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Soil biological health - what is it and how can we improve it?

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SOIL BIOLOGICAL HEALTH is a topic of great interest to sugarcane growers, although there is confusion as to what constitutes soil health. Many growers and consultants are unaware that beneficial organisms, rather than pathogens and pests, dominate the biological community in a healthy soil. Considering the vast diversity of soil organisms and their complex interactions, it is unsurprising that there is limited knowledge about how farming practices precisely impact on soil biological health, and how biological health can be achieved. The former Sugar Yield Decline Joint Venture (SYDJV) and subsequent activities have demonstrated that soil biological health represents a significant production constraint. The modern farming system (MFS), with controlled traffic, permanent beds, minimum tillage, legume break crops and crop residue retention, aims to overcome soil constraints, including soil biological health, by minimising problems arising from soil compaction, continuous monoculture and low levels of soil organic matter. In this paper we discuss key organisms that inhabit soils under sugarcane production and how soil biology responds to management practices. We highlight biological indicators of soil health, and their usefulness to growers for quantifying soil responses to changed farming practices. We outline research needs to advance the industry’s ability to manipulate soil biological health.
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SOIL BIOLOGICAL HEALTHWHAT IS IT
AND HOW CAN WE IMPROVE IT?
By
RICHARD BRACKIN1, SUSANNE SCHMIDT1, DAVID WALTER2,
SHAMSUL BHUIYAN3, SCOTT BUCKLEY1, JAY ANDERSON1
1The University of Queensland, Brisbane, 2The University of the Sunshine Coast, Sippy Downs,
3Sugar Research Australia, Woodford
r.brackin@uq.edu.au
KEYWORDS: Soil Food Web, Organic Matter,
Soil Health Indicators, Soil Biology.
Abstract
SOIL BIOLOGICAL HEALTH is a topic of great interest to sugarcane growers, although
there is confusion as to what constitutes soil health. Many growers and consultants are
unaware that beneficial organisms, rather than pathogens and pests, dominate the
biological community in a healthy soil. Considering the vast diversity of soil organisms
and their complex interactions, it is unsurprising that there is limited knowledge about
how farming practices precisely impact on soil biological health, and how biological
health can be achieved. The former Sugar Yield Decline Joint Venture (SYDJV) and
subsequent activities have demonstrated that soil biological health represents a
significant production constraint. The modern farming system (MFS), with controlled
traffic, permanent beds, minimum tillage, legume break crops and crop residue
retention, aims to overcome soil constraints, including soil biological health, by
minimising problems arising from soil compaction, continuous monoculture and low
levels of soil organic matter. In this paper we discuss key organisms that inhabit soils
under sugarcane production and how soil biology responds to management practices.
We highlight biological indicators of soil health, and their usefulness to growers for
quantifying soil responses to changed farming practices. We outline research needs to
advance the industry’s ability to manipulate soil biological health.
Introduction
The physical and chemical components of soil quality are well understood, and
quantification methods exist that are accessible to growers and consultants (Stirling et al. 2016).
Soil biological traits and their relationships with crops are more complex, and there are large
deficiencies in fundamental knowledge (Lehman et al., 2015).
Only about 100 000 species of soil fungi are known of an estimated 5 million species, and
4 500 identified species of soil bacteria contrast an estimated 1 billion species inhabiting soils
(Nielsen et al., 2016). Such knowledge gaps hinder the development of robust tools for
practitioners, and understanding of soil biological traits at the paddock scale is in its infancy.
Soil contains a vast diversity of organisms, with differing functions, requirements and life
cycles, and in which uncountable numbers of individual organisms exist and interact.
The diagram (Figure 1) shows the diverse sizes of the soil community across many orders of
magnitude from microscopic bacteria (~1 µm and below) to larger organisms such as earthworms,
which are several centimetres in length.
As a whole, the soil biological community provides a number of essential ecosystem
services, particularly decomposition of organic matter and release of nutrients for plant uptake, soil
formation, storage and recycling of nutrients, growth promotion and suppression of pests and
diseases, and the degradation of toxins (Table 1) (Stirling 2014).
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Fig. 1Soil organisms grouped by class, showing the size of body width. Bacteria in the
diagram represent all prokaryotes, bacteria and Archaea.
