Second acyl homoserine lactone production system in the extreme acidophile Acidithiobacillus ferrooxidans

Development and Control of Biofilms: Novel Strategies Using Natural Antimicrobials

Separation membranes have a wide application in the food industry, for instance, in the clarification/fractionation of milk, the concentration/separation of selected components, and wastewater treatment. They provide a large area for bacteria to attach and colonize. When a product comes into contact with a membrane, it initiates bacterial attachment/colonization and eventually forms biofilms. Several cleaning and sanitation protocols are currently utilized in the industry; however, the heavy fouling of the membrane over a prolonged duration affects the overall cleaning efficiency. In view of this, alternative approaches are being developed. Therefore, the objective of this review is to describe the novel strategies for controlling membrane biofilms such as enzyme-based cleaner, naturally produced antimicrobials of microbial origin, and preventing biofilm development using quorum interruption. Additionally, it aims to report the constitutive microflora of the membrane and the development of the predominance of resistant strains over prolonged usage. The emergence of predominance could be associated with several factors, of which, the release of antimicrobial peptides by selective strains is a prominent factor. Therefore, naturally produced antimicrobials of microbial origin could thus provide a promising approach to control biofilms. Such an intervention strategy could be implemented by developing a bio-sanitizer exhibiting antimicrobial activity against resistant biofilms.

The use of synthetic agonists of quorum sensing N- acyl homoserine lactone pathway improves the bioleaching ability in Acidithiobacillus and Pseudomonas bacteria

Metal solubilization from discarded electrical material and electronic devices (e-waste) using the bioleaching capabilities of bacterial cells is highly effective. However, gaps in understanding about the microbiological processes involved in the bioleaching reaction leads to less efficient metal solubilization in large-scale e-waste processing. In this study, bacterial species belonging to the genera Acidithiobacillus and Pseudomonas were used to leach copper and gold from discarded printed circuit boards (PCB). Through modulation of the cell-to-cell communication system in these bacteria, phenotypic traits directly involved in the bioleaching reaction were regulated in order to improve the metal solubilization. Addition of the long chain synthetic autoinducer molecule N-acyl homoserine lactone (AHL) of the quorum sensing pathway to the bioleaching reaction resulted in a significant enhancement of metal extraction from PCB. Factors such as: cell attachment to PCB, biofilm formation and hydrogen cyanide (HCN) production were regulated by the quorum sensing system and could be directly related to the improvement of metal bioleaching. Bioleaching reactions using bacterial quorum sensing modulation could represent a valuable tool in overcoming limitations at the industrial level imposed by microbiological traits that lead to inefficient metal bioleaching from e-waste.

Application of double-pulse laser-induced breakdown spectroscopy (DP-LIBS), Fourier transform infrared micro-spectroscopy and Raman microscopy for the characterization of copper-sulfides

The combined application of the structure sensitive techniques Fourier transform infrared μ-spectroscopy and Raman microscopy in conjunction with different approaches of laser-induced breakdown spectroscopy (LIBS) including the two-color double pulse (DP-LIBS) have been applied towards the characterization of whole ore copper-sulfide minerals. Discrete information from the surface of the whole ore minerals that lead to the establishment of infrared marker bands and from the surface of bioleached samples that allow the monitoring of jarosite and biofilm formation are provided by FTIR mapping experiments. Raman data can provide information related to the type of the mineral and of the secondary minerals formed on the surface of the ore. Of the four different LIBS approaches applied towards the characterization of the composition of the whole ore minerals, the DP-LIBS shows the highest sensitivity with increasing signals for both the Fe and Cu metals in the whole ore samples.

Raman and FTIR microspectroscopies, laser induced breakdown spectroscopy (LIBS) and DP-LIBS have been applied towards our understanding of the characterization of the structure and structure–function relationship in copper-sulfide minerals.

Effects of interactions between quorum sensing and quorum quenching on microbial aggregation characteristics in wastewater treatment: A review

Due to the increasingly urgent demand for effective wastewater denitrification and dephosphorization systems, there is a need to improve the performance of existing biological treatment technologies. As a bacteria-level communication mechanism, quorum sensing (QS) synchronizes gene expression in a density-dependent manner and regulates bacterial physiological behavior. On this basis, the QS-based bacterial communication mechanism and environmental factors affecting QS are discussed. This paper reviews the influence of QS on sludge granulation, biofilm formation, emerging contaminants (ECs) removal, and horizontal gene transfer in sewage treatment system. Furthermore, the QS inhibition strategies are compared. Based on the coexistence and balance of QQ and QS in the long-term operation system, QQ, as an effective tool to regulate the growth density of microorganisms, provides a promising exogenous regulation strategy for residual sludge reduction and biofilm pollution control. This paper reviews the potential of improving wastewater treatment efficiency based on QS theory and points out the feasibility and prospect of exogenous regulation strategy. PRACTITIONER POINTS: The mechanism of bacterial communication based on QS and the environmental factors affecting QS were discussed. The application of QS and QQ in improving the sludge performance of biological treatment systems was described. The significance of QS and QQ coexistence in sewage treatment process was described.

Genetic engineering of the acidophilic chemolithoautotroph Acidithiobacillus ferrooxidans

There are several natural and anthropomorphic environments where iron- and/or sulfur-oxidizing bacteria thrive in extremely acidic conditions. These acidophilic chemolithautotrophs play important roles in biogeochemical iron and sulfur cycles, are critical catalysts for industrial metal bioleaching operations, and have underexplored potential in future biotechnological applications. However, their unique growth conditions complicate the development of genetic techniques. Over the past few decades genetic tools have been successfully developed for Acidithiobacillus ferrooxidans, which serves as a model organism that exhibits both iron- and sulfur-oxidizing capabilities. Conjugal transfer of plasmids has enabled gene overexpression, gene knockouts, and some preliminary metabolic engineering. We highlight the development of genetic systems and recent genetic engineering of A. ferrooxidans, and discuss future perspectives.

