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Antibiotic resistance has been increasingly reported for a wide variety of bacteria of clinical significance. This widespread problem constitutes one of the greatest challenges of the twenty-first century. Faced with this issue, clinicians and researchers have been persuaded to design novel strategies in order to try to control pathogenic bacteria. Therefore, the discovery and elucidation of the mechanisms underlying bacterial pathogenesis and intercellular communication have opened new perspectives for the development of alternative approaches. Antipathogenic and/or antivirulence therapies based on the interruption of quorum sensing pathways are one of several such promising strategies aimed at disarming rather than at eradicating bacterial pathogens during the course of colonization and infection. This review describes mechanisms of bacterial communication involved in biofilm formation. An overview of the potential of marine bacteria and their bioactive components as QS inhibitors is further provided.

Axenic cultures are essential for studying microbial ecology, evolution, and genomics. Despite the importance of pure cultures, public culture collections are biased towards fast-growing copiotrophs, while many abundant aquatic prokaryotes remain uncultured due to uncharacterized growth requirements and oligotrophic lifestyles. Here, we applied high-throughput dilution-to-extinction cultivation using defined media that mimic natural conditions to samples from 14 Central European lakes, yielding 627 axenic strains. These cultures include 15 genera among the 30 most abundant freshwater bacteria identified via metagenomics, collectively representing up to 72% of genera detected in the original samples (average 40%) and are widespread in freshwater systems globally. Genome-sequenced strains are closely related to metagenome-assembled genomes (MAGs) from the same samples, many of which remain undescribed. We propose a classification of several novel families, genera, and species, including many slowly growing, genome-streamlined oligotrophs that are notoriously underrepresented in public repositories. Our large-scale initiative to cultivate the “uncultivated microbial majority” has yielded a valuable collection of abundant freshwater microbes, characterized by diverse metabolic pathways and lifestyles. This culture collection includes promising candidates for oligotrophic model organisms, suitable for a wide array of ecological studies aimed at advancing our ecological and functional understanding of dominant, yet previously uncultured, taxa. A large fraction of aquatic bacteria remains uncultured. Here, the authors cultivated 627 strains of abundant freshwater bacteria from 14 European lakes, thus generating a collection that includes many previously uncultured, oligotrophic bacteria that may serve as model organisms.

Here we used flow cytometry (FCM) and filtration paired with amplicon sequencing to determine the abundance and composition of small low nucleic acid (LNA)-content bacteria in a variety of freshwater ecosystems. We found that FCM clusters associated with LNA-content bacteria were ubiquitous across several ecosystems, varying from 50 to 90% of aquatic bacteria. Using filter-size separation, we separated small LNA-content bacteria (passing 0.4 µm filter) from large bacteria (captured on 0.4 µm filter) and characterized communities with 16S amplicon sequencing. Small and large bacteria each represented different sub-communities within the ecosystems’ community. Moreover, we were able to identify individual operational taxonomical units (OTUs) that appeared exclusively with small bacteria (434 OTUs) or exclusively with large bacteria (441 OTUs). Surprisingly, these exclusive OTUs clustered at the phylum level, with many OTUs appearing exclusively with small bacteria identified as candidate phyla (i.e. lacking cultured representatives) and symbionts. We propose that LNA-content bacteria observed with FCM encompass several previously characterized categories of bacteria (ultramicrobacteria, ultra-small bacteria, candidate phyla radiation) that share many traits including small size and metabolic dependencies on other microorganisms.

Phosphorus (P) enrichment to streams, lakes, and estuaries is increasing throughout the United States. P loading is typically viewed from a harmful algal bloom perspective; if added P causes excess growths of phytoplankton or macroalgae, it may become targeted for control. However, P loading also contributes to two other non–algae-based aquatic problems. Field and experimental evidence shows that P loading directly stimulates growth of aquatic bacteria, which can increase to concentrations that exert a significant biochemical oxygen demand on water bodies, contributing to hypoxia, a widespread impairment. Experimental evidence also demonstrates that fecal bacterial growth can be significantly stimulated by P loading, increasing health risks through exposure or the consumption of contaminated shellfish and causing economic losses from beach and shellfish area closures. Resource managers need to look beyond algal bloom stimulation and should consider the broader roles that excess P loading can have on ecosystem function and microbiological safety for humans.

