EMO BON Handbook Condensa ion, P o ocol o Me ada a and WaSOP 1 (Basic) sampling
This p o ocol o igina es om: h ps://www.emb c.eu/documen s/2024.04_EMOBON-Handbook_FINAL.pd
, and is modi ied o sampling in he Sub-A c ic T omsø a ea. Responsible o he modi ica ions and
e isions:
K is el Be g, Julie Bi z-Tho sen, Simon N. Schmid , and Kim P æbel
Resea ch G oup o Gene ics, UiT The A c ic Uni e si y o No way.
Con ac pe son: kim.p aebel@ui .no
Thi d e ision 26.11.2025, KP
Second e ision, 30.08.2021, SN
1) MATERIALS
Table 1: O e iew o ma e ials needed o pe o m p ope sampling
Ma e ials
Quan i y
Bleach
Pu i ied wa e (Milli-Q o Nanopu e)
Ni ile glo es, a ious sizes
50 ml alcon ubes
Wash bo le
Fo ceps
Scisso s
Plas ic bag o samples
Pe is al ic pump(s) and ela ed equipmen
Elec ic ape oll
Ga a- ape oll
Fil a ion ipods, 142mm
PC memb anes 3 μm, ø=142 mm
PC memb anes 0.2 μm, ø=142 mm
5 ml c yo ubes + caps
Pe manen ma ke s
T anspa en ape oll
6 l Niskin bo le
200 μm mesh ne
Sampling con aine s
Funnel
DNA/RNA Shield bo le
S e i ex il e s
140mm pe i dishes
D y pape
70 % e hanol
Bench co e /plas ic bags
Rack o ubes (50 ml and 5 ml)
Box o d y ice
CTD
Hoses
Rubbe band Niskin
Foil
2 li e s
20 li e s
1 box pe size
2
1
2
1
10 pe size
1
1
2
5
5
5
10
1
1
1
2
1
1
1
10
10
2
1
1 pk
1
1
1
1
1
2) PRIOR TO SAMPLING
When p epa ing he wo k su ace and cleaning, always wea glo es and adequa e p o ec ion.
• Clean able wi h 10% bleach solu ion ollowed by Milli-Q, and 70% E OH wash.
• Take a piece o bench-co e ( hick plas ic bags) and co e he wo k able.
• Find he pe is al ic pump, h ee casse es and ma ching ubes and se up o il a ion. Clean he
pump and ubes wi h 10% bleach ollowed by milli-Q wa e .
• P epa e wo 50 ml Falcon ubes, one wi h ~40 ml 10% bleach solu ion and one who will con ain
il e ed seawa e – label hese acco dingly on sides and on caps.
3) SAMPLING
Sampling consis s o me ada a-logging using he CTD and collec ing seawa e using he Niskin bo le.
• Take he ollowing equipmen wi h you o he sample si e:
o CTD and ope ( ope is ound in he ub wi h he equipmen o he Niskin bo le)
o Tub con aining he 6 li e Niskin bo le and line
o 20 li e Nalgene sampling con aine
o Funnel and il e ( ound on op he sampling con aine s)
o Ga a ape (i alone, o a ach he il e o unnel and unnel o sampling con aine i windy)
o One sp ay bo le wi h 10% bleach solu ion and one wi h milli-Q wa e
o Mobile phone ( o accu a e ime and da e logging o CTD da a e ie al)
o O he sa e y equipmen
o Ni ile glo es
• A ach he ope secu ely o he op o he CTD and make su e i is long enough o each he
sampling dep h. A ach he o he end o he ope secu ely o he pie /boa .
• Remo e he “ lushing sy inge” om he bo om o he CTD and s o e i secu ely.
• No e da e and ime (as speci ic as possible, use sc eensho o h ps:// ime.is o example) when
you u n on he CTD and when i is below he wa e su ace.
• Keep he CTD jus below he su ace o a leas one minu e o calib a e he equipmen , now
lowe he CTD o he sampling dep h (~2 me e s) Impo an : No e ime e y p ecisely s ay a
he sampling dep h o wo ull minu es.
• Pull he CTD ou o he wa e and u n i o , lush he bo om o he CTD using he “ lushing
sy inge” illed wi h milli-Q wa e a leas wo imes. The CTD also needs a p ope showe wi h ab
wa e , his can wi h ad an age be done du ing he long il e ing s eps o sa e ime.
• Wash unnel and il e wi h 10% bleach and inse wi h milli-Q.
• Sample con aine s we e cleaned p ope ly p io o s o age so no need o clean hose wi h bleach i
he lids a e a ached secu ely. I lids a e open ollow he cleaning p ocedu e o Niskin bo le.
• Clean he 6 li e Niskin bo le wi h 10% bleach, wai > 5minu es, and inse in he sea.
• Sample 2x6 li e using he Niskin bo le a he sample dep h a he chosen loca ion.
