Search

A genome analysis of Pseudomonas pseudoalcaligenes KF707, a PCBs degrader and metal-resistant soil microorganism, revealed the presence of two novel gene clusters named che2 and che3, which were predicted to be involved in chemotaxis-like pathways, in addition to a che1 gene cluster. We herein report that the histidine kinase coding genes, cheA2 and cheA3, have no role in swimming or chemotaxis in P. pseudoalcaligenes KF707, in contrast to cheA1. However, the cheA1 and cheA2 genes were both necessary for cell swarming, whereas the cheA3 gene product had a negative effect on the optimal swarming phenotype of KF707 cells.

Habitats defined as “extremes” exist across the entire planet. They can be widely different in their physico-chemical features as they include a diverse array of harsh parameters thought to preclude the existence of living organisms, such as temperature, pH, salinity, radiation, pressure, low water activity, low nutrients, and even the presence of toxic agents such as metals and/or metalloids. Organisms capable of surviving or thriving in those habitats are named “extremophiles” and the vast majority of them are prokaryotes, which is not surprising as they show a remarkable reservoir of genomes allowing them to grow in a great variety of hostile niches. Interestingly, several harsh conditions may occur simultaneously and the microorganisms able to withstand them are called “poly-extremophiles”. Although many bacterial species from all kinds of extreme environments have been isolated and described in the last decades, very little is known about the molecular strategies and physiology that allow them to grow in such critical conditions. The aim of this Research Topic on Microbial Life Under Stress (Volume II) is to address this issue by applying multidisciplinary approaches for integrating data from biochemical, genomic, transcriptomic, proteomic, bioinformatics, and evolutionary studies of bacteria from extreme and poly-extreme environments. This Research Topic consists of 14 original articles by numerous authors actively engaged in the study of microbiology, biochemistry, and omic-research of extremophiles. The present Editorial can be divided into four sections which include groups of articles on different genera and species of acidophiles, studies on microorganisms from arid/desiccated environments but also from habitats at low and high temperatures, and finally, a set of papers on extremophiles capable of coping with extreme levels of radiation, pressure, and toxic metals.

Abstract Bacteria belonging to Rhodococcus genus represent ideal candidates for microbial biotechnology applications because of their metabolic versatility, ability to degrade a wide range of organic compounds, and resistance to various stress conditions, such as metal toxicity, desiccation, and high concentration of organic solvents. Rhodococcus spp. strains have also peculiar biosynthetic activities that contribute to their strong persistence in harsh and contaminated environments and provide them a competitive advantage over other microorganisms. This review is focused on the metabolic features of Rhodococcus genus and their potential use in biotechnology strategies for the production of compounds with environmental, industrial, and medical relevance such as biosurfactants, bioflocculants, carotenoids, triacylglycerols, polyhydroxyalkanoate, siderophores, antimicrobials, and metal-based nanostructures. These biosynthetic capacities can also be exploited to obtain high value-added products from low-cost substrates (industrial wastes and contaminants), offering the possibility to efficiently recover valuable resources and providing possible waste disposal solutions. Rhodococcus spp. strains have also recently been pointed out as a source of novel bioactive molecules highlighting the need to extend the knowledge on biosynthetic capacities of members of this genus and their potential utilization in the framework of bioeconomy. Key points • Rhodococcus possesses promising biosynthetic and bioconversion capacities. • Rhodococcus bioconversion capacities can provide waste disposal solutions. • Rhodococcus bioproducts have environmental, industrial, and medical relevance.

Tellurite (TeO32−) is an oxyanion of increasing concern for soils and water bodies as tellurite is toxic to prokaryotes and eukaryotes. In cells of Rhodobacter capsulatus, a facultative anoxygenic photosynthetic bacterium which tolerates up to 1 mM tellurite, the assembly of c-type cytochromes (cyts) occurs in the periplasm and involves several proteins ensuring the correct redox-state of the c yt c m aturation process (Ccm). Here it is shown that a sub-lethal tellurite concentration (0.2 mM) reduces the amount of cyts c during the early growth-phase of R. capsulatus. This effect is due to a malfunction of the Ccm system and not to an effect on the transcriptional expression of the cyt c genes. Further, growth of mutants MT-G4/S4 and MD21, with mutations at the level of cyt c2 (ΔcycA) and of the Ccm system (ΔdsbA/ΔccdA), respectively, was more affected by tellurite than wild type cells. Both MT-G4/S4 and MD21 mutants, featured by a cyt c2 deficiency, showed a significant decrease in their capacity to reduce TeO32− into Te0, thereby implying the need of a full amount of periplasmic cyt c2 in the microbial-driven speciation of the metalloid. These findings show, for the first time, that tellurite processing by cells starts at the periplasmic level.