The phylum Planctomycetota is changing our understanding of bacterial metabolism, driving critical biogeochemical processes through the transformation of complex polymeric substrates into valuable bioactive compounds. Sophisticated methods for cultivation, genome sequencing and genetic strain engineering developed in the last two decades have stimulated detailed studies on cell propagation, metabolic capabilities and potential applications of phylum members beyond the mere isolation and characterization of novel taxa. This review synthesizes recent advances in understanding the Planctomycetota physiology with a focus on the degradation of phototroph-derived polysaccharides, anaerobic ammonium oxidation (anammox) and biosynthesis of secondary metabolites. New data especially collected over the last 5 years justifies more intensive research of the yet uncharacterized pathways of substrate uptake and utilization, as well as genome mining-assisted bioprospection to exploit the phylum's chemical repertoire. Key points • Planctomycetes can degrade high-molecular-weight sugars produced by algae • Anaerobic ammonium oxidation (anammox) is used in technical applications • The first secondary metabolites were discovered in the last 5 years

Concern about biodiversity loss has yielded a surge of studies on temporal change in α-diversity, whereas temporal β-diversity has gained less interest. We sampled bacterioplankton, biofilm, and riparian soil bacteria repeatedly across the open-water season in a pristine stream network to determine the level of temporal β-diversity in relation to stream network position and environmental variability. We tested the hypothesis that aquatic bacterial communities in isolated and environmentally heterogenous headwaters exhibit high temporal β-diversity while the better-connected and environmentally more stable mainstem sections support more stable communities, and soil communities bear no relationship to network position. As expected, temporal β-diversity decreased from headwaters toward mainstems for bacterioplankton. Against expectations, an opposite pattern was observed for biofilm. For bacterioplankton, temporal β-diversity was positively related to temporal variability in water chemistry. For biofilm bacteria, temporal variability was negatively related to variability in temperature. Temporal β-diversity of soil communities did not show any response to stream network position, but was strongly related to variability in the soil environment. The two aquatic habitats and riparian soils supported distinctly different bacterial communities. The number of ASVs shared between the soil and the aquatic communities decreased along the network, and more so for bacterioplankton. The higher temporal variability of bacterial communities in the headwaters likely results from temporally variable input of propagules from riparian soil, emphasizing the role of land–water connection and network position to bacterioplankton community composition. Overall, bacterial communities exhibited high temporal variability, highlighting the importance of temporal replication to fully capture their network-scale biodiversity.

Carotenoids are a large group of health-promoting compounds used in many industrial sectors, such as foods, feeds, pharmaceuticals, cosmetics, nutraceuticals, and colorants. Considering the global population growth and environmental challenges, it is essential to find new sustainable sources of carotenoids beyond those obtained from agriculture. This review focuses on the potential use of marine archaea, bacteria, algae, and yeast as biological factories of carotenoids. A wide variety of carotenoids, including novel ones, were identified in these organisms. The role of carotenoids in marine organisms and their potential health-promoting actions have also been discussed. Marine organisms have a great capacity to synthesize a wide variety of carotenoids, which can be obtained in a renewable manner without depleting natural resources. Thus, it is concluded that they represent a key sustainable source of carotenoids that could help Europe achieve its Green Deal and Recovery Plan. Additionally, the lack of standards, clinical studies, and toxicity analysis reduces the use of marine organisms as sources of traditional and novel carotenoids. Therefore, further research on the processing of marine organisms, the biosynthetic pathways, extraction procedures, and examination of their content is needed to increase carotenoid productivity, document their safety, and decrease costs for their industrial implementation.

