Biodiversity Data Journal : Data Paper (Biosciences)
Data Paper (Biosciences)
AxIOM: Amphipod crustaceans from insular Posidonia oceanica seagrass meadows
expand article infoLoïc N. Michel, Nicolas Sturaro, André Heughebaert§, Gilles Lepoint
‡ Laboratory of Oceanology, FOCUS research unit, University of Liege, Liege, Belgium
§ Belgian Biodiversity Platform, Bruxelles, Belgium
Open Access



The Neptune grass, Posidonia oceanica (L.) Delile, 1813, is the most widespread seagrass of the Mediterranean Sea. This foundation species forms large meadows that, through habitat and trophic services, act as biodiversity hotspots. In Neptune grass meadows, amphipod crustaceans are one of the dominant groups of vagile invertebrates, forming an abundant and diverse taxocenosis. They are key ecological components of the complex, pivotal, yet critically endangered Neptune grass ecosystems. Nevertheless, comprehensive qualitative and quantitative data about amphipod fauna found in Mediterranean Neptune grass meadows remain scarce, especially in insular locations.

New information

Here, we provide in-depth metadata about AxIOM, a sample-based dataset published on the GBIF portal. AxIOM is based on an extensive and spatially hierarchized sampling design with multiple years, seasons, day periods, and methods. Samples were taken along the coasts of Calvi Bay (Corsica, France) and of the Tavolara-Punta Coda Cavallo Marine Protected Area (Sardinia, Italy). In total, AxIOM contains 187 samples documenting occurrence (1775 records) and abundance (10720 specimens) of amphipod crustaceans belonging to 72 species spanning 29 families. The dataset is available at


Amphipoda, Crustacea, Posidonia oceanica, Seagrass, Mediterranean, Corsica, Sardinia, Islands, Revellata Bay, Tavolara - Punta Coda Cavallo Marine Protected Area, Hierarchical sampling design


The Neptune grass, Posidonia oceanica (L.) Delile, 1813, is the most widespread seagrass of the Mediterranean Sea. This foundation species forms large meadows that are of crucial ecological and economic importance. Their complex, multi-layered structure offers a suitable habitat to hundreds of animal and plant species, as well as micro-organisms (Buia et al. 2000). In addition, through the epiphytes that grow on all parts of the plants, its dead and decaying tissues and, to a lesser extent, its living tissues, P. oceanica supports elaborate food webs (Vizzini 2009. Thanks to these habitat and trophic services, Neptune grass meadows, which cover up to 50000 km2, are biodiversity hotspots in the Mediterranean Sea. Although these meadows are legally protected and included in numerous marine protected areas (MPAs), they are nevertheless threatened by direct and indirect impacts of multiple anthropogenic activities (Giakoumi et al. 2015).

In P. oceanica meadows, amphipods are one of the dominant groups of vagile invertebrates, forming an abundant and diverse taxocenosis (Gambi et al. 1992). They mostly feed on seagrass epiphytes with species-specific dietary preferences (Michel et al. 2015b). Through their feeding activity, they act as ecosystem engineers, as they exert selective top-down control on epiphytic assemblages and modulate nutrient availability for their seagrass host (Michel et al. 2015a). Overall, amphipod crustaceans can be considered key ecological components of the complex, pivotal, yet critically endangered Neptune grass ecosystems. Despite their ecological importance, quantitative and widely available data about amphipod fauna of Mediterranean Neptune grass meadows remain scarce. This is especially true for amphipod assemblages from meadows situated along the coasts of Mediterranean islands, whose structure has recently been showed to differ from their mainland counterparts (Bellisario et al. 2015). In this context, the aim of the AxIOM dataset is to make data collected in the framework of ecological studies freely available on the Global Biodiversity Information Facility (GBIF) portal.

General description


AxIOM is a sample-based dataset (n = 187 samples) documenting occurrences of amphipod crustaceans associated to Posidonia oceanica seagrass meadows from Mediterranean Islands (Corsica, Sardinia). In total, it contains 1775 records, documenting occurrence and abundance of 10720 amphipod specimens belonging to 72 species spanning 29 families. Samples were collected over different periods 3 consecutive years, both during the day and during the night. A nested hierarchical sampling design was set up, and multiple sampling methods were combined to ensure a holistic view of the taxocenosis. The dataset package is composed of two data files: one describing sampling events, and the other reporting occurrence data of amphipod crustaceans.

