In all studies, it is important to adapt the size and the
number of samples in order to consider the spatial heterogeneity existing in the soil (due both to the soil itself and the
presence of vegetation cover), so that this heterogeneity does
not hide the studied effect or get confused with it. To obtain a
representative sample of the study site, it is better to collect
several soil cores, group them, mix them, and sift them (with a
2 mm mesh sieve) to create a homogeneous sample before
starting the analysis. To avoid the contamination between
different sites, it is necessary between each site to clean the
auger by ridding it of a maximum of soil and possibly to rinse it
with ethanol (70 %) and then to dry it with a clean paper.
It is sometimes necessary to look the soil organization at a
microscale, the scale of the soil aggregate. In this case, soil
aggregates (for the desired size, often by a few millimeters)
(Grundmann and Debouzie 2000) are sorted from the soil core,
under a binocular loupe with sterile material before analysis.
Some approaches are intended to dissociate the
microorganisms located in or outside the aggregates (and therefore more or less exposed to mobile water with charged ions
and soluble elements circulating in the ground). In this case,
methods with moderate soil washing can be used to recover the
microorganisms localized on the surface of aggregates
(Ranjard et al. 1997), the microorganisms remaining with the
aggregates being predominantly those located inside.
17.2.2 Sampling Techniques in Aquatic
Environment
Although the development of automatic sensors now permits the
in situ acquisition of many hydrological parameters related to
the physiology of living organisms, water sampling still
represents a primary and obligatory step in the collection of
large amounts of data from the marine environment and especially for the collection of microorganisms. Collection can be
considered the process of obtaining an aliquot of the studied
aquatic environment. Sampling consists of retaining, preserving,
and storing a portion of this collected water for analytical
purposes. It should be noted that sampling is only relevant if
the water collection is conducted correctly and is representative
of the studied environment. In some cases, water collection and
sampling are merged, especially when contamination absolutely
has to be prevented. Collection and pretreatment of water
samples and sediment in the field present certain difficulties
in comparison to laboratory work. There are also difficulties
associated with working on a vessel, where the working
conditions are rarely comparable to those in laboratories. This
chapter documents methods and useful equipment for collecting
marine samples and processing them for various downstream
applications, including analyses of nutrients and gases, biomass
concentration, cell abundance and experimentation, both offshore rather than at the coast and in shallow lagoons.
17.2.2.1 Equipment for Water Collection
Collection of Surface Water by Hand
This procedure is only applicable to collection of surface water
from the water’s edge (e.g., at a beach or harbor deck) or from
a small boat at a short distance from the coast. This type of
sampling does not require specific equipment. A surface sample can be collected using a simple bucket, assuming that this
simple device is compatible with the subsequent analyses.
Nevertheless, if possible, it is better to collect water samples
directly in the flasks that will be used to store the samples, to
reduce contamination due to intermediate handling. In all
cases, the hands of the sampler have to be protected by polyethylene gloves, and sampling is performed by immersing the
bucket or bottle under the surface, as far as possible from the
boat or deck. A “fishing rod” system can be helpful in
collecting water at a distance from a boat or deck.
Sampling with Hydrological Bottles
This technique is used to collect water at depths below the
surface as well as at the surface when hand sampling is
impossible or inappropriate. First, the boat must be equipped
with a winch system to unwind a cable on which hydrological bottles are attached. On small boats, hand winches are
suitable for this purpose. In all cases, it is necessary to ensure
that the chemical quality of the cable is suitable for the
chemical analysis and experiments to be conducted on the
samples. In addition, it is essential to estimate the depth of
sampling accurately. One suitable approach is to equip the
winch with a counting pulley; another is to mark some
lengths along the cable. However, the best approach is to
install a pressure sensor or gauge at the end of the cable.
Nansen The first hydrological bottle was developed in 1910
by the oceanographer Fridtjof. This bottle was entirely made of
brass and remained the typical oceanographic instrument until
1966, when Shale Niskin designed a new bottle from a PVC
Box 17.1 (continued)
The extension of research on the deep biosphere
through these techniques will allow to describe the
immense biodiversity of the subsurface of our planet
and try to understand how bacterial communities have
persisted in such extremely nutrient-limited environment, isolated from any contribution from the surface
for tens of thousands, even hundreds of millions of
years. The adventure is just beginning.
