{"id":10135,"date":"2022-02-18T11:07:23","date_gmt":"2022-02-18T10:07:23","guid":{"rendered":"https:\/\/preprod.stygofaune-france.org\/environments-and-species\/sampling-equipment-and-protocols\/"},"modified":"2026-02-23T22:09:18","modified_gmt":"2026-02-23T21:09:18","slug":"sampling-equipment-and-protocols","status":"publish","type":"page","link":"https:\/\/preprod.stygofaune-france.org\/en\/environments-and-species\/sampling-equipment-and-protocols\/","title":{"rendered":"Sampling equipment and protocols"},"content":{"rendered":"<section\n        class=\"edito align-flex-center mb-80 bg-none\"\n>\n    <div class=\"edito__left-content\"\n         data-effect=\"fade-in-up-smooth\"\n         data-delay=\"1\"     >\n                    \n    \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/materiel-collecte.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Sampling equipment according to the habitats sampled\nOn the low wall: Cvetkov net or phreatobiological net. To the right of the photo: Bou-Rouch pump. \n\"        >\n    \n    <picture\n            class=\"picture-element size-large  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/materiel-collecte-300x225.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/materiel-collecte.jpg\"\n             alt=\"Mat\u00e9riel de collecte en fonction des habitats collect\u00e9s\"\n             loading=\"lazy\"\n             width=\"884\"\n             height=\"664\"\n        \/>\n    <\/picture>\n    <\/a>\n            <\/div>\n        <div class=\"edito__right-content\"\n         data-effect=\"fade-in-right\"\n         data-delay=\"1\"     >\n                    \n    \n<div class=\"paragrah \"\n     >\n    <h2>Sampling equipment<\/h2>\n<p>To collect the samples used to assess the aquatic fauna present at each site, specialised equipment and technical methods have been implemented.<\/p>\n<p>Depending on the type of habitat surveyed, different sampling devices are used:<\/p>\n<ul>\n<li>hand net,<\/li>\n<li>Cvetkov net or phreatobiological net,<\/li>\n<li>wide-opening net,<\/li>\n<li>Bou-Rouch probe\/pump,<\/li>\n<li>surface pump<\/li>\n<\/ul>\n<p>In all cases, the mesh size of the nets and filtration sieves is less than or equal to 250 microns, fine enough to capture the target stygobiotic species.<\/p>\n\n<\/div>            <\/div>\n<\/section>\n<section\n        class=\"text-full-width  bg-third mb-80 \"\n        >\n    <div class=\"text-full-width__content\">\n                    \n    \n<div class=\"paragrah mb-40\"\n     >\n    <h2 style=\"text-align: center;\">Sampling protocols<\/h2>\n<p style=\"text-align: center;\">Sampling procedures comply with the European Standard Protocol, developed during the PASCALIS programme and coordinated, among others, by the LEHNA team (see <a href=\"https:\/\/www.researchgate.net\/publication\/267567541_Sampling_Manual_for_the_Assessment_of_Regional_Groundwater_Biodiversity\">MALARD et al., 2002<\/a>).<\/p>\n\n<\/div>                    \n    <div class=\"key-figures-element mb-40 \">\n            <div class=\"key-figures-element__item with-icon\">\n            <div>\n                                <div class=\"key-figures-element__content\">\n                                            \n    \n<div class=\"paragrah \"\n     >\n    <h3>Springs<\/h3>\n<p>For springs, the protocol must be adapted to the outlet facies, ensuring sampling at the most upstream and darkest physically accessible point, using a:<\/p>\n<ul>\n<li>&#8220;hand net&#8221; used as a filtering trap, positioned (like a Surber net) across a water flow, if it is strong enough (rheotic facies) to carry in elements put into suspension upstream by scraping\/stirring the substrate;<\/li>\n<li>&#8220;hand net&#8221; used as a sieve and fed with substrate samples, if the water flow is weak (lentic facies), diffuse, or the water volume is very large (specifically when a &#8220;spring eye&#8221; cannot be distinguished or accessed).<\/li>\n<\/ul>\n\n<\/div>                                            \n    <div class=\"pictures__group  flex-end\"\n     >\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-a-main.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Hand net\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-a-main-300x226.