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Gulf of Mexico blue hole harbors high levels of novel microbial lineages


Exploration of oxygen-depleted marine environments has consistently revealed novel microbial taxa and metabolic capabilities that expand our understanding of microbial evolution and ecology. Marine blue holes are shallow karst formations characterized by low oxygen and high organic matter content. They are logistically challenging to sample, and thus our understanding of their biogeochemistry and microbial ecology is limited. We present a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico). Dissolved oxygen became depleted at the hole’s rim (32 m water depth), remained low but detectable in an intermediate hypoxic zone (40–75 m), and then increased to a secondary peak before falling below detection in the bottom layer (80–110 m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species. Microbial communities in the bottom layer contained heretofore undocumented levels of the recently discovered phylum Woesearchaeota (up to 58% of the community), along with lineages in the bacterial Candidate Phyla Radiation (CPR). Thirty-one high-quality metagenome-assembled genomes (MAGs) showed extensive biochemical capabilities for sulfur and nitrogen cycling, as well as for resisting and respiring arsenic. One uncharacterized gene associated with a CPR lineage differentiated hypoxic from anoxic zone communities. Overall, microbial communities and geochemical profiles were stable across two sampling dates in the spring and fall of 2019. The blue hole habitat is a natural marine laboratory that provides opportunities for sampling taxa with under-characterized but potentially important roles in redox-stratified microbial processes.

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Fig. 1: A conceptual diagram of the Amberjack blue hole showing the approximate water column layers as determined by physical and chemical stratification.
Fig. 2: The blue hole water column in September 2019 was highly stratified, with physical and chemical differences starting at the rim (at 32 m, indicated by a dashed line).
Fig. 3: Microbial communities represented three water column depth groupings: shallow (0–32 m), middle (40–70 m), and deep (80–95 m).
Fig. 4: Depth profiles of microbial taxa relative abundances in the Amberjack water column.
Fig. 5: Phylogenomic analysis of the Woesearchaeotal MAG and ninety publicly available MAGs from a range of biomes show the AJ population is most closely related to Woesearchaeota from other marine water columns, including a low oxygen water mass in the Arabian Sea.
Fig. 6: A comparison of gene content in each of the twelve MAGs recovered from the deep metagenomes shows three MAGs (BH21, BH22, and BH28) have a higher fraction of genes belonging to “Genetic Information Processing” than “Metabolism,” which is the opposite pattern of all other MAGs.
Fig. 7: Heat map of gene relative abundances in each of the four metagenomes.

Code availability

Python scripts used for calculating gene relative abundances, comparing these abundances across metagenomes, and calculating and comparing gene content in MAGs are available in the corresponding author’s GitHub repository:


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We thank the captains of the R/V William R. Mote and R/V Eugenie Clark for their support and professionalism, and staff at Mote Marine Lab for their work in sample collection and processing. We are also indebted to all of the volunteer technical divers who made this mission possible. We are grateful to Dr. Navid Constantinou for his help modeling the wind speeds required for the turnover of the water column. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.


This work was funded by the National Oceanic and Atmospheric Administration Office of Exploration and Research [7NA18OAR0110291].

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Patin, N.V., Dietrich, Z.A., Stancil, A. et al. Gulf of Mexico blue hole harbors high levels of novel microbial lineages. ISME J (2021).

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