Methods for sampling and analysis of

organic wetland soils in Uganda

Jenny Farmer (University of Aberdeen, Scotland, and Carbon

Foundation of East Africa, Uganda)

Charlie Langan (Carbon Foundation of East Africa, Uganda)

Mark Stewart Kibirango (National Agricultural Research

Organisation, Kawanda Laboratories, Uganda)

Version 1, August 2016

Contents 1 Introduction .................................................................................................................................... 3

1.1 Background to this document ................................................................................................. 3

1.2 Wetlands in Uganda ................................................................................................................ 3

1.3 Wetland soils ........................................................................................................................... 4

1.3.1 Organic soils .................................................................................................................... 4

1.3.2 Organic soils in Uganda ................................................................................................... 5

1.3.3 Wetland soils data in Uganda .......................................................................................... 6

2 Field sampling ................................................................................................................................. 9

2.1 Research objectives ................................................................................................................. 9

2.2 Planning................................................................................................................................... 9

2.3 Field campaigns ..................................................................................................................... 11

2.3.1 Equipment ..................................................................................................................... 11

2.3.2 Field team...................................................................................................................... 12

2.3.3 Sampling methods ........................................................................................................ 13

3 Soil data collection ........................................................................................................................ 18

3.1.1 Field based observations ............................................................................................... 18

3.1.2 Laboratory analysis ....................................................................................................... 19

4 Appendix 1 .................................................................................................................................... 23

4.1 Basic characterisation ........................................................................................................... 23

4.2 Von Post scale ....................................................................................................................... 23

4.3 Modified Troels Smith humicity score ................................................................................... 24

5 Appendix 2 .................................................................................................................................... 25

6 References ..................................................................................................................................... 26

1 Introduction

1.1 Background to this document

This document has been developed during the Alternative Carbon Investments in Ecosystems for

Poverty Alleviation (ALTER) research project in Uganda. ALTER is a 3 year research project based in

Ethiopia and Uganda which aims to demonstrate that there are real and lasting benefits for wide

scale poverty alleviation, particularly for the rural poor, by tackling soil degradation at a range of

scales, from field to landscape, using opportunities within existing agricultural areas as well as

severely degraded land. While the project has focused on studying dryland mineral soils in Ethiopia,

it has focused on organic wetland soils in Uganda.

During the first 6 months of the project ALTER researchers from the University of Aberdeen and the

Carbon Foundation of East Africa worked to collate existing information on the wetlands and organic

soils of Uganda, and socio-economic data linked to poverty (Langan and Farmer 2013). It was found

that there is very little data on wetland soils in Uganda. At a national level the national soil surveys

contained no records of soil sampling in the wetland areas. Inquiries with national agencies,

Universities, research agencies, NGO’s and local government offices also yielded no detailed studies.

A few individual research projects by researchers and students were found to have collected some

data on wetland soils, but the research was very limited in its extent.

Based on this, it was concluded that there was a large gap in wetland soils research in Uganda, in

particular of the organic soils which can be found in wetland areas of the country. Wetland soils can

be organic or mineral, or a mixture of the two due to sediment deposition in wetland areas. The

sampling and analytical procedures for these are all different, and it is important that the

appropriate methods are used. During the course of the ALTER research project, researchers have

worked to develop the sampling protocols appropriate for sampling Uganda’s organic wetland soils,

which have been trialled and tested in the field in wetlands sites in Kabale District. These protocols

have been based on internationally used methods for organic soil sampling, modified and adapted to

suit local field conditions and available equipment. In collaboration with the National Agricultural

Research Organisation’s laboratories at Kawanda, laboratory analytical procedures for organic soil

analysis have also been refined for specific use in Uganda.

This document is focused specifically on the protocols and methods for sampling and analysis of

organic wetland soils in Uganda, based on experiences in Kabale during the ALTER project. In the

coming years it is hoped to expand this document to provide details on sampling of all wetland soil

types and field conditions across Uganda.

1.2 Wetlands in Uganda

Wetlands in Uganda take on a variety of forms, across the wide lowland plains in the East (such as in

Pallisa), around lake edges (as around Lake Nakivale), and in valley bottoms (such as in Kabale). The

most recent inventory of wetlands in Uganda conducted by the Wetlands Management Department

(WMD), found that 10.9% of Uganda was covered with wetlands in 2008 (26,308 km2). This was a

30% reduction from the first national survey in 1994, which showed wetland coverage over 37,575

km2 (WMD 2008)1. Many small-scale wetlands were not included in this inventory, even though they

1 The 1994 inventory was based on both digital mapping and ground-truthing, the 2008 inventory on digital mapping only

provide valuable services and benefits to surrounding communities. Of Uganda’s total wetland area,

78% is classed as seasonal wetlands, and 23% as permanent (WMD 2008). Natural vegetation type

varies across wetland areas, predominantly grassland, papyrus and woodland, but also palms,

thickets and floating vegetation such as lilies. Vegetation succession is dependent on the water table

conditions which regulates plant communities (Petr, 2000 and UNEP Vol. IX). The role of

geomorphological, hydrological and vegetation characteristics play a significant part in the properties

on the underlying wetland soils.

1.3 Wetland soils

1.3.1 Organic soils

Formation of organic soils

Organic (peat) soils are typically formed under waterlogged conditions, where the water table level

is above the surface of the soil, thus creating anaerobic conditions whereby microbial decomposition

of the soil is limited. As dead plant material falls to the floor, it builds up under the water,

disintegrating rather than decomposing, leading to a continual accumulation of organic matter over

time which creates soils which are highly organic in their nature. Peat can accumulate at a rate of

anything between 0.5-3mm yr-1 (Sorensen, 1993). If the wetland is minerotrophic (receiving run-off

from outside the wetland area such as from hillslopes or rivers) then there is likely to be some

deposition of mineral sediments and nutrients into the organic soil layers.

