Mushroom Biology and Mushroom Products. Sánchez et al. (eds). 2002
UAEM. ISBN 968-878-105-3
NEAR INFRARED SPECTROSCOPY - AN ADAPTIVE PROCESS CONTROL SYSTEM
FOR AGARICUS BISPORUS COMPOST PRODUCTION
H. S. S. Sharma 1,2, M. Kilpatrick 3, G. Lyons 2 and J. Murray 3
Applied Plant Science Division, Department of Agriculture and Rural Development for N. Ireland
and 2Department of Applied Plant Science, School of Agriculture and Food Science, Queens
University, Newforge Lane, Belfast BT9 5PX, UK. 3Applied Plant Science Division, Department of
Agriculture for Northern Ireland, Loughgall, Co. Armagh, BT61 8JB, UK.
<s.sharma@qub.ac.uk>
1
ABSTRACT
The application of near infrared spectroscopy (NIRS) as a rapid tool for assessing substrate quality
has been investigated over the past 5 years in collaboration with major compost producers in
Northern Ireland. NIR calibrations for dry matter, pH, nitrogen, carbon, ash, microbial population
and fibre fractions using spectra of fresh composts have been developed and validated using a wide
range of phase I and II samples. Additional calibration for forecasting productivity of mushroom
yield has also been developed and this is currently being validated to improve accuracy of
prediction. The application of NIR technology to control process conditions, such as environmental
and physical characteristics during production, is feasible by using calibrations for key quality
parameters. A review of the different compost production systems and potential benefits of
integrating NIR monitoring and tunnel control sensors, to provide more flexibility during the
fermentation process is discussed.
INTRODUCTION
Researchers have known for some time that composts with defined composition could be produced,
to satisfy the ecological and nutritional needs of different mushroom strains under different growing
conditions. However, until now, such a substrate could not be prepared due to lack of suitable tools
to monitor and control substrate production rapidly or in real time. The introduction of spectroscopy
in the early 1980s and 90s as an analytical tool for process control has allowed many industries,
such as petrochemical, pharmaceutical, food and biotechnology to exploit the benefits of using
spectroscopy (Davis and Grant 1987, Osborne et al. 1992, Schilling et al. 1996). Spectroscopy is
the only suitable technique available that has the flexibility to cope with the demands of assessing
quality of the materials during production. The application of near infrared spectroscopy, as a tool
for assessing substrate quality, has been investigated over the past 5 years in collaboration with
major compost producers in Northern Ireland. NIR calibrations for dry matter (moisture content),
pH, nitrogen dry matter (NDM), carbon, ash, microbial population and fibre fractions using spectra
of fresh composts have been developed and validated using a wide range of phase I and II samples.
In addition calibration for predicting potential mushroom yield of compost has also been developed
from a number of compost comparative trials.
This presentation is aimed at exploring potential benefits of integrating NIRS hardware and
software to onboard monitoring and control systems for either phase II or an indoor composting
chamber. This opens up the possibility of controlling the different phases of substrate production by
using an online NIRS system in real time. Although NIRS is more suitable for integrating with an
indoor composting system or Phase II process stage, the instrument is flexible enough to be used as
an offline system for monitoring substrate quality during windrow and bunker Phase I.
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SUBSTRATE PRODUCTION SYSTEMS
Windrow method
Phase I: NIRS can assess the input materials i.e. mixed wet straw, chicken litter and gypsum for
moisture content, nitrogen dry matter, ash and fibre fractions to provide guide lines on the duration
of this phase. Microbial activity causes the stacks to self-heat, making the straw soften and become
more water absorbent. These rough stacks are maintained for 4-6 days with periodic mechanical
turning to prevent anaerobosis at a moisture level of 70-75%. The temperature at the centre of the
stack may reach 80C causing a reduction in microbial activity in this zone. Therefore frequent
turning is required to mix the cooler outer zones of compost with the hotter inner areas. Turning
also aerates the windrow and the fact that natural ventilation occurs between turns ensures that
oxygen is available for microbial activity. The key changes at this stage of production are driven by
the activities of thermophilic microorganisms resulting in modifying pH, temperature and breaking
down the cellulosic substrate. NIR probes can monitor the increase in ammonia concentration and
the formation of humus, which is a dark layer (Eddy and Jacobs 1976, Iiyama et al. 1996) made up
of bacterial cells, fungal spores and hyphal fragments embedded in a matrix of amorphous material
on the surface of straw. The deposition of humus is linked to microbial activity, which is dependent
on the availability of water-soluble carbohydrate and polyphenols and ammonium nitrogen under
favourable conditions. Monitoring of all three parameters using NIR probes positioned at various
depths could provide a rapid indication of the activity of mesophilic and thermophilic
microorganisms. In addition, duration of process could be determined on the basis of an optimum
range of target parameters at phase I. Furthermore, this application could be complemented with
smell, visual and physical observations of the substrate.
