Microbial biogeography of the eastern Yucatán carbonate aquifer
Bibliographic record
Abstract
ABSTRACT Constraining the spatial distribution of microorganisms and their ecological interactions is crucial for informing biogeochemistry. To that end, we explore horizontal and vertical patterns of microbial biogeography in the eastern Yucatán carbonate aquifer by examining the relative abundance of microbial taxavia16S rRNA gene sequencing. As one of the largest anchialine groundwater systems on Earth, the density-stratified Yucatán aquifer consists of a meteoric lens overlying saline groundwater. The myriad sinkholes (cenotes) of the eastern peninsula lead into a vast network of subsurface conduits. Several studies describe microbial communities within specific regions of the aquifer, yet fundamental questions remain regarding the ecology and distribution of biogeochemically relevant microbes. Our analysis demonstrates that this aquifer hosts a distinct microbiome from nearby seawater, with regionalism observed across cave systems and vertical water column zones. We apply novel software to construct taxonomic co-occurrence networks at different scales and categorize highly connected groups of taxa into potential niches. Our network analysis approach suggests that ubiquitous, metabolically flexible taxa such as the familyComamonadaceaeact as ecological linchpins across several niches, often directly or indirectly co-occurring with taxa capable of anammox (e.g.,Gemmataceae), methanotrophy (e.g.,Methyloparacoccus), or organoheterotrophy. Furthermore, communities from a deep, pit-like cenote open to the surface show the strongest niche partitioning between water column zones, differing from those encountered throughout the mostly dark and oligotrophic aquifer system, including another deep pit cenote with no direct surface opening. Our results suggest that members of a core microbiome could modulate different biogeochemical regimes depending on location, acting as reservoirs of metabolic potential in disparate environments of this groundwater system. IMPORTANCE The extensive Yucatán carbonate aquifer, located primarily in southeastern Mexico, is pockmarked by numerous sinkholes (cenotes) that lead to a complex web of underwater caves. The aquifer hosts a diverse yet understudied microbiome throughout its highly stratified water column, which is marked by a meteoric lens floating on intruding seawater owing to the coastal proximity and high permeability of the Yucatán carbonate platform. Here, we present a biogeographic survey of bacterial and archaeal communities from the eastern Yucatán aquifer. We apply a novel network analysis software that models ecological niche space from microbial taxonomic abundance data. Our analysis reveals that the aquifer community is composed of several distinct niches that follow broader regional and hydrological patterns. This work lays the groundwork for future investigations to characterize the biogeochemical potential of the entire aquifer with other systems biology approaches.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".