Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1

A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse

Algae-dominated ecosystems are fundamentally influenced by their microbiome. We lack information on the identity and function of bacteria that specialize in consuming algal-derived dissolved organic matter in high algal density ecosystems such as outdoor algal ponds used for biofuel production. Here, we describe the metagenomic and metaproteomic signatures of a single bacterial strain that bloomed during a population-wide crash of the diatom, Phaeodactylum tricornutum, grown in outdoor ponds. 16S rRNA gene data indicated that a single Kordia sp. strain (family Flavobacteriaceae) contributed up to 93% of the bacterial community during P. tricornutum demise. Kordia sp. expressed proteins linked to microbial antagonism and biopolymer breakdown, which likely contributed to its dominance over other microbial taxa during diatom demise. Analysis of accompanying downstream microbiota (primarily of the Rhodobacteraceae family) provided evidence that cross-feeding may be a pathway supporting microbial diversity during diatom demise. In situ and laboratory data with a different strain suggested that Kordia was a primary degrader of biopolymers during algal demise, and co-occurring Rhodobacteraceae exploited degradation molecules for carbon. An analysis of 30 Rhodobacteraceae metagenome assembled genomes suggested that algal pond Rhodobacteraceae commonly harbored pathways to use diverse carbon and energy sources, including carbon monoxide, which may have contributed to the prevalence of this taxonomic group within the ponds. These observations further constrain the roles of functionally distinct heterotrophic bacteria in algal microbiomes, demonstrating how a single dominant bacterium, specialized in processing senescing or dead algal biomass, shapes the microbial community of outdoor algal biofuel ponds.IMPORTANCEAquatic biogeochemical cycles are dictated by the activity of diverse microbes inhabiting the algal microbiome. Outdoor biofuel ponds provide a setting analogous to aquatic algal blooms, where monocultures of fast-growing algae reach high cellular densities. Information on the microbial ecology of this setting is lacking, and so we employed metagenomics and metaproteomics to understand the metabolic roles of bacteria present within four replicated outdoor ponds inoculated with the diatom Phaeodactylum tricornutum. Unexpectedly, after 29 days of cultivation, all four ponds crashed concurrently with a "bloom" of a single taxon assigned to the Kordia bacterial genus. We assessed how this dominant taxon influenced the chemical and microbial fate of the ponds following the crash, with the hypothesis that it was primarily responsible for processing senescent/dead algal biomass and providing the surrounding microbiota with carbon. Overall, these findings provide insight into the roles of microbes specialized in processing algal organic matter and enhance our understanding of biofuel pond microbial ecology.

Friends and foes: symbiotic and algicidal bacterial influence on Karenia brevis blooms

Harmful Algal Blooms (HABs) of the toxigenic dinoflagellate Karenia brevis (KB) are pivotal in structuring the ecosystem of the Gulf of Mexico (GoM), decimating coastal ecology, local economies, and human health. Bacterial communities associated with toxigenic phytoplankton species play an important role in influencing toxin production in the laboratory, supplying essential factors to phytoplankton and even killing blooming species. However, our knowledge of the prevalence of these mechanisms during HAB events is limited, especially for KB blooms. Here, we introduced native microbial communities from the GoM, collected during two phases of a Karenia bloom, into KB laboratory cultures. Using bacterial isolation, physiological experiments, and shotgun metagenomic sequencing, we identified both putative enhancers and mitigators of KB blooms. Metagenome-assembled genomes from the Roseobacter clade showed strong correlations with KB populations during HABs, akin to symbionts. A bacterial isolate from this group of metagenome-assembled genomes, Mameliella alba, alleviated vitamin limitations of KB by providing it with vitamins B1, B7 and B12. Conversely, bacterial isolates belonging to Bacteroidetes and Gammaproteobacteria, Croceibacter atlanticus, and Pseudoalteromonas spongiae, respectively, exhibited strong algicidal properties against KB. We identified a serine protease homolog in P. spongiae that putatively drives the algicidal activity in this isolate. While the algicidal mechanism in C. atlanticus is unknown, we demonstrated the efficiency of C. atlanticus to mitigate KB growth in blooms from the GoM. Our results highlight the importance of specific bacteria in influencing the dynamics of HABs and suggest strategies for future HAB management.