Involvement of a Quorum Sensing Signal Molecule in the Extracellular Amylase Activity of the Thermophilic Anoxybacillus amylolyticus

Anoxybacillus amylolyticus is a moderate thermophilic microorganism producing an exopolysaccharide and an extracellular α-amylase able to hydrolyze starch. The synthesis of several biomolecules is often regulated by a quorum sensing (QS) mechanism, a chemical cell-to-cell communication based on the production and diffusion of small molecules named “autoinducers”, most of which belonging to the N-acyl homoserine lactones’ (AHLs) family. There are few reports about this mechanism in extremophiles, in particular thermophiles. Here, we report the identification of a signal molecule, the N-butanoyl-homoserine lactone (C4-HSL), from the milieu of A. amylolyticus. Moreover, investigations performed by supplementing a known QS inhibitor, trans-cinnamaldehyde, or exogenous C4-HSL in the growth medium of A. amylolyticus suggested the involvement of QS signaling in the modulation of extracellular α-amylase activity. The data showed that the presence of the QS inhibitor trans-cinnamaldehyde in the medium decreased amylolytic activity, which, conversely, was increased by the effect of exogenous C4-HSL. Overall, these results represent the first evidence of the production of AHLs in thermophilic microorganisms, which could be responsible for a communication system regulating thermostable α-amylase activity.

Cell Density-dependent Anammox Activity of Candidatus Brocadia sinica Regulated by N-acyl Homoserine Lactone-mediated Quorum Sensing

The activity of anaerobic ammonia-oxidizing (anammox) bacteria is considered to depend on cell density; however, this has not yet been confirmed due to the fastidious nature of anammox bacteria (e.g., slow growth, oxygen sensitivity, and rigid aggregate formation). In the present study, the cell density-dependent occurrence of anammox activity (^14-15N₂ gas production rate) was investigated using planktonic enrichment cultures of Candidatus Brocadia sinica. This activity was detectable when the density of cells was higher than 10⁷‍ ‍cells‍ ‍mL^–1 and became stronger with increases in cell density. At the cell densities, the transcription of the BROSI_A1042 and BROSI_A3652 genes, which are potentially involved in the biosynthesis and reception of N-acyl homoserine lactone (AHL), was detectable in Brocadia sinica cells. The presence of AHL molecules in the MBR culture of B. sinica was confirmed by an AHL reporter assay and gas chromatography mass spectrometry analysis. The exogenous addition of the MBR culture extract and AHL molecules (a cocktail of C₆, C₈, C₁₀, and C₁₂-homoserine lactones) increased the specific ^14-15N₂ production rate of B. sinica. These results suggest that the specific anammox activity of B. sinica is regulated by AHL-mediated quorum sensing.

Newly Isolated Acidithiobacillus sp. Ksh From Kashen Copper Ore: Peculiarities of EPS and Colloidal Exopolysaccharide

A novel strain of an iron- and sulfur-oxidizing bacterium was isolated from a natural biotope at Kashen copper ore (Martakert Province, Republic of Artsakh). The strain is able to grow and oxidize ferrous ions in the range of pH 1.4-2.6 with optimal pH 2.0. The optimal temperature for growth is 35°C. Acidithiobacillus sp. Ksh has shown the highest activity for pyrite oxidation among other strains. It also demonstrated high activity in oxidation for copper and copper-gold bearing ores (Armenia). The isolate Acidithiobacillus sp. Ksh was identified as Acidithiobacillus ferrooxidans based on phylogenetic and physiological studies. Comparative studies of EPS production by cells grown on ferrous ions or pyrite were carried out. The chemical composition of capsular and colloidal EPS produced by Acidithiobacillus (At.) ferrooxidans Ksh were revealed to be proteins and carbohydrates. Exosaccharide produced by At. ferrooxidans Ksh is present mainly as polysaccharide in contrast to Leptospirillum (L.) ferriphilum CC, which is oligosaccharide. The structural difference of colloidal particles of these polysaccharides was due to the degree of hydration of the saccharide molecules.

The substrate-dependent regulatory effects of the AfeI/R system in Acidithiobacillus ferrooxidans reveals the novel regulation strategy of quorum sensing in acidophiles

A LuxI/R‐like quorum sensing (QS) system (AfeI/R) has been reported in the acidophilic and chemoautotrophic Acidithiobacillus spp. However, the function of AfeI/R remains unclear because of the difficulties in the genetic manipulation of these bacteria. Here, we constructed different afeI mutants of the sulfur‐ and iron‐oxidizer A. ferrooxidans, identified the N‐acyl homoserine lactones (acyl‐HSLs) synthesized by AfeI, and determined the regulatory effects of AfeI/R on genes expression, extracellular polymeric substance synthesis, energy metabolism, cell growth and population density of A. ferrooxidans in different energy substrates. Acyl‐HSLs‐mediated distinct regulation strategies were employed to influence bacterial metabolism and cell growth of A. ferrooxidans cultivated in either sulfur or ferrous iron. Based on these findings, an energy‐substrate‐dependent regulation mode of AfeI/R in A. ferrooxidans was illuminated that AfeI/R could produce different types of acyl‐HSLs and employ specific acyl‐HSLs to regulate specific genes in response to different energy substrates. The discovery of the AfeI/R‐mediated substrate‐dependent regulatory mode expands our knowledge on the function of QS system in the chemoautotrophic sulfur‐ and ferrous iron‐oxidizing bacteria, and provides new insights in understanding energy metabolism modulation, population control, bacteria‐driven bioleaching process, and the coevolution between the acidophiles and their acidic habitats.

