Domain-specific osmoadaptation revealed by metatranscriptomic analysis in hypersaline environments.

High-throughput RNA-seq enables the analysis of gene expression in complex, culture-independent microbial communities. In this study, we used this approach to explore the microbial adaptation to salinity changes in hypersaline environments using samples collected from the Santa Pola ponds (Alicante, Spain). Two metatranscriptomic experiments were conducted: (i) salt concentration from 20 to 30%, mimicking summer evaporation, and (ii) dilution from 30 to 25%, simulating rainfall.

Metagenome-Assembled Genomes (MAGs): Advances, Challenges, and Ecological Insights.

Metagenome-assembled genomes (MAGs) have revolutionized microbial ecology by enabling the genome-resolved study of uncultured microorganisms directly from environmental samples. By leveraging high-throughput sequencing, advanced assembly algorithms, and genome binning techniques, researchers can reconstruct microbial genomes without the need for cultivation. These methodological advances have expanded the known microbial diversity, revealing novel taxa and metabolic pathways involved in key biogeochemical cycles, including carbon, nitrogen, and sulfur transformations.

Molecular adaptations specific to extreme halophilic archaea could promote high perchlorate tolerance.

Perchlorate is a strong chaotropic agent that causes macromolecule denaturation, DNA damage, and oxidative stress. However, perchlorate deliquescence is thought to promote the formation of liquid salt brines, even at hyper-arid and cold environments, such as the Martian regolith. For that reason, the detection of high levels of perchlorate at different locations on the Martian surface led to hypotheses about the existence of Martian microenvironments compatible with life, especially with those organisms tolerant to hyper-salinity and perchlorate.

Decoding the general role of tRNA queuosine modification in eukaryotes.

Transfer RNA (tRNA) contains modified nucleosides essential for modulating protein translation. One of these modifications is queuosine (Q), which affects NAU codons translation rate. For decades, multiple studies have reported a wide variety of species-specific Q-related phenotypes in different eukaryotes, hindering the identification of a general underlying mechanism behind that phenotypic diversity.

Structure and dispersion of the conjugative mobilome in surface ocean bacterioplankton.

Mobile genetic elements (MGEs), collectively referred to as the "mobilome", can have a significant impact on the fitness of microbial communities and therefore on ecological processes. Marine MGEs have mainly been associated with wide geographical and phylogenetic dispersal of adaptative traits. However, whether the structure of this mobilome exhibits deterministic patterns in the natural community is still an open question.

tRNA queuosine modification is involved in biofilm formation and virulence in bacteria.

tRNA modifications are crucial for fine-tuning of protein translation. Queuosine (Q) modification of tRNAs is thought to modulate the translation rate of NAU codons, but its physiological role remains elusive. Therefore, we hypothesize that Q-tRNAs control those physiological processes involving NAU codon-enriched genes (Q-genes).

Isolation of novel cold-tolerance genes from rhizosphere microorganisms of Antarctic plants by functional metagenomics.

The microorganisms that thrive in Antarctica, one of the coldest environments on the planet, have developed diverse adaptation mechanisms to survive in these extreme conditions. Through functional metagenomics, in this work, 29 new genes related to cold tolerance have been isolated and characterized from metagenomic libraries of microorganisms from the rhizosphere of two Antarctic plants. Both libraries were hosted in two cold-sensitive strains of DH10B Δ and DH10B Δ.

Heterologous Expression of the Phytochelatin Synthase from and Its Effect on Different Stress Factors in .

Phytochelatins (PCs) are cysteine-rich small peptides, enzymatically synthesized from reduced glutathione (GSH) by cytosolic enzyme phytochelatin synthase (PCS). The open reading frame (ORF) of the gene from the microalgae was heterologously expressed in strain DH5α, to analyze its role in protection against various abiotic agents that cause cellular stress. The transformed strain showed increased tolerance to exposure to different heavy metals (HMs) and arsenic (As), as well as to acidic pH and exposure to UVB, salt, or perchlorate.

Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile.

Perchlorate is an oxidative pollutant toxic to most of terrestrial life by promoting denaturation of macromolecules, oxidative stress, and DNA damage. However, several microorganisms, especially hyperhalophiles, are able to tolerate high levels of this compound. Furthermore, relatively high quantities of perchlorate salts were detected on the Martian surface, and due to its strong hygroscopicity and its ability to substantially decrease the freezing point of water, perchlorate is thought to increase the availability of liquid brine water in hyper-arid and cold environments, such as the Martian regolith.

Identification of a self-sufficient cytochrome P450 monooxygenase from Cupriavidus pinatubonensis JMP134 involved in 2-hydroxyphenylacetic acid catabolism, via homogentisate pathway.

The self-sufficient cytochrome P450 RhF and its homologues belonging to the CYP116B subfamily have attracted considerable attention due to the potential for biotechnological applications based in their ability to catalyse an array of challenging oxidative reactions without requiring additional protein partners. In this work, we showed for the first time that a CYP116B self-sufficient cytochrome P450 encoded by the ohpA gene harboured by Cupriavidus pinatubonensis JMP134, a β-proteobacterium model for biodegradative pathways, catalyses the conversion of 2-hydroxyphenylacetic acid (2-HPA) into homogentisate. Mutational analysis and HPLC metabolite detection in strain JMP134 showed that 2-HPA is degraded through the well-known homogentisate pathway requiring a 2-HPA 5-hydroxylase activity provided by OhpA, which was additionally supported by heterologous expression and enzyme assays.

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments.

Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory.

Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae.

Transcriptomic sequencing together with bioinformatic analyses and an automated annotation process led us to identify novel phytochelatin synthase (PCS) genes from two extremophilic green algae (Chlamydomonas acidophila and Dunaliella acidophila). These genes are of intermediate length compared to known PCS genes from eukaryotes and PCS-like genes from prokaryotes. A detailed phylogenetic analysis gives new insight into the complicated evolutionary history of PCS genes and provides evidence for multiple horizontal gene transfer events from bacteria to eukaryotes within the gene family.

Functional metagenomics of extreme environments.

The bioprospecting of enzymes that operate under extreme conditions is of particular interest for many biotechnological and industrial processes. Nevertheless, there is a considerable limitation to retrieve novel enzymes as only a small fraction of microorganisms derived from extreme environments can be cultured under standard laboratory conditions. Functional metagenomics has the advantage of not requiring the cultivation of microorganisms or previous sequence information to known genes, thus representing a valuable approach for mining enzymes with new features.

Extracellular DNA release by undomesticated Bacillus subtilis is regulated by early competence.

Extracellular DNA (eDNA) release is a widespread capacity described in many microorganisms. We identified and characterized lysis-independent eDNA production in an undomesticated strain of Bacillus subtilis. DNA fragments are released during a short time in late-exponential phase.

The role of nitric-oxide-synthase-derived nitric oxide in multicellular traits of Bacillus subtilis 3610: biofilm formation, swarming, and dispersal.

Background: Bacillus subtilis 3610 displays multicellular traits as it forms structurally complex biofilms and swarms on solid surfaces. In addition, B. subtilis encodes and expresses nitric oxide synthase (NOS), an enzyme that is known to enable NO-mediated intercellular signalling in multicellular eukaryotes.

Cannibalism: a social behavior in sporulating Bacillus subtilis.

A social behavior named cannibalism has been described during the early stages of sporulation of the Gram-positive Bacillus subtilis. This phenomenon is based on the heterogeneity of sporulating populations, constituted by at least two cell types: (1) sporulating cells, in which the master regulator of sporulation Spo0A is active, and (2) nonsporulating cells, in which Spo0A is inactive. Sporulating cells produce two toxins that act cooperatively to kill the nonsporulating sister cells.