Despite their small size (when considering individual bacteria or fungal hyphae), soil
microbes strongly influence soil structure (Ritz and Young, 2004) and are instrumental for the
build-up of soil organic matter (Fontaine and Barot, 2005). Specific groups of microbes are
responsible for more specialised functions, including the conversion of atmospheric nitrogen into
reactive nitrogen that crops can use (biological nitrogen fixation), nitrification, and suppression of
pathogens (Stirling et al., 2016). Certain organism groups are responsible for negative soil
biological function including crop diseases.
In general, soil microbes are limited by energy (not nutrients) and most of their activities are
centred around obtaining energy, either through consuming organic material, oxidising inorganic
substrates (i.e. nitrification), or taking energy directly from living plants (which are often energy
rich but nutrient limited) (Brackin et al., 2014; Hobbie and Hobbie, 2013). This can occur through
negative interactions such as pathogenicity or predation, but also via co-operative interactions
where microbes ‘trade’ nutrients with plants for energy e.g. by consuming energy-rich sugars and
other chemicals exuded by roots, or through more specialised structures such as rhizobia (that form
nitrogen fixing root nodules) and mycorrhizal associations (Stirling et al., 2016). Microbes also
compete with other soil organisms for resources (Dunn et al., 2006).
Substantial evidence exists that agricultural land use selects for different microbial
communities than those that develop in soils under native vegetation (Brackin et al., 2013; Jesus et
al., 2009; Nourbakhsh 2007). Microbe populations are reduced by 5070% in sugarcane soils
compared with adjacent forest soils (Brackin et al., 2014; Dominy et al., 2002; Holt and Mayer,
1998), resulting in sugarcane soils having lower substrate conversion (i.e. microbial enzyme)
activities and reduced capacity for litter decomposition (Brackin et al., 2013).
Reasons include:
(i) Plant litter inputs are reduced and less diverse in agricultural than natural systems;
(ii) Tillage negatively impacts on fungal hyphal networks and the larger soil fauna
(which may take a long time to re-establish);
(iii) Nutrients are supplied separately to carbon as mineral fertilisers rather than bound
together in organic materials as occurs in natural ecosystems; and
(iv) Many soil microbes are well adapted to decomposing organic materials; however,
their populations tend to decline with reduced substrate availability in agricultural
systems.
Instead, intensive monoculture systems tend to promote pathogenic soil microbes that specialise
in infecting a narrow range of host crops (Shipton 1977). As a result, pathogens are more competitive
and there are fewer organisms that control pathogen populations where a single crop is grown.
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We define biologically healthy soils as those which support large and diverse microbial
communities, suppress pathogens, and support healthy crop development. Generally, the best
examples of these soils are those that are under (or have been recently cleared from) native
vegetation or pasture, experience low disturbance, and have high inputs of diverse organic
materials.
Table 1The role of soil organisms in ecosystem services (modified from Stirling 2014).
Decomposition of organic matter
Soil organisms macerate and decompose plant and animal residues. It is probably the
most important function of the soil biological community.
Soil formation, and stabilisation of aggregates
Soil microorganisms produce polysaccharide glues that shape soil structure and form
aggregates. Networks of fungal hyphae bind mineral and organic particles together
helping form macro-aggregates. The larger soil fauna act asengineers’, by moving or
ingesting soil, or creating mounds, casts and burrows.
Production, uptake and transfer of nutrients
Many soil organisms impact directly on plant nutrition. For example, many bacteria
are involved in nitrogen cycling; arbuscular mycorrhizal fungi promote the crops’
uptake of phosphorus and other nutrients; siderophore-producing bacteria chelate iron
and other bound nutrients to increase the availability for plants; and certain fungi and
bacteria solubilise phosphates, making them available to plants.
Storage and cycling of nutrients
When organic matter is decomposed, complex organic molecules are broken down
and eventually mineralised into smaller organic substances. During this process, some
nutrients are immobilised (i.e. incorporated into living cells). This process governs
the supply of nutrients to plants and nutrient equilibrium levels in soil are governed
by the soil biota.
