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

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

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

Holm, Johanna B.; Paragkamian, Savvas; Humphreys, Mike; Chatterjee, Apaala; Yarwood, Stephanie; Gaimaro, Josh; Stavroulaki, Melanthia; Tsaparis, Dimitris; Plaitis, Manolis; Kasapidis, Panagiotis; Darivianakis, Stelios; Kotoulas, Georgios; Magoulas, Antonios; Oulas, Anastasis; Kyrpiotakis, Zacharias; Pavlidis, Pavlos; ten Hoopen, Petra ORCID: https://orcid.org/0000-0003-4242-4015; Cochrane, Guy; Kooistra, H. C. F. Wiebe; Schriml, Jason R.; Schriml, Bronwen E.; Lagkouvardos, Ilias; Gkorezis, Panos; Davies, Neil; Laney, Christine; Stanish, Lee; Sutton, Granger; Tighe, Scott; Mizrachi, Ilene Karsch; Parks, Donovan; Yilmaz, Pelin; Carey, Chelsea; Buttigieg, Pier; Goldstein, Philip; Pafilis, Evangelos; Schriml, Lynn M.. 2025 First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity. Environmental Microbiome, 20, 95. 11, pp. 10.1186/s40793-025-00752-z

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Official URL: https://doi.org/10.1186/s40793-025-00752-z

Abstract/Summary

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).

Item Type:

Publication - Article

Digital Object Identifier (DOI):

10.1186/s40793-025-00752-z

ISSN:

2524-6372

Additional Keywords:

Soil metagenome, Island, Crete, Metadata standards Citizen science

NORA Subject Terms:

Agriculture and Soil Science
Biology and Microbiology

Date made live:

01 Aug 2025 10:49 +0 (UTC)