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1. Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

   https://doi.org/10.3762/bjoc.20.146  

   Zhong, Weimao; Agarwal, Vinayak (January 2024, Beilstein Journal of Organic Chemistry)

   Microbulbiferis a genus of halophilic bacteria that are commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly,Microbulbifergenomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic novelty. In this review, we summarize the distribution ofMicrobulbiferbacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated fromMicrobulbiferstrains. We argue that these bacteria have been hiding in plain sight, and contemporary efforts into their genome and metabolome mining are going to lead to a proliferation ofMicrobulbifer-derived natural products in the future. We also describe, where possible, the ecological interactions of these bacteria in marine microbiomes. 

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2. Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech

   https://doi.org/10.3390/md21010053  

   Deutsch, Jessica M.; Green, Madison O.; Akavaram, Priyanka; Davis, Ashleigh C.; Diskalkar, Sarth S.; Du Plessis, Isabelle A.; Fallon, Hannah A.; Grason, Emma M.; Kauf, Emma G.; Kim, Zoe M.; et al (January 2023, Marine Drugs)

   Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies. 

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3. Effect of various types of extracellular DNA on V. hyugaensis biofilm formation

   https://doi.org/10.1128/msphere.00035-23  

   Gu_Liu, Carmen; Maresso, Anthony W (August 2023, mSphere)

   Imperiale, Michael J (Ed.)

   ABSTRACT Marine bacteria face a constant influx of new extracellular DNA (exDNA) due to the massive viral lysis that occurs in the ocean on a daily basis. Generally, biofilms have shown to be induced by self-secreted exDNA. However, the effect of various types of exDNA with varying lengths, self vs non-self, as well as guanine-cytosine content (GC) content on biofilm formation has not been explored, despite being a critical component of the extracellular polymeric substance. To test the effect of such exDNA on biofilms, a marine bioluminescent bacterium (Vibrio hyugaensis) was isolated from the Sippewissett Salt Marsh, USA, and treated with various types of exDNA. We observed rapid pellicle formation with distinct morphologies only in cultures treated with herring sperm gDNA, anotherVibriospp. gDNA, and an oligomer of 61–80% GC content. With pH measurements before and after the treatment, we observed a positive correlation between biofilm formation and the change to a more neutral pH. Our study highlights the importance of studying DNA-biofilm interaction by carefully examining the physical properties of the DNA and by varying its content, length, and source. Our observation may serve as the basis for future studies that seek to interrogate the molecular explanation for the various types of exDNA and their effects on biofilm formation. IMPORTANCEBacteria mostly exist as biofilm, a protective niche that promotes protection from the environment and nutrient uptake. By forming these structures, bacteria have caused recalcitrant antibiotic-resistant infections, contamination of dairy and seafood, and fouling equipment in the industry. A critical component that makes up the extracellular polymeric substances, the structural component of a biofilm, is the extracellular DNA secreted by the bacteria found in the biofilm. However, previous studies on DNA and biofilm formation have neglected the unique properties of nucleic acid and its high diversity. Our study aims at disentangling these DNA properties by monitoring their effect at inducing biofilm formation. By varying length, self vs non-self, and GC percentage, we used various microscopy techniques to visualize the structural composition of aVibrio hyugaensisbiofilm. We observed DNA-dependent biofilm stimulation in this organism, a novel function of DNA in biofilm biology. 

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4. Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis

   https://doi.org/10.1093/ismejo/wrag091  

   De_Santiago, Alejandro; Barnes, Shelby; Pereira, Tiago José; Marcellino-Barros, Mirayana; Durden, Lekeah; Han, Min Khant; Thrash, J Cameron; Bik, Holly M (April 2026, The ISME Journal)

   Abstract Despite growing insights into the composition of marine invertebrate microbiomes, our understanding of their ecological and evolutionary patterns remains poor, owing to limited sampling depth and low-resolution datasets. Previous studies have provided conflicting results that both confirm and deny the existence of phylosymbiosis between marine invertebrates and marine bacteria. Here, we investigated potential animal-microbe symbioses in Pseudoalteromonas, a bacterial genus consistently identified as a core microbiome taxon in diverse invertebrates. Using a pangenomic analysis of 236 free-living and invertebrate-associated bacterial strains (including two new nematode-associated isolates generated in this study), we confirm that Pseudoalteromonas is a symbiont with substantial evidence of phylosymbiosis across at least three marine invertebrate phyla (e.g., Nematoda, Mollusca, and Cnidaria). Patterns of symbiosis were consistent irrespective of geography (including in Antarctica), with FISH images from nematodes indicating that bacterial symbionts form biofilms in the mouth and esophagus and are sometimes present in female nematode ovaries exhibiting stunted development. The evolutionary history of Pseudoalteromonas is marked by substantial host-switching and lifestyle transitions, and host-associated genomes suggest that these bacteria are facultative symbionts involved in nutritional symbioses. In marine environments, we hypothesize that horizontally acquired symbionts may have co-evolved with invertebrates, using host mucus as a physical niche and food source, while providing their animal hosts with Vitamin B, amino acids, and bioavailable carbon compounds in return. 

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5. Heterotrophic bacteria trigger transcriptome remodelling in the photosynthetic picoeukaryote Micromonas commoda

   https://doi.org/10.1111/1758-2229.13285  

   Hamilton, Maria; Ferrer‐González, Frank Xavier; Moran, Mary Ann (June 2024, Environmental Microbiology Reports)

   Abstract Marine biogeochemical cycles are built on interactions between surface ocean microbes, particularly those connecting phytoplankton primary producers to heterotrophic bacteria. Details of these associations are not well understood, especially in the case of direct influences of bacteria on phytoplankton physiology. Here we catalogue how the presence of three marine bacteria (Ruegeria pomeroyiDSS‐3,Stenotrophomonassp. SKA14 andPolaribacter dokdonensisMED152) individually and uniquely impact gene expression of the picoeukaryotic algaMicromonas commodaRCC 299. We find a dramatic transcriptomic remodelling byM. commodaafter 8 h in co‐culture, followed by an increase in cell numbers by 56 h compared with the axenic cultures. Some aspects of the algal transcriptomic response are conserved across all three bacterial co‐cultures, including an unexpected reduction in relative expression of photosynthesis and carbon fixation pathways. Expression differences restricted to a single bacterium are also observed, with the FlavobacteriiaP. dokdonensisuniquely eliciting changes in relative expression of algal genes involved in biotin biosynthesis and the acquisition and assimilation of nitrogen. This study reveals thatM. commodahas rapid and extensive responses to heterotrophic bacteria in ways that are generalizable, as well as in a taxon specific manner, with implications for the diversity of phytoplankton‐bacteria interactions ongoing in the surface ocean. 

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