Biodi e si y Da a Jou nal 13: e148981
doi: 10.3897/BDJ.13.e148981
Da a Pape
A long- e m ecological esea ch da ase om he
ma ine gene ic moni o ing p og amme ARMS-
MBON 2020-2021
Jus ine Pagnie , Louise Allcock, Ibon Cancio , E a Cha zinikolaou , Gio gos Cha zigeo giou ,
Na han Alexis Mi chell Ch ismas , Fede ica Cos an ini , Thanos Dailianis , Klaas Deneud , Oihane
Díaz de Ce io , Ma kos Digenis , Ka ina Ex e , Vasilis Ge o asileiou , Jose González Fe nández
Lau a Kauppi , Kleoniki Keklikoglou , Jon Ben K is o e sen , Rune Lagaisse , Bo u Ma ič, Jonas
Mo elmans , Es e ania Pa edes , Ch is ina Pa loudi , Alessand o Piazza , Anne Ma ie Powe ,
And eja Ramšak , Ioulia San i , Jos ein Solbakken , Melan hia S a oulaki , Pe e An on Upadhyay
S æh , Ja ie Tajadu a , Jesus Souza T oncoso , Ka e ina Vasileiadou , Emmanouela Ve nadou ,
Ma hias Obs
‡ Uni e si y o Go henbu g, SciLi eLab, Go henbu g, Sweden
§ Go henbu g Global Biodi e si y Cen e, Go henbu g, Sweden
| Uni e si y o Galway, Galway, I eland
¶ Uni e si y o he Basque Coun y (UPV/EHU), Leioa, Spain
# Plen zia Ma ine S a ion (PiE-UPV/EHU), Plen zia, Spain
¤ Ins i u e o Ma ine Biology, Bio echnology and Aquacul u e (IMBBC), Hellenic Cen e o Ma ine Resea ch (HCMR),
He aklion, G eece
« Royal Bo anic Ga den Edinbu gh, Edinbu gh, Uni ed Kingdom
» Depa men o Biological, Geological and En i onmen al Science, Uni e si y o Bologna, Ra enna, I aly
˄ Flande s Ma ine Ins i u e (VLIZ), Oos ende, Belgium
˅ Depa men o En i onmen , Facul y o En i onmen , Ionian Uni e si y, Zakyn hos, G eece
¦ Cen o de In es igación Ma iña, Uni e sidade de Vigo, Vigo, Spain
ˀ T ä minne Zoological S a ion, Uni e si y o Helsinki, Hanko, Finland
ˁ Na ional Ins i u e o Biology, Ma ine Biology S a ion Pi an, Pi an, Slo enia
₵ Eu opean Ma ine Biological Resou ce Cen e (EMBRC), Pa is, F ance
ℓ Depa men o Ecoscience, Ma ine Di e si y and Expe imen al Ecology, Aa hus uni e si y, Aa hus, Denma k
₰ Uni e si y o Go henbu g, Go henbu g, Sweden
‡,§ | ¶,# ¤ ¤
« » ¤ ˄
¶,# ¤,˅ ˄ ˅,¤ ¦
ˀ¤ ¤ ˄ ˁ
˄¦₵» |
ˁ ₵,¤ ˀ¤
ℓ¶,# ¦ ¤ ¤
₰,§
© Pagnie J e al. This is an open access a icle dis ibu ed unde he e ms o he C ea i e Commons A ibu ion License (CC BY
4.0), which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided he o iginal au ho and sou ce a e
c edi ed.
Co esponding au ho : Jus ine Pagnie (jus ine.pagnie @gu.se), Ma hias Obs (ma hias.obs @ma ine.gu.se)
Academic edi o : Sa ah Faulwe e
Recei ed: 06 Feb 2025 | Accep ed: 01 Jul 2025 | Published: 21 No 2025
Ci a ion: Pagnie J, Allcock L, Cancio I, Cha zinikolaou E, Cha zigeo giou G, Ch ismas NM, Cos an ini F,
Dailianis T, Deneud K, Díaz de Ce io O, Digenis M, Ex e K, Ge o asileiou V, González Fe nández J, Kauppi
L, Keklikoglou K, K is o e sen JB, Lagaisse R, Ma ič B, Mo elmans J, Pa edes E, Pa loudi C, Piazza A,
Powe AM, Ramšak A, San i I, Solbakken J, S a oulaki M, S æh PU, Tajadu a J, Souza T oncoso J,
Vasileiadou K, Ve nadou E, Obs M (2025) A long- e m ecological esea ch da ase om he ma ine gene ic
moni o ing p og amme ARMS-MBON 2020-2021. Biodi e si y Da a Jou nal 13: e148981.