Characteristics of organic soils

The definition of an organic, or peat, soil varies somewhat as there are a number of international soil

classification systems. Both the FAO soil classification and USDA soil taxonomy system class them

under Histosols, defined as having more than 40cm of organic soil material in the surface 80cm, with

organic soil material having 12-18% organic carbon. Peat soils have similarly been defined by others

as those having an organic layer more than 50cm deep, with this organic layer comprising more than

30% organic material (18% carbon content, Agus et al., 2011).

The composition of the soil depends on the original parent vegetation and environmental conditions

at that time. Down a full peat profile (which can cover time periods of thousands of years) changes in

both of these can be observed. The maturity of the peat material, or its level of decomposition or

disintegration can also be observed down the profile, ranging from fibric (least disintegrated), to

hemic and sapric (most disintegrated). Organic soils are carbon rich due to the high levels of organic

material present (approximately 50% of organic material is carbon). They are typically acidic, due to

the high presence of organic compounds. The principal mineral components found in organic soils

are carbon, hydrogen, oxygen and nitrogen, the presence of any others depends predominantly on

mineral soil mixing e.g. from erosion elsewhere in the catchment or riverine deposition.

Degradation of organic soils

As a wetland is drained, the organic soil is exposed to the atmosphere beginning a process of

decomposition of the previously unexposed plant material. Considerable carbon losses result, as the

organic material undergoes rapid microbial decomposition. Organic material decomposes at different

rates, with more easily decomposable material (more active) having a higher turnover rate than the

more stable material (Whitbread, 1992). Nutrient changes can also occur due to the change in field

conditions and land use (Holden, Chapman, & Labadz, 2004), and in some areas a build-up of

pathogens and soil borne diseases occurs due to the loss of flooding regimes (Andriesse, 1988).

Wetland areas which receive run-off from outside of the wetland system will receive additional

nutrients as sediment is deposited, they will likely also receive pests and pathogens too. Without

regular flooding these can build up in the soil.

Drainage changes the hydrological properties of the soil, and can cause changes such as irreversible

drying where the soil loses its water holding capacity and becomes resistant to rewetting. This has

significant implications for the ability of the soil to recover from a drainage event.

Figure 1 Water logged conditions resulting in peat formation (L), and drainage affected organic wetland soils exposed to the air, resulting in irreversible change (R)

1.3.2 Organic soils in Uganda

Data on wetland soils in Uganda is extremely limited. Wetland soils across the country comprise of

different soil properties, ranging from high to low organic matter contents, often with underlying

base-clay layers, some experiencing build-up of sediment eroded from elsewhere in the catchment.

Organic soils underpin some of these wetland ecosystems, and are high in soil organic carbon (SOC)

due to lack of decomposition of dead plant material under the waterlogged conditions, although

data on this is lacking for Uganda (Marchant, Taylor, & Hamilton, 1997). In addition to the soil,

floating wetland vegetation can have a thick rhizome mat, made up of live and dead roots and

organic matter.

In the lowland wetlands (1,240 to 1,900 m above sea level) there is relatively rapid decomposition of

the thin layer of organic material, below which is a deep layer of clay (UNEP Vol. IX). In upland

wetlands (over 1,900 m above sea level) a thicker layer of organic material (peat) built up over time is

present. Organic soil depth in Uganda’s wetlands is highly variable and research is very limited with

studies showing a range of wetland organic soil depths, some more than 20 m deep (Farmer et al.

2015, Marchant et al. 1997; AERDP 2004), with estimates of 1.3- 1.5 Gt of SOC reported to be

sequestered in these soils in Uganda (Joosten, 2009; Page, Rieley, & Banks, 2011). These peat

deposits contain extensive historical data on past climate and vegetation regimes as the plant

material is preserved over thousands of years (the oldest deposits so far studied show over 23,000

years of historical information, Taylor, 1990), yet have only received limited research attention

(Hamilton & Taylor, 1986).

1.3.2.1 Organic soils and ecosystem services

Ecosystem services are defined as the benefits people obtain from ecosystems, covering

provisioning, regulating, supporting and cultural services (MEA 2005). Wetlands in Uganda, in both

their intact and modified states, deliver key ecosystem services derived from the soils. Intact

wetlands supply a diverse variety of services across all ecosystem service categories. Most

importantly, the supporting services maintain the general condition of the wetland. Ecosystem

services from intact wetlands are often public goods or open access resources benefiting a range of

stakeholders. After land use conversion to agriculture, there is a systematic skew towards

provisioning ecosystem services, with significantly reduced supporting, regulating and cultural

services. There is also a shift in the beneficiaries of these services. The introduction of alternative

land management practices in wetlands can be maintained in a sustainable balance, benefiting

communities whilst preserving the wetland ecosystem, as has been done historically and

traditionally within Uganda in the past (Iyango et al., n.d.). However, Uganda is currently seeing an

increase in the unsustainable use of wetland resources.

Considering the supporting role that soil formation plays in wetland systems, it can be argued that

soil quality is important in the supply of all wetland ecosystem services. Organic matter in these soils

is maintained by the balance of inputs to the soil from plants, and the

decomposition from soil micro-organisms. The chemical balance of the

organic matter regulates this microbial activity, and in organic soils where

carbon makes up the major proportion of the soil organic matter, any

changes to this element (e.g. due to drainage of soil) will affect the

functionality and composition of soil microorganisms (Kutsch et al. 2009).

Figure 2 demonstrates the linkages of the supporting role that soil carbon

plays in the wetland ecosystem, leading to human wellbeing as a result of

poverty alleviation (ALTER 2013).

Climate regulation is a principal ecosystem service provided by wetlands.

As organic material is preserved under the waterlogged conditions it

creates a significant stock of carbon. The carbon stock in organic soils of

Uganda is estimated at 1.3 Gt, giving it the 20th largest peat based carbon

stock of all countries in the world (Joosten, 2009). Methane, nitrous oxide

and carbon dioxide emissions are all emitted from these soils, depending

on the water table level, with carbon dioxide being the principal gas

emitted once drainage has occurred (Hergoualc’h & Verchot, 2013).

