Cairano et al. (2026) Temporal changes in the water quality and ecology of an alluvial aquifer through an agricultural crop cycle

Identification

• Journal: The Science of The Total Environment
• Year: 2026
• Authors: Maria Di Cairano, Grant C. Hose, Kathryn Korbel
• DOI: 10.1016/j.scitotenv.2026.181433

Research Groups

• School of Natural Sciences, Macquarie University, NSW, Australia.
• School of Life and Environmental Sciences, The University of Sydney, NSW, Australia.

Short Summary

This study investigates the spatial and temporal impacts of an annual cotton cropping cycle on a shallow alluvial aquifer's water quality and biodiversity using eDNA metabarcoding. The findings reveal that irrigation water infiltration alters groundwater chemistry and biotic communities, which exhibit an "ecological memory" of agricultural practices.

Objective

• To characterize the spatial and temporal variation in aquifer water quality and the distribution of groundwater biota (prokaryotes and eukaryotes) over an annual irrigated cropping cycle.
• To determine if shifts in groundwater biota are correlated with changes in water quality induced by agricultural practices.

Study Configuration

• Spatial Scale: A 212 m linear transect of eight monitoring wells extending from the Namoi River toward an irrigated cotton farm in northern New South Wales, Australia.
• Temporal Scale: One annual cycle (August 2017 to August 2018), with five sampling events (P1–P5) covering fallow, irrigation/growing, and harvesting periods.

Methodology and Data

• Models and Analysis: Greenfield Hybrid Analysis Pipeline (GHAP) for taxonomic identification; Functional Annotation of Prokaryotic Taxa (FAPROTAX); Non-metric multidimensional scaling (nMDS); PERMANOVA and distance-based linear models (DISTLM).
• Data sources:
  • Field Observations: Groundwater levels (m AHD) and physico-chemical parameters (T, pH, EC, DO) measured via handheld meters.
  • Chemical Analysis: Nutrients ($NH4-N$, $NO2-N$, $NO_3-N$, TP, DOC) analyzed via APHA methods; stable isotopes ($\delta^{18}O$ and $\delta^2H$) measured using a liquid water isotope analyzer.
  • Biological Data: Environmental DNA (eDNA) extracted from 1 L water samples; metabarcoding of 16S rDNA (prokaryotes) and 18S rDNA (eukaryotes) using Illumina MiSeq sequencing.

Main Results

• Hydrology: Groundwater levels declined significantly over the year due to regional drought, though levels were highest during the irrigation period (December 2017).
• Water Chemistry: Electrical conductivity (EC) decreased with distance from the river (range: 448–1590 $\mu S/cm$), while ammonium ($NH_4-N$) concentrations increased closer to the irrigated field (up to 0.21 mg/L).
• Isotopic Evidence: Stable isotope signatures ($\delta^{18}O$ and $\delta^2H$) confirmed the infiltration of evaporated irrigation water into the aquifer, distinguishing it from regional Great Artesian Basin groundwater.
• Biotic Shifts: Prokaryotic communities varied significantly with distance from the river ($p = 0.018$) and sampling period ($p = 0.018$). Taxa such as Chlamydiales and Desulfobacterales increased in relative abundance closer to the field.
• Agricultural Indicators: Cotton (Gossypium hirsutum) DNA and associated pathogens (e.g., Alternaria alternata) were detected in groundwater, particularly during irrigation periods.
• Ecological Memory: Biotic communities showed legacy effects, remaining relatively stable over time despite fluctuating conditions, suggesting a "memory" of long-term agricultural pressure.

Contributions

• Provides a high-resolution temporal and spatial analysis of groundwater ecosystem responses to a specific agricultural crop cycle.
• Demonstrates the efficacy of eDNA metabarcoding in detecting both direct (crop DNA) and indirect (community shifts) impacts of irrigation on aquifers.
• Identifies "ecological memory" in groundwater microbes, highlighting that subsurface ecosystems may not respond immediately to seasonal changes but rather reflect long-term land-use legacies.

Funding

• Australian Research Council Linkage Grant (LP190100927).
• International Macquarie University Research Excellence Scholarship (iMQRES).
• National Collaborative Research Infrastructure Strategy (NCRIS) Groundwater Project.
• Cotton Catchment Communities CRC (Projects 2.02.03 and 2.02.21).

Citation

@article{Cairano2026Temporal,
  author = {Cairano, Maria Di and Hose, Grant C. and Korbel, Kathryn},
  title = {Temporal changes in the water quality and ecology of an alluvial aquifer through an agricultural crop cycle},
  journal = {The Science of The Total Environment},
  year = {2026},
  doi = {10.1016/j.scitotenv.2026.181433},
  url = {https://doi.org/10.1016/j.scitotenv.2026.181433}
}

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