Agarolytic culturable bacteria associated with three antarctic subtidal macroalgae

Optimizing agarase production from Microbulbifer sp. using response surface methodology and machine learning models

Agarase enzymes are critical in industries like food, cosmetics, and medicine where they play a critical role in DNA recovery, food gelling, cosmetic formulations, and waste treatment. However, current agarase sources often face limitations related to low yields, inconsistent activity, and high production costs. Therefore, there is a need to identify and optimize more efficient microbial sources for industrial-scale agarose production. This study is an exhaustive investigation into the optimized production of extracellular agarase from a microbial source. Through qualitative-quantitative analysis, the study optimizes the growth conditions of Microbulbifer sp. for enhanced agarase production. Response surface methodology is used to investigate the interactive effects of key parameters to get the optimized conditions as 0.3% agar, pH 7, 25°C temperature, and 36-hour incubation time, confirmed by a verification experiment yielding 317.97 μmol min-1 agarase activity (F-value of 44.75 and an R-squared of 0.9827). The study also explores various machine learning algorithms where radial basis function neural network performed best with R-squared values of 0.989 and low mean squared error of 0.44, indicating the reliability and robustness of predicting agarase activity with high accuracy and generalization. The optimized production conditions and machine learning predictions offer significant improvements in the scalability and efficiency of agarase production with incubation time and temperature having the most dominating effect on agarase production. These findings would help in scaling up production and real-time adjustments during bioreactor operations in an industrial setup.

Polysaccharide degradation in an Antarctic bacterium: Discovery of glycoside hydrolases from remote regions of the sequence space

Glycoside hydrolases (GHs) are enzymes involved in the degradation of oligosaccharides and polysaccharides. The sequence space of GHs is rapidly expanding due to the increasing number of available sequences. This expansion paves the way for the discovery of novel enzymes with peculiar structural and functional properties. This work is focused on two GHs, Ps_GH5 and Ps_GH50, from the genome of the Antarctic bacterium Pseudomonas sp. ef1. These enzymes are in an unexplored region of the sequence space of their respective GH families, not allowing a reliable sequence-based function prediction. For this reason, a computational pipeline was developed that combines deep learning "dynamic docking" on AlphaFold 3D models with physics-based molecular dynamics simulations to infer their substrate specificity. From in silico screening of a repertoire of potential oligosaccharides, only xylooligosaccharides for Ps_GH5 and galactooligosaccharides for Ps_GH50 emerged as catalytically competent substrates. Biochemical characterization agrees with computational simulations indicating that Ps_GH5 is an endo-β-xylanase, and Ps_GH50 is active mainly on small galactooligosaccharides. In conclusion, this study identifies two novel GHs subfamilies placed in remote regions of the sequence space and highlights the efficacy of substrate specificity prediction by computational approaches in the discovery of new enzymes.

Exploring Diversity and Polymer Degrading Potential of Epiphytic Bacteria Isolated from Marine Macroalgae

The macroalgae surface allows specific bacterial communities to colonize, resulting in complex biological interactions. In recent years, several researchers have studied the diversity and function of the epiphytic bacteria associated with algal host, but largely these interactions remain underexplored. In the present study we analysed the cultivable diversity and polymer degradation potential of epiphytic bacteria associated with five different marine macroalgae (Sargassum, Ulva, Padina, Dictyota and Pterocladia sp.) sampled from the central west coast of India. Out of the total 360 strains isolated, purified and preserved, about 238 strains were identified through 16S rRNA gene sequence analysis and processed for polymer (cellulose, pectin, xylan and starch) degrading activities. Phylogeny placed the strains within the classes Actinobacteria, Bacilli, Alpha-proteobacteria, and Gamma-proteobacteria and clustered them into 45 genera, wherein Vibrio, Bacillus, Pseudoalteromonas, Alteromonas, Staphylococcus and Kocuria spp. were the most abundant with 20 strains identified as potentially novel taxa within the genera Bacillus, Cellulosimicrobium, Gordonia, Marinomonas, Vibrio, Luteimonas and Pseudoalteromonas. In terms of polymer hydrolysis potential, 61.3% had xylanase activity, while 59.7%, 58.8%, and 52.2% had amylase, cellulase, and pectinase activity, respectively. Overall, 75.6% of the strains degraded more than one polysaccharide, 24% degraded all polymers, while nine strains (3.8%) degraded raw sugarcane bagasse. This study showed great potential for seaweed-associated bacteria in the bio-remediation of agro-waste based raw materials, which can be employed in the form of green technology.