760
F. Joux et al.
number of samples in order to consider the spatial heterogeneity existing in the soil (due both to the soil itself and the
presence of vegetation cover), so that this heterogeneity does
not hide the studied effect or get confused with it. To obtain a
representative sample of the study site, it is better to collect
several soil cores, group them, mix them, and sift them (with a
2 mm mesh sieve) to create a homogeneous sample before
starting the analysis. To avoid the contamination between
different sites, it is necessary between each site to clean the
auger by ridding it of a maximum of soil and possibly to rinse it
with ethanol (70 %) and then to dry it with a clean paper.
It is sometimes necessary to look the soil organization at a
microscale, the scale of the soil aggregate. In this case, soil
aggregates (for the desired size, often by a few millimeters)
(Grundmann and Debouzie 2000) are sorted from the soil core,
under a binocular loupe with sterile material before analysis.
Some approaches are intended to dissociate the
microorganisms located in or outside the aggregates (and therefore more or less exposed to mobile water with charged ions
and soluble elements circulating in the ground). In this case,
methods with moderate soil washing can be used to recover the
microorganisms localized on the surface of aggregates
(Ranjard et al. 1997), the microorganisms remaining with the
aggregates being predominantly those located inside.
17.2.2 Sampling Techniques in Aquatic
Environment
Although the development of automatic sensors now permits the
in situ acquisition of many hydrological parameters related to
the physiology of living organisms, water sampling still
represents a primary and obligatory step in the collection of
large amounts of data from the marine environment and especially for the collection of microorganisms. Collection can be
considered the process of obtaining an aliquot of the studied
aquatic environment. Sampling consists of retaining, preserving,
and storing a portion of this collected water for analytical
purposes. It should be noted that sampling is only relevant if
the water collection is conducted correctly and is representative
of the studied environment. In some cases, water collection and
sampling are merged, especially when contamination absolutely
has to be prevented. Collection and pretreatment of water
samples and sediment in the field present certain difficulties
in comparison to laboratory work. There are also difficulties
associated with working on a vessel, where the working
conditions are rarely comparable to those in laboratories. This
chapter documents methods and useful equipment for collecting
marine samples and processing them for various downstream
applications, including analyses of nutrients and gases, biomass
concentration, cell abundance and experimentation, both offshore rather than at the coast and in shallow lagoons.
17.2.2.1 Equipment for Water Collection
Collection of Surface Water by Hand
This procedure is only applicable to collection of surface water
from the water’s edge (e.g., at a beach or harbor deck) or from
a small boat at a short distance from the coast. This type of
sampling does not require specific equipment. A surface sample can be collected using a simple bucket, assuming that this
simple device is compatible with the subsequent analyses.
Nevertheless, if possible, it is better to collect water samples
directly in the flasks that will be used to store the samples, to
reduce contamination due to intermediate handling. In all
cases, the hands of the sampler have to be protected by polyethylene gloves, and sampling is performed by immersing the
bucket or bottle under the surface, as far as possible from the
boat or deck. A “fishing rod” system can be helpful in
collecting water at a distance from a boat or deck.
Sampling with Hydrological Bottles
This technique is used to collect water at depths below the
surface as well as at the surface when hand sampling is
impossible or inappropriate. First, the boat must be equipped
with a winch system to unwind a cable on which hydrological bottles are attached. On small boats, hand winches are
suitable for this purpose. In all cases, it is necessary to ensure
that the chemical quality of the cable is suitable for the
chemical analysis and experiments to be conducted on the
samples. In addition, it is essential to estimate the depth of
sampling accurately. One suitable approach is to equip the
winch with a counting pulley; another is to mark some
lengths along the cable. However, the best approach is to
install a pressure sensor or gauge at the end of the cable.
Nansen The first hydrological bottle was developed in 1910
by the oceanographer Fridtjof. This bottle was entirely made of
brass and remained the typical oceanographic instrument until
1966, when Shale Niskin designed a new bottle from a PVC
Box 17.1 (continued)
The extension of research on the deep biosphere
through these techniques will allow to describe the
immense biodiversity of the subsurface of our planet
and try to understand how bacterial communities have
persisted in such extremely nutrient-limited environment, isolated from any contribution from the surface
for tens of thousands, even hundreds of millions of
years. The adventure is just beginning.
760
F. Joux et al.