SpoIIIE and a novel type of DNA translocase, SftA, couple chromosome segregation with cell division in Bacillus subtilis.

Cell division must only occur once daughter chromosomes have been fully separated. However, the initiating event of bacterial cell division, assembly of the FtsZ ring, occurs while chromosome segregation is still ongoing. We show that a two-step DNA translocase system exists in Bacillus subtilis that couples chromosome segregation and cell division.

SOLID2: an antibody array-based life-detector instrument in a Mars Drilling Simulation Experiment (MARTE).

A field prototype of an antibody array-based life-detector instrument, Signs Of LIfe Detector (SOLID2), has been tested in a Mars drilling mission simulation called MARTE (Mars Astrobiology Research and Technology Experiment). As one of the analytical instruments on the MARTE robotic drilling rig, SOLID2 performed automatic sample processing and analysis of ground core samples (0.5 g) with protein microarrays that contained 157 different antibodies.

Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene.

When Pseudomonas putida KT2440 cells encounter toluene in the growth medium, they perceive it simultaneously as a potential nutrient to be metabolized, as a membrane-damaging toxic drug to be extruded, and as a macromolecule-disrupting agent from which to protect proteins. Each of these inputs requires a dedicated transcriptional response that involves a large number of genes. We used DNA array technology to decipher the interplay between these responses in P.

High- and low-threshold genes in the Spo0A regulon of Bacillus subtilis.

The master regulator for entry into sporulation in Bacillus subtilis is the response regulator Spo0A, which directly governs the expression of about 121 genes. Using cells in which the synthesis of Spo0A was under the control of an inducible promoter or in which production of the regulatory protein was impaired by a promoter mutation, we found that sporulation required a high (threshold) level of Spo0A and that many genes in the regulon differentially responded to high and low doses of the regulator. We distinguished four categories of genes, as follows: (i) those that required a high level of Spo0A to be activated, (ii) those that required a high level of Spo0A to be repressed, (iii) those that were activated at a low level of the regulator, and (iv) those that were repressed at a low dose of the regulator.

Genes involved in formation of structured multicellular communities by Bacillus subtilis.

The spore-forming bacterium Bacillus subtilis is capable of assembling multicellular communities (biofilms) that display a high degree of spatiotemporal organization. Wild strains that have not undergone domestication in the laboratory produce particularly robust biofilms with complex architectural features, such as fruiting-body-like aerial projections whose tips serve as preferential sites for sporulation. To discover genes involved in this multicellular behavior and to do so on a genome-wide basis, we took advantage of a large collection of mutants which have disruptions of most of the uncharacterized genes in the B.

The sigmaE regulon and the identification of additional sporulation genes in Bacillus subtilis.

We report the identification and characterization on a genome-wide basis of genes under the control of the developmental transcription factor sigma(E) in Bacillus subtilis. The sigma(E) factor governs gene expression in the larger of the two cellular compartments (the mother cell) created by polar division during the developmental process of sporulation. Using transcriptional profiling and bioinformatics we show that 253 genes (organized in 157 operons) appear to be controlled by sigma(E).

The regulation of microcin B, C and J operons.

Microcins are ribosomally encoded small peptide antibiotics produced by Gram(-) enterobacteria. Microcin production-biosynthesis, maturation and secretion to the medium-is encoded by gene clusters organized in operons. Production of the best known plasmid-encoded microcins (MccB, MccC and MccJ) switches on when cells reach the stationary growth phase.

Genome-wide analysis of the stationary-phase sigma factor (sigma-H) regulon of Bacillus subtilis.

Sigma-H is an alternative RNA polymerase sigma factor that directs the transcription of many genes that function at the transition from exponential growth to stationary phase in Bacillus subtilis. Twenty-three promoters, which drive transcription of 33 genes, are known to be recognized by sigma-H-containing RNA polymerase. To identify additional genes under the control of sigma-H on a genome-wide basis, we carried out transcriptional profiling experiments using a DNA microarray containing >99% of the annotated B.