum or an addition of pyrite leach liquor from L. ferriphilum. Data show that the number of attached S. thermosulfidooxidans on pyrite increases, if the pyrite had been pre-colonized by living biofilms of L. ferriphilum, while it decreases if the pre-colonized biofilms had been inactivated. Coaggregation between S. thermosulfidooxidans and L. ferriphilum occurs during the dual-species biofilm formation, but different effects on bioleaching were noted, if the preculture of L. ferriphilum had been different. If L. ferriphilum had been pre-colonized on a pyrite, significantly negative effect was shown. However, if the two species were simultaneously inoculated into a sterile leaching system, the bioleaching efficiency was better than that of a pure culture of S. thermosulfidooxidans. The effect might be related to a metabolic preference of S. thermosulfidooxidans. If S. thermosulfidooxidans performed leaching in a filtered pyrite leachate from L. ferriphilum, the cells preferred to oxidize RISCs instead of ferrous ion and the number of attached cells decreased compared with the control. This study gives an indication that in a short-term multi-species leaching system the role of S. thermosufidooxidans may be related to the time of its introduction.

Archaeal biofilm formation

Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.