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-a-main-150x150.jpg\"\n             alt=\"Filet \u00e0 mains utilis\u00e9 comme pi\u00e8ge filtrant et positionn\u00e9 au travers d'un flux d'eau pour la collecte \u00e0 vue de la faune aquatique.\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n    <\/div>                                    <\/div>\n            <\/div>\n        <\/div>\n            <div class=\"key-figures-element__item with-icon\">\n            <div>\n                                <div class=\"key-figures-element__content\">\n                                            \n    \n<div class=\"paragrah mb-20\"\n     >\n    <h3>Groundwater<\/h3>\n<p>For groundwater, sampling is typically carried out from above:<\/p>\n<ul>\n<li>using a phreatobiological net (Cvetkov-type net) fitted with a rope of variable length; appropriate handling allows the water column to be stirred\/filtered, thereby suspending and filtering fauna likely to rest on the bottom and walls.<\/li>\n<li>by pumping from a piezometer using a manual surface pump (the same type of pump as that used with the Bou-Rouch probe), connected to a flexible hose (30 mm external diameter) ending in a screened section. The hose is lowered to the bottom of the piezometer in order to collect the bottom sediments where the target organisms are found, rather than those only present in the water column. <\/li>\n<\/ul>\n\n<\/div>                                            \n    <div class=\"pictures__group  flex-end\"\n     >\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-cvetkov.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Cvetkov net\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-cvetkov-300x300.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-cvetkov-150x150.jpg\"\n             alt=\"Filet Cvetkov \u00a0: d\u00e9tail et maniement in situ\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-phreatobiologique.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Phreatobiological net: detail and in situ handling\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-phreatobiologique-300x293.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/filet-phreatobiologique-150x150.jpg\"\n             alt=\"Filet phr\u00e9atobiologique, \u00e9quip\u00e9 d'un cordage pour collecter la faune\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompage-piezometre.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Pumping from a piezometer\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompage-piezometre-300x249.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompage-piezometre-150x150.jpg\"\n             alt=\"Pompage dans un pi\u00e9zom\u00e8tre (captage AEP -r\u00e9seau d'adduction d'eau potable du Syndicat des Eaux d'Alviganc-Montvalent, 46)\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n    <\/div>                                    <\/div>\n            <\/div>\n        <\/div>\n            <div class=\"key-figures-element__item with-icon\">\n            <div>\n                                <div class=\"key-figures-element__content\">\n                                            \n    \n<div class=\"paragrah mb-20\"\n     >\n    <h3>Underground rivers<\/h3>\n<p>For underground rivers, the sampling methodology consists of placing a:<\/p>\n<ul>\n<li>hand net positioned across the water flow (like a Surber net in a rheotic environment), in front of which the surface of the sediment or any living substrates present in the streambed (stones, rocks, dead wood, etc.) are stirred.<\/li>\n<\/ul>\n\n<\/div>                                            \n    <div class=\"pictures__group  flex-start\"\n     >\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/plongee-resurgence-sorpt.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Dive in a pool of water, Sorpt resurgence (municipality of Chasteaux, 19)\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-right with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/plongee-resurgence-sorpt-225x300.