Phase II: The phase I compost must undergo a pasteurisation process to eradicate pathogens and
pests that survive the initial stage of production. If through restricted ventilation, the oxygen content
of the compost is low during phase II, anaerobic conditions prevail and the compost temperature
drops, possibly leading to the production of toxic compounds that inhibit the growth of mushroom
mycelium. Phase II is a highly aerobic, thermophilic, solid substrate process usually lasting for 5-8
days (Fermor et al. 1985). The pasteurisation stage is achieved by raising the air temperature to
58C using steam and maintaining this temperature for 8-10 hours. Pasteurisation is followed by
conditioning, the process whereby the compost is converted into a selective substrate for the growth
of the mushroom mycelium. Moisture content at the end of phase II is linked to microbial activity,
which is dependent on availability of oxygen and optimum temperature. During phase II, readily
available carbohydrates are utilised and the microorganisms convert ammonia and nitrates to
proteins, changing the pH from alkaline to near neutral by the end of the process. The key factors
during pasteurisation and conditioning stages are ammonia, temperature, microbial activity, oxygen,
nitrogen dry matter and moisture content. NIR probes can monitor most of the parameters listed
above and changes in the parameters can be observed in real time. This could provide accurate
information on the gradual reduction of microbial activity and the associated degree of selectivity
imparted to the compost.
In-vessel Phase I composting
In recent years, variations on the scheme suggested by Sinden and Hauser in 1953 for compost
preparation have evolved in the industry. There has been a gradual move away from outdoor
compost preparation to partial or complete indoor production, aimed at reducing odour (von
Minnigerode 1981, Miller et al. 1990) to comply with environmental pollution legislation. Some
producers are now changing to Phase I production in positively aerated chambers (in-vessel or
bunker production; Figure 1) facilitating better control, producing a more uniform substrate (Noble
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and Gaze 1994). Wetted straw, poultry litter and gypsum are mixed on a blending line and the mixture is then
piled into rough stacks for 48-72 hours. The compost is then filled into concrete bunkers, walled on three
sides and fitted with air ducts in the floor at a density of 16 units m-2 (Sharma et al. 2000a). NIR probes can
be positioned at different depths in the bunker to develop a profile of the differences in compost mass. Air is
pumped through the ducts during composting and airflow is controlled by changes in substrate temperature
and oxygen concentration. This in turn could be integrated to the NIR probes measuring moisture content,
microbial activity, ammonia and other related changes in the substrate. The compost remains in the first
bunker for 4 days and rapidly attains a uniform temperature of 80C. After this period the compost is removed
and transferred to an adjacent bunker and water (10 litres t -1) is added to compensate for moisture loss as a
result of air-flow desiccation. After a further 4 days, the compost is emptied from the second bunker onto a
concrete apron for 6-12 hours to allow cooling and natural re-inoculation before Phase II. All process steps
including the transferring of material between bunkers are aimed at providing an optimum substrate
environment for rapid microbial activity and this can be carried out in conjunction with an NIRS based
decision support system.
Figure 1. Schematic representation of a bunker system.
