New Biocalcifying Marine Bacterial Strains Isolated from Calcareous Deposits and Immediate Surroundings

Marine bacterial biomineralisation by CaCO3 precipitation provides natural limestone structures, like beachrocks and stromatolites. Calcareous deposits can also be abiotically formed in seawater at the surface of steel grids under cathodic polarisation. In this work, we showed that this mineral-rich alkaline environment harbours bacteria belonging to different genera able to induce CaCO3 precipitation. We previously isolated 14 biocalcifying marine bacteria from electrochemically formed calcareous deposits and their immediate environment. By microscopy and µ-Raman spectroscopy, these bacterial strains were shown to produce calcite-type CaCO3. Identification by 16S rDNA sequencing provided between 98.5 and 100% identity with genera Pseudoalteromonas, Pseudidiomarina, Epibacterium, Virgibacillus, Planococcus, and Bhargavaea. All 14 strains produced carbonic anhydrase, and six were urease positive. Both proteins are major enzymes involved in the biocalcification process. However, this does not preclude that one or more other metabolisms could also be involved in the process. In the presence of urea, Virgibacillus halodenitrificans CD6 exhibited the most efficient precipitation of CaCO3. However, the urease pathway has the disadvantage of producing ammonia, a toxic molecule. We showed herein that different marine bacteria could induce CaCO3 precipitation without urea. These bacteria could then be used for eco-friendly applications, e.g., the formation of bio-cements to strengthen dikes and delay coastal erosion.

The Unusual Lipid A Structure and Immunoinhibitory Activity of LPS from Marine Bacteria Echinicola pacifica KMM 6172T and Echinicola vietnamensis KMM 6221T

Gram-negative bacteria experiencing marine habitats are constantly exposed to stressful conditions dictating their survival and proliferation. In response to these selective pressures, marine microorganisms adapt their membrane system to ensure protection and dynamicity in order to face the highly mutable sea environments. As an integral part of the Gram-negative outer membrane, structural modifications are commonly observed in the lipopolysaccharide (LPS) molecule; these mainly involve its glycolipid portion, i.e., the lipid A, mostly with regard to fatty acid content, to counterbalance the alterations caused by chemical and physical agents. As a consequence, unusual structural chemical features are frequently encountered in the lipid A of marine bacteria. By a combination of data attained from chemical, MALDI-TOF mass spectrometry (MS), and MS/MS analyses, here, we describe the structural characterization of the lipid A isolated from two marine bacteria of the Echinicola genus, i.e., E. pacifica KMM 6172T and E. vietnamensis KMM 6221T. This study showed for both strains a complex blend of mono-phosphorylated tri- and tetra-acylated lipid A species carrying an additional sugar moiety, a d-galacturonic acid, on the glucosamine backbone. The unusual chemical structures are reflected in a molecule that only scantly activates the immune response upon its binding to the LPS innate immunity receptor, the TLR4-MD-2 complex. Strikingly, both LPS potently inhibited the toxic effects of proinflammatory Salmonella LPS on human TLR4/MD-2.