Preliminary antibacterial metabolite production screening unveiled that  B. amyloliquefaciens MTCC 12,713 associated with the intertidal red alga Kappaphycus alverezii exhibited potential inhibitory effects against drug-resistant pathogens methicillin-resistant Staphylococcus aureus , vancomycin-resistant Enterococcus faecalis , Pseudomonas aeruginosa , and Klebsiella pneumoniae. Four homologous siderophore types of bacillibactins were isolated from a heterotrophic marine bacterium through bioactivity-guided purification. All detectable natural product gene clusters in B. amyloliquefaciens MTCC 12,713 were analyzed by sequencing the complete genome of the bacterium. The studied compounds displayed broad spectrum bactericidal activity against multidrug-resistant strains with a range of minimum inhibitory concentration values from 1.56 to 6.25 µg/mL, whereas standard antibiotic chloramphenicol was active at 6.25 to 12.5 µg/mL. Structure-bioactivity relationship assessment showed that higher electronic values were responsible for antibacterial properties against the nosocomial pathogens. The 2, 3-dihydroxybenzoate ( dhb )-assisted biosynthetic pathway of catecholate-enclosed bacillibactins was proposed through the bacillibactin synthase multienzyme complex catalysis followed by dimerization of dhbACEBF operons with 16 genes (~ 12 kb bacterial genome). The present findings recognized an undescribed 4-methoxy-11′-pentanoyloxy-bacillibactin C as a source of potential antibacterial agent for use against drug-resistant pathogens for pharmaceutical applications. Key points • Bacillus amyloliquefaciens in association with Kappaphycus alverezii was isolated • Four antibacterial bacillibactin analogs were identified from symbiotic bacterium • 4-Methoxy-11′-pentanoyloxy-bacillibactin C showed potential antibacterial activity

The composition and function of bacterial communities in recirculating aquaculture systems (RAS) vary significantly across operational phases and treatment units. Yet the causal links between these bacterial dynamics and nitrogen removal mechanisms remain obscure. In this study, we demonstrated dynamic shifts in bacterial community composition and nitrogen removal function within RAS throughout cultivation and in each unit, by water quality monitoring, 16 S rRNA gene sequencing, metagenomics, 15 N isotope tracing and kinetic modeling. Bacterial community composition shifted temporally, marked by a decline in r-strategists and increases in both α- and β-diversity from the start-up to the culture phase, a succession primarily driven by salinity, total dissolved solids, and conductivity. Ecologically, this transition is indicative of a shift in dominant life-history strategies, from an r-selected pioneer community to a K-selected, more stable and resilient community. Denitrification, anammox, and nitrification dominated nitrogen removal pathways, collectively representing 45.2% of the nitrogen-cycling functional genes. In addition, there was significant spatiotemporal heterogeneity in bacterial nitrogen removal. Spatially, aquatic bacteria exhibited higher denitrification activity, while biofilm-attached anammox bacteria of K-strategist demonstrated disproportionately high metabolic activity relative to their low abundance; this was probably regulated by biofilm-associated quorum sensing. Temporally, the ammonia-oxidizing bacteria (AOB) enabled an initial rapid ammonia degradation, whereas nitrite-oxidizing bacteria (NOB) and denitrifiers dominated later-stage decreases in nitrite and nitrate, indicating that the bacterial nitrogen removal function responded to nutrient dynamics. This study demonstrated the coupling mechanisms between ecological adaptation strategies of bacterial communities and nitrogen removal function in RAS, thereby establishing a basis for precision management technologies targeting functional bacteria. Graphical abstract Diagram of bacterial dynamics and nitrogen removal function in RAS. Spatially, variations in nitrogen removal functions between aquatic and biofilm-attached bacteria were demonstrated. Temporally, shifts of water quality, bacterial community composition and nitrogen removal functions in fish culture tank across the culture cycling were revealed.

Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.