Novel Strategy for Improvement of the Bioleaching Efficiency of Acidithiobacillus ferrooxidans Based on the AfeI/R Quorum Sensing System

Acidithiobacillus ferrooxidans is an acidophilic and chemolithotrophic sulfur- and iron-oxidizing bacterium that has been widely used in the bioleaching process for extracting metals. Extracellular polymeric substances (EPS) are essential for bacteria-ore interactions, and the regulation of EPS synthesis could be an important way of influencing the efficiency of the bioleaching process. Therefore, exploring and utilizing the regulatory pathways of EPS synthesis to improve the bacterial bioleaching capability have posed a challenge in the study and application of bioleaching bacteria. Here, several engineering strains were constructed using genetic manipulation methods. And we revealed the regulatory function of the AfeI/R quorum sensing (QS) system in EPS synthesis and biofilm formation of A. ferrooxidans, and the AfeI/R-mediated EPS synthesis could influence bacteria-substrate interactions and the efficiency of bioleaching. Finally, an AfeI/R-mediated bioleaching model was proposed to illustrate the role of QS system in this process. This study provided new insights into and clues for developing highly efficient bioleaching bacteria and modulating the bioleaching process.

Identification of quorum sensing signal AHLs synthases in Candidatus Jettenia caeni and their roles in anammox activity

Acyl-homoserine lactone (AHL)-based quorum sensing (QS) in the anaerobic ammonium oxidizing (anammox) consortia has attracted increasing attention. However, AHL synthase in anammox bacteria and the relationship between AHL synthetic genes and anammox activity are still not clear because anammox bacteria have not been isolated from the consortia. Two novel synthases of AHLs (JqsI-1 and JqsI-2), which are HdtS-type rather than the widely studied LuxI-type, were identified in anammox bacteria Candidatus Jettenia caeni and synthesized four AHLs. There was a correlation between AHL concentration, in situ transcriptional expression of the AHL synthase genes (jqsI-1 and jqsI-2) and genetic marker of anammox activity (hydrazine synthase gene, hzsA). And AHL add-back studies demonstrated that AHL influence the expression of hzsA to regulate anammox bacterial activity. This study provides insight into the QS communication pathway of anammox bacteria for wastewater treatment.

Assessment of Bioleaching Microbial Community Structure and Function Based on Next-Generation Sequencing Technologies

It is widely known that bioleaching microorganisms have to cope with the complex extreme environment in which microbial ecology relating to community structure and function varies across environmental types. However, analyses of microbial ecology of bioleaching bacteria is still a challenge. To address this challenge, numerous technologies have been developed. In recent years, high-throughput sequencing technologies enabling comprehensive sequencing analysis of cellular RNA and DNA within the reach of most laboratories have been added to the toolbox of microbial ecology. The next-generation sequencing technology allowing processing DNA sequences can produce available draft genomic sequences of more bioleaching bacteria, which provides the opportunity to predict models of genetic and metabolic potential of bioleaching bacteria and ultimately deepens our understanding of bioleaching microorganism. High-throughput sequencing that focuses on targeted phylogenetic marker 16S rRNA has been effectively applied to characterize the community diversity in an ore leaching environment. RNA-seq, another application of high-throughput sequencing to profile RNA, can be for both mapping and quantifying transcriptome and has demonstrated a high efficiency in quantifying the changing expression level of each transcript under different conditions. It has been demonstrated as a powerful tool for dissecting the relationship between genotype and phenotype, leading to interpreting functional elements of the genome and revealing molecular mechanisms of adaption. This review aims to describe the high-throughput sequencing approach for bioleaching environmental microorganisms, particularly focusing on its application associated with challenges.

Profiles of quorum sensing (QS)-related sequences in phycospheric microorganisms during a marine dinoflagellate bloom, as determined by a metagenomic approach

The complicated relationships among environmental microorganisms are regulated by quorum sensing (QS). Understanding QS-based signals could shed light on the interactions between microbial communities in certain environments. Although QS characteristics have been widely discussed, few studies have been conducted on the role of QS in phycospheric microorganisms. Here, we used metagenomics to examine the profile of AI-1 (AinS, HdtS, LuxI) and AI-2 (LuxS) autoinducers from a deeply sequenced microbial database, obtained from a complete dinoflagellate bloom. A total of 3001 putative AI-1 homologs and 130 AI-2 homologs were identified. The predominant member among the AI groups was HdtS. The abundance of HdtS, AinS, and LuxS increased as the bloom developed, whereas the abundance of LuxI showed the opposite trend. Phylogenetic analysis suggested that HdtS and LuxI synthase originated mainly from alpha-, beta-, and gamma-Proteobacteria, whereas AinS synthase originated solely from Vibrionales. In comparison to AI-1, the sequences related to AI-2 (LuxS) demonstrated a much wider taxonomic coverage. Some significant correlations were found between dominant species and QS signals. In addition to the QS, we also performed parallel analysis of the quorum quenching (QQ) sequences. In comparison to QS, the relative abundance of QQ signals was lower; however, an obvious frequency correlation was observed. These results suggested that QS and QQ signals co-participate in regulating microbial communities during an algal bloom. These data helped to reveal the characteristic behavior of algal symbiotic bacteria, and facilitated a better understanding of microbial dynamics during an algal bloom event from a chemical ecological perspective.

