Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia

Abstract

Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.

Two Novel, Flavin-Dependent Halogenases from the Bacterial Consortia of Botryococcus braunii Catalyze Mono- and Dibromination

“…The newly identified hits from the B. braunii bacterial consortia cluster close to Trp halogenases, but build their own clade together with BrvH. BrvH was found to be very similar to hits 24 and 21 (pairwise identity of 95% and 64%, respectively), which represent flavin-dependent halogenases encoded in the metagenome-assembled genomes (MAG 10 and MAG 21, respectively [59]) of Brevundimonas and Sphingomonas. Thus, these enzymes might represent their own group within the flavin-dependent halogenases with likely similar substrate preferences.…”

“…We screened metagenomic data sets of Botryococcus braunii consortia [59] for novel, flavin-dependent halogenases by applying our pHMM strategy [33], which is based on the PFAM database (http://pfam.xfam.org/, accessed on 8 April 2021) tryptophan-halogenase model (Trp_halogenase, PF04820), to increase the scope of possible halogenases. The metagenomes of four Botryococcus braunii consortia were analysed; they contained at least 33 distinct bacterial species, as indicated by 16 S rDNA amplicon and metagenome sequencing analyses [59]. For the analysis of the metagenomes, according to Neubauer et al, the pHMM was employed, which was based on Trp halogenases and was optimised in a two-step approach [33].…”

“…Thus, these enzymes might represent their own group within the flavin-dependent halogenases with likely similar substrate preferences. According to antiSMASH analyses (antibiotics & Secondary Metabolite Analysis Shell [63]), both MAGs encode several metabolic gene clusters for bacteriocins and antibiotic compounds [59,64]. In addition, the MAG similar to Sphingomonas contains a gene cluster potentially responsible for siderophore synthesis.…”

“…Metagenomic datasets of Botryococcus braunii consortia, deposited under the Bio-ProjectID PRJEB26344 [59], were used for the search of novel flavin-dependent halogenases. The analyses were performed according to the previously described pHMM strategy [33], which is based on the PFAM (http://pfam.xfam.org, 2016) tryptophan-halogenase model (Trp_halogenase, PF04820).…”

“…The analyses were performed according to the previously described pHMM strategy [33], which is based on the PFAM (http://pfam.xfam.org, 2016) tryptophan-halogenase model (Trp_halogenase, PF04820). The dataset of the MAG21 (similar to the genus Sphingomonas) can be found under the deposited BioProject ID PRJEB26345 [59], and was used for the antiSMASH (https://antismash.secondarymetabolites.org, 2020) analysis (using default settings) [63]. Amino acid sequence alignments were performed using NCBI ( www.ncbi.nlm.nih.gov, accessed on 8 April 2021, Bethesda, MD, USA, 2020) NR [81] and MultAlin [82].…”