Project description


Multidisciplinary study of trophic diversity and functional role of amphipod crustaceans associated to Posidonia oceanica meadows AND Multiscale variability of amphipod assemblages in Posidonia oceanica meadows: A comparison between different protection levels


Loïc N. Michel, Nicolas Sturaro and Gilles Lepoint

Design description: 

The AxIOM dataset was generated during two doctoral research programmes that took place at University of Liège, Belgium. The first one focused on ecology of amphipod crustaceans from Posidonia oceanica meadows, on their place in the food web and on their role in the ecosystem (Michel 2011). The second one focused on the multiscale variability patterns of amphipod assemblages associated to P. oceanica meadows, and their potential responses among different protection levels (Sturaro 2012).


Belgian Fund for Scientific Research (F.R.S.-FNRS) research fellow grant nr. FC74734; Belgian Fund for Research in Industry and Agriculture (FRIA) doctoral grant.

Sampling methods


AxIOM contains 187 sampling events, spanning 3 consecutive years. Sampling took place in two regions: Corsica (Calvi Bay) and Sardinia (Tavolara-Punta Coda Cavallo Marine Protected Area, TMPA). Samples were taken during different periods of the year (November, March, June, July, August) to acknowledge seasonal variation of communities (Gambi et al. 1992). Since amphipod assemblages from Posidonia oceanica meadows also exhibit diel variations (Sánchez-Jerez et al. 1999), samples were taken during both day and night. To ensure efficient and representative sampling of the amphipod taxocenosis, 4 complementary methods were used: hand-towed net, litter collection, air-lift and 2 slightly different types of light traps. In both investigated regions, a nested hierarchical sampling design was setup to fully capture the spatial variability of amphipod community structure over multiple scales spanning four orders of magnitude (1 to 1000 metres; Sturaro et al. 2015). Sampling stations encompass various levels of environmental protection and anthropogenic pressure, including integral reserve (TMPA zone A), partial reserve (TMPA zone B), general reserve (TMPA zone C), unprotected pristine zone (Calvi Bay) and heavily impacted zone (Gulf of Olbia).

Sampling description: 

Most samples were taken following a nested hierarchical sampling design that focused on variability at 4 spatial scales, ranging from 1 to 1000 metres. In each sampling region (Corsica and Sardinia), zones separated by > 1000 m were chosen. In each zone, 2 sites (separated by ~ 100 m) were picked. Inside each site, 2 or 4 sectors (separated by ~10 m) were randomly selected within each site. Each sector was delimited by a permanent frame circumscribing an area of 9 m2. Depending on the method used, sampling events either covered a full sector or were taken randomly inside a sector and separated by ~1 m were collected. Details of the sampling design are given in Sturaro et al. (2015), Sturaro et al. (2014) Levels of this design are documented in the "event.txt" file of the dataset using matching hierarchized parent event IDs.

All sampling was performed by SCUBA diving at depths ranging from 10.4 to 15 metres. Detailed methodology for the hand-towed net (labelled "Net" in the "samplingProtocol" column of the "event.txt" file of the dataset), the air-lift ("Airlift") and the first type of light traps ("Trap1") can be found in Michel et al. (2010).

Litter collection ("Litter") consisted in hand-picking of litter fragments. A 25 x 40 cm quadrate was randomly thrown in the meadow, to estimate sampling area, and all litter present among this meadow patch was handpicked by fistfuls, and quickly placed in a container. By doing so, vagile organisms associated to litter fragments were also collected. This procedure was repeated until a standardized container of 2 litres was filled.

The second type of light traps ("Trap2", Fig. 1) were made of two nested 1 litre translucent plastic containers. The top container was pierced with vertical rectangular slits (1 cm wide x 12 cm long), and was then inserted in the bottom one. Traps were anchored using metal stakes (∅: 3 mm) that were directly stuck in the matte. Each trap presented vertical rectangular slits (1 cm wide x 15 cm long) in its upper part. A diving emergency light stick was fixed in the bottom part of each trap. These sticks emit light for >12 hours, and the vagile invertebrates, attracted by the light, entered the trap through the slits. They gathered in the bottom part, the presence of a bottleneck in the middle of the trap limiting their potential escape. Traps were placed at twilight and recovered the next morning.