h ps://doi.o g/10.3897/BDJ.13.e148981
Abs ac
Con inuing he in e na ional e o s o he ARMS Ma ine Biodi e si y Obse a ion Ne wo k
(ARMS-MBON), we p esen da a om he second sampling campaign, coming om 56
Au onomous Ree Moni o ing S uc u es (ARMS) deployed in 2020 and 2021 along
Eu opean coas s unde he Eu opean Ma ine Omics Biodi e si y Obse a ion Ne wo k
(EMO BON). The da ase includes in o ma ion on sampling loca ions and condi ions,
sample a chi ing and quali y epo s o collec ed samples. Da a and me ada a a e openly
accessible and can be downloaded om he associa ed Gi Hub eposi o y. Sequence
da a can be accessed ia he Eu opean Nucleo ide A chi e (ENA) h ough he
co esponding accession numbe s. Images o ARMS pla es a e s o ed on Plu oF and can
be downloaded h ough links p o ided in his pape . Sequence da a we e p ocessed and
explo ed wi h he PEMA pipeline, esul ing in 17,194, 7,235 and 5,261 unique ASVs/
OTUs o COI, 18S and ITS, espec i ely. In his da ase , ARMS e ealed he p esence o
o e 61 euka yo ic phyla, aligning wi h ou p e ious sampling campaign. Amongs hese
phyla, 35 had sequences iden i ied o he species le el. Wi h his da ase and i s
associa ed pape , we p o ide a s anda dised esou ce o ma ine biodi e si y moni o ing
and scien i ic analyses o ben hic biodi e si y. The p esen ed da a p oduc suppo s
u u e s udies on he s a us and changes in species composi ion, dis ibu ion and gene ic
di e si y.
In oduc ion
In an e a o signi ican global changes, he s udy and conse a ion o biodi e si y ha e
become a majo ocus o scien is s wo ldwide. Only ecen ly ha e he in ica e
connec ions be ween he heal h o hese ecosys ems and human well-being s a ed o
gain a en ion in public heal h discou se and decision-making, in he ligh o he One
Heal h concep (Ho on e al. 2014). Oceans, his o ically o e looked in conse a ion
e o s, co e o e 90% o he biosphe e and a e c i ical habi a s eeming wi h wildli e
(Cowan 1997). To his da e, mo e han 240,000 ma ine species ha e been desc ibed
(Ahyong e al. 2024) and an a e age o 2,332 new species a e disco e ed e e y yea
(Bouche e al. 2023). Howe e , he dis ibu ion and ecology o mos known species in he
2Pagnie J e al
global ocean is s ill, o a la ge ex en , unknown (Guidi e al. 2020), while da a desc ibing
he popula ion size and dis ibu ion ange a e lacking o he majo i y o ma ine species
(Mo a e al. 2011, Ab eu e al. 2022. In es iga ing species dis ibu ion, ange, abundance
and gene ic di e si y is, he e o e, a c i ical ield o ac ion o he conse a ion o ma ine
sys ems.
Howe e , mos ma ine habi a s ace inc easing h ea s, such as biodi e si y loss and
deg ada ion (Maza is e al. 2019, Luypae e al. 2020, O’Ha a e al. 2021), while
p ocesses, such as clima e change, can signi ican ly and ab up ly al e he communi y
composi ion and ood web s uc u e. Coas al a eas a e pa icula ly ulne able due o
hei p oximi y o human ac i i ies, o ins ance, ou ism and indus ial de elopmen
(Ha is e al. 2022, G een e al. 2022, González He nández e al. 2023) and hei
sensi i i y o clima e change (Bu ke e al. 2009). Unde s anding he dynamics be ween
human ac i i ies and ecosys em esponse is mo e impo an han e e . To his end, he
amewo ks o Essen ial Biodi e si y Va iables (EBVs; Geijzendo e e al. 2016, P oença
e al. 2017, Kissling e al. 2018a, Kissling e al. 2018b), Essen ial Ocean Va iables (EOVs;
Milosla ich e al. (2018), Mulle -Ka ge e al. (2018)), Essen ial Clima e Va iables (ECVs;
Bojinski e al. (2014), Zeng e al. (2019)) and Essen ial Ecosys em Se ice Va iables
(EESVs; Bal ane a e al. (2022)) ha e eme ged o p o ide key me ics o moni o ing
biodi e si y and oceanic changes a egional and global scales. EBVs aim o cap u e
c i ical aspec s o biodi e si y change, such as species popula ions and gene ic di e si y,
while EOVs ocus on oceanic p ocesses and ecosys em heal h. Gi en he complexi y o
ma ine en i onmen s and he o en sub le na u e o hei ecological shi s, hese
amewo ks highligh he necessi y o inno a i e moni o ing echniques and widely
adhe ed p o ocols capable o deli e ing high- esolu ion insigh s in o biodi e si y pa e ns
and changes. These echniques mus ope a e on la ge scales and deli e high- esolu ion
da a o e ec i ely cap u e he apid loss o biodi e si y and suppo conse a ion e o s,
esea ch and policy. Gene ic me hods, such as DNA/eDNA me aba coding, ha e been
de eloped and a e inc easingly used as hey become cheape and mo e e icien , while
p o iding high axonomic esolu ion (Tabe le e al. 2012, Ruppe e al. 2019). Mo eo e ,
consensus s anda disa ion and public p o ocols ha e o be applied so esul s can be
compa able ac oss ime and space. Howe e , i is impo an o no e ha s anda disa ion
e o s o DNA/eDNA me aba coding a e s ill ongoing, wi h me hodological choices (such
as ma ke selec ion, p ime design, sampling s a egy and bioin o ma ic p ocessing)
con inuing o in luence esul s and compa abili y. Recen e iews and pilo s udies
emphasise he need o ha monisa ion o p o ocols and highligh cu en challenges and
knowledge gaps ha mus be add essed o widesp ead adop ion in ma ine biodi e si y
moni o ing ( an de Loos and Nijland 2021, Gold e al. 2022).
