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We reply to the comments made by Benvenuti et al. (2022) about our paper on the Italian natural history museums and scientific collections and the need of a centralized hub and repository. While agreeing that digitization is a useful tool to valorize each museum and collection, we still believe that the suggestion of a centralized hub is valid and necessary. This would largely help in boosting coordination among museums, sharing personnel and resources, and in providing a place to deposit scientific collections that do not fit the scope of smaller museums.

In Italy, differently from other countries, a national museum of natural history is not present. This absence is due, among other reasons, to its historical political fragmentation up to 1870, which led to the establishment of medium-sized museums, mostly managed by local administrations or universities. Moreover, a change of paradigm in biological research, at the beginning of the 20th century, contributed to privilege experimental studies in universities and facilitated the dismissal of descriptive and exploratory biology, which formed the basis of the taxonomic research carried out by natural history museums. Consequently, only a few museums have a provision of curatorial staff, space and material resources adequate to maintain their original mission of discovering the natural world, by conducting a regular research activity accompanied by field campaigns. The creation of a national research centre for the study of biodiversity, facilitating interconnections among the existing natural history museums could be a solution and is here supported, together with a centralised biorepository to host collections and vouchers, to the benefit of current and future taxonomic research and environmental conservation. Such an institution should find place and realisation within the recently proposed National Biodiversity Future Center (NBFC) planned within the National Plan of Recovery and Resilience (PNRR). Pending upon the creation of this new national centre, a network among the existing museums should coordinate their activities.

Natural sciences usually proceed through the analysis of facts that are then assembled into a general framework, often called a “theory”. I have tried here to assemble the “tiny facts” that I have uncovered in my career and to organize them into a holistic perspective. I have chosen to start from the “big picture”, i.e., the functioning of ecosystems, to focus then on details regarding the expression of biodiversity, from the role of life cycles in ecosystem functioning, to the way of assessing biodiversity based on the accurate knowledge of its evolution in time. The Historical Biodiversity Index allows to compare the potential biodiversity (all the species recorded from the studied habitat type) with the realized biodiversity (the species found by sampling in that habitat). The study of natural history might lead to unexpected ecological connections, such as the dynamics of plankton (the most important ecological phenomenon of the whole planet) and the composition of resting stage banks, or the keystone role of the interstitial fauna in determining the diversity of plankton. The oceanic realm is in three dimensions and must be considered as a volume rather than as an area. Living systems, though, change constantly and a fourth dimension (time) is crucial to understand their structure and function. The cells of ecosystem functioning, based on connectivity, are proposed as natural spatial units for both management and protection from human impacts.

Zooplankton molecular analyses allow for accurate species identification with a proper molecular signature, complementing classic phenotypic-based taxonomy (α taxonomy). For the first time in the Mediterranean Sea, cytochrome oxidase I (COI) gene sequences of calanoid copepods were associated with morphological identification, HD and SEM images, using a fully integrated approach to assess taxonomic diversity. Such method was applied to selected species, generating consensus sequences from the Gulf of Naples (Central Tyrrhenian Sea, Western Mediterranean Sea) also including reference barcodes of three target species (Nannocalanus minor, Pleuromamma gracilis and the non-indigenous species (NIS) Pseudodiaptomus marinus) that are new for the Mediterranean area. The new barcodes were selected including: dominant and rare species; species that were originally described in the study area as type locality, but lacking a molecular description; emergent NIS and potential species complex. The integration between morphological and molecular identification by tree placement, using species-specific highly conserved oligonucleotides, also provided new and high-quality references of the most common and abundant copepod genera and species in the Mediterranean Sea. Our regional reference library was then integrated and analyzed with global data reference available on BOLD database to explore the presence of potential cryptic species and biogeographic patterns and links among geographically distant populations of copepods. Overall, this study provides valuable insight into the actual copepod taxonomic diversity and contributes to building baseline knowledge to monitor coastal biodiversity in neritic areas worldwide, where copepods are of paramount ecological importance, paving the way for future metabarcoding studies.

Biodiversity is a broad concept that encompasses the diversity of nature, from the genetic to the habitat scale, and ensures the proper functioning of ecosystems. The Mediterranean Sea, one of the world’s most biodiverse marine basins, faces major threats, such as overexploitation of resources, pollution and climate change. Here we provide the first multi-taxa inventory of marine organisms and coastal terrestrial flora recorded in southeastern Salento (Ionian Sea, Italy), realized during the project “Biodiversity MARE Tricase”, which provided the first baseline of species living in the area. Sampling was carried out by SCUBA and free diving, fishing gears, and citizen science from 0 to 70 m. Overall, 697 taxa were found between March 2016 and October 2017, 94% of which were identified to the species level. Of these, 19 taxa represented new records for the Ionian Sea (36 additional new records had been reported in previous publications on specific groups, namely Porifera and Mollusca Heterobranchia), and two findings represented the easternmost records in the Mediterranean Sea (Helicosalpa virgula and Lampea pancerina). For eight other taxa, our findings represented the only locality in the Ionian Sea, besides the Straits of Messina. In addition to the species list, phenological events (e.g., blooms, presence of reproductive traits and behaviour) were also reported, with a focus on gelatinous plankton. Our results reveal that even for a relatively well-known area, current biodiversity knowledge may still be limited, and targeted investigations are needed to fill the gaps. Further research is needed to understand the distribution and temporal trends of Mediterranean biodiversity and to provide baseline data to identify ongoing and future changes.