Figure 1.  

Schematic representation of the second type of light traps used in this study. All measurements are expressed in centimetres. A: bottom container, B: top container, C: diving emergency light stick, D: vertical slits, E: bottleneck, F: bottom, G: Posidonia oceanica leaves, H: metal stake.

Quality control: 

Sampling protocols were standardized to avoid biases. Amphipods were and identified using primarily the keys of the Mediterranean amphipod fauna of Bellan-Santini et al. (1982), Bellan-Santini et al. (1989), Bellan-Santini et al. (1993), Bellan-Santini et al. (1998) and the interactive key of Myers et al. (2001). In some cases, more recent diagnoses and redescriptions of species were also used. This was notably the case for the genera Apherusa (Krapp-Schickel and Sorbe 2006) and Caprella (Guerra-García and Takeuchi 2002, Krapp-Schickel and Takeuchi 2005, Krapp-Schickel and Vader 1998, Krapp et al. 2006). After identification, specimens were randomly selected to be re-examined by either first or last author in order to check identification accuracy. Species names were matched against the authoritative, expert-driven World Register of Marine Species (WoRMS).

Step description: 

After collection, all samples were sieved on 400 µm nylon mesh to eliminate sediment and fine particulate organic matter. They were subsequently fixed for >24 hours in a formaldehyde solution (4% in 0.22 µm-filtered seawater). Samples were then sorted to isolate amphipods and transfer them to a preservation solution consisting of 70% ethanol in distilled water to which 1% glycerine was added to prevent evaporation. After identification, specimens were stored in this preservation solution in airtight vials.

Geographic coverage


AxIOM contains samples taken in Posidonia oceanica seagrass meadows from Mediterranean Islands. Two regions were investigated: Corsica (Calvi Bay) and Sardinia (Tavolara-Punta Coda Cavallo marine protected area).

Calvi Bay lies in the Ligurian Sea (western Mediterranean), on the north-western coast of Corsica (France; 42°35'N, 8°45'E). It is bound by Punta Revellata Cape in the West, and by Punta Spanu Cape in the East. Temperature of water is typically minimal in February (12°C) and maximal in August (26°), with a notable vertical thermal stratification from May to September. Salinity of the water of Calvi Bay is around 38 and shows no major seasonal variation. Calvi Bay is an oligotrophic area and shows low inorganic nutrient and particulate organic matter concentrations (Lepoint et al. 2004).

In Calvi Bay, Posidonia oceanica meadows cover 4.94 km2, i.e. about 50% of the area of the bay. They are found at depths ranging from 3 to 38 m. Meadows mostly grow on soft bottoms and show, in most places, a continuous extension, but local erosion (“intermattes”) occurs (Abadie et al. 2015). Meadows of Calvi Bay are relatively dense, and show an important foliar biomass and production despite the oligotrophic character of the area (Gobert et al. 2003). Overall, the coastal areas surrounding the bay are weakly urbanised and the ecological status of seawater of Calvi Bay is considered as good (Gobert et al. 2009).

The Tavolara-Punta Coda Cavallo Marine Protected Area (TMPA) lies in the Thyrrenian Sea (western Mediterranean), on the north-eastern coast of Sardinia (Italy; 40°56'N, 09°44'E). TMPA covers 153.57 km2 and extends along 76 km of coastline. It is located south of the Gulf of Olbia, a heavily urbanized area undergoing anthropogenic pressures from discrete (wastewater discharge and industrial activities) and diffuse (ships and coastal tourism) sources. It comprises the islands of Tavolara, Molara and Molarotto. It was established in 1997, although enforcement of protection effectively began in 2003-2004. Three zones featuring different protection regimes have been defined.

