Shotgun metagenomic sequencing reveals the full taxonomic, trophic, and functional diversity of a coral reef benthic cyanobacterial mat from Bonaire, Caribbean Netherlands

Anthropogenic forcing is spurring cyanobacterial proliferation in aquatic ecosystems worldwide. While planktonic

cyanobacterial blooms have received substantial research attention, benthic blooms of mat-forming

cyanobacteria have received considerably less attention, especially benthic mat blooms on coral reefs.

Resultingly, numerous aspects of coral reef benthic cyanobacterial bloom ecology remain unknown, including

underlying biodiversity in the mat communities. Most previous characterizations of coral reef cyanobacterial

mat composition have only considered the cyanobacterial component. Without an unbiased characterization of

full community diversity, we cannot predict whole-community response to anthropogenic inputs or effectively

determine appropriate mitigation strategies. Here, we advocate for the implementation of shotgun sequencing

techniques to study coral reef cyanobacterial mats worldwide, utilizing a case study of a coral reef benthic

cyanobacterial mat sampled from the island of Bonaire, Caribbean Netherlands. Read-based taxonomic profiling

revealed that Cyanobacteria was present at only 47.57% relative abundance in a coral reef cyanobacterial mat,

with non-cyanobacterial members of the sampled mat community, including diatoms (0.78%), fungi (0.25%), Archaea

(0.34%), viruses (0.08%), and other bacteria (45.78%), co-dominating the community.We found numerous

gene families for regulatory systems and for functional pathways (both aerobic and anaerobic). These gene families

were involved in community coordination; photosynthesis; nutrient scavenging; and the cycling of sulfur,

nitrogen, phosphorous, and iron. We also report bacteriophage (including prophage) sequences associated

with this subtidal coral reef cyanobacterial mat, which could contribute to intra-mat nutrient cycling and

bloom dynamics. Overall, our results suggest that Cyanobacteria-focused analysis of coral reef cyanobacterial

mats underestimates mat diversity and fails to capture community members possessing broad metabolic