Indoor Composting
This method involves the controlled breakdown of raw materials through each phase inside a
chamber, as the process cycle can be completed in ten to fourteen days and odour production can be
controlled throughout. For a short composting process to be successful, the best possible
homogeneity of raw ingredients is important from the outset (Laborde 1994). Mixing is undertaken
in one operation at the start, with the raw materials being shredded and wetted by being passed into
a large auger type screw mixer. NIR probes can monitor the variations in the composition of the raw
materials for moisture, nitrogen, ash and fibre content, and could even be integrated to the sample
hopper to change the flow rate of the materials based on set limits of the parameters. Heat
generated by microbial breakdown of substrate causes the compost temperature to rise and
subsequent loss of moisture due to evaporation could be controlled by sending correcting signals to
actuators (water valves) to achieve optimum set points. Two protocols of temperature control for
indoor composting have been adopted. The first method is known as the Low Temperature (LT)
method (Gerrits and van Griensven 1990, Nair and Price 1993). Temperature is maintained at 48C
for seven days in aerobic conditions with a disinfection peak at 58C during the process. The
chopped raw materials are treated with a patented biological inoculum consisting of a mixture of
thermophilic microorganisms, enzymes and a lipid support base. The second method, known as the
High Temperature (HT) technique, was largely developed at INRA, France (Laborde et al. 1989). It
consists of two phases, Phase I is performed at 75-80C for 5-7 days in conditions of moderate
aerobosis, with an oxygen level of 8% in the compost. Phase II is undertaken at 48-50C for 4-7
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days with or without a brief pasteurisation at 58C during the process. Between the two phases a
biological activator is added at the end of Phase I to re-inoculate the compost with essential
microorganisms: this is only carried out if a temperature of 75-80C has been maintained evenly
throughout the compost, causing substrate sterilisation (Laborde 1994). An Industrial variation on
this technique, involves passing small quantities of cold air below the compost heap, lowering the
base temperature to 45-50C, whilst the allowing the mid and upper areas to reach 75-80C. A
balanced biomass that reinoculates the compost at tunnel emptying is thus maintained in the cooler
zone. In this latter instance, there is no need for a biological activator.
As in windrow, phase I and II tunnels, microbial succession drives the breakdown of substrate
during indoor composting and the same key parameters define the process. The substrate produced
by indoor composting is different in terms of colour, physical and chemical properties and
microbial biomass compared to compost prepared by traditional methods. Changing the process
from an outdoor (windrow system) to an environment friendly and resource saving indoor process
has resulted in a different pattern of succession, leading to overall reduction in compost quality.
This is most likely due to difficulty in monitoring and controlling breakdown of the substrate. As in
phase II application, similar NIR probes can also be installed at various depths inside the chamber
to monitor all key parameters listed above. The integration of NIRS system and tunnel control
sensors will be most advantageous for indoor systems as the production phases can be monitored
and if necessary remedial actions can be taken rapidly.
NEAR INFRARED SPECTROSCOPY
The spectral data from the materials at each stage of production could be used for monitoring
changes in important parameters and control the process based on specified range of quality
parameters and environmental conditions. Currently, not all changes in NIR spectra of compost can
be explained by the existing knowledge of the production process and in addition, the spectrum
contains extensive information on the substrate that has yet to be fully understood. Complex
biochemical changes are taking place, which cannot be measured by the existing analytical tools
(Sharma et al. 2000b). The spectrum contains fingerprints of all the microbial, biochemical and
physical changes taking place, during the preparation of compost and the spectral
markers/characteristics shift in correspondence to the transformation within the substrate. The
influence of these factors on the spectrum can be described as multidimensional and the data
matrices obtained can only be analysed using complex algorithms, such as principal component
analysis and partial least squares regression methods (Barnes et al. 1989, Williams 1987, Windham
et al. 1989).
Analytical methods currently available for quality control during production are pH, NDM,
ammonia, conductivity and ash (Sharma 1991). The value of NIRS as a rapid, inexpensive,
environment friendly instrumental method has been widely accepted as an alternative to traditional
wet techniques for determining nitrogen and fibre fractions. The recent advances made in the
development of NIR probes (e.g. diffuse reflectance, transmission/interactance fibre optic modules)
for online analysis in chemical, pharmaceutical and animal feed industries have shown that the
technology could be applied to compost production as part of a routine quality control system.