Zone A (5.29 km2) is an integral reserve and no-take/no-access zones. Access of zone A is restricted to scientists, reserve staff and police authorities. Zone B (31.13 km2) is a partial reserve where access is permitted, but only professional fishermen inhabiting the nearby coastal villages are allowed to fish. Zone C (117.15 km2) is a general reserve where access as well as professional and recreational fishing are allowed under restricted conditions defined by the MPA management consortium.

In TMPA, temperature of water is nearly the same as Calvi Bay, with variation between 14°C and 26°C. Salinity is around 38 and is constant the whole year. P. oceanica meadows cover a total surface of 4415 Ha and are found at depths ranging from 0.5 to 41 m (Tavolara-Punta Coda Cavallo Marine Protected Area management consortium pers. comm.). At sampling depth, shoot density, leaf and epiphyte biomasses do not show differences among protection levels (Sturaro et al. 2014).


40.859253 and 42.579722 Latitude; 8.725000 and 9.777583 Longitude.

Taxonomic coverage


This dataset comprises 72 amphipod species (including 2 subspecies of Caprella acanthifera) belonging to 51 genera and 29 families.

Taxa included:
Rank Scientific Name Common Name
kingdom Animalia Animals
phylum Arthropoda Arthropods
subphylum Crustacea Crustaceans
superclass Multicrustacea
class Malacostraca
subclass Eumalacostraca
superorder Peracarida
order Amphipoda Amphipods
suborder Gammaridea
suborder Senticaudata
infraorder Gammarida
infraorder Hadziida
infraorder Talitrida
superfamily Aoroidea
superfamily Caprelloidea
superfamily Corophioidea
superfamily Gammaroidea
superfamily Hadzioidea
superfamily Liljeborgioidea
superfamily Photoidea
superfamily Talitroidea
family Ampeliscidae
family Amphilochidae
family Ampithoidae
family Aoridae
family Atylidae
family Calliopiidae
family Caprellidae
family Corophiidae
family Cyproideidae
family Dexaminidae
family Gammaridae
family Hyalidae
family Iphimediidae
family Ischyroceridae
family Leucothoidae
family Liljeborgiidae
family Lysianassidae
family Maeridae
family Megaluropidae
family Nuuanuidae
family Oedicerotidae
family Opisidae
family Photidae
family Phoxocephalidae
family Podoceridae
family Pontogeneiidae
family Stenothoidae
family Uristidae
family Urothoidae
genus Ampelisca
genus Amphilochus
genus Ampithoe
genus Aora
genus Apherusa
genus Apocorophium
genus Apolochus
genus Atylus
genus Caprella
genus Cymadusa
genus Deflexilodes
genus Dexamine
genus Ericthonius
genus Eusiroides
genus Gammarella
genus Gammaropsis
genus Gammarus
genus Gitana
genus Guernea
genus Harpinia
genus Hippomedon
genus Hyale
genus Iphimedia
genus Ischyrocerus
genus Jassa
genus Lembos
genus Leptocheirus
genus Leucothoe
genus Liljeborgia
genus Lysianassa
genus Lysianassina
genus Maera
genus Megaluropus
genus Metaphoxus
genus Microdeutopus
genus Microjassa
genus Nannonyx
genus Normanion
genus Nototropis
genus Orchomene
genus Peltocoxa
genus Perioculodes
genus Phtisica
genus Pseudolirius
genus Pseudoprotella
genus Siphonoecetes
genus Stenothoe
genus Synchelidium
genus Tmetonyx
genus Tritaeta
genus Urothoe
species Ampelisca diadema (Costa, 1853)
species Ampelisca rubella A. Costa, 1864
species Amphilochus manudens Bate, 1862
species Ampithoe helleri Karaman, 1975
species Ampithoe ramondi Audouin, 1826
species Aora gracilis (Bate, 1857)
species Aora spinicornis Afonso, 1976
species Apherusa chiereghinii Giordani-Soika, 1949
species Apocorophium acutum (Chevreux, 1908)
species Apolochus neapolitanus (Della Valle, 1893)
species Atylus massiliensis Bellan-Santini, 1975
species Atylus vedlomensis (Bate & Westwood, 1862)
species Caprella acanthifera Leach, 1814
species Caprella equilibra Say, 1818