Purification and characterization of 1-acyl-sn-glycerol-3-phosphate acyltransferase with a substrate preference for polyunsaturated fatty acyl donors from the eicosapentaenoic acid-producing bacterium Shewanella livingstonensis Ac10

1-Acyl-sn-glycerol-3-phosphate acyltransferase (designated as PlsC in bacteria) catalyzes the acylation of lysophosphatidic acid and is responsible for the de novo production of phosphatidic acid, a precursor for the synthesis of various membrane glycerophospholipids. Because PlsC is an integral membrane protein, it is generally difficult to solubilize it without causing its inactivation, which has been hampering its biochemical characterization despite its ubiquitous presence and physiological importance. Most biochemical studies of PlsC have been carried out using crude membrane preparations or intact cells. In this study, we succeeded in solubilization and purification of a recombinant PlsC in its active form from the eicosapentaenoic acid-producing bacterium Shewanella livingstonensis Ac10 using 6-cyclohexyl-1-hexyl-β-d-maltoside as the detergent. We characterized the purified enzyme and found that it has a substrate preference for the acyl donors with a polyunsaturated fatty acyl group, such as eicosapentaenoyl group. These results provide a new method for purification of the PlsC family enzyme and demonstrate the occurrence of a new PlsC with unique substrate specificity.

Acidithiobacillus ferrooxidans and its potential application

The widely distributed Acidithiobacillus ferrooxidans (A. ferrooxidans) lives in extremely acidic conditions by fixing CO₂ and nitrogen, and by obtaining energy from Fe²⁺ oxidation with either downhill or uphill electron transfer pathway and from reduced sulfur oxidation. A. ferrooxidans exists as different genomovars and its genome size is 2.89-4.18 Mb. The chemotactic movement of A. ferrooxidans is regulated by quorum sensing. A. ferrooxidans shows weak magnetotaxis due to formation of 15-70 nm magnetite magnetosomes with surface functional groups. The room- and low-temperature magnetic features of A. ferrooxidans are different from other magnetotactic bacteria. A. ferrooxidans has potential for removing sulfur from solids and gases, metals recycling from metal-bearing ores, electric wastes and sludge, biochemical production synthesizing, and metal workpiece machining.

Strand-specific RNA-seq analysis of the Acidithiobacillus ferrooxidans transcriptome in response to magnesium stress

Bioleaching is a promising process for 350 million tons Jinchuan low-grade pentlandite. But, Jinchuan pentlandite has lots of magnesium and high concentration of Mg²⁺ is harmful to bioleaching microorganisms. Thus, finding a way to improve the adaption of microorganisms to Mg²⁺ is a key for bioleaching. In the study, we found that oxidizing activity, bioleaching ability and biofilm formation of A.f were inhibited by Mg²⁺ stress. In addition, we analyzed mRNA and small RNA (sRNA) of Acidithiobacillus ferrooxidans (A.f) under Mg²⁺ stress by strand-specific RNA-sequencing (ssRNA-seq). After the bioinformatics process, 2475 coding genes were obtained, and there were 33 differential expression genes (DEGs) in 0.1 M-VS-Con, including 28 down-regulated and 5 up-regulated, whereas 52 DEGs were obtained in 0.5 M-VS-Con, including 28 down-regulated and 24 up-regulated. Gene ontology analysis showed most of DEGs were involved in catalytic activity, metabolic process and single-organism process. Furthermore, we identified 636 sRNA and some differential expression sRNA that may respond to Mg²⁺ stress. Further analysis of DEGs suggested that Mg²⁺ stress reduced biofilm formation perhaps through inhibiting Type IV Pili-related gene expression and inhibited bacterial activity perhaps through affecting carbon fixation. The study provided the foundation to understand the mechanisms of Mg²⁺ resistance in A.f and may be helpful to improve bioleaching ability for pentlandit.

Large Diversity and Original Structures of Acyl-Homoserine Lactones in Strain MOLA 401, a Marine Rhodobacteraceae Bacterium

Quorum sensing (QS) is a density-dependent mechanism allowing bacteria to synchronize their physiological activities, mediated by a wide range of signaling molecules including N-acyl-homoserine lactones (AHLs). Production of AHL has been identified in various marine strains of Proteobacteria. However, the chemical diversity of these molecules still needs to be further explored. In this study, we examined the diversity of AHLs produced by strain MOLA 401, a marine Alphaproteobacterium that belongs to the ubiquitous Rhodobacteraceae family. We combined an original biosensors-based guided screening of extract microfractions with liquid chromatography coupled to mass spectrometry (MS), High Resolution MS/MS and Nuclear Magnetic Resonance. This approach revealed the unsuspected capacity of a single Rhodobacteraceae strain to synthesize 20 different compounds, which are most likely AHLs. Also, some of these AHLs possessed original features that have never been previously observed, including long (up to 19 carbons) and poly-hydroxylated acyl side chains, revealing new molecular adaptations of QS to planktonic life and a larger molecular diversity than expected of molecules involved in cell–cell signaling within a single strain.

The Systematic Investigation of the Quorum Sensing System of the Biocontrol Strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 Unveils aurI to Be a Biosynthetic Origin for 3-Oxo-Homoserine Lactones

The shoot endophytic biocontrol strain Pseudomonas chlororaphis subsp. aurantiaca PB-St2 produces a wide range of exoproducts, including enzymes and antibiotics. The production of exoproducts is commonly tightly regulated. In order to get a deeper insight into the regulatory network of PB-St2, the strain was systematically investigated regarding its quorum sensing systems, both on the genetic and metabolic level. The genome analysis of PB-St2 revealed the presence of four putative acyl homoserine lactone (AHL) biosynthesis genes: phzI, csaI, aurI, and hdtS. LC-MS/MS analyses of the crude supernatant extracts demonstrated that PB-St2 produces eight AHLs. In addition, the concentration of all AHL derivatives was quantified time-resolved in parallel over a period of 42 h during the growth of P. aurantiaca PB-St2, resulting in production curves, which showed differences regarding the maximum levels of the AHLs (14.6 nM– 1.75 μM) and the production period. Cloning and heterologous overexpression of all identified AHL synthase genes in Escherichia coli proved the functionality of the resulting synthases PhzI, CsaI, and AurI. A clear AHL production pattern was assigned to each of these three AHL synthases, while the HdtS synthase did not lead to any AHL production. Furthermore, the heterologous expression study demonstrated unequivocally and for the first time that AurI directs the synthesis of two 3-oxo-AHLs.