Uganda was reported to have the 12th highest emissions from degrading

peat of all countries in the world (Joosten, 2009), as a result of drainage of

the organic wetland soils and the oxidation of the soil carbon stocks. This

has significant implications for climate change impacts.

1.3.3 Wetland soils data in Uganda

Some data related to wetlands, their uses and the socio-economic dependencies of the people living

around them does exist for Uganda. However, data collection has been patchy, scattered between

Figure 2 Links between soil carbon and human well being

different institutions, and is often driven by donor projects rather than institutional strategic plans.

There have been commendable efforts to conduct national soil and wetland surveys across Uganda,

however large time gaps between surveys make it difficult to consistently monitor change. Along

with national surveys, a number of individual research and conservation projects have collected data

for baseline and impact surveys, along with

MSc or PhD studies.

The availability of maps is limited; the

National Ordinance Survey carried out in the

1950s and 60s remains the major source for

maps of the country, however this did not

document any sampling of the wetland

organic soils, as evidenced by the gaps in

memoirs recording the details of the study

(Harrop, 1960). The process of digitising

these original soil maps has begun, with the

central and eastern areas of Uganda already

completed, although there is uncertainty as

to the time frame on digitising the remaining

areas, to date this work has been conducted

through a collaboration between NEMA and

NARO. A new national soils inventory is

currently being implemented, but again

without any sampling in wetland areas. The

Wetlands Management Department has

developed maps of national wetland

coverage for the country, the most recent

from 2008 (Figure 3). Wetlands International

has recently developed peat maps for the

tropics, including one for Uganda, which details the peat coverage, certainty in the coverage and the

level of peat degradation.

Some individual projects have analysed surface soil samples in wetland systems (Kanyiginya,

Kansiime, Kimwaga, & Mashauri, 2010; Lind & Visser, 1962). There have been very few individual

research projects that have taken peat cores in the country (Marchant et al., 1997), and no national-

level field campaign. One individual energy report shows results from peat analysis at nine points

across the country (AERDP, 2004).

In 1996, wetland status reports were produced at District level for key districts, each of these

detailing the wetlands within the District. Within these there is a one-page description for each

wetland in the District, with a description of the physical features of the wetlands, under which a

comment on soils was included e.g. ‘soils contain peat’, or ‘soils are course texture and contain peat’

(NWCMP, 1996a, b).

Aniku (1996) reports on the wetland soils of Uganda, describing the 18 soil series found in wetlands.

Descriptions are focused on the location of each soil series, their formation, fertility and uses. For

some soils the typical pH and saturation are described. Under this categorisation most soils are a

Figure 3 Wetland areas in Uganda. Wetlands Management Department, 2008

form of clay loam, some with sand. One wetland soil is described as ‘papyrus peat’, and is recorded

to cover 1,046 km2 of the country. This peat is said to be found in valleys of the Kigezi, Ankole and

Buganda regions and along the waterlogged fringes of Lake Victoria and Lake Kyoga, formed from

papyrus residues and river alluvium (Aniku, 1996). Aniku (1996) comments that the deeper peat

found in the Kigezi highlands is due to lower temperatures, compared to the other, warmer, areas

where peat is shallower.

The lack of any detailed analysis on the depth, structure and elements found in the wetland soils can

be assumed to be due to the difficult field conditions within the wetlands. Although there is the

capacity at the National Agricultural Research Laboratories at Kawanda and Makerere University

laboratories to analyse soils, the equipment for sampling peat soils at depth in the field has not been

available in country.

Table 1 Summary of national level wetland soils information

Data type Format Description Source

Soils data Hard copy maps and memoirs

Maps developed in the 1950’s and 60’s, with accompanying notes on the areas sampled. The soil across Uganda is mapped, and although some notes on the peat soils were made, there is no accompanying analysis of these soils.

Photographs of the maps available online. Hard copies available to view at the National Agricultural Research Organisation soils laboratories. Memoirs are held at Kawanda, with the hope that one day they will be digitised.

Soils data Digital map

Digital maps for four of the plates of the original soil maps for the country, covering central and eastern areas.

Kawanda/NARO

Peat coverage Digital map

Map with areas of peat in Uganda Kawanda/NARO

Wetlands coverage

Map Wetlands coverage maps for Uganda- 1994, 2008. Permanent and seasonal wetland coverage. Sub-county level.

Wetlands Management Department/ NFA Biomass Survey

Wetlands inventory data

Database Details on wetland type, ecological features, wetland uses, wetland degradation, wetland conservation activities. Held within the NWIS.

Wetlands Management Department

Peat coverage Digital map

Coverage of peat in Uganda, with details on the certainty of peat being present and the level of degradation

Wetlands International (in preparation)

2 Field sampling

Here we discuss the details of sampling organic wetland soils, including some of the key

considerations when developing a research plan, approaches to fieldwork, and options for soil

analysis.

2.1 Research objectives

There are many reasons as to why people would want to sample organic soils. The main reasons that

these soils have been studied in the past in Uganda include:

- for paleo-ecological research linked to past climate and vegetation regimes, and historical

environmental degradation (Hamilton & Taylor, 1986; Marchant et al., 1997; Morrison &

Hamilton, 1974; Morrison, 1968; Taylor, 1990)

- understanding the impacts of land use change on soil carbon and the links to poverty,

greenhouse gas emissions and climate change (ALTER research project, 2013-2016)

- nutrient retention studies (on wetland soils, but not on organic wetland soils, Kanyiginya et

al., 2010)

Across the world other reasons for studies on organic soils include (but are not limited to):

- nature and formation of peat soil to understand ecosystem sustainability (Page, Rieley,

Shotyk, & Weiss, 1999; Shimamura & Momose, 2005)

- understanding biogeochemical processes (e.g. of soil microbes such as methanogens

(Freitag, Toet, Ineson, & Prosser, 2010)

- carbon budgets and greenhouse gas benefits (Fred Worrall, Reed, Warburton, & Burt, 2003)

