Detection of hydrocarbon-degrading bacteria on deepwater corals of the northeast Atlantic using CARD-FISH

A targeted approach to enrich host-associated bacteria for metagenomic sequencing

Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.

Enhanced crude oil degradation by remodeling of crude oil-contaminated soil microbial community structure using sodium alginate/graphene oxide/Bacillus C5 immobilized pellets

Bioaugmentation (BA) of oil-contaminated soil by immobilized microorganisms is considered to be a promising technology. However, available high-efficiency microbial agents remain very limited. Therefore, we prepared a SA/GO/C5 immobilized gel pellets by embedding the highly efficient crude oil degrading bacteria Bacillus C5 in the SA/GO composite material. The optimum preparation conditions of SA/GO/C5 immobilized gel pellets were: SA 3.0%, GO 25.0 μg/mL, embedding amount of C5 6%, water bath temperature of 50°C, CaCl₂ solution concentration 3% and cross-linking time 20 h. BA experiments were carried out on crude oil contaminated soil to explore the removal effect of SA/GO/C5 immobilized pellets. The results showed that the SA/GO/C5 pellets exhibited excellent mechanical strength and specific surface area, which facilitated the attachment and growth of the Bacillus C5. Compared with free bacteria C5, the addition of SA/GO/C5 significantly promoted the removal of crude oil in soil, reaching 64.92% after 30 d, which was 2.1 times the removal rate of C5. The addition of SA/GO/C5 promoted the abundance of soil exogenous Bacillus C5 and indigenous crude oil degrading bacteria Alcanivorax and Marinobacter. In addition, the enrichment of hydrocarbon degradation-related functional abundance was predicted by PICRUSt2 in the SA/GO/C5 treatment group. This study demonstrated that SA/GO/C5 is an effective method for remediating crude oil-contaminated soil, providing a basis and option for immobilized microorganisms bioaugmentation to remediate organic contaminated soil.