Probing the whole ore chalcopyrite-bacteria interactions and jarosite biosynthesis by Raman and FTIR microspectroscopies

The whole ore chalcopyrite-bacteria interaction and the formation of the extracellular polymeric substances (EPS) during the bioleaching process by microorganisms found in the mine of Hellenic Copper Mines in Cyprus were investigated. Raman and FTIR microspectroscopies have been applied towards establishing a direct method for monitoring the formation of secondary minerals and the newly found vibrational marker bands were used to monitor the time evolution of the formation of covellite, and the K(+) and NH4(+)-jarosites from the chalcopyrite surfaces. The Raman data indicate that the formation of K(+)-jarosite is followed by the formation of NH4(+)-jarosite. The variation in color in the FTIR imaging data and the observation of the amide I vibration at 1637cm(-1) indicate that the microorganisms are attached on the mineral surface and the changes in the frequency/intensity of the biofilm marker bands in the 900-1140cm(-1) frequency range with time demonstrate the existence of biofilm conformations.

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.

Construction and phenotypic characterization of M68, an RruI quorum sensing knockout mutant of the photosynthetic alphaproteobacterium Rhodospirillum rubrum

Many bacterial species communicate using a complex system known as quorum sensing (QS) in which gene expression is controlled in response to cell density. In this study an N-acylhomoserine lactone (AHL) synthase (Rru_A3396) knockout mutant (M68) of Rhodospirillum rubrum S1H (WT) was constructed and characterized phenotypically under light anaerobic conditions. Results showed that R. rubrum WT produces unsubstituted, 3-OH and 3-oxo-substituted AHLs with acyl chains ranging from 4 to 14 carbons, with 3-OH-C8 being the most abundant. Growth, pigment content and swimming motility were found to be under the control of this LuxI-type QS system. In addition, cultivation in a low shear environment put forward the aggregative phenotype of M68 and linked biofilm formation to QS in R. rubrum S1H. Interestingly, QS-mutant M68 continued to produce decreased levels of 3-OH-C8-HSL, probably due to the presence of an extra HdtS-type AHL synthase.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Potential Emergence of Multi-quorum Sensing Inhibitor Resistant (MQSIR) Bacteria

Expression of certain bacterial genes only at a high bacterial cell density is termed as quorum-sensing (QS). Here bacteria use signaling molecules to communicate among themselves. QS mediated genes are generally involved in the expression of phenotypes such as bioluminescence, biofilm formation, competence, nodulation, and virulence. QS systems (QSS) vary from a single in Vibrio spp. to multiple in Pseudomonas and Sinorhizobium species. The complexity of QSS is further enhanced by the multiplicity of signals: (1) peptides, (2) acyl-homoserine lactones, (3) diketopiperazines. To counteract this pathogenic behaviour, a wide range of bioactive molecules acting as QS inhibitors (QSIs) have been elucidated. Unlike antibiotics, QSIs don't kill bacteria and act at much lower concentration than those of antibiotics. Bacterial ability to evolve resistance against multiple drugs has cautioned researchers to develop QSIs which may not generate undue pressure on bacteria to develop resistance against them. In this paper, we have discussed the implications of the diversity and multiplicity of QSS, in acting as an arsenal to withstand attack from QSIs and may use these as reservoirs to develop multi-QSI resistance.

Shotgun proteomics study of early biofilm formation process of Acidithiobacillus ferrooxidans ATCC 23270 on pyrite

Acidithiobacillus ferrooxidans is a chemolithoautotrophic, mesophilic Gram-negative bacterium able to oxidize ferrous iron, sulfur, and metal sulfides. It forms monolayer biofilms where extracellular polymeric substances are essential for cell attachment and metal sulfide leaching. High-throughput proteomics has been applied to study the early process of biofilm formation on pyrite by At. ferrooxidans ATCC 23270. After 24 h contact with the mineral, planktonic and sessile (biofilm) cell subpopulations were separated and proteins extracted. In total, 1319 proteins were detected in both samples. Sixty-two of these were found to be increased in biofilms. Additionally, 25 proteins were found to be decreased in the biofilm cell subpopulation. Three transcriptional factors were found to be increased or decreased among both cell subpopulations, suggesting their potential involvement in the regulation of these processes. Although no significant differences were observed for the known proteins related to ferrous iron and sulfur oxidation pathways among both cell subpopulations, the results presented here show that the early steps of At. ferrooxidans biofilm formation consist of a set of metabolic adaptations following cell attachment to the mineral surface. Functions such as extracellular polymeric substances biosynthesis seem to be pivotal. This first high-throughput proteomic study may also contribute to the annotation of several unknown At. ferrooxidans proteins found.

Quorum sensing in extreme environments

Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities and environmental conditions on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments.

AHL signaling molecules with a large acyl chain enhance biofilm formation on sulfur and metal sulfides by the bioleaching bacterium Acidithiobacillus ferrooxidans

Biofilm formation plays a pivotal role in bioleaching activities of bacteria in both industrial and natural environments. Here, by visualizing attached bacterial cells on energetic substrates with different microscopy techniques, we obtained the first direct evidence that it is possible to positively modulate biofilm formation of the extremophilic bacterium Acidithiobacillus ferrooxidans on sulfur and pyrite surfaces by using Quorum Sensing molecules of the N-acylhomoserine lactone type (AHLs). Our results revealed that AHL-signaling molecules with a long acyl chain (12 or 14 carbons) increased the adhesion of A. ferrooxidans cells to these substrates. In addition, Card-Fish experiments demonstrated that C14-AHL improved the adhesion of indigenous A. ferrooxidans cells from a mixed bioleaching community to pyrite. Finally, we demonstrated that this improvement of cell adhesion is correlated with an increased production of extracellular polymeric substances. Our results open up a promising means to develop new strategies for the improvement of bioleaching efficiency and metal recovery, which could also be used to control environmental damage caused by acid mine/rock drainage.