What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria

Macroalgal surface constitutes a peculiar ecological niche and an advantageous substratum for microorganisms able to degrade the wide diversity of algal glycans. The degrading enzymatic activities of macroalgal epiphytes are of paramount interest for the industrial by-product sector and biomass resource applications. We characterized the polysaccharide hydrolytic profile of bacterial isolates obtained from three macroalgal species: the red macroalgae Asparagopsis taxiformis and Sphaerococcus coronopifolius (Rhodophyceae) and the brown Halopteris scoparia (Phaeophyceae), sampled in South Portugal. Bacterial enrichment cultures supplemented with chlorinated aliphatic compounds, typically released by marine algae, were established using as inoculum the decaying biomass of the three macroalgae, obtaining a collection of 634 bacterial strains. Although collected from the same site and exposed to the same seawater seeding microbiota, macroalgal cultivable bacterial communities in terms of functional and phylogenetic diversity showed host specificity. Isolates were tested for the hydrolysis of starch, pectin, alginate and agar, exhibiting a different hydrolytic potential according to their host: A. taxiformis showed the highest percentage of active isolates (91%), followed by S. coronopifolius (54%) and H. scoparia (46%). Only 30% of the isolates were able to degrade starch, while the other polymers were degraded by 55-58% of the isolates. Interestingly, several isolates showed promiscuous capacities to hydrolyze more than one polysaccharide. The isolate functional fingerprint was statistically correlated to bacterial phylogeny, host species and enrichment medium. In conclusion, this work depicts macroalgae as holobionts with an associated microbiota of interest for blue biotechnologies, suggesting isolation strategies and bacterial targets for polysaccharidases' discovery.

Diversity of epiphytic bacterial communities on male and female Porphyra haitanensis

Purpose

To study the structure of the epiphytic bacterial community of the male and female Porphyra haitanensis, in order to explore the similarities and differences of epiphytic bacterial community structure between dioecious macroalgae.

Methods

Collection of male and female Porphyra haitanensis from the intertidal zone of Niushan Island, Fujian, China. Epiphytic bacteria were collected and studied, and the community composition and diversity of epiphytic bacteria were explored using high-throughput sequencing technology.

Results

There was no significant difference between male and female Porphyra haitanensis on α-diversity and β-diversity. Proteobacteria and Bacteroidetes were the core microbiota in male and female Porphyra haitanensis. Bacteria from the Maribacter (male 14.87%, female 1.66%) and the Tenacibaculum (male 1.44%, female 25.78%) were the most indicative epiphytic bacterial taxa on male and female Porphyra haitanensis.

Conclusions

Sex differences have some influence on the construction of epiphytic bacterial communities in Porphyra haitanensis, but they are not the decisive factors affecting the construction of epiphytic bacterial communities in Porphyra haitanensis.

Isolation and Characterisation of the Agarolytic Bacterium Pseudoalteromonas Ruthenica

Agar is a polysaccharide that primarily constitutes the cell wall of red algae. It is a good source of carbon and energy for many microbes. In the present study, an agarolytic bacterium, UQAD-3, was obtained from the waters of Al-Uqair, the Arabian Gulf, Al-Ahsaa, Saudi Arabia. UQAD-3 exhibited agarolytic activity when grown on agar as the sole source of carbon and energy. The strain was identified as Pseudoalteromonas ruthenica based on comparative analysis of the 16S rRNA, with 99.6% similarity. This finding was further confirmed by phylogenetic analyses based on 16S rRNA gene sequences, which highlighted that UQAD-3 was assembled within the Pseudoalteromonas clade and constituted a monophyletic subcluster with P. ruthenica, KMM 300T. The strain was further characterised biochemically using the Biolog Gen III microtest system. UQAD-3 showed positive reactions to 16 (17%) of the 94 diverse traits assessed. Good growth was reported in 10% NaCl indicating its moderate halophilic nature. These observations indicate the agarolytic potential of the strain and opens new horizons for industrial applications in the future.