The wide anthropogenic use of selenium compounds represents the major source of selenium pollution world- wide, causing environmental issues and health concerns. Microbe-based strategies for metal removal/recovery have received increasing interest thanks to the association of the microbial ability to detoxify toxic metal/ metalloid polluted environments with the production of nanomaterials. This study investigates the tolerance and the bioconversion of selenite (SeO32−) by the aerobically grown Actinomycete Rhodococcus aetherivorans BCP1 in association with its ability to produce selenium nanoparticles and nanorods (SeNPs and SeNRs). The BCP1 strain showed high tolerance towards SeO32− with a Minimal Inhibitory Concentration (MIC) of 500 mM. The bio- conversion of SeO32− was evaluated considering two different physiological states of the BCP1 strain, i.e. un- conditioned and/or conditioned cells, which correspond to cells exposed for the first time or after re-inoculation in fresh medium to either 0.5 or 2 mM of Na2SeO3, respectively. SeO32− bioconversion was higher for conditioned grown cells compared to the unconditioned ones. Selenium nanostructures appeared polydisperse and not ag- gregated, as detected by electron microscopy, being embedded in an organic coating likely responsible for their stability, as suggested by the physical-chemical characterization. The production of smaller and/or larger SeNPs was influenced by the initial concentration of provided precursor, which resulted in the growth of longer and/or shorter SeNRs, respectively. The strong ability to tolerate high SeO32− concentrations coupled with SeNP and SeNR biosynthesis highlights promising new applications of Rhodococcus aetherivorans BCP1 as cell factory to produce stable Se-nanostructures, whose suitability might be exploited for biotechnology purposes.

Microbial degradation of 1,1,2,2-tetrachloroethane has been rarely analysed under aerobic conditions. In this work, the catabolic potential of a TeCA-degrading aerobic propanotroph consortium (C2) and the optimal bioreactor configuration for an on-site TeCA-bioremediation strategy with C2 were defined. More specifically, the diversity of alkane-oxidizing bacteria in C2 was assessed by means of clone libraries of genes coding for alkane monooxygenases (MOs) of different families (AlkB-like alkane hydroxylase, soluble di-iron MO and cytochromes P450). A large number of alkane MO sequences retrieved in this study showed the highest similarity with reference sequences belonging to Rhodococcus genus, suggesting a key role of this genus in TeCA/propane co-metabolism, while the remaining alkane MO sequences were mainly attributed to other Actinobacteria, to Bradhyrizobiaceae, and Cupriavidus genus. Further, the feasibility of an on-site TeCA bioremediation strategy with C2 was evaluated by simulating a continuous-flow aerobic co-metabolic process with different bioreactor configurations. Our results show that the configuration with a suspended-cell continuous stirred-tank reactor (CSTR) followed by a suspended-cell plug-flow reactor (PFR) was the one giving the best performance with consortium C2.

Members of the genus Rhodococcus have metabolic versatility and unique adaptation capacities to fluctuating environmental conditions, enabling the colonization of a wide variety of environments; they also play an important role in nutrient cycling and have potential applications in bioremediation, biotransformations and biocatalysis. Rhodococcus spp. are mainly distributed in soil, water and marine sediments, although some of them are also pathogens for humans, animals and plants. Consistent with the wide catabolic diversity, Rhodococcus spp. possess large and complex genomes (up to 10.1 Mbp), which contain a multiplicity of catabolic genes, high genetic redundancy of biosynthetic pathways and large catabolic plasmids, the latter encoding peculiar metabolic and physiological traits. Recently, the progress in sequencing technology led to a dramatic increase in the number of sequenced Rhodococcus genomes, which have been investigated through diverse bioinformatic approaches. In particular, whole-genome comparative and genome-based functional studies were associated to omic technologies for the study of the global Rhodococcus cell response with the aim of providing insight into the genetic basis of specific catabolic capacities and phenotypic traits. Lastly, genome-based advances in Rhodococcus engineering led to the first design of molecular toolkits for tunable and targeted genome editing. Besides this, genome-based metabolic models were developed to make metabolic predictions of the Rhodococcus cell response to specific growth conditions. Both the synthetic and system approaches offered new opportunities for genome-scale rational design of Rhodococcus cell for environmental and industrial applications.