Process optimisation: The input raw materials must be checked not only for quality and composition
but also for identity. Quality of wheat straw can be variable depending on variety, application of
fungicides/growth hormones, storage conditions after harvesting, age and variety (Sharma et al.
2000c). Significantly, the NIR spectra are also different for these samples as the cellulose and
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hemicellulose contents are variable. In addition, the quality of the chicken litter can also vary
depending on the bedding materials (i.e. wood chips or straw) and the ingredients of feed used.
Visible-NIR spectrometers could be used for the determination of colour, nitrogen, moisture
content, fibre fractions, ash, other components of the raw materials used for preparing compost and
potential yield (Sharma and Kilpatrick 2000, Sharma et al. 1999, Sharma and Kilpatrick 1999,
Sharma and Lyons 1999).
a)
c)
a)
(c)
b)
d)(d)
Figure 2. Experimental (a) replicated tunnels showing inside of a (b) chamber equipped with (c)
monitoring and (d) control facilities.
During the composting process, an ecological succession of microorganisms drive the breakdown of
raw materials i.e. wheat straw and chicken litter/horse/pig manure. Use of suitable raw materials is
the key to optimising the production of high quality substrate for cultivating mushroom. This will
provide quality standards with guidelines and formulations for optimising the process. However, in
practice composters have to prepare the best possible substrate using available raw materials. A
knowledge-based adaptive production system could be developed to optimise the process based on
quality of the input raw materials. This will permit efficient utilisation of the available raw materials
by monitoring changes in key parameters.
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Calibration development: Online monitoring of the production stages could be carried out using
sensitive NIR probes. For analysis of the spectra from fresh samples, individual calibration
equations for each of the key parameters such as NDM, moisture content, ash, fibre fractions and
others, have to be developed from the database. The spectral data could be assessed using these
calibrations. All components of the test substrates will have their own spectral images for a given
period during production. The initial calibrations necessary for measuring key parameters can be
developed using a bench top model (such as Foss, 6500 NIR system). The instrument can scan fresh
samples taken at different stages of production starting from input raw material to the final
substrate. Since two moisture peaks dominate NIR spectra, accuracy for measuring moisture content
should be high. At high moisture content (above 75 %) the relationships between NIR spectra and
other key compost parameters such as pH, NDM, carbon, ash, microbial population and ammonia
may not be linear and selected segments of the spectra may have to be used for the development of
robust calibrations (Sharma 2000).
Development of calibration equations for use in phase II or indoor composting will require
monitoring of the changes in substrate during preparation using a wide range of recipes. The
resulting database will be needed for establishing an optimum range for each parameter at every
stage of the production process. This can only be carried out in replicated tunnels equipped with
monitoring and control facilities (Figure 2). However, tentative NIR calibrations could also be
developed using maximum and minimum limits set for each parameter based on existing databases
held by the industry.
COMPUTERISED ENVIRONMENTAL CONTROL.
To remain competitive, computer control systems are now an integral part of the manufacturers
battle to keep compost production in balance with end-point mushroom quality. Nowhere is this
more evident than the Netherlands where 100% of compost production farms and 80% of
mushroom growing units are equipped with computerised control (Lamber 2000). All computerised
systems, operate sophisticated sensing equipment to measure environmental parameters (air
temperature, humidity, compost temperature O2, etc.) and send correcting signals to tunnel actuators
(motorised valves, steam, cooling, ventilation flaps etc.) to achieve optimum set-points. The
controlling programme adjusts prioritised parameters for specific production stages. Computers
check the climate virtually continuously, regulating various climatic factors simultaneously, and in
relation to each other. Thus, the success of any computer-controlled system depends primarily on
the quality of the program used.