The Au onomous Ree Moni o ing S uc u es Ma ine Biodi e si y Obse a ion Ne wo k
(ARMS-MBON), ini ia ed in 2018, ca ies ou con inuous gene ic moni o ing o ha d-
bo om communi ies ac oss Eu ope (Obs e al. 2020) using s anda dised p o ocols
(Suppl. ma e ial 1). Following he ini ial concep ual ou lines by Obs e al. (2020) and
San i e al. (2023), he da a om he i s sampling campaign (2018-2020) we e published
in Da aghmeh e al. (2025). The occu ence da a om his i s da ase a e a ailable on
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 3
he Global Biodi e si y In o ma ion Facili y (GBIF), he Ocean Biodi e si y In o ma ion
Sys em (OBIS, Eu OBIS) ollowing he links in Suppl. ma e ial 2. These i s yea s o e ed
aluable pe spec i es on he pan-Eu opean gene ic di e si y o ha d-bo om ben hic
ecosys ems, demons a ed he e ec i eness o DNA me aba coding in imp o ing
adi ional moni o ing echniques and highligh ed he obs acles aced in es ablishing a
s anda dised ma ine moni o ing ne wo k.
ARMS-MBON began unde he ASSEMBLE Plus p ojec (2017-2022) and is now
coo dina ed by he Eu opean Ma ine Biological Resou ces Cen e (EMBRC) unde he
Eu opean Ma ine Omics Biodi e si y Obse a ion Ne wo k (EMO BON) p og amme, led
by EMBRC (San i e al. 2023). EMO BON collec s samples om he wa e column (Wa),
so subs a es (So) and ha d subs a es using ARMS (Ha), aiming o allow esea che s o
explo e ma ine di e si y ac oss di e en habi a s. The eby, EMO BON ac i ely con ibu es
o he UN Decade o Ocean Science o Sus ainable De elopmen and he global Ocean
Biomolecula Obse ing Ne wo k ini ia i e, which is one o he ac ions endo sed by he
Decade (OBON; Meye e al. (2023)).
Building on he ounda ions laid by his ini ial ARMS-MBON sampling campaign, he
cu en da a pape p esen s he second ARMS-MBON da a elease, ocusing on 56
ARMS deployed along Eu opean coas s om 2020 o 2021. The da ase includes
ma e ial samples, me ada a, images, sequence da a, de i ed axonomic obse a ions
and documen a ion, all adhe ing o FAIR p inciples (Tanhua e al. 2019). This da ase
con ibu es o he EBV amewo k by p o iding high- esolu ion gene ic da a ha suppo
moni o ing o gene ic di e si y, species occu ence and communi y composi ion. Th ough
s anda dised sampling and open-access da a, i enables long- e m, spa ially compa able
assessmen s o ben hic biodi e si y, aligning wi h key EBV classes, such as Gene ic
Composi ion and Species Popula ions.
Value o he da ase
The da ase p esen ed in his pape holds signi ican alue o bo h ma ine ecology
esea ch and ma ine conse a ion p og ammes. I p o ides s anda dised, high- esolu ion
gene ic da a on ben hic species ac oss Eu opean coas s. The da a epo ed he e a e
compa able wi h he p e ious and subsequen da ase s om EMO BON obse a o ies
and, he eby, allow o he moni o ing o he s a us and changes o ben hic biodi e si y.
This da ase enhances biodi e si y moni o ing by con ibu ing o Essen ial Biodi e si y
Va iables (EBVs) and p o iding da a on species occu ence, alpha/be a di e si y and
gene ic di e si y, add essing knowledge gaps in ma ine species dis ibu ion and di e si y
h ough 56 ARMS deploymen s. I suppo s scien i ic esea ch, conse a ion planning
and global in e ope abili y by in eg a ing wi h ini ia i es like he Ocean Biodi e si y
In o ma ion Sys em (OBIS), he Global Biodi e si y In o ma ion Facili y (GBIF), he
Eu opean Ma ine Obse a ion and Da a Ne wo k (EMODne ) and he Eu opean Digi al
Twin o he Ocean (EU DTO), see Da a Resou ces 7 o 9.
4Pagnie J e al
Ul ima ely, his da ase p o ides a c i ical esou ce o unde s anding and p o ec ing
ma ine biodi e si y in an e a o apid en i onmen al change, o e ing long- e m alue o
biodi e si y esea ch, ecosys em managemen and global conse a ion e o s.
Me hods
Sampling, ARMS p ocessing and image da a
The o iginal obse a o y design, ieldwo k me hodologies and sample p ocessing
p ocedu es as well as ins uc ions o biobanking and da a managemen ha e been
desc ibed in Obs e al. (2020). Du ing his second ARMS MBON campaign, ieldwo k,
image da a collec ion and sample collec ion ollowed he same guidelines as o he i s
sampling campaign (Da aghmeh e al. 2025), mainly guided by he ARMS MBON
Handbook 2.0 and he EMO BON Handbook 2.0 ha can be accessed on he ARMS-
MBON Gi Hub eposi o y, he EMO BON websi e and he Ocean Bes P ac ices pla o m
(see Suppl. ma e ial 1 o all use ul links).
