AxIOM: Amphipod crustaceans from insular Posidonia oceanica seagrass meadows.

BACKGROUND: 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 http://ipt.biodiversity.be/resource?r=axiom.

Introduction

The Neptune grass, (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, 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 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

Purpose

AxIOM is a sample-based dataset (n = 187 samples) documenting occurrences of amphipod crustaceans associated to 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

Title

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

Personnel

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 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 meadows, and their potential responses among different protection levels (Sturaro 2012).

Funding

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

Study extent

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 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: 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 (Krapp-Schickel and Sorbe 2006) and (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

Description

AxIOM contains samples taken in 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, 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. 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).

Coordinates

40.859253 and 42.579722 Latitude; 8.725000 and 9.777583 Longitude.

Taxonomic coverage

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

Temporal coverage

Data range: 2006 11 15 – 2008 8 19.

Collection data

Collection name

AxIOM

Collection identifier

ULGOceano001

Specimen preservation method

Ethanol 70% in distilled water + 1% glycerin

Usage rights

Use license

Other

IP rights notes

Creative Commons CC BY

Data resources

Data package title

AxIOM: Amphipod crustaceans from insular seagrass meadows

Resource link

http://ipt.biodiversity.be/resource?r=axiom

Number of data sets

1

Data set 1.

Data set name

AxIOM: Amphipod crustaceans from insular seagrass meadows

Data format

Darwin Core

Number of columns

30

Download URL

http://ipt.biodiversity.be/resource?r=axiom, www.gbif.org/dataset/b146a93c-657b-4768-aa51-9cabe3dac808

Description

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 http://tdwg.github.io/dwc/terms/. AxIOM has the Global Biodiversity Information Facility Universally Unique Identifier (GBIF UUID) b146a93c-657b-4768-aa51-9cabe3dac808.

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

Data set 1.

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