Alkanes are widely distributed in the environment as they not only constitute the large fraction of crude oil but are also produced by many living organisms. They are saturated hydrocarbons of different sizes and structures, which pose a variety of challenges to degradative microorganisms due to their physicochemical properties, i.e., the extremely limited solubility and the high energy required for activation. The hydrophobic cell surface of Rhodococcus spp., the ability to produce biosurfactants, and the possession of a wide range of oxygenases allow coping with such challenges. In particular, monooxygenase enzymes are involved in the activation of alkanes by converting them into alcohols, which undergo a series of oxidation steps before being converted to fatty acids. Rhodococcus alkane monooxygenases belong to different families (i.e., AlkB-like monooxygenase, soluble di-iron monooxygenase, cytochrome P450), have different genetic organization, and are subject to different regulatory mechanisms, which are poorly known. Because of their long-term survival capacity, broad catabolic abilities, and effective contact mechanisms with hydrocarbon molecules, alkanotrophic Rhodococcus strains have biotechnology applications and potential in bioremediation and biotransformation reactions.

The oxyanion tellurite (TeO32-) is extremely toxic to bacterial cells. In Rhodobacter capsulatus, tellurite enters the cytosol by means of the high uptake-rate acetate permease RcActP2, encoded by one of the three actP genes present in this species (actP1, actP2 and actP3). Conversely, in Escherichia coli a low rate influx of the oxyanion is measured, which depends mainly on the phosphate transporter EcPitA, even though E. coli contains its own EcActP acetate permease. Here we report that when the actP2 gene from R. capsulatus is expressed in wild-type E. coli HB101 and in E. coli JW3460 δpitA mutant, the cellular intake of tellurite increases up to four times, suggesting intrinsic structural differences between EcActP and RcActP2. Indeed, a sequence analysis indicated the presence in RcActP2 of an insert of 15-16 residues, located between trans-membrane (TM) helices 6 and 7, which is absent in both EcActP and RcActP1. Based on this observation, the molecular models of homodimeric RcActP1 and RcActP2 were calculated and analyzed. In the RcActP2 model, the insert induces a perturbation in the conformation of the loop between TM helices 6 and 7, located at the RcActP2 dimerization interface. This perturbation opens a cavity on the periplasmic side that is closed, instead, in the RcActP1 model. This cavity also features an increase of the positive electric potential on the protein surface, an effect ascribed to specific residues Lys261, Lys281 and Arg560. We propose that this positively charged patch in RcActP2 is involved in recognition and translocation of the TeO32- anion, attributing to RcActP2 a greater ability as compared to RcActP1 to transport this inorganic poison inside the cells.

Members of the deep-branching order Thermotogales are widespread in various terrestrial, submarine and subterrestrial extreme environments. This bacterial order included both thermophilic and hyperthermophilic anaerobic microorganisms so far pertaining to ten genera. It is only recently (2011) that cultivation of a mesophilic member of this order belonging to a novel genus, Mesotoga, has been successful. All members, with the exception of Mesotoga spp., are recognized as high hydrogen producers having possible applications in biotechnology with a peculiar emphasis for members of the genus Thermotoga (e.g. T. maritima and T. neapolitana). The ecology, phylogeny and metabolism linked to hydrogen production of these bacteria, are reviewed.

Caves are dark and oligotrophic habitats where chemotrophic microbial communities interact with the inorganic mineral rocks and cooperate organizing themselves in complex biological formations, which are visible in caves as biofilms, biodeposits or biospeleothems. In these environments, microorganisms contribute to the turnover of the matter and activate peculiar enzymatic reactions leading to the modification of the mineral rocks and to the production of metabolites with possible industrial and pharmaceutical interest. In this PhD thesis, various molecular and geomicrobiological approaches were used to investigate the microbial diversity and potential activities in different cave systems, i.e. the orthoquartzite cave Imawarì Yeuta, the sufidic cave Fetida and the ice cave Cenote Abyss. This is aimed at gathering indications on the possible interactions that support microbial growth and its impact in cave environments. As a result, microbial taxa and functions associated to light-independent chemolithotroph and heterotrophic activities were identified in the three caves, indicating the involvement of microorganisms in i) silica mobilization and amorphization processes and the formation of a novel type of silica-based stromatolite in Imawarì Yeuta Cave, ii) the formation of three types of biofilm/biodeposit involved in sulphur cycle and in the speleogenesis of Fetida Cave, iii) the development of biofilms and their maintenance under psychrophilic conditions in samples collected from ice in Cenote Abyss. Additionally, the metabolic potentials of around one hundred isolates derived from these cave systems were evaluated in terms on anti-microbial activity. The results pointed out that unexplored and oligotrophic caves are promising environments for novel bioactive molecules discovery.