- suitability for agricultural use and practices (Biasi et al., 2008; McBride, 2001)

- effects of change (e.g. effect on soil nutrients (Craft & Richardson, 1993), effect on

greenhouse gas emissions (Audet, Elsgaard, Kjaergaard, Larsen, & Hoffmann, 2013;

Jauhiainen, Takahashi, Heikkinen, Martikainen, & Vasander, 2005; F Worrall, Bell, & Bhogal,

2010))

There are a number of models which have been developed for modelling organic soil processes and

the impacts of changes in land use and climate, enabling researchers to scale up field results across

space and time (Farmer, Matthews, Smith, Smith, & Singh, 2011). Examples of these include

modelling changes in organic soil carbon stocks using the ECOSSE model (Smith et al., 2010),

assessing greenhouse gas emissions from organic soils using the PEATLAND model (van Huissteden,

van Den Bos, & Marticorena Alvarez, 2006) and the MERES model for rice paddies on wetland soils

(Matthews et al., 2000). Typically these models require information on climate (rainfall and

temperature2), land use, plant inputs, soil properties (e.g. bulk density and carbon content) and soil

water content over a range of time scales (Farmer et al., 2011).

2.2 Planning

The development of a sampling plan will depend on the research questions, research objectives and

budgetary restrictions (both in terms of time and money) of the researcher. It is important to try to

2 Weather data is available from NARO weather stations, the Department of Meteorology or online from the US NCDC at

http://www7.ncdc.noaa.gov/CDO/cdoselect.cmd?datasetabbv=GSOD&countryabbv=&georegionabbv

identify where research can feed in to national and local strategic objectives. The researcher should

also take into account the data needs of any models which they wish to use, evaluating existing

available data and data gaps that need to be filled.

Whilst considering these, it is important to collect samples which are representative of the study

area. There can be considerable differences in soil properties within one wetland study area. The

work of Farmer et al. (2015) demonstrated significant variability within the Rushebeya-Kanyabaha

wetland system in Kabale District, with large differences in soil physical and chemical properties and

peat depths- a result of both natural and anthropogenic conditions.

Key considerations when developing a sample plan:

- Spatial variability; What is the size of the area of study? Generally, the larger the study area

the more likely there will be greater variability in the soils.

o What is the expected spatial variability of the soils?

Is there natural variability? For example, the edge of a wetland compared to

the middle could be expected to show differences in organic soil depth and

mixing of mineral soil. If there is already some information on the soil or land

use then this can be used to determine the extent of the sampling. If there is

no information then sampling could be done in two field campaigns, one

round to try to gain some insight into spatial variability, the results of which

can then be used to help design the more extensive second round of data

collection. Soils can have high local heterogeneity, so triplicate sampling may

be necessary to investigate this.

Is there human induced variability, historically and currently?

What is the history of the study area? Have some areas been used in

different ways in the past? Again, this may influence surface soil

properties and sampling plans should take this potential variability

into account.

Are there multiple land uses within the area of study? If so, sampling

should take this into account as different land uses will have

different influences on the surface soil properties.

- Temporal variability;

o Is time of day or time of year likely to affect results? For example, sampling just after

a heavy rain, or after a farmer has applied fertiliser may influence soil moisture or

nutrient results- it depends if these are important factors for the researcher to

consider. Sampling during the drt seasons may make fieldwork easier- in terms of

access to sites and also not losing field days to rain, but may lead to collection of

data that is not representative of the year. Rainy season compared to dry season will

result in different soil moisture contents in all wetland soils, and cultivated wetland

soils will show differences in micro-topography depending on time of planting,

harvesting etc. linked to the seasons.

Whether spatial and temporal variability is an important consideration in the sampling plan will

depend on the research objectives and reasons for sampling.

2.3 Field campaigns

2.3.1 Equipment

The equipment required for soil sampling depends on the sampling plan. For example, if peat depth

is the only information required, then sample bags and labels are not needed. If only sampling the

soil surface, then multiple auger rods for sampling deep peat are not required. Only carry the

equipment needed, as moving in this field environment can be challenging, and when returning from

the field the field team will have the extra weight of samples to carry back. When preparing to go to

the field, a checklist of the required field-kit should be checked to ensure all field-kit is packed (Table

2). This includes making sure that there is enough of everything e.g. sample bags, for the field visit.

Table 2 Suggested field kit for sampling organic wetland soils

Kit item Notes

Auger head For sampling the soil core. Recommended is the Eijkelkamp Russian style peat auger3.

Pre-marked auger rods Total number depends on the depth required for sampling. Marked to show each depth increment.

Auger handle Necessary for helping push and pull the auger rods.

Auger rope In case of loss of auger head, to pull it back to the surface.

Spanners Multiple sizes required- for the auger head, auger rods, and (where applicable) for the auger rope.

Grease For lubricating the rods where they join.

Sack To place under auger as it is opened in case any sample falls out.

Tape measure For measuring depth increments of the sample e.g. measuring the 50cm core into 10cm increments. Also used to measure water table depth above or below the soil surface.

Spatula/knife For cutting up the core.

Sample bags For putting soil sample into. Paper bags are not suitable for wet soils.

Permanent markers Good quality permanent markers for labelling sample bags.

Larger bags For putting multiple soil samples into e.g. all the samples from one core can be put into one larger, pre- labelled bag.

Sack/bigger travel bag Larger bags can go into a bigger bag e.g. a sack, for ease of transport.

Jerry can For collecting water for rinsing auger head.

Basin For rinsing auger head in.

GPS device To record location of sample.

Camera To photograph each sample and site.

Field data entry sheets/notebook/smart phone

Depending on the method of data recording, either pre-print datasheets, fill information in a notebook, or enter data into pre-prepared smartphone based forms.

Ball point pens For recording information in datasheets or notebook. Note, ball point are better than ink pens as the ink will not run if the papers get wet.

Masking tape For labelling and sealing larger sample bags.

