Turf algae redefine the chemical landscape of temperate reefs, limiting kelp forest recovery.

In temperate regions experiencing rapid ocean warming, kelp forests are being replaced by chemically rich turf algae. However, the extent to which these turf algae alter the surrounding chemical environment or affect the rebound potential of kelp forests (through chemically mediated interactions) remains unknown. Here, we used underwater visual surveys, comprehensive chemical profiling, and laboratory experiments to reveal that turf algae release bioactive compounds into the water that fundamentally alter the reef "chemical landscape" and directly suppress kelp recruitment.

The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake.

Background: Venoms and their associated glands and delivery structures have evolved numerous times among animals. Within these venom systems, the molecular, cellular, and morphological components interact and co-evolve to generate distinct, venom phenotypes that are increasingly recognized as models for studying adaptive evolution. However, toxins are often unevenly distributed across venom-producing tissues in patterns that are not necessarily adaptive but instead likely result from constraints associated with protein secretion.

Metabolomic signatures of pathogen suppression effect of Baltic eelgrass meadows in surrounding seawater.

Organic molecules exuded into water column by marine organisms represent a significant portion of marine dissolved organic matter (DOM) that modulates biochemical interactions. Secreted allelochemicals have been suggested to be involved in regulation of pathogen abundance in seagrass meadows, however, seagrass exometabolome has remained unstudied. We aimed to identify seagrass exometabolites, within and outside meadows, and explore their potential involvement in pathogen suppression under varying environmental conditions.

Oxidation state of bioavailable dissolved organic matter influences bacterioplankton respiration and growth efficiency.

Oxygen consumption by oceanic microbes can predict respiration (CO production) but requires an assumed respiratory quotient (RQ; ΔO/ΔCO). Measured apparent RQs (ARQs) can be impacted by various processes, including nitrification and changes in dissolved organic matter (DOM) composition, leading to discrepancies between ARQ and actual RQ. In DOM remineralization experiments conducted in the eastern North Atlantic Ocean, ARQs averaged 1.

Comparative Multi-Omics Survey Reveals Novel Specialized Metabolites and Biosynthetic Gene Clusters Under GacS Control in Pseudomonas donghuensis Strain SVBP6.

In Pseudomonas donghuensis SVBP6, isolated from an agricultural field, the well-conserved Gac-Rsm pathway upregulates biosynthesis of the antifungal compound 7-hydroxytropolone (7-HT). However, 7-HT does not fully explain the strain's Gac-Rsm-dependent antimicrobial activity. Here, we combined comparative transcriptomic, proteomic, and metabolomic approaches to identify novel GacS-dependent biosynthetic gene clusters (BGC) and/or extracellular specialized metabolites.

Two-Dimensional Liquid Chromatography Tandem Mass Spectrometry Untangles the Deep Metabolome of Marine Dissolved Organic Matter.

Dissolved organic matter (DOM) is an ultracomplex mixture that plays a central role in global biogeochemical cycles. Despite its importance, DOM remains poorly understood at the molecular level. Over the last decades, significant efforts have been made to decipher the chemical composition of DOM by high-resolution mass spectrometry (HR-MS) and liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS).

Statistical analysis of feature-based molecular networking results from non-targeted metabolomics data.

Feature-based molecular networking (FBMN) is a popular analysis approach for liquid chromatography-tandem mass spectrometry-based non-targeted metabolomics data. While processing liquid chromatography-tandem mass spectrometry data through FBMN is fairly streamlined, downstream data handling and statistical interrogation are often a key bottleneck. Especially users new to statistical analysis struggle to effectively handle and analyze complex data matrices.

High-Resolution Tandem Mass Spectrometry-Based Analysis of Model Lignin-Iron Complexes: Novel Pipeline and Complex Structures.

Understanding the chemical nature of soil organic carbon (SOC) with great potential to bind iron (Fe) minerals is critical for predicting the stability of SOC. Organic ligands of Fe are among the top candidates for SOCs able to strongly sorb on Fe minerals, but most of them are still molecularly uncharacterized. To shed insights into the chemical nature of organic ligands in soil and their fate, this study developed a protocol for identifying organic ligands using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UHPLC-HRMS/MS) and metabolomic tools.

Reproducible mass spectrometry data processing and compound annotation in MZmine 3.

Untargeted mass spectrometry (MS) experiments produce complex, multidimensional data that are practically impossible to investigate manually. For this reason, computational pipelines are needed to extract relevant information from raw spectral data and convert it into a more comprehensible format. Depending on the sample type and/or goal of the study, a variety of MS platforms can be used for such analysis.

Isolation and Characterization of an Antioxidant Aryl Polyene Pigment from Antarctic Bacterium Lysobacter sp. A03.

Lysobacter is known as a bacterial genus with biotechnological potential, producing an array of enzymes, antimicrobial metabolites, and bioactive antioxidant compounds, including aryl polyene (APE) pigments that have been described as protecting substances against photooxidative damage and lipid peroxidation. In this study, the pigment extracted from keratinolytic Lysobacter sp. A03 isolated from Antarctic environment was characterized.