species Caprella tavolarensis Sturaro & Guerra-García, 2012
species Cymadusa crassicornis (Costa, 1853)
species Deflexilodes griseus (Della Valle, 1893)
species Dexamine spiniventris (Costa, 1853)
species Dexamine spinosa (Montagu, 1813)
species Ericthonius punctatus (Bate, 1857)
species Eusiroides dellavallei Chevreux, 1899
species Gammarella fucicola (Leach, 1814)
species Gammaropsis dentata Chevreux, 1900
species Gammaropsis maculata (Johnston, 1828)
species Gammaropsis palmata (Stebbing & Robertson, 1891)
species Gammarus aequicauda (Martynov, 1931)
species Gammarus crinicornis Stock, 1966
species Gammarus insensibilis Stock, 1966
species Gitana sarsi Boeck, 1871
species Guernea (Guernea) coalita (Norman, 1868)
species Harpinia zavodniki Karaman, 1987
species Hippomedon massiliensis Bellan-Santini, 1965
species Hippomedon oculatus Chevreux & Fage, 1925
species Hyale camptonyx (Heller, 1866)
species Hyale schmidti (Heller, 1866)
species Iphimedia minuta G.O. Sars, 1882, 1883
species Ischyrocerus inexpectatus Ruffo, 1959
species Jassa ocia (Bate, 1862)
species Lembos websteri Bate, 1857
species Leptocheirus guttatus (Grube, 1864)
species Leptocheirus pectinatus (Norman, 1869)
species Leucothoe spinicarpa (Abildgaard, 1789)
species Liljeborgia dellavallei Stebbing, 1906
species Lysianassa costae (Milne Edwards, 1830)
species Lysianassa pilicornis (Heller, 1866)
species Lysianassina longicornis (Lucas, 1846)
species Maera grossimana (Montagu, 1808)
species Megaluropus massiliensis Ledoyer, 1976
species Metaphoxus simplex (Bate, 1857)
species Microdeutopus anomalus (Rathke, 1843)
species Microdeutopus similis Myers, 1977
species Microjassa cumbrensis (Stebbing & Robertson, 1891)
species Nannonyx propinquus Chevreux, 1911
species Normanion chevreuxi Diviacco & Vader, 1988
species Nototropis guttatus Costa, 1853
species Orchomene humilis (Costa, 1853)
species Orchomene similis (Chevreux, 1912)
species Peltocoxa gibbosa (Schiecke, 1977)
species Peltocoxa marioni Catta, 1875
species Perioculodes aequimanus (Korssman, 1880)
species Phtisica marina Slabber, 1769
species Podocerus variegatus Leach, 1814
species Pseudolirius kroyeri (Haller, 1897)
species Pseudoprotella phasma (Montagu, 1804)
species Siphonoecetes (Centraloecetes) dellavallei Stebbing, 1899
species Stenothoe cavimana Chevreux, 1908
species Stenothoe eduardi Krapp-Schickel, 1975
species Stenothoe monoculoides (Montagu, 1815)
species Synchelidium haplocheles (Grube, 1864)
species Synchelidium longidigitatum Ruffo, 1947
species Tmetonyx nardonis (Heller, 1866)
species Tritaeta gibbosa (Bate, 1862)
species Urothoe elegans (Bate, 1857)
subspecies Caprella acanthifera acanthifera Leach, 1814
subspecies Caprella acanthifera discrepans Mayer, 1890

Temporal coverage

Data range: 
2006-11-15 - 2008-8-19.

Collection data

Collection name: 
Collection identifier: 
Specimen preservation method: 
Ethanol 70% in distilled water + 1% glycerin

Usage rights

Use license: 
IP rights notes: 

Creative Commons CC BY

Data resources

Data package title: 
AxIOM: Amphipod crustaceans from insular Posidonia oceanica seagrass meadows
Number of data sets: 
Data set name: 
AxIOM: Amphipod crustaceans from insular Posidonia oceanica seagrass meadows
Data format: 
Darwin Core

The dataset is composed of two files. The first one is named "event.txt". It gathers data about sampling events (n=187). "Event.txt" has 282 rows and 18 columns. The second file is named "occurrence.txt". It contains occurrence records (n=1775) of amphipod specimens. "Occurrence.txt" has 1776 rows and 13 columns. For more information about Darwin Core terms, please refer to AxIOM has the Global Biodiversity Information Facility Universally Unique Identifier (GBIF UUID) b146a93c-657b-4768-aa51-9cabe3dac808.