Tarpaulin To keep the rain off. Depends on site location and sampling plan (when sampling at depth then sampling in the rain is not recommended).

Gloves For protecting hands in densely vegetated wetland sites.

Panga For clearing paths through dense wetland sites.

3 Information available from https://www.eijkelkamp.com/files/media/Gebruiksaanwijzingen/EN/m1-

0409epeatsamplerset.pdf

Figure 4 (From top left in a clockwise direction) Using a tape measure to measure out the core and then either a plastic card or a knife to cut the core. Attaching the auger handle. Using spanners to attach a new auger rod, premarked with masking tape. Gum boats, still very wet feet, but useful for keeping spanners in! Auger rods, handle and rope. Sample bags, larger bags, masking tape, pen and note book.

2.3.2 Field team

A strong field team is a must for this work! The soil depth to be sampled will determine the number

of fieldworkers required. Typically:

- Clean hands: One person as note taker and bag labeller. One person for dictating sample

observations to the note taker and putting the sample into the sample bags (typically the

lead researcher).

- Auger team: One person on the auger head, responsible for getting it into and out of the soil

without opening or closing. If sampling soil surface only, then only one more additional

person is needed. However, the effort of pushing the auger down through the peat increases

quickly with soil depth. If sampling up to about 4 m then two more additional people are

needed. If sampling beyond 4 m then 4 additional people are needed, potentially 5 if

sampling down to 10m.

Figure 5 (From top left in a clockwise direction) Everyone has a role to play and the field team can easily reach 7 people. Pushing the auger into the soil can be hard work. Dictating sample observations and measuring sample for bagging. Clearing a path to the sample location can take a long time in dense vegetation. A full, energetic team required for sampling deep peats (note the person handling the auger head, others helping to guide the rods and two people using a pole to support the rods.

2.3.3 Sampling methods

The methods for sampling will depend on the research objectives and field conditions. However, in

general the following apply to all field sites and sampling.

2.3.3.1 Avoiding site contamination

When arriving at the sample location, the site should not be contaminated in any way. Field teams

should not go to the toilet anywhere within the sampling area (bearing in mind if sampling along a

transect or at multiple points within an area, the sampling area can be quite large). No litter should

be left in the field site, and any contamination from the grease should be minimised. Care should

also be taken not to disturb vegetation unnecessarily, maintaining the natural condition of the site as

much as possible.

Care should be taken at each sample point to make sure that the surface soil is not compacted or

disturbed by the field team. No-one should stand on or near to the sample point especially when

surface soil sampling is taking place. When sampling beyond the soil surface some effort is required

to pull the auger up and will require the team to stand near the sample point- but care should be

taken not to be too close when the auger is being brought up to the surface and not to stand on the

sample point in-between sampling.

2.3.3.2 Use of the auger

Manual soil sampling can be done using soil rings or an auger. Soil rings are only really appropriate

when sampling to a shallow depth (above the surface of the water table). Mineral soil augers are

very different to peat augers and not appropriate for sampling organic soils as they do not capture a

volumetric sample, do not seal the sample in (organic soils are wet and will fall out), and do not allow

accurate sampling of sub-increments of the sample. There are two classical types of peat auger; a

Hillier auger and a Russian (Macaulay) auger. The Russian auger is preferred as it allows sampling of

intact cores, allowing for observations on peat stratification. It also has the lowest risk of sample

contamination. In sites where there is a high clay content it may be difficult to pass the auger

through the soil profile as the soil will have a higher bulk density than the organic soils it has been

designed for.

The corer of a Russian auger typically takes a sample of 50cm length. Rods are then attached to the

auger head to enable sampling down the profile in 50cm increments. The auger rods should be pre-

marked and labelled for ease of field sampling. Each rod should be labelled in numerical order of

assembly, and on each rod the 50cm depth increments should be marked. Thus, the field team will

easily know which rod to attach next, and how deep to insert the rods into the soil.

If the water table is above the surface of the water, the height of the water above the soil surface

should be measured and the auger inserted to the surface of the soil, not the water. E.g. if the water

is 10 cm above the surface of the soil, the auger will need to be inserted 10 cm above the 50 cm

marker on the rod (or for visual ease, 40 cm below the next marker).

The auger should be clean, and inserted into the soil open. As it is lowered into the soil it can be

prevented from twisting closed by lowering it with a slight anti-clockwise twist. Once the sample

depth is reached (as marked on the auger rods), the auger should be twisted in a clockwise direction

until resistance is felt. It only needs a 180° twist to close the auger, however if the handle or a rod

has just been attached it may be a bit loose and require a bigger twist. Once twisted closed, the

auger can be pulled up, maintaining a slight clockwise twist to ensure the auger stays closed. As it

nears the surface it is important to ensure that it does not open as it is pulled out of the ground.

Once the auger is out of the ground, it should be held flat as soon as possible. Any soil on the outside

of the auger should be wiped off (not washed) and then the sack placed flat under the auger head

and the team readied for opening of the auger- as the auger is opened the team must adjust their

hold on the rods and auger head to ensure the soil sample is kept flat and level.

Once the auger is open a photograph should be immediately taken of the whole sample for future

reference, and in particular the colour of the peat noted, as this can change considerably over a

matter of seconds. It is important to make these observations quickly as when the peat is exposed to

the air immediate oxidation can take place, changing the colour of the soil.

In some cases it may be that the full 50cm core is to be sampled, in which case it can be treated as a

whole and all the sample inside the auger put into the sample bag. In other cases the research may

require smaller samples e.g. 10cm increments, or increments based on soil properties. In this case

the depth increments that are to be taken from the sample should be measured out and the core cut

into these sections. Field based observations of each sample should be noted and then the sample

placed in the labelled sample bag. All sample bags must be pre-labelled before the sample is put

inside to ensure correct labelling of samples.

Sampling can continue down the profile, by adding more auger rods to reach deeper until the

researcher has collected the samples they require. When sampling surface soils this may just be to 1

m, whereas sampling the full profile can reach over 10 m.

