Villela, H. | Search bioRxiv

bioRxiv2025

Modular metagenomic analysis of pan-domain symbioses with MAGUS

Metagenomic analysis of deeply sequenced, eukaryotic-dominant symbiotic communities can be difficult for many metagenomic workflows. Here, we present MAGUS, a bioinformatic toolkit that uses a suite of custom bioinformatic methods for iterative genome assembly and filtering of pan-domain communities, where eukaryotes, bacteria, viruses, and functionally annotated gene catalogs are resolved and analyzed over a series of interconnected, modular software components. We evaluated MAGUS using deeply sequenced (median depth: 579 million reads) ten samples of hard corals, soft corals, and hydrozoans, which comprise complex, eukaryote-dominated symbiotic communities. We successfully resolved phylogenetically comparable host (N = 10), algal (N = 6), bacterial (N = 55), and viral (N = 160,925) genomes, as well as a gene catalog comprising 15,369,684 non-redundant genes (7.6% functionally annotated). MAGUS is available on GitHub (https://github.com/two-frontiers-project/2FP_MAGUS/).

bioinformatics↗

bioRxiv2018

Biophysical and physiological causes of coral reef microbialization

Coral reefs are declining globally as their primary producer communities shift from stony coral to fleshy macroalgae dominance. Previously, we have shown that the rise of fleshy macroalgae produces dissolved organic carbon (DOC) that lead to microbialization and coral death. Here we test the hypothesis that the biophysical cause of bacterial biomass accumulation is a relative decrease in electron acceptors relative to electron donors due to O2 loss from macroalgae. We show that 37 % of photosynthetic O2 produced by reef fleshy macroalgae is lost in the form of gas through ebullition from algae surfaces. O2 loss increases DOC:O2 ratios, decoupling the photosynthetically fixed carbon from oxidative potential for respiration. This biogeochemical environment drives heterotrophic microbes to increase cell-specific DOC consumption and cell sizes, accumulating biomass. In contrast, corals do not lose oxygen and support the growth of smaller and fewer bacteria. In situ biomass and metagenomic analyses of 87 reefs across the Pacific and Caribbean show that on algae-dominated reefs bacteria accumulate organic carbon through a Warburg-like increase in aerobic glycolytic metabolism. Because of its biophysical basis, microbialization is predicted to occur in other marine ecosystems shifting primary producer assemblages, such as planktonic communities in warming and acidifying conditions.

ecology↗