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/plongee-resurgence-sorpt-150x150.jpg\"\n             alt=\"Plong\u00e9e subaquatique ou sp\u00e9l\u00e9oplong\u00e9e dans une vasque d\u2019eau, r\u00e9surgence de la source karstique du Sorpt (commune de Chasteaux, 19)\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n    <\/div>                                    <\/div>\n            <\/div>\n        <\/div>\n            <div class=\"key-figures-element__item with-icon\">\n            <div>\n                                <div class=\"key-figures-element__content\">\n                                            \n    \n<div class=\"paragrah mb-20\"\n     >\n    <h3>Surface watercourses<\/h3>\n<p>In the bed of surface watercourses, sampling is carried out using a:<\/p>\n<ul>\n<li>probe\/pump (Bou-Rouch type), operated by driving a screened metal tube deep into the substrate (20\u2013120 cm), drawing water using a pump mounted on the other end, and then filtering the sample at the pump outlet.<\/li>\n<\/ul>\n\n<\/div>                                            \n    <div class=\"pictures__group  flex-end\"\n     >\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch-maniement.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Bou-Rouch pump: operation\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch-maniement-300x225.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch-maniement-150x150.jpg\"\n             alt=\"Pompe Bou-Rouch\u00a0: maniement\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n            <div class=\"pictures__item\">\n            \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Bou-Rouch pump: detail\n\"        >\n    \n    <picture\n            class=\"picture-element size-thumbnail  align-none with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch-157x300.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/pompe-bou-rouch-150x150.jpg\"\n             alt=\"D\u00e9tail de la Pompe Bou-Rouch, avec pompe d'aspiration \u00e0 piston, tube m\u00e9tallique pointu et avec une partie cr\u00e9pin\u00e9e \u00e0 la base et t\u00eate de frappe\"\n             loading=\"lazy\"\n             width=\"150\"\n             height=\"150\"\n        \/>\n    <\/picture>\n    <\/a>\n        <\/div>\n    <\/div>                                    <\/div>\n            <\/div>\n        <\/div>\n    <\/div>\n                    \n    <div class=\"focus  program\">\n            <span class=\"material-icons-outlined\">biotech<\/span>\n        <div class=\"focus__content\">\n        <h4>Are other sampling methods used?<\/h4>\n<p>As soon as conditions allow (immersion in an underground or near-dark environment, with no prior disturbance of the habitat), in addition to the sampling methods mentioned above, it is possible to carry out &#8220;visual&#8221; collection (with the naked eye or a magnifying glass) by carefully observing the substrate walls and all living supports present (dead wood, stones, etc.).<\/p>\n\n    <\/div>\n<\/div>            <\/div>\n\n<\/section>\n<section\n        class=\"text-full-width  bg-none mb-80 \"\n        data-effect=\"fade\" data-delay=\"1\" >\n    <div class=\"text-full-width__content\">\n                    \n    \n\n    <a href=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/sonde-multi-parametres.jpg\"\n   class=\"picture-element__link  glightbox \"\n   data-title=\"Multi-parameter probe (\u00a9 HANNA instruments)\n\"        >\n    \n    <picture\n            class=\"picture-element size-medium mb-20 align-left with-link\">\n        <source srcset=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/sonde-multi-parametres-221x300.jpg\" media=\"(max-width:475px)\"\/>\n        <img decoding=\"async\" src=\"https:\/\/preprod.stygofaune-france.org\/app\/uploads\/sonde-multi-parametres-221x300.jpg\"\n             alt=\"Sonde multi-param\u00e8tres (\u00a9 HANNA instruments)\"\n             loading=\"lazy\"\n             width=\"221\"\n             height=\"300\"\n        \/>\n    <\/picture>\n    <\/a>\n                    \n    \n<div class=\"paragrah mb-20\"\n     >\n    <h2 class=\"p1\">Field measurements and data collection<\/h2>\n<h3 class=\"p1\"><span class=\"s1\">Physico-chemical analyses<\/span><\/h3>\n<p class=\"p1\">Before each sampling event, the physico-chemical parameters of temperature (T\u00b0), acidity (pH) and electrical conductivity (Ev) are measured on site (as close as possible to mid-depth in the water column) using a field multi-parameter probe.