Some sampling may require duplicate or triplicate cores to be taken located nearby to each other to

test for heterogeneity in the soils.

Figure 6 Sample photograph of full 50cm sample and pre-labelled sample bag

2.3.3.3 Avoiding sample contamination

It is very important that contamination of samples is avoided. In between each sample, the auger

should be washed and cleaned thoroughly. When inserting the auger into the soil, it is important to

avoid surface material such as plants from getting stuck in the auger. However, it will undoubtedly

collect some soil as it passes through the profile to the depth to be sampled. Once the auger is open

the researcher should look for any possible contamination (often in the top of the sample). This

should be excluded from the sample which is put into the sample bag. It is very important that any

exclusion of contaminated sample is noted, as this can affect results e.g. if there was contamination

in the 50-100cm increment at 50-55cm, exclude the 50-55cm part of the sample and note that the

sample is actually representative of 55-100cm only. If contamination is included, it will give

inaccurate results in laboratory analysis.

Some sampling may require duplicate cores to be taken, where two cores are taken as close to each

other as possible with a depth overlap (usually about 20cm) to ensure complete profile stratigraphy

with no material lost (e.g. due to contamination).

Figure 7 Contamination (black surface soil) in the core sample taken at 500 cm

2.3.3.4 Sample increments

Depending on the research objectives, samples can be collected in specific increments e.g. 10cm or

50cm increments, or based on observable differences in the soil. Due to historical differences in

vegetation which formed the peat, past water level regimes, fire events, or deposition of mineral soil

due to short or long term events it is often possible to see different “layers” in the soil. Thus, within a

50cm increment there may be quite different soil properties observable, which might make more

sense to sample individually to capture the specific properties. E.g. the first 10cm may be reddy

brown with charcoal layers, then the next 20cm are very watery and dark and then the remaining

20cm have woody pieces in them. Laboratory analysis may show considerable differences in soil

properties of each of these layers and thus by sampling this as one 50cm piece or in specified

increments some of the finer details of the peat properties may be lost. Alternatively, the smaller the

sample collected the higher the likelihood of error in the analysis. Also, smaller samples mean more

samples per core, which can be costly. However, whether to sample in specific depth increments or

in observable strata depends on the research objectives and budget, and a balance with improved

accuracy in results.

Figure 8 Different observable layers in the soil profile- it is recommended that sampling takes these layers into account

2.3.3.5 Sampling at depth

When trying to sample the full peat profile, deeper peat deposits can be challenging to sample

accurately. Peat deposits can measure over 10 m in depth, and accurately sampling beyond this

depth is very difficult.

There are a couple of options for sampling deep peats (Figure 9). One is to use pole supports. This

can be done by using a couple of young Eucalyptus poles with forked ends to help support the auger

rods in the air. One or two members of the field team will be needed to help lift the auger rods up

using the pole/s, and to help keep the auger rods upright as they go into and out of the soil. As the

auger is coming out of the soil it is very important that the pole is used to keep the rods as straight as

possible for as long as possible.

The second option is to insert about 4-5m of rod into the soil, and then attach more rods to the top

of these until the desired depth is met. Then as the rods are being brought out of the soil the rods

can be unscrewed in sections. Care must be taken to ensure that the unscrewing does not open the

auger head- so one person must hold the lower section of rods firmly with a spanner so it doesn’t

untwist. Also care must be taken to not let go of the auger rods as they may drop down into the

sample hole.

Figure 9 Sampling deep peats using a Eucalyptus pole to support the auger rods (L), and using spanners to attach rods in sections (R)

3 Soil data collection

3.1.1 Field based observations

The state of the soil is typically described based on the condition of the plant material in the peat

and the state of disintegration. Field based observations can be made based on the visual condition

of the soil and by touching the soil. Depending on laboratory analysis required for the samples, care

should be taken not to lose any of the sample material during the field-based observations (e.g.

squeezing the peat to observe the humicity will result in loss of water which will affect the wet

weight of the sample). All field based observations will be a useful record to help with interpretation

of any laboratory results. It is recommended that the observations below are noted for each sample

as soon as the auger is opened, before they are put into sample bags:

- Photograph (record the photo ID in the field notes)

- Increment (e.g. 0-50 cm) and sub increment being recorded (e.g. 0-15 cm)

- Level of decomposition: This can be based on the most basic classifications of peat

maturity/decomposition of “irreversibly dried”, “fibric”, “hemic” or “sapric”, or can be more

detailed by using the Von Post scale on a scale of 1-10 (von Post, 1922), or the modified

Troels-Smith method for humicity on a scale of 0-4 (Kershaw, 1997). All of these approaches

are somewhat subjective and qualitative. In tropical peats the basic classification of peat

maturity is commonly used (Agus, Hairiah, & Mulyani, 2011). The Von Post scale is a more

globally used approach, although it was originally designed for Swedish peats and is

generally applied to temperate peat soils. See Appendix 1 for further details of these

different methods.

Figure 10 Three class of decomposition (L to R) fibric, hemic, sapric.

- Clay: Note if there is any clay observable in the sample and a description of it e.g. slope clay

from hillside run-off (typically found in the surface layers), base clay (the clay found below

the peat layer) or indistinguishable clay.

Figure 11 Three clays (L to R); mineral soil deposit from hill slope run-off in surface sample, indistinguishable clay layer mid-sample and grey base clay below the peat profile.

- Colour: This can be based on a Munsel colour chart, however this chart doesn’t often

contain colour ranges appropriate for organic soils in Uganda. The researcher can record

their own colour observations (although this is somewhat subjective) e.g. dark brown,

brown, light brown, and also note the clay colour e.g. orange clay is more indicative of

hillslope run-off into the wetland, compared to grey clay which is typically found at the

interface at the bottom of the peat. These observations can be later compared with the

photograph.

- Moisture: Indicate if the soil is air dried, compacted dry (often in deeper deposits),

moderately moist, amorphous (wet but still with peat) or aqueous (completely watery e.g.

lake water). Further laboratory analysis will give the true moisture content.

