Exploring Marine Microbial Diversity: An In-depth Assessment Overview of Representative Sampling Strategies

Zrinka Ljubešić¹Marija Gligora Udovic¹FÜSUN AKGÜL²Ariola Bacu³Ana R. Díaz-Marrero⁴Dragana Drakulović⁵Stefano Fazi⁶Susana P. Gaudêncio⁷Filip Grgurević¹Anamarija Kolda⁸Tihomir Makovec⁹Lucie Novoveska¹⁰Donata Overlinge¹¹Ivo Safarik¹²Joana R Sousa⁷Olivier P Thomas¹³Maggie Reddy¹³Giovanna Cristina Varese¹⁴Marlen Ines Vasquez¹⁵Ana Rotter^9*

• ¹University of Zagreb, Zagreb, Croatia
• ²Mehmet Akif Ersoy University, Burdur, Türkiye
• ³Department of Biotechnology, Faculty of Natural Sciences, University of Tirana, Tirana, Tirana, Albania
• ⁴Institute of Natural Products and Agrobiology, Spanish National Research Council (CSIC), San Cristóbal de La Laguna, Spain
• ⁵Institute of Marine Biology, University of Montenegro, Kotor, Montenegro
• ⁶Water Research Institute, National Research Council - IRSA-CNR, Rome, Italy
• ⁷NOVA University of Lisbon, Lisbon, Lisboa, Portugal
• ⁸Rudjer Boskovic Institute, Zagreb, Croatia
• ⁹Marine Biology Station Piran, National Institute of Biology (Slovenia), Piran, Slovenia
• ¹⁰ScotBio, Livingston, United Kingdom
• ¹¹Marine Research Institute, Klaipeda University, Klaipeda, Klaipeda, Lithuania
• ¹²Department of Nanobiotechnology, Biology Centre, ISB, CAS, Ceske Budejovice, Czechia
• ¹³University of Galway, Galway, County Galway, Ireland
• ¹⁴University of Turin, Turin, Piedmont, Italy
• ¹⁵Cyprus University of Technology, Limassol, Limassol, Cyprus

Abstract 1. The assessment of marine microbial biodiversity is crucial for determining either the environmental status (ecological or biodiversity research) or as a first step in the biodiscovery process (biotechnological research). Regardless of the research purpose, the first step in a biodiversity assessment is the sampling, which can range from ad hoc sampling expeditions to long-term monitoring campaigns. In spite of its demands for funds, infrastructure, expertise, equipment, and personnel, sampling is often not adequately planned. This results in increased likelihood for biased sampling, which can lead to misinterpretation of results, omission of valuable specimens and an unrepresented collection of stored samples, all particularly important for the assessment of microbial biodiversity. For these reasons, we are proposing a conceptual framework to assist in better preparation of sampling, consisting of pre-sampling, sampling and post sampling steps. The manuscript guides the reader through all the necessary steps, regardless of the sampling habitat (from water column to sediment), the sampling techniques and the preservation and storage approaches including inoculation, culture and biorepositories. Such a harmonized approach can be of benefit for (i) researchers in the field of ecology/biotechnology, (ii) industrial companies requiring information on the providers and availability of data, and (iii) governance structures and funders, in the light of open science principles.