Quorum sensing in the context of food microbiology

Food spoilage may be defined as a process that renders a product undesirable or unacceptable for consumption and is the outcome of the biochemical activity of a microbial community that eventually dominates according to the prevailing ecological determinants. Although limited information are reported, this activity has been attributed to quorum sensing (QS). Consequently, the potential role of cell-to-cell communication in food spoilage and food safety should be more extensively elucidated. Such information would be helpful in designing approaches for manipulating these communication systems, thereby reducing or preventing, for instance, spoilage reactions or even controlling the expression of virulence factors. Due to the many reports in the literature on the fundamental features of QS, e.g., chemistry and definitions of QS compounds, in this minireview, we only allude to the types and chemistry of QS signaling molecules per se and to the (bioassay-based) methods of their detection and quantification, avoiding extensive documentation. Conversely, we attempt to provide insights into (i) the role of QS in food spoilage, (ii) the factors that may quench the activity of QS in foods and review the potential QS inhibitors that might "mislead" the bacterial coordination of spoilage activities and thus may be used as biopreservatives, and (iii) the future experimental approaches that need to be undertaken in order to explore the "gray" or "black" areas of QS, increase our understanding of how QS affects microbial behavior in foods, and assist in finding answers as to how we can exploit QS for the benefit of food preservation and food safety.

Engineering microbial consortia to enhance biomining and bioremediation

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.

Quorum quenching revisited--from signal decays to signalling confusion

In a polymicrobial community, while some bacteria are communicating with neighboring cells (quorum sensing), others are interrupting the communication (quorum quenching), thus creating a constant arms race between intercellular communication. In the past decade, numerous quorum quenching enzymes have been found and initially thought to inactivate the signalling molecules. Though this is widely accepted, the actual roles of these quorum quenching enzymes are now being uncovered. Recent evidence extends the role of quorum quenching to detoxification or metabolism of signalling molecules as food and energy source; this includes “signalling confusion”, a term coined in this paper to refer to the phenomenon of non-destructive modification of signalling molecules. While quorum quenching has been explored as a novel anti-infective therapy targeting, quorum sensing evidence begins to show the development of resistance against quorum quenching.

Mineral-microbe interactions: biotechnological potential of bioweathering

Mineral-microbe interaction has been a key factor shaping the lithosphere of our planet since the Precambrian. Detailed investigation has been mainly focused on the role of bioweathering in biomining processes, leading to the selection of highly efficient microbial inoculants for the recovery of metals. Here we expand this scenario, presenting additional applications of bacteria and fungi in mineral dissolution, a process with novel biotechnological potential that has been poorly investigated. The ability of microorganisms to trigger soil formation and to sustain plant establishment and growth are suggested as invaluable tools to counteract the expansion of arid lands and to increase crop productivity. Furthermore, interesting exploitations of mineral weathering microbes are represented by biorestoration and bioremediation technologies, innovative and competitive solutions characterized by economical and environmental advantages. Overall, in the future the study and application of the metabolic properties of microbial communities capable of weathering can represent a driving force in the expanding sector of environmental biotechnology.

Quorum sensing: regulating the regulators

Many bacteria use 'quorum sensing' (QS) as a mechanism to regulate gene induction in a population-dependent manner. In its simplest sense this involves the accumulation of a signaling metabolite during growth; the binding of this metabolite to a regulator or multiple regulators activates induction or repression of gene expression. However QS regulation is seldom this simple, because other inputs are usually involved. In this review we have focussed on how those other inputs influence QS regulation and as implied by the title, this often occurs by environmental or physiological effects regulating the expression or activity of the QS regulators. The rationale of this review is to briefly introduce the main QS signals used in Gram-negative bacteria and then introduce one of the earliest understood mechanisms of regulation of the regulator, namely the plant-mediated control of expression of the TraR QS regulator in Agrobacterium tumefaciens. We then describe how in several species, multiple QS regulatory systems can act as integrated hierarchical regulatory networks and usually this involves the regulation of QS regulators. Such networks can be influenced by many different physiological and environmental inputs and we describe diverse examples of these. In the final section, we describe different examples of how eukaryotes can influence QS regulation in Gram-negative bacteria.

Quorum-sensing system in Acidithiobacillus ferrooxidans involved in its resistance to Cu²⁺

AIMS

 The purpose of this study was to search for the relationship between quorum sensing (QS) and Cu²⁺ resistance in Acidithiobacillus ferrooxidans.

METHODS AND RESULTS

 Resistance to Cu²⁺ of A. ferrooxidans significantly decreased with the treatment dose of a synthetic QS blocker (5Z)-4-bromo-5-(bromomethylene)-2(5H)-furanone (FUR). Relative differences in expression of the QS genes afeI, afeR and Cu²⁺ resistance-associated genes afe0329, afe0454 were examined in the presence of Cu²⁺ and/or FUR compound. The expression of QS genes afeI and afeR increased significantly with 50 mmol l⁻¹ Cu²⁺ in the culture, while for samples treated with both 50 mmol l⁻¹ Cu²⁺ and 0.01 μg ml⁻¹ FUR compound, they showed little changes compared with control, and the expression of afe0329 and afe0454 genes increased slightly either. These results showed that QS system was positively related to the mechanism of Cu²⁺ resistance.

CONCLUSIONS

QS system in A. ferrooxidans involved in its resistance to Cu²⁺.

SIGNIFICANCE AND IMPACT OF THE STUDY

 The mechanisms of Cu²⁺ resistance in A. ferrooxidans could be revealed on a population level rather than on a single-cell level. Our work also provides useful data for further selection of A. ferrooxidans strains with suitable Cu²⁺ resistance that could probably increase the bioleaching efficiency.