Figure 12 Different classes of observable soil moisture: Top (L to R)- aqueous, amorphous. Bottom (L to R)- moderate, compacted dry, air dry.

- Material and percentage: Note any distinguishable material present and a rough percentage

that it makes of the total sample e.g. fine roots 20% and wood 5%. Material typically

observed in organic soils of Uganda include charcoal, wood, fine roots, aerenchyma roots

(tube-like roots of the papyrus plant) and unidentifiable plant material. Also note any

presence of sand, stone and clay. This can be compared later with the level of

decomposition, as a ‘double check’ on the level of decomposition.

An example field form can be found in Appendix 2.

3.1.2 Laboratory analysis

Any samples to be sent for further analysis should be placed in pre-labelled sample bags. For the

laboratory analysis outlined below, samples should be refrigerated at 4°C and taken to the laboratory

as soon as possible. Some components of the soil can undergo change as a result of being exposed to

the air, in particular soil carbon, hence the need for refrigeration for sample preservation until the

time of analysis. There are a number of procedures which can be applied to organic soils when in the

laboratory, depending on the requirements of the researcher.

3.1.2.1 Soil moisture and bulk density

The most basic analysis is drying of the soils in a moisture extraction oven (that used at Kawanda is

Harrow Scientific) at 105 °C until all moisture is lost, giving the soil moisture content and bulk

density. Soil moisture content is useful as it can give insight into the hydrological characteristics of

the system, suitability for plant growth and can be used when trying to gain insight into soil carbon

cycling (e.g. as a factor in CO2 and CH4 emissions).

Soil moisture content is calculated as:

𝑀𝐶 = 𝑀𝑤𝑠−𝑀𝑑𝑠𝑀𝑑𝑠/100

(1)

where 𝑀𝐶 is the soil moisture content (%), 𝑀𝑤𝑠 is the sample wet weight (g) and 𝑀𝑑𝑠 is the sample

dry weight (g).

Bulk density is the measure of the dry weight of soil in a specific volume of soil, and is an indication

of the level of soil compaction. Bulk density values can give soil porosity (an inverse relationship) and

can be used in calculations of nutrient stocks within the soil e.g. nitrogen or carbon stocks.

Bulk density is calculated as:

𝐵𝐷 = 𝑀𝑑𝑠/𝑉𝑠 (2)

where 𝐵𝐷 is the bulk density (g cm-3) and 𝑉𝑠 is the sample volume (cm3). Typical values for tropical

organic soils range between 0.05 and 0.2 g cm-3 (Farmer et al., 2014), but these can go higher with

mineral soil mixing (Page et al., 2011). The average bulk density recorded in a peat core in Ruhuma

wetland was 0.10 g cm-3.

Figure 13 Soil samples ready for drying in the oven. Note that peat samples are wet and thus are in plastic sample bags and aluminium trays for support.

3.1.2.2 Organic matter and carbon content

Of particular interest to a lot of organic soil researchers is the organic matter and carbon content of

the soil. As discussed in Farmer et al., (2014) there are a number of methods available for the

analysis of the C content of soils, usually presented as a proportion of the soil organic matter

(Schumacher, 2002). For mineral soils the Walkley Black method is most commonly used (Walkley

and Black, 1934), and is a popular method of analysis used in Uganda. However, it is not appropriate

for use on organic soils as it is not a true measure of total organic carbon. In tropical peats, analysis is

usually undertaken using either loss on ignition (LoI) (e.g. in Satrio et al., 2009; Ywih et al., 2009) or

elemental analysis (e.g. in Brady, 1997; Shimada et al., 2001). Elemental analysis is the most accurate

of all methods available but requires expensive, sensitive equipment which is currently not available

in Uganda. It involves combustion of samples at high temperatures, followed by gas chromatography

or infrared detection of the carbon oxides. Loss on ignition requires samples to be ground and sieved

through a 2mm sieve, and then combusted at 550°C, where the residual ash content is used to

determine the organic matter content, from which the organic carbon is calculated using a

conversion factor (Agus et al. 2011). This can be done in a muffle furnace, which is available at the

National Agricultural Research Organisation’s laboratories at Kawanda. Comparison of carbon

contents from 25 samples using both loss on ignition (in the Kawanda laboratories) and elemental

analysis (in The James Hutton Institute laboratories, Scotland) showed no significant difference

between methods. Thus, loss on ignition is recommended as the most appropriate method of

analysis for organic soils in Uganda.

Figure 14 Sub-samples placed in crucibles in muffle furnace for loss on ignition

Using loss on ignition, the ash content (𝑝𝑎𝑠ℎ, %) is calculated as:

𝑝𝑎𝑠ℎ =𝑀𝑎𝑠ℎ

𝑀𝑑𝑠 × 100 (3)

where 𝑀𝑎𝑠ℎ is the ash mass after combustion (g).

Organic matter content (𝑂𝑀, %) is then calculated as:

𝑂𝑀 = 100 − 𝑝𝑎𝑠ℎ (4)

From this, the carbon content can be calculated as:

𝐶𝑜𝑟𝑔 =𝑂𝑀

𝑅𝑂𝑀:𝐶 (5)

where 𝐶𝑜𝑟𝑔 is the carbon content (%) and 𝑅𝑂𝑀:𝐶 is the conversion factor used to establish the 𝐶𝑜𝑟𝑔

of the total organic matter. The conversion factor recommended for organic soils in Uganda is a

factor of 1.88, as determined by Farmer and Kibirango based on a comparison of results from 78

samples from Kabale analysed using loss on ignition (at Kawanda laboratories) and elemental

analysis (at the James Hutton Institute laboratories, Scotland). Other values in the literature for

tropical peats include 1.724, 1.878 and 1.922 (Agus et al., 2011; Farmer et al., 2014; Maswar, 2011),

but the factor of 1.88 is most appropriate as it was developed from Ugandan soils.