Comparative analysis of biofilm bacterial communities developed on different artificial reef materials

AIMS

Artificial reefs play a vital role in restoring and creating new habitats for marine species by providing suitable substrates, especially in areas where natural substrates have been degraded or lost due to declining water quality, destructive fishing practices, and coral diseases. Artificial reef restoration aimed at coral larval settlement is gaining prominence and initially depends on the development of biofilms on reef surfaces. In this study, we hypothesized that different artificial reef materials selectively influence the composition of biofilm bacterial communities, which in turn affected coral larval settlement and the overall success of coral rehabilitation efforts. To test this hypothesis, we evaluated the impact of six different reef-made materials (porcelain, granite, coral skeleton, calcium carbonate, shell cement, and cement) on the development of biofilm bacterial communities and their potential to support coral larval settlement.

METHODS AND RESULTS

The biofilm bacterial communities were developed on different artificial reef materials and studied using 16S rRNA gene amplicon sequencing and analysis. The bacterial species richness and evenness were significantly (P < 0.05) low in the seawater, while these values were high in the reef materials. At the phylum level, the biofilm bacterial composition of all materials and seawater was majorly composed of Pseudomonadota, Cyanobacteria, and Bacteroidetes; however, significantly (P < 0.05) low Bacteroidetes were found in the seawater. At the genus level, Thalassomonas, Glaciecola, Halomicronema, Lewinella, Hyphomonas, Thalassospira, Polaribacter, and Tenacibaculum were significantly (P < 0.05) low in the coral skeleton and seawater, compared to the other reef materials. The genera Pseudoaltermonas and Thalassomonas (considered potential inducers of coral larval settlement) were highly abundant in the shell-cement biofilm, while low values were found in the biofilm of the other materials.

CONCLUSION

The biofilm bacterial community composition can be selective for different substrate materials, such as shell cement exhibited higher abundances of bacteria known to facilitate coral larval settlement, highlighting their potential in enhancing restoration outcomes.

Purification and Properties of a Plasmin-like Marine Protease from Clamworm (Perinereis aibuhitensis)

Marine organisms are a rich source of enzymes that exhibit excellent biological activity and a wide range of applications. However, there has been limited research on the proteases found in marine mudflat organisms. Based on this background, the marine fibrinolytic enzyme FELP, which was isolated and purified from clamworm (Perinereis aibuhitensis), has exhibited excellent fibrinolytic activity. We demonstrated the FELP with a purification of 10.61-fold by precipitation with ammonium sulfate, ion-exchange chromatography, and gel-filtration chromatography. SDS-PAGE, fibrin plate method, and LC-MS/MS indicated that the molecular weight of FELP is 28.9 kDa and identified FELP as a fibrinolytic enzyme-like protease. FELP displayed the maximum fibrinolytic activity at pH 9 (407 ± 16 mm2) and 50 °C (724 ± 27 mm2) and had excellent stability at pH 7-11 (50%) or 30-60 °C (60%), respectively. The three-dimensional structure of some amino acid residues of FELP was predicted with the SWISS-MODEL. The fibrinolytic and fibrinogenolytic assays showed that the enzyme possessed direct fibrinolytic activity and indirect fibrinolysis via the activation of plasminogen; it could preferentially degrade Aα-chains of fibrinogen, followed by Bβ- and γ-chains. Overall, the fibrinolytic enzyme was successfully purified from Perinereis aibuhitensis, a marine Annelida (phylum), with favorable stability that has strong fibrinolysis activity in vitro. Therefore, FELP appears to be a potent fibrinolytic enzyme with an application that deserves further investigation.