Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism

Abstract

Background: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

Results: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

Conclusion: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.

Keywords: Asparagopsis taxiformis; Halopteris scoparia; Sphaerococcus coronopifolius; Dehalogenation; Halogenation; Holobiont; Macroalgae; Metagenome-assembled genomes (MAGs); Microbiome; Organohalogens.

Fig. 1

Chord diagram showing the observed prokaryotic phyla based on the taxonomic classification of the SSU rRNA sequences identified in the metagenomic contigs. It illustrates their distribution among the macroalgae-associated microbiomes. Inside the circle: in green the phyla assigned to Sphaerococcus coronopifolius, in blue and in orange those assigned to Halopteris scoparia and Asparagopsis taxiformis, respectively

Fig. 2

Gene density values of target genes annotated within the Sphaerococcus coronopifolius (Sc, blue bar), Asparagopsis taxiformis (At, red bar), and Halopteris scoparia (Hs, gray bar) sequenced metagenomes. The list indicates the recommended name of the 81 encoded BRENDA enzymes and their associated complete EC number (X.X.X.X). The list shows the enzymes considering enantiomers (R/S), substituent numerical position, and alphabetical order. Annotated BRENDA-EC42 subgroup functions: ^^ dehalogenases, * halogenases, and gene density values (genes/Mbp)

Fig. 3

Gene density values for potential degradative and biosynthetic clusters involved in halogen metabolism depicted for the Sphaerococcus coronopifolius (Sc, blue bar), Asparagopsis taxiformis (At, red bar), and Halopteris scoparia (Hs, gray bar) metagenomes. A Degradative gene clusters (numbered from 1 to 23) along with the chemical types of halogenated molecules degraded. B Biosynthetic gene clusters (numbered from 1 to 9) and chemical types of halogenated metabolites produced. The cluster gene density values are shown as genes/Mbp. The clusters are arranged in descending order of their density values

Fig. 4

Phylogenetic tree showing the relationships between the 98 MAGs and the distribution of BRENDA-EC161 functions density annotated for each MAG, particularly dehalogenases and halogenases (BRENDA-EC42) and hydrolytic and non-hydrolytic dehalogenases gene densities. The 2 phyla including clades enriched in BRENDA-EC161 functions are shown in pink (Actinobacteriota) and light orange (Proteobacteria). MAGs assigned orders are also indicated. (detailed gene density values are in Additional file 1: Table S8). Ref* indicates an unsupervised reference genome of the public KBase genomes database used in phylogenetic tree building. Sc, Sphaerococcus coronopifolius; At, Asparagopsis taxiformis; Hs, Halopteris scoparia

Fig. 5

Phylogenetic tree showing for each MAG the lowest taxon assigned by GTDB-Tk and the clustered target genes according to the potential type of degraded or synthesized halogenated molecule. From inner to outside: MAGs numbered and macroalga host, colored taxonomic orders, lowest taxon assigned by GTDB-Tk (empty box indicates a novel family), MAG quality (the arrow indicates high-quality MAG), and the bar chart representing cluster density (with synthesized compounds in the inner circle and degraded compounds in the outer circle) for each MAG, aligned accordingly. The names of the compounds are listed in descending order of the detected cluster density values across all MAGs. Ref* indicates an unsupervised reference genome of the public KBase genomes database used in phylogenetic tree building. Sc, Sphaerococcus coronopifolius; At, Asparagopsis taxiformis; Hs, Halopteris scoparia