Gene al desc ip ion o he sampling campaign
The p esen ed da a a e de i ed om 56 ARMS uni s, co esponding o 56 indi idual
sampling e en s. These include 55 unique Uni IDs, as wo sampling e en s occu ed a
he same ARMS loca ion (BelgiumCoas _AJJCD78, one deploymen in 2020 and one in
2021, see Suppl. ma e ial 3).
Geog aphic co e age
The da ase ’s geog aphical ange includes 13 obse a o ies, ac oss 10 coun ies,
co e ing six eco egions (Table 1, Fig. 1). Fo mo e in o ma ion abou he obse a o ies
and si es, see Gi Hub links in Suppl. ma e ial 1.
Locali y Coun y Coo dina es Eco egion Deploymen da es (deploymen -- e ie al)
Ra ennaM I aly 44.492426N;
12.287623E
Ad ia ic Sea (22/04/2021 -- 22/07/2021)
Ra ennaH I aly 44.421488N;
12.209497E
Ad ia ic Sea (22/04/2021 -- 22/07/2021)
Vigo Spain 42.2284N;
-8.7787W
Sou h
Eu opean
A lan ic Shel
(06/07/2020 -- 06/10/2020)
Table 1.
Table 1. Locali y and geog aphical coo dina es o he obse a o ies collec ing ARMS samples
du ing he second sampling campaign. Eco egions a e acco ding o Spalding e al. (2007).
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 5
Locali y Coun y Coo dina es Eco egion Deploymen da es (deploymen -- e ie al)
C e e C e e 35.343153N;
25.136605E
Aegean Sea (03/09/2020 -- 22/01/2021);
Plymou h Uni ed
Kingdom
50.3673N;
-4.1554W
Cel ic Seas (17/07/2020 -- 21/09/2020); (17/07/2020 -- 21/09/2020);
(17/07/2020 -- 23/09/2020)
PiEGe xo Spain 43.33858N;
-3.014639W
Sou h
Eu opean
A lan ic Shel
(24/06/2020 -- 03/11/2020);
Belgium
Coas
Belgium 51.43333 N;
2.808331 E
No h Sea (06/05/2020 -- 12/10/2020); (25/02/2021 -- 19/08/2021);
(17/06/2020 -- 09/03/2021); (22/04/2021 -- 08/10/2021)
Galway I eland 53.315443N;
-9.671564W
Cel ic Seas (21/07/2020- 08/07/2021); (21/07/2020 -- 07/07/2021);
(23/07/2020 -- 08/07/2021)
Pi an Slo enia 45.54875N;
13.5507E
Ad ia ic Sea (11/06/2020 -- 28/07/2021); (22/06/2021 -- 27/10/2021);
(23/02/2021 -- 22/06/2021)
TZS Finland 59.841505N;
23.248879E
Bal ic Sea (08/06/2020 -- 17/11/2020); (08/06/2020 -- 18/11/2020);
(08/06/2020 -- 20/11/2020);
Kos e Sweden 58.875155N;
11.103194E
No h Sea (16/07/2020 -- 08/06/2021)
SWC Sweden 57.1107004N;
12.2439775E
No h Sea (31/01/2020 --18/05/2020); (06/02/2020 -- 20/05/2020);
(06/02/2020 -- 29/05/2020); (05/03/2020 -- 04/06/2020);
(31/01/2020 -- 18/05/2020); (28/02/2020 -- 27/05/2020);
(01/04/2020 -- 15/07/2020); (13/02/2020 -- 03/06/2020)
Lim jo d Denma k 56.89985 N;
9.05663333 E
No h Sea (10/11/2020 -- 15/11/2021)
Tempo al co e age
The da ase is composed o da a om ARMS uni s deployed in 2020 and o he s in 2021
and e ie ed du ing bo h yea s. These ARMS uni s we e deployed du ing pe iods
anging be ween 66 days in Plymou h, UK and 412 days in Pi an, Slo enia (Fig. 2). In
ac , in ea lie phases o ARMS MBON, di e en me hodologies we e es ed (e.g. sho e
deploymen s o alien species moni o ing s. longe deploymen s o long- e m
biodi e si y moni o ing). Addi ionally, longe deploymen s a e needed a ce ain no he n
obse a o ies (e.g. S alba d) o ensu e su icien communi y de elopmen . Deploymen
ime was also in luenced by local cons ain s a he di e en pa ne s a ions. Howe e , as
mo e expe ience and in o ma ion is ga he ed ac oss he ne wo k, he goal is o
s anda dise deploymen du a ion in he u u e.
In he da ase p esen ed by Da aghmeh e al. (2025), no signi ican linea associa ion
be ween deploymen du a ion and he numbe o species iden i ied o he ASV/OTU
6Pagnie J e al
ichness was de ec ed. Deploymen du a ion is, howe e , an impo an measu e o
ack
depending on which s udies a e pe o med wi h ARMS da a.
Gene al in o ma ion on he obse a o ies and ARMS deploymen s (e.g. coo dina es,
habi a ype, deploymen dep h) and on he sampling e en s and hei esul ing ma e ial
samples (e.g. da e o deploymen and e ie al, ma e ial sample IDs, p ese a i e used)
can be ound on he Gi Hub eposi o y (see Suppl. ma e ial 1 o espec i e links) and in
Suppl. ma e ial 3.