Interactions of Botryococcus braunii cultures with bacterial biofilms

Unicellular microalgae generally grow in the presence of bacteria, particularly when they are farmed massively. This study analyzes the bacteria associated with mass culture of Botryococcus braunii: both the planktonic bacteria in the water column and those forming biofilms adhered to the surface of the microalgal cells (∼10⁷-10⁸ culturable cells per gram microalgae). Furthermore, we identified the culturable bacteria forming a biofilm in the microalgal cells by 16S rDNA sequencing. At least eight different culturable species of bacteria were detected in the biofilm and were evaluated for the presence of quorum-sensing signals in these bacteria. Few studies have considered the implications of this phenomenon as regards the interaction between bacteria and microalgae. Production of C4-AHL and C6-AHL were detected in two species, Pseudomonas sp. and Rhizobium sp., which are present in the bacterial biofilm associated with B. braunii. This type of signal was not detected in the planktonic bacteria isolated from the water. We also noted that the bacterium, Rhizobium sp., acted as a probiotic bacterium and significantly encouraged the growth of B. braunii. A direct application of these beneficial bacteria associated with B. braunii could be, to use them like inoculants for large-scale microalgal cultures. They could optimize biomass production by enhancing growth, particularly in this microalga that has a low growth rate.

Biofilm development in the extremely acidophilic archaeon 'Ferroplasma acidarmanus' Fer1

'Ferroplasma acidarmanus' Fer1 is an iron-oxidizing extreme acidophile isolated from the Iron Mountain mine, California, USA. This archaeon is predominantly found in biofilm-associated structures in the environment, and produces two distinct biofilm morphologies. Bioinformatic analysis of the 'F. acidarmanus' Fer1 genome identified genes annotated as involved in attachment and biofilm formation. No putative quorum sensing signaling genes were identified and no N-acyl homoserine lactone-like compounds were found in 'F. acidarmanus' Fer1 biofilm supernatant. Scanning confocal microscopy analysis of biofilm development on the surface of pyrite demonstrated the temporal and spatial development of biofilm growth. Furthermore, two-dimensional polyacrylamide gel electrophoresis was used to examine differential protein expression patterns between biofilm and planktonic populations. Ten up-regulated proteins were identified that included six enzymes associated with anaerobic growth, suggesting that the dominating phenotype in the mature biofilm was associated with anaerobic modes of growth. This report increases our knowledge of the genetic and proteomic basis of biofilm formation in an extreme acidophilic archaeon.

Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community

Background

Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Río Tinto (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria Leptospirillum spp. (L. ferrooxidans and L. ferriphilum) and Acidithiobacillus ferrooxidans are abundant. These microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of Leptospirillum spp. as part of its natural extremely acidophilic community.

Results

Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of L. ferrooxidans. Genes up-regulated in the filamentous biofilm are involved in cellular functions related to biofilm formation and maintenance, such as: motility and quorum sensing (mqsR, cheAY, fliA, motAB), synthesis of cell wall structures (lnt, murA, murB), specific proteases (clpX/clpP), stress response chaperons (clpB, clpC, grpE-dnaKJ, groESL), etc. Additionally, genes involved in mixed acid fermentation (poxB, ackA) were up-regulated in the biofilm. This result, together with the presence of small organic acids like acetate and formate (1.36 mM and 0.06 mM respectively) in the acidic (pH 1.8) water stream, suggests that either L. ferrooxidans or other member of the microbial community are producing acetate in the acidophilic biofilm under microaerophilic conditions.

Conclusions

Our results indicate that the acidophilic filaments are dynamic structures in which different mechanisms for biofilm formation/dispersion are operating. Specific transcriptomic fingerprints can be inferred for both planktonic and sessile cells, having the former a more active TCA cycle, while the mixed acid fermentation process dominate in the latter. The excretion of acetate may play a relevant ecological role as a source of electron donor for heterotrophic Fe³⁺ reducers like some Alphaproteobacteria, Acidobacterium spp. and Sulfobacillus spp., also present in the biofilm. Additionally, acetate may have a negative effect on bioleaching by inhibiting the growth of chemolithotrophic bacteria.

Growth phase-dependent biosynthesis of Nep, a halolysin-like protease secreted by the alkaliphilic haloarchaeon Natrialba magadii

AIMS

The alkaliphilic haloarchaeon Natrialba magadii secretes a halolysin-like protease (Nep) that is active and stable in high salt and in organic solvents, which represents a potential resource for biocatalysis in low water activity conditions. In this study, the effect of the growth stage on Nep biosynthesis was examined.

METHODS AND RESULTS

Nep mRNA and extracellular protease activity were measured by RT-PCR and azocaseinolytic activity determination, respectively. Increased abundance in Nep mRNA was observed in Nab. magadii cells with culture age, which correlated with accumulation of extracellular protease activity. Moreover, a 'stationary phase behavior' on synthesis of Nep was evidenced in low-density cultures incubated with stationary phase medium.

CONCLUSIONS

nep gene expression is up-regulated during the transition to the stationary phase in response to 'factors' (metabolite and/or regulatory molecule) occurring in high-density cultures of Nab. magadii. Although the identity of these molecules remains to be determined, preliminary evidence suggests that they are hydrophobic and stable in high salt and high pH values (3.5 mol l(-1) NaCl, pH 10).

SIGNIFICANCE AND IMPACT OF STUDY

This study contributes to gain insight into the regulation of haloarchaeal protease biosynthesis, facilitating the large-scale production of this extremozyme for basic studies or potential applications.