• Emp y he Niskin bo le in o he unnel h ough he il e and in o he sample con aine , i he il e s
ge s clogged up, inse and clean be ween samples. Clean Niskin bo le wi h 10% bleach and
showe wi h ab wa e . This can wi h ad an age be done du ing he long il e ing s eps.
4) FILTERING
B ing all equipmen back om he sampling si e.
• Swi l he seawa e con aine o homogenize he wa e , ill a small aliquo con aine (e.g. a clean 1
l ja ) wi h seawa e , a ack a s e i ex il e o each o he ube ends and place he il e on he
edge o he h ee 1-li e ja s aped oge he . S a he pump on 60 pm and pump un il he wa e
le el in all h ee ja s ha e eached he black line (each s e i ex il e has now il e ed minimum
500 ml wa e ), he ini ial ja mus be e illed acco dingly, bu was e as li le seawa e as possible.
Remembe o ill one o he p e iously labeled alcon ubes wi h ~40 ml il e ed seawa e ( un-
h ough om one o hese s e i ex il e s).
• Remo e he s e i ex il e s om he ubes and pu hem in o alcon ubes labeled acco dingly.
• Clean ubes wi h 10% bleach solu ion and milli-Q wa e be o e disassembling he cons uc ion.
Re u n ubes and casse es o hei dedica ed zip-lock bags, bu lea e one casse e ou o he
nex il a ion se up.
• Find h ee new, wide , ubes in a bag labeled GO-sampling and a ach hem o he casse e and
he pe is al ic pump like igu e 1 below (do no add PC il e s ye ):
Figu e 1: Simpli ica ion o il e ing se up.
• Clean he il a ion appa a uses and ubes using 10% bleach solu ion and lush ho oughly wi h
milli-Q, and ca. 500ml sample seawa e , be o e applying he il e s.
• Clean o ceps in he alcon ubes con aining 10% bleach and inse in he il e ed seawa e alcon
ube. S o e in bleach a e use.
• Apply il e s using he clean o ceps in he o de shown in igu e 1.
• P ope ly mix he seawa e sampling con aine . Use he 10 li e Nalgene sampling bo le as was e
bo le and o measu e ou 5 li e s.
• Add elec onic ape o he h eads o he en ila ion al es and secu e hem using a w ench (do
no disassemble al es a e il a ion – lea e on un il nex sampling). Tigh en knobs and secu e
ube endings. Lea e he en ila ion al es open (lea e s aigh up in he ai ).
• S a il a ion o he i s 5 l seawa e a 60 pm, howe e , he speed may be adjus ed acco dingly
depending on he amoun o pa icles in he wa e (highe speed in win e , slowe in sp ing).
When wa e lows egula ly h ough he en ila ion al es, close hem.
• Co e he mou h o he sampling con aine du ing il a ion (e.g pa a ilm, in oil).
• When he il a ion s ep is inished, guide he emaining wa e h ough he ubes and allow ai o
un h ough he sys em (wi h he al es closed) o a while be o e eleasing he al es and he
p essu e in he sys em.
• Clean o ceps and scisso s in 10% bleach and inse in il e ed seawa e .
• Open ipod holde s and emo e il e (one a a ime!) using he o ceps. Pu he i s il e in a
140mm pe i dish and cu i in wo equally sized pieces using he scisso s. Place each hal (o
“ eplica e”) in sepa a e labeled 5 ml c yo ubes acco ding o Figu e 2. I is ecommended o oll
he il e s like ciga e e pape and olding while a oiding o mash i down he ube. Repea o he
second il e . Replica es 1 and 2 a e placed in DNA/RNA shield ully co e ing he il e while
eplica e 3 and 4 a e no . Place he c yo ubes on d y ice as soon as possible.
• Run 2 li e s o milli-Q wa e h ough he sys em wi hou any il e s.
• Repea he abo e men ioned s eps o a second un using ano he 5 li e s o seawa e o
eplica ed 3 and 4. Do no add DNA/RNA shield on hese samples. Place on d y ice as soon as
possible.
• Run 2 li e s o milli-Q wa e h ough he sys em wi hou any il e s.
• Run 5 li e s o milli-Q wa e h ough he sys em wi h il e s ( hese se e as nega i e con ols).
Nega i e con ols will be placed in DNA/RNA shield like eplica es 1 and 2, bu wi hou being cu
in wo. Place on d y ice as soon as possible.
• Disassemble ipods and pumps, clean se up and wo kspace acco dingly ( inse all pa s wi h 70
% e hanol and allow o d y, possibly o e nigh ) and s o e p ope ly.
• No e down CTD sampling imes in he small yellow book and ake a pho o o he page.
• Upda e he ma e ials lis o he nex isi !
Figu e 2: Summa y o he sampling p ocedu e. Look o e he samples he e, his is impo an .