Labo a o y p o ocols o amplicon sequencing
Un il 2021, ma e ial samples had been sen o he Hellenic Cen e o Ma ine Resea ch
(HCMR), C e e, G eece, o sequencing. This da ase is, he e o e, composed o he h ee
inal sequencing ba ches p ocessed in his acili y, in Sep embe 2020, Ap il 2021 and
Augus 2023. The HCMR ins i u e conduc ed amplicon sequencing o 162 ma e ial
samples ollowing he ARMS-MBON Molecula S anda d Ope a ional P ocedu e (see
Suppl. ma e ial 1 o link). DNA me aba coding was pe o med on he euka yo ic
mi ochond ial and nuclea ma ke genes cy och ome c oxidase subuni I (COI), 18S RNA
(18S) and o 68 samples, on he in e nal ansc ibed space (ITS) egion. The COI
Figu e 1.
Loca ions o obse a o ies ha deployed ARMS uni s du ing he 2020–2021 ARMS-MBON
sampling campaign. The wo Ra enna (I aly) obse a o ies a e p esen ed as a single en i y
he e due o hei p oximi y. TZS - T ä minne Zoological S a ion. SWC - Swedish Wes Coas .
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 7
p ime s p ima ily a ge me azoans, 18S ampli ies a b oad ange o euka yo es including
p o is s and me azoans and ITS was used o be e de ec ungi and
o he
mic oeuka yo es. The ITS ma ke was used exclusi ely du ing he p ojec ’s ea ly s ages
and is cu en ly no longe in use; his da a pape , he e o e, p esen s he las esul s o
his ma ke .
Figu e 2.
Sampling e en s o he second ARMS-MBON sampling campaign. Axis on he le shows
Obse a o yID_Uni ID combina ions, axis on he igh shows g oupings o obse a o ies in o
la ge egions. Red semici cle: ime o deploymen . Blue semici cle: ime o e ie al. Whe e
ed and blue semici cles mee , a new ARMS uni was deployed o a consecu i e pe iod a he
same spo upon e ie al o he i s uni . Whe e lines con ain mo e han wo semici cles (see
Gul O Pi an_LukaKP), mul iple uni s we e deployed a he exac same spo a he same ime,
bu we e e ie ed a di e en ime poin s.
8Pagnie J e al
Fo he COI ma ke gene, he mlCOIin F and jgHCO2198 p ime s (Le ay e al. 2013
,
Gelle e al. 2013) we e used and o 18S RNA, All18SF and All18SR (Ha dy e al. 2010)
we e chosen. Sequencing was pe o med wi h Illumina MiSeq ollowing he ARMS
MBON Molecula S anda d Ope a ing P ocedu es.
All aw sequence da a om success ul sequencing e en s a e now publicly accessible in
he Eu opean Nucleo ide A chi e (ENA) (see Da a esou ces sec ion below). Sequences
om nega i e con ols a e also a ailable. Addi ional de ails on how he sequence da a
we e demul iplexed, including whe he he eads include p ime sequences, a e
documen ed in Suppl. ma e ial 4.
Da a managemen
Da a managemen ollowed he same wo k low as o ou i s da a elease, whe e he
whole p ocedu e has been desc ibed and documen ed (Da aghmeh e al. 2025). In sho ,
e en me ada a (obse a o y, e en and sample me ada a, ENA accession numbe s o
sequencing da a) we e eco ded on he ARMS-MBON p ojec Googleshee and ARMS
pla e images and associa ed sp eadshee s we e uploaded o he Plu oF pla o m (h ps://
plu o .u .ee/). A e quali y con ol (i.e. checking o inconsis en o ma s, missing en ies o
incomple e ones), all me ada a and image da a en e ed on Plu oF and all sp eadshee
da a we e ha es ed and uploaded o he ARMS-MBON Gi Hub space (see Suppl.
ma e ial 1 o links). When o ganising he da a on Gi Hub, we c ea ed new eposi o ies,
speci ic o his second da a elease, bu ollowing he same s uc u e as o he i s (
Da aghmeh e al. 2025). Each eposi o y o he second da a elease was hen packaged
as a Resea ch Objec C a e (RO-C a e; Soiland-Reyes e al. (2022)) o p oduce machine-
accessible and in e ope able da ase s. Raw sequence da a a e accessible on he
Eu opean Nucleo ide A chi e ia he accession numbe s ound on Gi Hub. The
occu ence da a ob ained om he p ocessing is in eg a ed in he Global Biodi e si y
In o ma ion Facili y (GBIF) and on he Eu opean Ocean Biodi e si y In o ma ion Sys em
(OBIS), see Da a Resou ces 7 o 9.
Biobanking
All pa ne s we e asked o keep a leas one back-up eplica e o each sample, s o ed in
a eeze a -20°C, as well as a digi al copy o all o iginal images om he sampling e en
and he p ocessed pla es.
All collec ions o ARMS samples we e ca ied ou wi h he necessa y ABS na ional
pe mi s. These allow he ele an s a ions o collec he samples in o de o u ilise he
gene ic ma e ial o axonomic iden i ica ion pu poses. I anyone wishes o ob ain and
p ocess any eplica e ma e ial as s o ed in he indi idual pa ne s a ions, please no e
ha any e-u ilisa ion needs o be e-nego ia ed wi h ABS compe en au ho i ies in he
p o iding coun ies.