Quorum sensing and social networking in the microbial world

For many years, bacterial cells were considered primarily as selfish individuals, but, in recent years, it has become evident that, far from operating in isolation, they coordinate collective behaviour in response to environmental challenges using sophisticated intercellular communication networks. Cell-to-cell communication between bacteria is mediated by small diffusible signal molecules that trigger changes in gene expression in response to fluctuations in population density. This process, generally referred to as quorum sensing (QS), controls diverse phenotypes in numerous Gram-positive and Gram-negative bacteria. Recent advances have revealed that bacteria are not limited to communication within their own species but are capable of 'listening in' and 'broadcasting to' unrelated species to intercept messages and coerce cohabitants into behavioural modifications, either for the good of the population or for the benefit of one species over another. It is also evident that QS is not limited to the bacterial kingdom. The study of two-way intercellular signalling networks between bacteria and both uni- and multicellular eukaryotes as well as between eukaryotes is just beginning to unveil a rich diversity of communication pathways.

Selection and evaluation of reference genes for improved interrogation of microbial transcriptomes: case study with the extremophile Acidithiobacillus ferrooxidans

Background

Normalization is a prerequisite for accurate real time PCR (qPCR) expression analysis and for the validation of microarray profiling data in microbial systems. The choice and use of reference genes that are stably expressed across samples, experimental conditions and designs is a key consideration for the accurate interpretation of gene expression data.

Results

Here, we evaluate a carefully selected set of reference genes derived from previous microarray-based transcriptional profiling experiments performed on Acidithiobacillus ferrooxidans and identify a set of genes with minimal variability under five different experimental conditions that are frequently used in Acidithiobacilli research. Suitability of these and other previously reported reference genes to monitor the expression of four selected target genes from A. ferrooxidans grown with different energy sources was investigated. Utilization of reference genes map, rpoC, alaS and era results in improved interpretation of gene expression profiles in A. ferrooxidans.

Conclusion

This investigation provides a validated set of reference genes for studying A. ferrooxidans gene expression under typical biological conditions and an initial point of departure for exploring new experimental setups in this microorganism and eventually in other closely related Acidithiobacilli. The information could also be of value for future transcriptomic experiments in other bacterial systems.

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

BACKGROUND

Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.

RESULTS

The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.

CONCLUSION

Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

Two dissimilar N-acyl-homoserine lactone acylases of Pseudomonas syringae influence colony and biofilm morphology

Plant aerial surfaces comprise a complex habitat for microorganisms, and many plant-associated bacteria, such as the pathogen Pseudomonas syringae, exhibit density-dependent survival on leaves by utilizing quorum sensing (QS). QS is often mediated by diffusible signals called N-acyl-homoserine lactones (AHLs), and P. syringae utilizes N-3-oxo-hexanoyl-dl-homoserine lactone (3OC6HSL) to control traits influencing epiphytic fitness and virulence. The P. syringae pathovar syringae B728a genome sequence revealed two putative AHL acylases, termed HacA (Psyr_1971) and HacB (Psyr_4858), which are N-terminal nucleophile hydrolases that inactivate AHLs by cleaving their amide bonds. HacA is a secreted AHL acylase that degrades only long-chain (C > or = 8) AHLs, while HacB is not secreted and degrades all tested AHLs. Targeted disruptions of hacA, hacB, and hacA and hacB together do not alter endogenous 3OC6HSL levels under the tested conditions. Surprisingly, targeted disruptions of hacA alone and hacA and hacB together confer complementable phenotypes that are very similar to autoaggregative phenotypes seen in other species. While AHL acylases might enable P. syringae B728a to degrade signals of competing species and block expression of their QS-dependent traits, these enzymes also play fundamental roles in biofilm formation.

Isolation and characterization of an autoinducer synthase from Acinetobacter baumannii

The opportunistic human pathogen Acinetobacter baumannii strain M2 was found to produce distinct acyl-homoserine lactone (AHL) signals based on the use of an Agrobacterium tumefaciens traG-lacZ biosensor. An A. baumannii gene, designated abaI, was cloned and directed AHL production in recombinant Escherichia coli. The AbaI protein was similar to members of the LuxI family of autoinducer synthases and was predicted to be the only autoinducer synthase encoded by A. baumannii. The primary AHL signal directed by AbaI was identified by mass spectrometry as being N-(3-hydroxydodecanoyl)-L-HSL (3-hydroxy-C(12)-HSL). Minor amounts of at least five additional AHLs were also identified. The expression of abaI at the transcriptional level was activated by ethyl acetate extracts of culture supernatants or by synthetic 3-hydroxy-C(12)-HSL. An abaI::Km mutant failed to produce any detectable AHL signals and was impaired in biofilm development.

Biomining in the Post-Genomic Age: Advances and Perspectives

Systems Microbiology is a new way to approach research in microbiology. The idea is to treat the microorganism or community as a whole, integrating fundamental biological knowledge with OMICS research (genomics, proteomics, transcriptomics, metabolomics) and bioinformatics to obtain a global picture of how a microbial cell operates in the community. The oxidative reactions resulting in the extraction of dissolved metal values from ores is the outcome of a consortium of different microorganisms. Therefore, this bioleaching community is particularly amenable for the application of Systems Microbiology. As more genomic sequences of different biomining microorganisms become available, it will be possible to define the molecular adaptations of bacteria to their environment, the interactions between the members of the community and to predict favorable or negative changes to efficiently control metal solubilization. Some key phenomena to understand the process of biomining are biochemistry of iron and sulfur compound oxidation, bacteria-mineral interactions (chemotaxis, cell-cell communication, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. These variables should be considered in an integrative way from now on. Together with recently developed molecular methods to monitor the behavior and evolution of microbial participants during bioleaching operations, Systems Microbiology will offer a comprehensive view of the bioleaching community. The power of the OMICS approaches will be briefly reviewed. It is expected they will provide not only exciting new findings but also will allow predictions on how to keep the microbial consortium healthy and therefore efficient during the entire process of bioleaching.