Bacterial Nanotubes as Intercellular Linkages in Marine Assemblages

Several types of bacterial appendages, e.g., pili and fimbriae, are known for their role in promoting interactions and aggregation with particles and bacteria in the ocean. First discovered in Bacillus subtilis and Escherichia coli, but novel to marine bacteria, bacterial nanotubes are hollow tubular structures connecting cell pairs that allow for the internal transport of cytoplasmic metabolites across the connecting structure. While the significance of nanotubes in exchange of cytoplasmic content has been established in non-marine bacteria, their occurrence and potential ecological significance in marine bacteria has not been reported. Using multiple high-resolution microscopy methods (atomic force microscopy, scanning, and transmission electron microscopy), we have determined that marine bacteria isolates and natural assemblages from nearshore upper ocean waters can express bacterial nanotubes. In marine isolates Pseudoalteromonas sp. TW7 and Alteromonas sp. ALTSIO, individual bacterial nanotubes measured 50–160 nm in width and extended 100–600 nm between connected cells. The spatial coupling of different cells via nanotubes can last for at least 90 min, extending the duration of interaction events between marine bacteria within natural assemblages. The nanomechanical properties of bacterial nanotubes vary in adhesion and dissipation properties, which has implication for structural and functional variability of these structures in their ability to stick to surfaces and respond to mechanical forces. Nanotube frequency is low among cells in enriched natural assemblages, where nanotubes form short, intimate connections, <200 nm, between certain neighboring cells. Bacterial nanotubes can form the structural basis for a bacterial ensemble and function as a conduit for cytoplasmic exchange (not explicitly studied here) between members for multicellular coordination and expression. The structural measurements and nanomechanical analyses in this study also extends knowledge about the physical properties of bacterial nanotubes and their consequences for marine microenvironments. The discovery of nanotube expression in marine bacteria has significant potential implications regarding intimate bacterial interactions in spatially correlated marine microbial communities.

Exploring bioactive pigments from marine bacterial isolate from the Indonesian seas

Marine microbes offer a significant source for biodiscovery due to their rich biodiversity and genetic capacity. Particularly, microbial pigments of marine origin are getting more attention in current research due to their widely perceived application as natural food colorants, antioxidant, antimicrobial, and many more. In the past five years, our research group has successfully characterised various bioactive pigments isolated from marine bacteria, including Erythrobacter flavus strain KJ5 that produces unique sulphur-containing carotenoids, Pseudoalteromonas rubra strain PS1 and SB14 that contain antimicrobial prodiginine, and Seonamhaeicola algicola strain CCI for high content of zeaxanthin. This paper describes the challenges we encountered in conducting research in exploring bioactive pigments especially with focus on carotenoid research, reviewed critically on strategy we developed for isolation of isolate as well as identification and elucidation of the pigments, and consideration for future research.

D-alanine metabolism via D-Ala aminotransferase by marine Gammaproteobacteria , Pseudoalteromonas sp. CF6-2

As the most abundant D-amino acid (DAA) in the ocean, D-alanine (D-Ala) is a key component of peptidoglycan in bacterial cell wall. However, the underlying mechanisms of bacterial metabolization of D-Ala through microbial food web remain largely unknown. In this study, the metabolism of D-Ala by marine bacterium Pseudoalteromonas sp. CF6-2 was investigated. Based on genomic, transcriptional and biochemical analyses combined with gene knockout, D-Ala aminotransferase was found to be indispensable for the catabolism of D-Ala in strain CF6-2. Investigation on other marine bacteria also showed that D-Ala aminotransferase gene is a reliable indicator for their ability to utilize D-Ala. Bioinformatic investigation revealed that D-Ala aminotransferase sequences are prevalent in genomes of marine bacteria and metagenomes, especially in seawater samples, and Gammaproteobacteria represents the predominant group containing D-Ala aminotransferase. Thus, Gammaproteobacteria is likely the dominant group to utilize D-Ala via D-Ala aminotransferase to drive the recycling and mineralization of D-Ala in the ocean. IMPORTANCE As the most abundant D-amino acid in the ocean, D-Ala is a component of marine DON (Dissolved organic nitrogen) pool. However, the underlying mechanism of bacterial metabolization of D-Ala to drive the recycling and mineralization of D-Ala in the ocean is still largely unknown. The results in this study showed that D-Ala aminotransferase is specific and indispensable for D-Ala catabolism in marine bacteria, and that marine bacteria containing D-Ala aminotransferase genes are predominantly Gammaproteobacteria widely distributed in global oceans. This study reveals marine D-Ala utilizing bacteria and the mechanism of their metabolization of D-Ala. The results shed light on the mechanisms of recycling and mineralization of D-Ala driven by bacteria in the ocean, which are helpful in understanding oceanic microbial-mediated nitrogen cycle.