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 9
Ecological pa e ns obse ed in he da ase e ealed dis inc communi y composi ions
ac oss ma ke s and axonomic g oups. The COI da ase was domina ed by A h opoda,
Cnida ia, Annelida and Mollusca, while 18S was la gely composed o A h opoda,
Mollusca, Cho da a and Myzozoa and ITS was hea ily skewed owa ds Ascomyco a and
Figu e 5.
UpSe plo showing he numbe o species iden i ied using he h ee ma ke genes: COI, 18S
and ITS. G een ba s ep esen he numbe o species iden i ied (based on he applied
con idence h eshold) ha a e sha ed ac oss he a ious combina ions o ma ke gene
da ase s. The ma ix below he ba plo indica es which combina ions o ma ke genes
co espond o each ba . Ba s on he le display he o al numbe o species iden i ied wi hin
each ma ke gene da ase . No ably, no species we e ound o be common ac oss all h ee
da ase s.
16 Pagnie J e al
Basidiomyco a (Fig. 4). These di e ences highligh he complemen a y na u e o he
ma ke genes and ein o ce he need o a mul i-ma ke app oach in ben hic
biodi e si y
assessmen s. Fu he mo e, mos species de ec ed we e unique o each ma ke , wi h
minimal o e lap, sugges ing ha each ma ke p o ides access o dis inc po ions o he
communi y (Fig. 5). The da a also con i med he de ec ion o 61 euka yo ic phyla, wi h 35
o hem ha ing ASVs/OTUs iden i ied o species le el, p o iding a b oad axonomic
esolu ion ha aligns wi h ea lie indings in he ne wo k (Da aghmeh e al. 2025).
Raw da a and he subsequen PEMA ou pu s p esen ed he e a e compa able o ou i s
da a elease (Da aghmeh e al. 2025) and o o he simila s udies (Le ay and Knowl on
2015, Gielings e al. 2021, Coke e al. 2023). Mo e speci ically, o COI and ITS, he
mean sequencing dep h pe sample was a simila ange o ha epo ed in Da aghmeh
e al. (2025) (Suppl. ma e ial 8). Howe e , i was lowe o 18S, which could be due o
lowe sequencing quali y. These pa e ns likely e lec di e ences in sample quali y,
sequencing condi ions o lib a y p epa a ion ac oss he da es and sugges po en ial
ba ch e ec s ha should be accoun ed o when pe o ming u he s a is ical analyses.
Addi ionally, he a e age numbe o ASVs/OTUs pe sample was 60% lowe in he
second elease o COI, 17% lowe o 18S and he same o ITS (Suppl. ma e ial 9). The
numbe o species de ec ed, howe e , was simila be ween bo h da ase s o 18S
(Wilcoxon, p = 0.68) and COI (Wilcoxon, p = 0.94). Di e ences be ween da ase s can be
due o di e en sequencing quali y o di e ences in sample p epa a ion p o ocols,
sequencing pla o ms o bioin o ma ics p ocessing pipelines (Smi h and Peay 2014, Sims
e al. 2014), which, howe e , has no been he case in his s udy. Va iabili y in
sequencing pe o mance ac oss ma ke s may also e lec inhe en di e ences in p ime
e iciency, a ge gene di e si y o ampli ica ion success, all o which can in luence he
eco e y o ASVs/OTUs. Mul i-ma ke s a egies ha e been ecommended o imp o e
axonomic co e age (Po as e al. 2022) and p o ide mo e accu a e communi y
composi ion es ima es (Gün he e al. 2018, S e anni e al. 2018).
The ARMS-MBON moni o ing ne wo k has unde gone signi ican g ow h and
de elopmen since i s ini ial yea s, ma ked by he addi ion o new obse a o ies and an
inc easingly s uc u ed app oach o sample collec ion, da a managemen and analysis.
This expansion has g ea ly en iched ou da ase , enhancing ou capaci y o long- e m
moni o ing o ma ine ecosys ems. The in eg a ion in o he EMO BON ne wo k in 2021,
which conduc s ex ensi e wa e and sedimen sampling ac oss Eu ope, ep esen s a
majo ad ancemen .
Mo eo e , ou ongoing e o s o e ine me hodologies a e suppo ed by he collec i e
expe ise and insigh s om he pa ne s’ ieldwo k and da a analysis expe iences. This
con inuous imp o emen cycle no only s eng hens he moni o ing capabili ies o ARMS-
MBON, bu also ensu es ha ou me hods emain a he o e on o ma ine biodi e si y
esea ch. The syne gy be ween ARMS-MBON and EMO BON, alongside ou commi men
o me hodological ad ancemen s, allow us o make subs an ial con ibu ions o he
unde s anding and p ese a ion o ma ine ecosys ems.