The carbon content can be used with bulk density results to calculate carbon stocks in the peat core:

𝐶𝑠𝑡𝑜𝑐𝑘 = ∑(𝐴𝑛 × 𝐻𝑛 × 𝐵𝐷𝑛 × 𝐶𝑜𝑟𝑔 𝑛) (6)

where 𝐶𝑠𝑡𝑜𝑐𝑘 here is the carbon stock in g C per area (𝐴), 𝐴 is the area sampled (with a Russian

sampler this is typically 9.82cm2), 𝐻𝑛 is the height of the sample increment (cm) and 𝐵𝐷𝑛 and 𝐶𝑜𝑟𝑔 𝑛

are the bulk density and carbon contents for that increment. This can then be scaled up to give

results over larger areas e.g. farmer’s fields, or per ha, which is more useful.

3.1.2.3 Other nutrients

Further nutrient analysis can also be performed on the soils. This may be required for insight into the

suitability of organic soils for plant growth (such as crops), to study the sustainability of current land

uses (for example, where land users complain of poor plant growth) or for insight into soil properties

for future land management scenarios. Key nutrients such as N, Mg, Ca, P and K can also be analysed

using standard analytical procedures The available cations (Ca, Mg, K) and available P are extracted

using the mehlich 3 extraction method with pH 2.5. Total nitrogen is analysed using a

sulphuric/selenium digestion mixture, digested at 330oC and later quantified colorimetrically using

the salicylate method. pH is read from a 1:5 soil:water extract

3.1.2.4 Other analysis

Any further analysis, such as elemental analysis, isotopic analysis and radio carbon dating of peats

requires shipping of samples outside of Uganda. Methods of sample collection, storage and shipping

involves specific protocols and sample treatment. Reasons for this additional analysis could be to

study the historical formation of the soil (aging the carbon in the peat, and studying pollen particles

found in the soil) or to study the losses of carbon from the soil under land use scenarios (e.g. aging

the carbon being lost through water, or aging the peat down the profile).

4 Appendix 1

There are a number of different methods for determining peat humicity. “Basic characterisation” is

the recommended method to apply to organic wetland soils in Uganda. Although basic, it provides a

simple approach. However, depending on the demands of the research objectives a more detailed

approach such as that of the von Post scale or the Troels Smith score may be more appropriate.

4.1 Basic characterisation

This simple approach, when coupled with other field-observations on colour and material, gives

insight into the decomposition of the soils.

Scale Description

Irreversible drying Peat which has been exposed to the air due to drainage and has taken on a grainy form (similar to dried coffee grains), with no obvious plant structure to the grains.

Fibric Fairly undecomposed/disintegrated peat. Fibres present in over 2/3 of the sample.

Hemic Intermediate levels of disintegration/decomposition. Fibres present in 1/3 to 2/3 of the sample.

Sapric Most highly disintegrated/decomposed peat. Fibres present in less than 1/3 of the sample. Likely to be found in the deepest/oldest peat deposits.

4.2 Von Post scale

This scale is commonly used in temperate zones for peat decomposition classification (Scottish Peat

Surveys, 1968). The high number of classes can make it difficult to apply, and is subjective.

Scale Description

H1 Completely undecomposed peat which, when squeezed, releases almost clear water. Plant remains easily identifiable. No amorphous material present.

H2 Almost entirely undecomposed peat which, when squeezed, releases clear or yellowish water. Plant remains still easily identifiable. No amorphous material present

H3 Very slightly decomposed peat which, when squeezed, releases muddy brown water, but from which no peat passes between the fingers. Plant remains still identifiable, and no amorphous material present

H4 Slightly decomposed peat which, when squeezed, releases very muddy dark water. No peat is passed between the fingers but the plant remains are slightly pasty and have lost some of their identifiable features.

H5 Moderately decomposed peat which, when squeezed, releases very “muddy” water with a very small amount of amorphous granular peat escaping between the fingers. The structure of the plant remains is quite indistinct although it is still possible to recognize certain features. The residue is very pasty.

H6 Moderately highly decomposed peat with a very indistinct plant structure. When squeezed, about one-third of the peat escapes between the fingers. The residue is very pasty but shows the plant structure more distinctly than before squeezing

H7 Highly decomposed peat. Contains a lot of amorphous material with very faintly recognizable plant structure. When squeezed, about one-half of the peat escapes between the fingers. The water, if any is released, is very dark and almost pasty.

H8 Very highly decomposed peat with a large quantity of amorphous material and very indistinct plant structure. When squeezed, about two-thirds of the peat escapes

between the fingers. A small quantity of pasty water may be released. The plant material remaining in the hand consists of residues such as roots and fibers that resist decomposition.

H9 Practically fully decomposed peat in which there is hardly any recognizable plant structure. When squeezed it is a fairly uniform paste.

H10 Completely decomposed peat with no discernible plant structure. When squeezed, all the wet peat escapes between the fingers

4.3 Modified Troels Smith humicity score

Scores are given based on the nature and amount of material passing through the fingers on

squeezing (Kershaw, 1997).

Score Description

0 Fresh peat yielding clean water

1 Slightly decomposed peat yielding dark coloured, turbid water

2 Decomposed peat yielding half its mass

3 Very decomposed peat yielding three quarters its mass

4 Totally decomposed peat yielding almost all its mass

5 Appendix 2

Example of a field form for recording field based observations of samples:

Survey title: Date:

GPS ID: Transect ID: Core ID:

Site photos ID’s:

Depth increment

Sample Photo ID

Sub-increment Decomposition Colour Moisture Material and %

0-50

Depth increment

Sample Photo ID

Sub-increment Decomposition Colour Moisture Material and %

50-100

Depth increment

Sample Photo ID

Sub-increment Decomposition Colour Moisture Material and %

100-150

Depth increment

Sample Photo ID

Sub-increment Decomposition Colour Moisture Material and %

150-200

Depth increment

Sample Photo ID

Sub-increment Decomposition Colour Moisture Material and %

200-250

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