Current applications
Compost preparation
During Phase I, the use of computer control in automated logistic processes using programmable
logical controllers (PLC’s) i.e. filling, emptying equipment and transportation belts is rapidly
becoming standard practice world-wide. In addition, microprocessors for environmental control,
function to supply optimum oxygen for the biological processes occurring during pre-wetting and
fermentation processes. Computerised integration operates through the fan system controlling
compost temperature, supply system pressure and oxygen levels in the compost. To encourage the
natural exothermic action of thermophilic microorganisms during Phase I, the preferred control
260
Ambient
weather
Alarm and
System
manager

SENSORS
Control
Panel
Central
computer
monitoring
and control
system
Compost
tunnel
FAN CAPACITY
AIR DAMPER
POSITION
COOLING VALVE
POSITION
STEAM VALVE
POSITION
AVERAGE COMPOST
TEMPERATURE (4)
BOTTOM INBLOW AIR
TEMPERATURE 1 and 2
TOP RETURN AIR TEMPERATURE
OXYGEN CONCENTRATION
AIR QUANTITY
NIR PROBES (6)
Figure 3. Schematic flow of NIRS monitoring system for indoor (or phase II) compost production.
Dry matter
NDM
Ash
Carbon
Thermophiles
pH
Conductivity
Fibre fractions
Data analysis
and prediction
Multi-channel
NIRS
Fibre optic
interface
Blending with
chicken litter and
gypsum
Indoor
Composting
Chamber
Figure 4. Schematic representation of a compost tunnel monitoring system for environmental
control.
parameters are oxygen and temperature. Use of steam has widely been rejected (Op den Camp et
al. 1991) as this increases the compost moisture content through condensation creating strong
resistance to air-flow that can ultimately lead to anaerobiosis
Phase II and III tunnels
Climate control for Phase II bulk pasteurisation systems is extensively used in Industry. Controlling
parameters include compost and air temperature, humidity, air volume and oxygen levels (Figure
3). Control programmes generally regulate recursively – taking into account the values of the
immediate preceding period – thereby attenuating reactions and avoiding sudden changes.
Regulation of temperature and ventilation are the most important factors and by evaluating
differences between air and compost temperatures, a measure of the microbial activity of the
261
compost is taken into account. Choices are incorporated into controlling programs on the methods
of, for example, cooling regulation. During spawn-run, options of both mechanical cooling and
cooling with outside air are available. Generally, outside air is used only if the heat content of that
air is lower than the heat content of the tunnel air. The underlining principal is that as mycelial
growth is encouraged by CO2 the quantity of fresh air should be limited during this phase. PLC’s
are also utilised in automating logistic processes and increasingly ammonia scrubbers and
biofiltration systems are climate controlled.
Future applications
To date, little attempt has been made integrating compost analysis with controlling priorities, but
with increased understanding of compost fermentation processes and ever more sophisticated
sensing/analytical equipment, this becomes a realistic possibility. To varying degrees, managers
may currently base decisions for regulating control after consideration of the compost analysis. For
example, during Phase II a higher minimum air damper and/or fan position may be set when the
moisture content of Phase I compost is above optimum. Similarly, a specified period of cooling
with outside air may be determined preferable to mechanical cooling in an attempt to decrease
moisture levels in wetter than optimum Phase III composts and vice versa.
Sophisticated precedents are being developed in other spheres of mushroom production where Time
Domain Reflectometry (Beyer 2000) is being investigated for in situ rapid determination of casing
moisture content with a view to ultimately linking analysis to automated watering systems. NIRS
has been shown capable of providing analytical information on a wide range of compost parameters.
Development of sensing equipment now permits NIRS to be adapted for online analysis (Figure 4).
Further development of appropriate calibration equations in replicated tunnels equipped with
monitoring and control facilities could provide the optimum range for each parameter at every stage
of the production process. Subsequently, this information could be utilised to determine more
effective, interactive manipulation and prioritisation of computerised environmental control
parameters to achieve a measured end-point.
CONCLUSION
Integration of NIR monitoring and tunnel control systems will be advantageous for optimising
compost production and such a system using existing hardware and software can be supplied by
instrument manufacturers to compost producers. However without an extensive database on the key
changes taking place during composting, the accuracy and potential benefits of the system could not
be fully exploited by the industry. This necessitates collaborative ventures between the researchers,
instrument manufacturers and compost producers to develop a database on quality standards for
commonly used raw materials and calibration equations for all key parameters during the three
phases of substrate production.
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