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 17
The ARMS-MBON ne wo k is well-equipped o p o ide comp ehensi e da a o s udying
biodi e si y pa e ns in ma ine ecosys ems o e he long e m. Fo ins ance, i has al eady
been shown ha ARMS-BON ne wo k da a a e use ul o he iden i ica ion o NIS (
Da aghmeh e al. 2025, Pagnie e al. 2025). Using a a ie y o me hodologies, ARMS-
MBON can gene a e de ailed insigh s in o species dis ibu ion, communi y s uc u e and
gene ic di e si y. The ne wo k’s ex ensi e a ay o obse a o ies acili a es he collec ion
o high- esolu ion, spa ially-di e se da a, which is c i ical o unde s anding he complex
dynamics o ma ine biodi e si y. Addi ionally, he da a gene a ed align closely wi h
Essen ial Biodi e si y Va iables (EBVs), ensu ing compa ibili y wi h global biodi e si y
moni o ing amewo ks and enhancing he u ili y o he da ase o la ge-scale ecological
assessmen s. This obus and expanding da ase enables igo ous s a is ical analyses,
p o iding aluable in o ma ion on bo h sho - e m pa e ns and long- e m ends.
In addi ion o he ex ensi e gene ic da a p o ided in his second da a elease, we also
include a comp ehensi e se o high- esolu ion images om he deployed ARMS uni s.
While hese images emain unde u ilised in cu en analyses, hey o e signi ican
po en ial o complemen a y esea ch. In ac , s udies showed ha ARMS pho o-analyses
can be used o compa e ma ine ben hic communi ies (Da id e al. 2019). Visual da a can
p o ide c ucial con ex o he gene ic indings by documen ing he physical appea ance
o he communi ies, o e ing insigh s in o species beha iou , habi a s uc u es and
possible en i onmen al changes o e ime. Fu he mo e, he images could be used o
c oss- e e encing wi h gene ic da a o imp o e species iden i ica ion and alida e he
p esence o non-indigenous species (NIS) de ec ed ia me aba coding (Blai e al. 2024).
This isual documen a ion also holds alue o he de elopmen o mo e in eg a i e
app oaches o biodi e si y moni o ing ha combine gene ic, ecological and isual da a.
We encou age he b oade scien i ic communi y o explo e he ich po en ial o his image
da ase in u u e esea ch.
Bene i s sha ing s a emen
ARMS-MBON and EMO BON ep esen a la ge-scale esea ch collabo a ion wi h
scien is s om ac oss Eu ope and beyond. All ne wo k pa ne s o he obse a o ies
men ioned in his manusc ip p o ided gene ic samples and a e included as co-au ho s.
All con inuously gene a ed aw and p ocessed da a om his ne wo k a e sha ed wi h he
public and scien i ic communi y (see abo e). Ou esea ch add esses he u gen need o
la ge-scale and long- e m moni o ing o ma ine bio ic communi ies h ough ex ensi e
collabo a i e e o s.
Con lic s o in e es
The au ho s decla e ha he esea ch was conduc ed in he absence o any comme cial
o inancial ela ionships ha could be cons ued as a po en ial con lic o in e es .
18 Pagnie J e al
Da a Resou ces
Da a and me ada a a e accessible h ough he ollowing:
- Resou ce 1: Gene ic da a
see below
- Resou ce 2: Sample me ada a:
h ps://gi hub.com/a ms-mbon/da a_ elease_002
- Resou ce 3: Bioin o ma ics da a and me ada a (inpu s, ou pu s, pa ame e s):
h ps://gi hub.com/a ms-mbon/analysis_ elease_002
- Resou ce 4: Code used o he pos -PEMA analyses:
h ps://gi hub.com/a ms-mbon/code_ elease_002
- Resou ce 5: Sample access (Fo physical samples, eques s can be di ec ed o he
co esponding au ho o he ins i u ions esponsible o sample a chi ing, as de ailed in
he da ase documen a ion: All pa ne s we e asked o keep a leas one back-up
eplica e o each sample, s o ed in a eeze a -20°C, as well as a digi al copy o all
o iginal images om he sampling e en and he p ocessed pla es):
h ps://www.emb c.eu
- Resou ce 6: Image da a (Images o ARMS pla es om his da a se a e s o ed on Plu oF
and can be downloaded using he links p o ided in he dedica ed CSV ile below):
h ps://gi hub.com/a ms-mbon/da a_ elease_002/blob/main/ImageDa a_ elease002.cs
- Resou ce 7: IMIS eco d o COI (whe e Da win Co e A chi e iles can be downloaded,
links o GBIF, OBIS and Eu OBIS eco ds can be ound):
h ps://www. liz.be/en/imis?module=da ase &dasid=8922
- Resou ce 8: IMIS eco d o 18S (whe e Da win Co e A chi e iles can be downloaded,
links o GBIF, OBIS and Eu OBIS eco ds can be ound):
h ps://www. liz.be/en/imis?module=da ase &dasid=8918
- Resou ce 9: IMIS eco d o ITS (whe e Da win Co e A chi e iles can be downloaded,
links o GBIF, OBIS and Eu OBIS eco ds can be ound):
h ps://www. liz.be/en/imis?module=da ase &dasid=8921
A long- e m ecological esea ch da ase om he ma ine gene ic moni o ing ... 19
Resou ce 1
Download URL
All he aw sequence iles and nega i e con ols o his s udy we e submi ed o he
Eu opean Nucleo ide A chi e (ENA) wi h he umb ella s udy accession numbe
PRJEB72316 (publicly a ailable a h p://www.ebi.ac.uk/ena/da a/ iew/PRJEB72316).