Genome analysis of Pseudomonas strain 4B with broad antagonistic activity against toxigenic fungi.

Pseudomonas sp. 4B isolated from the effluent pond of a bovine abattoir was investigated as antifungal against toxigenic fungi. The complete genome of Pseudomonas 4B was sequenced using the Illumina MiSeq platform.

Evaluation of Data-Dependent MS/MS Acquisition Parameters for Non-Targeted Metabolomics and Molecular Networking of Environmental Samples: Focus on the Q Exactive Platform.

Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations.

Native metabolomics identifies the rivulariapeptolide family of protease inhibitors.

The identity and biological activity of most metabolites still remain unknown. A bottleneck in the exploration of metabolite structures and pharmaceutical activities is the compound purification needed for bioactivity assignments and downstream structure elucidation. To enable bioactivity-focused compound identification from complex mixtures, we develop a scalable native metabolomics approach that integrates non-targeted liquid chromatography tandem mass spectrometry and detection of protein binding via native mass spectrometry.

Proteomic dataset of exposed to sublethal concentrations of free and nanoencapsulated nisin.

The cellular proteins of exposed to free and liposome-encapsulated nisin at sublethal concentration were hydrolyzed by trypsin and examined by tandem mass spectrometry (MS/MS) to obtain proteomic data. In the present study, we use the STRING v11.05 database analyze the interactions among the 78 upregulated proteins from obtained after treatment with sublethal concentrations of free and nanoliposome-encapsulated nisin.

Listeria monocytogenes exposed to antimicrobial peptides displays differential regulation of lipids and proteins associated to stress response.

With the onset of Listeria monocytogenes resistance to the bacteriocin nisin, the search for alternative antimicrobial treatments is of fundamental importance. In this work, we set out to investigate proteins and lipids involved in the resistance mechanisms of L. monocytogenes against the antimicrobial peptides (AMPs) nisin and fengycin.

Genomic characterization and production of antimicrobial lipopeptides by Bacillus velezensis P45 growing on feather by-products.

Aims: To investigate the potential of novel Bacillus velezensis P45 as an eco-friendly alternative for bioprocessing poultry by-products into valuable antimicrobial products.

Methods And Results: The complete genome of B. velezensis P45 was sequenced using the Illumina MiSeq platform, showing 4455 protein and 98 RNA coding sequences according to the annotation on the RAST server.

Antimicrobial activity of DC and its synergistic interaction with nisin against food-related bacteria.

The antimicrobial activities of DC essential oil (EO) and hydroalcoholic extract (HE) were evaluated. The EO showed broad antimicrobial activity and its synergistic combination with nisin was tested. Major components of EO were nerolidol, beta-pinene and D-limonene, while artepillin C, rutin and cafeic acid were major phenolics of HE.

Proteomic analysis reveals differential responses of Listeria monocytogenes to free and nanoencapsulated nisin.

The ability of Listeria monocytogenes grow on ready-to-eat food is a major concern in food safety. Natural antimicrobials, such as nisin, can be used to control this pathogen, but the increasing reports of nisin tolerance and resistance make necessary novel approaches to increase its effectiveness, such as encapsulation. The goal of this study was to investigate how L.

Proteomic analysis of exposed to free and nanostructured antimicrobial lipopeptides.

In this work, the effect of antimicrobial lipopeptide P34 on Listeria monocytogenes was evaluated for the first time through a proteomics approach. Bacteria were treated with sub-lethal doses of peptide P34 (F-P34) and P34 encapsulated into nanoliposomes (N-P34), while empty nanoliposomes (NE) and fresh buffer were used as controls. The proteomic analysis allowed the detection of one group of proteins commonly differentially represented in response to free and encapsulated P34 exposure.

Nisin influence on the expression of Listeria monocytogenes surface proteins.

In this work, a comparative analysis of the peripheral cell component (PCC) proteins of Listeria monocytogenes was carried out. The study was conducted on two set of samples consisting of bacteria treated with sub-lethal concentration of nisin and untreated bacteria as control. PCC proteins were extracted by Tris-Urea-EDTA treatment and then subjected to trypsin digestion and mass spectrometry analysis.

Diversity of cyclic antimicrobial lipopeptides from Bacillus P34 revealed by functional annotation and comparative genome analysis.

Cyclic lipopeptides (CLPs) from Bacillus strains have demonstrated a wide range of bioactivities making them interesting candidates for different applications in the pharmaceutical, food and biotechnological industries. Genome sequencing, together with phylogenetic analysis of the Bacillus sp. P34, isolated from a freshwater fish gut, showed that the bacterial strain belongs to the Bacillus velezensis group.

Marine bacteria as source of antimicrobial compounds.

The marine environment encompasses a huge biological diversity and can be considered as an underexplored location for prospecting bioactive molecules. In this review, the current state of art about antimicrobial molecules from marine bacteria has been summarized considering the main phylum and sources evolved in a marine environment. Considering the last two decades, we have found as most studied group of bacteria producers of substances with antimicrobial activity is the Firmicutes phylum, in particular strains of the genus.