<\/p>\n<p class=\"p1\">A large volume of water is collected (always as close as possible to mid-depth in the water column) in order to measure, using field kits, the parameters of dissolved oxygen (O<span class=\"s1\"><sub>2<\/sub><\/span>), ammonium (NH<span class=\"s1\"><sub>4<\/sub><\/span>+), phosphate (PO<span class=\"s1\"><sub>4<\/sub><sup>3-<\/sup><\/span>), calcium carbonate (CaCo<span class=\"s1\"><sub>3<\/sub><\/span>), sulfate (SO<span class=\"s1\"><sub>4<\/sub><sup>2-<\/sup><\/span>), nitrate (NO<span class=\"s1\"><sub>3<\/sub><sup>2-<\/sup><\/span>) and nitrite (NO<span class=\"s1\"><sub>2<\/sub><sup>&#8211;<\/sup><\/span>).<\/p>\n<p class=\"p1\">A 1 L water sample will be set aside and stored in a bottle (double-capped and labelled) so that the recorded measurements can be checked later, if necessary.<\/p>\n<h3>Preservation, sorting &amp; identification of samples<\/h3>\n<p>After filtration, the sampling residue is placed in a medium-capacity bottle (200 to 500 ml, double-capped and labelled) and immediately fixed on site by adding 99.9% alcohol in sufficient quantity (after dilution) to obtain a preservation solution of at least 70% alcohol.<\/p>\n<p>After sorting under a stereomicroscope, specimens are stored by major taxonomic groups in 2 ml microtubes designed for long-term preservation (O-ring seal), labelled inside and out, and completely filled with 99.9% alcohol.<\/p>\n<p>Midway through and at the end of sampling, they are then sent for confirmation\/identification to the <a href=\"https:\/\/preprod.stygofaune-france.org\/reseau-stygofaune\/\">taxonomic experts associated with the study programme<\/a>.<\/p>\n\n<\/div>                    \n    <div class=\"focus mb-20 info\">\n            <span class=\"material-icons-outlined\">lightbulb<\/span>\n        <div class=\"focus__content\">\n        <p>Please note that once removed from their environment, all specimens must be preserved in a solution of \u2265 70% alcohol; otherwise their DNA molecules may degrade, compromising subsequent genetic (sequencing) analyses.<\/p>\n\n    <\/div>\n<\/div>                    \n    \n<div class=\"paragrah \"\n     >\n    <h3>Data recording<\/h3>\n<p>In parallel with sampling, a field <strong>&#8220;Sampling Sheet&#8221;<\/strong> is completed for each site, in order to immediately record, in addition to the measured physico-chemical water parameters, the sampling conditions and the main characteristics of the sampling point, as well as a faunal and floral survey of the immediate surroundings.<\/p>\n<p>The information collected on site is used, among other things, to produce a <strong>&#8220;Topo Sheet&#8221;<\/strong> for each site, which brings together data on:<\/p>\n<ul>\n<li>toponymy,<\/li>\n<li>topography,<\/li>\n<li>geolocation,<\/li>\n<li>geology-hydrogeology,<\/li>\n<li>as well as historical and heritage data,<\/li>\n<li>and a photographic illustration of the site.<\/li>\n<\/ul>\n<p>Data relating to the identification of the collected <a href=\"https:\/\/\/\/preprod.stygofaune-france.org\/milieux-et-especes\/especes\/\">aquatic fauna<\/a> are recorded in a <strong>&#8220;Sorting &amp; Identification Sheet&#8221;<\/strong> which, in addition to the counts for each major identified taxon, reproduces the working photographs taken under the microscope and assigns each site and each specimen a unique preservation code.<\/p>\n\n<\/div>            <\/div>\n\n<\/section>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":10091,"parent":10098,"menu_order":19,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"class_list":["post-10135","page","type-page","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/pages\/10135","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/comments?post=10135"}],"version-history":[{"count":2,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/pages\/10135\/revisions"}],"predecessor-version":[{"id":10146,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/pages\/10135\/revisions\/10146"}],"up":[{"embeddable":true,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/pages\/10098"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/media\/10091"}],"wp:attachment":[{"href":"https:\/\/preprod.stygofaune-france.org\/en\/wp-json\/wp\/v2\/media?parent=10135"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}