Resou ce iden i ie
The accession numbe s o he componen p ojec s unde he umb ella s udy a e
PRJEB37740, PRJEB37757, PRJEB33796, PRJEB37754, PRJEB37756, PRJEB37757,
PRJEB72186, PRJEB37740, PRJEB37741, PRJEB37753, PRJEB72187, PRJEB37756,
PRJEB37754 and PRJEB37744.
Da a o ma
FASTQ
Conclusion
In conclusion, he second da a elease o ARMS-MBON p o ides an en iched and
con inued da ase o ben hic biodi e si y in Eu ope, including bo h aw and p ocessed
amplicon sequencing da a alongside high- esolu ion images. This elease highligh s he
ne wo k’s commi men o ad ancing ma ine biodi e si y moni o ing h ough igo ous
me hodologies and in eg a ion wi h global amewo ks, such as EBVs. By os e ing
accessibili y, in e ope abili y and sus ainabili y, ARMS-MBON con inues o make
signi ican con ibu ions o unde s anding and p ese ing ma ine ecosys ems.
Usage Righ s
CC BY 4.0
Da a accessibili y s a emen
All da a p esen ed in his manusc ip a e publicly a ailable wi h a CC BY licence (see
main ex and Supplemen a y Ma e ial o de ailed desc ip ions). S anda d ope a ing
p ocedu es and p o ocols a e a ailable on he dedica ed ARMS-MBON Gi Hub eposi o y
(h ps://gi hub.com/a ms-mbon/documen a ion). All me ada a and access o all image
da a gene a ed du ing his sampling campaign o ARMS-MBON o da e can be ound on
Gi Hub (h ps://gi hub.com/a ms-mbon/da a_ elease_002). All gene ic aw da a
gene a ed by ARMS-MBON o da e can be accessed on he Eu opean Nucleo ide
A chi e (ENA) h ough he accession numbe s p o ided ia he Gi Hub eposi o y (h ps:/
/gi hub.com/a ms-mbon/da a_ elease_002) and unde he umb ella s udy PRJEB72316
(h ps://www.ebi.ac.uk/ena/b owse / iew/PRJEB72316). Me ada a, access o image da a
20 Pagnie J e al
and accession numbe s o gene ic da a speci ically o he da ase p esen ed in his
manusc ip a e p o ided in he Supplemen a y Files and a e also a ailable on he
espec i e Gi Hub eposi o y (h ps://gi hub.com/a ms-mbon/da a_ elease_002). All
PEMA-p ocessed da a a e accessible h ough he Gi Hub eposi o y (h ps://gi hub.com/
a ms-mbon/analysis_ elease_002) and occu ences da a will be accessible ia GBIF and
OBIS.
Acknowledgemen s
The ARMS-MBON ne wo k was es ablished unde he in as uc u e p og amme
ASSEMBLE Plus (g an no. 730984). This wo k used esou ces p o ided by he
Eu opean Ma ine Omics Biodi e si y Obse a ion Ne wo k (EMO BON) p ojec ,
coo dina ed by he Eu opean Ma ine Biological Resou ce Cen e (EMBRC). Da a
publica ion and analysis a e unded by he p ojec s DTO-BioFlow (g an ag eemen no.
101112823) and MARCO-BOLO (g an ag eemen no. 101082021). Funding o
indi idual ARMS obse a o ies was p o ided by he INTERREG p ojec GEANS (No h
Sea P og amme o he Eu opean Regional De elopmen Fund o he Eu opean Union),
he Swedish Agency o Ma ine and Wa e Managemen (g an no. 3181-2019), he
Flande s Li eWa ch con ibu ion (Resea ch Founda ion Flande s g an I000819N) and he
Aquanis 2.0 p ojec (FONDATION To al). We hank Da iusz Nowak, Eoin MacLoughlin,
D . Mae e Edwa ds, S o m McDonald, Sam A oullouss, Susan Whelan, Domonique
Gillen, Dayle Leona d, Jamie Maxwell and Declan Mo issey o hei in aluable
con ibu ions o he sampling a he Galway obse a o y. Da a managemen and
compu a ional esou ces we e p o ided by he Swedish Biodi e si y Da a In as uc u e
(g an no. 2019-00242) and by a dis ibu ed in as uc u e in Spain, including da a
cen es a Picasso (Malaga), CICA (Se ille), eBRIC (Huel a) and he Uni e si y o
G anada. We also hank he Li eWa ch eam o he Spanish node o p o iding ools and
esou ces o p ocess he da a, as well as in aluable help and suppo along he way. We
hank Nau as Da aghmeh o w i ing he backbone o he da a analysis code and his
con ibu ion o es ablish he da a elease amewo k h ough his wo k on he i s ARMS-
MBON da a pape . Guiding documen s o ob ain ABS clea ance o access o gene ic
esou ces we e de eloped unde he p ojec s INTERREGEBB (EAPA_501/2016) and
H2020 EOSC-Li e (g an no. 824087). This wo k was also suppo ed by he SciLi eLab &
Wallenbe g Da a D i en Li e Science P og am (g an : KAW2024.0159).
Con lic s o in e es
The au ho s ha e decla ed ha no compe ing in e es s exis .
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