First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity

Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition. We performed a single-day, island-wide soil microbiota investigation, the first of its kind, to address this challenge by eliminating sources of variability including seasonality, weather conditions, anthropogenic or land use changes over time, and ecological succession of microbial communities. This island collection event (Island Sampling Day, ISD) was conducted in conjunction with the annual meeting of the Genomic Standards Consortium, on the island of Crete, and utilized standard data and metadata collection protocols. We generated amplicon sequences (V3-V4 regions of the 16 S ribosomal RNA gene) and a metadata-enriched dataset from 435 soil samples across 72 sites and four distinct ecozones for future whole-island microbiome studies. Here we report on the study design and sample collection process along with our initial examination of the ecological drivers of soil microbial community variability (e.g., elevation, soil types, soil pH, soil moisture, vegetation type, land use) across the Crete ecozones (defined by elevation and distinct habitats).

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Publication Details

Journal
Environmental Microbiome
Published
2025-07-24
DOI
https://doi.org/10.1186/s40793-025-00752-z
Primary Topic
Microbial Community Ecology and Physiology
Type
article
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article

First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity

Savvas Paragkamian, Lee F. Stanish, Chelsea J. Carey, Ilene Karsch‐Mizrachi et al.
Environmental Microbiome
Microbial Community Ecology and Physiology
article

First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity

Savvas Paragkamian, Lee F. Stanish, Chelsea J. Carey, Ilene Karsch‐Mizrachi, Georgios Kotoulas, Evagelos Pafilis, Christine Laney, Scott Tighe, Stelios Darivianakis, Panagiotis Kasapidis, Johanna B. Holm, Petra ten Hoopen, Stephanie A. Yarwood, Donovan H. Parks, Neil M Davies, Philip Goldstein, Apaala Chatterjee, Ilias Lagkouvardos, Melanthia Stavroulaki, Antoniοs Magoulas, Guy Cochrane, Anastasis Oulas, Dimitris Tsaparis, Lynn M. Schriml, Pier Luigi Buttigieg, Pelin Yilmaz, M. W. Humphreys, Pavlos Pavlidis, Granger Sutton, Jason R. Schriml, Zacharias Kyrpiotakis, H C F Wiebe Kooistra, Bronwen E Schriml, Panos Gkorezis, Josh Gaimaro, Manolis Plaitis
article en

Abstract

Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition. We performed a single-day, island-wide soil microbiota investigation, the first of its kind, to address this challenge by eliminating sources of variability including seasonality, weather conditions, anthropogenic or land use changes over time, and ecological succession of microbial communities. This island collection event (Island Sampling Day, ISD) was conducted in conjunction with the annual meeting of the Genomic Standards Consortium, on the island of Crete, and utilized standard data and metadata collection protocols. We generated amplicon sequences (V3-V4 regions of the 16 S ribosomal RNA gene) and a metadata-enriched dataset from 435 soil samples across 72 sites and four distinct ecozones for future whole-island microbiome studies. Here we report on the study design and sample collection process along with our initial examination of the ecological drivers of soil microbial community variability (e.g., elevation, soil types, soil pH, soil moisture, vegetation type, land use) across the Crete ecozones (defined by elevation and distinct habitats).

Environmental MicrobiomeVol. 20(1)
University of California, Riverside (US), University of Vermont (US), University of Maryland, Baltimore (US), Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung (DE), J. Craig Venter Institute (US), European Bioinformatics Institute (GB), British Antarctic Survey (GB), University of Maryland Center for Environmental Science (US), The University of Queensland (AU), University of Colorado Boulder (US), Stazione Zoologica Anton Dohrn (IT), National Ecological Observatory Network (US), Hellenic Mediterranean University (GR), Max Planck Institute for Marine Microbiology (DE), National Center for Biotechnology Information (US), Cardiovascular Center Frankfurt (DE), Hellenic Centre for Marine Research (GR), Cyprus Institute of Neurology and Genetics (CY), University of Maryland, College Park (US), Hasselt University (BE), Foundation for Research and Technology Hellas (GR), University of California, Berkeley (US)
Life in Land
Openalex Percentile: Top 82%
Microbial Community Ecology and Physiology
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