Column label Column description
event.txt:eventID Identification code of the sampling event (primary key).
event.txt:parentEventID Identification code of broader, parent events that group several sampling events. To reflect the nested hierarchical sampling design (cf. "Sampling description" section of this manuscript), parent events ID were built using up to five groups of character linked, in order, to the sampling region (Corsica or Sardinia), zone, site, sector, and sampling year.
event.txt:samplingProtocol Name of the method used to obtain the sample (cf. "Sampling description" section of this manuscript).
event.txt:sampleSizeValue Numerical value of the sampling area.
event.txt:sampleSizeUnit Unit used to express the sampling area (square meters).
event.txt:samplingEffort Brief description of the amount of effort expended to obtain the sample.
event.txt:eventDate Sampling event date. Light trap samples are taken over a full night, and therefore have two consecutive values. Precise dates were not recorded for the air-lift samples, and a date range spanning the whole sampling campaign is given instead.
event.txt:eventTime Time interval in which the sample was taken.
event.txt:eventRemarks For sampling events: the period of the day in which the sample was taken (day or night). For parent events: the concerned level of the nested hierarchical sampling design (cf. "Sampling description" section of this manuscript).
event.txt:waterBody Name of the marine area in which the sample was taken.
event.txt:island Name of the island in which the sample was taken.
event.txt:countryCode ISO 3166-1-alpha-2 code of the country in which the sample was taken.
event.txt:minimumDepthInMeters Minimum sampling depth, in meters.
event.txt:maximumDepthInMeters Maximum sampling depth, in meters.
event.txt:decimalLatitude Geographic latitude, in decimal degrees.
event.txt:decimalLongitude Geographic longitude, in decimal degrees.
event.txt:geodeticDatum Geodetic datum on which the geographic coordinates given in "decimalLatitude" and "decimalLongitude" are based (WGS84).
occurence.txt:basisOfRecord Nature of the occurrence record (preserved specimen)
occurence.txt:occurrenceID Globally unique and persistent identification number of the occurrence
occurence.txt:recordNumber Identification number given to the occurrence at the time of record
occurence.txt:individualCount Number of sampled specimen(s)
occurence.txt:sex Sex of sampled specimen(s)
occurence.txt:lifeStage Life stage of sampled specimen(s)
occurence.txt:eventID Identification code of the sampling event (foreign key).
occurence.txt:scientificName Binomial scientific name of the occurrence
occurence.txt:family Family of the occurrence
occurence.txt:genus Genus of the occurrence
occurence.txt:specificEpithet Species epithet of the occurrence
occurence.txt:infraspecificEpithet occurence.txt:Subspecies epithet of the occurrence
occurence.txt:taxonRank Lowest taxonomical level to which the specimen(s) could be identified


Authors warmly thank Dimitri Brosens and Peter Desmet (Instituut voor Natuur- en Bosonderzoek - INBO) for their help during preparation of this paper of the associated dataset and Renzo Biondo (Laboratory of Oceanology, ULg) for his technical assistance in the conception and building of sampling gear. They are also grateful to the staff of the STARESO Research station and to Augusto Navone, Pieraugusto Panzalis and Salvatore Vitale (Consorzio di Gestione Area Marina Protetta Tavolara-Punta Coda Cavallo, Olbia, Italy) for their hospitality and help during the fieldwork. At the time of sampling, LNM and NS were respectively supported by a Belgian Funds for Scientific Research (F.R.S.-FNRS) research fellow grant and a Belgian Fund for Research in Industry and Agriculture (FRIA) grant. GL is a F.R.S.-FNRS research associate. This is MARE publication nr. 335.

Author contributions

LNM, GL & NS conceived the sampling design and performed the sampling. LNM & NS performed identification of specimens under supervision of GL. AH and LNM prepared, formatted, mapped and published the dataset. LNM, NS, AH & GL wrote the paper. LNM & NS contributed equally to the manuscript and share first authorship.