Herbivory
Many soil organisms obtain sustenance from living roots. Most cause little damage to
crops, but some are important pests and pathogens.
Plant growth promotion and suppression of pests and pathogens
Rhizosphere inhabitants produce plant growth-promoting substances and endophytic
microorganisms induce resistance to pathogens.
Degradation of toxic compounds
Soil organisms produce enzymes that break down pesticides, pollutants and other
contaminants.
Biology of sugarcane soils
Biological components of soil quality decline were identified as early as 1930 in the
Australian Sugar Industry. Bell (1935) demonstrated in field and glasshouse experiments that virgin
land produced greater cane yields than long-term cane land. He found that long-term cane soil
responded strongly to fumigation (while forest soil did not), demonstrating a biological cause of
yield limitation.
This research was disrupted by WWII, and by the 1950s and 1960s, fertiliser application
rates were the primary avenue explored for improving soil fertility. Growers were encouraged to
increase fertiliser applications and avoid rotations (Yates 1963), and very low fertiliser prices
allowed growers to fertilise at high rates (Barrie 1963).
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The increases in nutrient-input facilitated yield increases, but also masked the early signs of
the negative impacts of the intensification of the sugarcane monoculture (Garside et al., 2007;
Pankhurst et al., 2003).
A substantial effort into researching soil quality in the sugar industry took place in the late
1990s (the Yield Decline Joint Venture). This program found a broad range of soil constraints in
long-term sugarcane soils, falling into biological, chemical and physical categories. It was
confirmed that a lack of crop rotations from sugarcane monoculture results in changes to the soil
biological community composition that included a build-up of pathogens (Pankhurst et al., 2005;
Stirling, 2008), and decreased overall microbial populations (Holt and Mayer, 1998). Sugarcane
soils (and agricultural soils generally) have lower content of organic carbon compared with soils
under native vegetation or pasture (Dominy et al., 2002; Stirling et al., 2010). Because soil carbon
is the main energy source for soil microbes, loss of soil carbon and soil microbial populations are
strongly linked (Dominy et al., 2002).
Here we discuss some of the organisms that occur in soils under sugarcane production, the
key management options that influence their populations, the tools available for quantifying
changes in soil organism populations, and the need for a comprehensive approach to soil biology
research in sugarcane systems.
Key components of soil biology
Bacteria
Bacteria and Archaea (we use the collective term ‘bacteria’) constitute the greatest
component of soil microorganisms with population densities often several orders of magnitude
greater than fungi in number but not in biomass (Stirling et al., 2016). Bacteria have a large
metabolic diversity and fulfil a vast range of functions in soils, from decomposing organic matter
(making nutrients available to other soil organisms and roots), driving the soil nitrogen cycle,
synthesising plant growth promoting substances, being food sources for other organisms,
pathogens, or suppressing pests and diseases (Stirling et al., 2016).
There has been considerable interest in endophytic nitrogen-fixing bacteria for several
decades to supplement nitrogen supply in sugarcane. Brazilian studies suggest substantial
contributions can be made to the crop N budget (Boddey et al., 1995; Boddey et al., 1991).
However, these methodologies rely on numerous assumptions and are prone to error (Soper et al.,
2015). Australian research with Brazilian and Australian sugarcanes have failed to detect significant
nitrogen fixation (Walsh et al., 2006) or increases in the abundance or activity of N-fixing bacteria
in soils receiving low N fertiliser rates (Yeoh et al., 2015).
A number of plant growth promoting rhizobacteria (PGPR) have been isolated from
sugarcane roots and can promote vigour in controlled conditions in laboratory or glasshouse, either
through nitrogen fixation, hormone production or both (Mehnaz, 2011; Paungfoo-Lonhienne et al.,
2014). While there is good evidence that PGPR can substantially stimulate yield increases in
laboratory or glasshouse (Siddiqui, 2005), few PGPR have been trialled successfully in commercial
sugarcane crops. Across numerous crops, variable results occur and reasons include that
competitive interactions from other microorganisms can prevent benefits from PGPR (Saharan and
Nehra, 2011).
In Brazil, bacterial inocula of five or more PGPR including putative N-fixing
Gluconacetobacter, Azospirillum, Herbaspirillum and Bulkholderia species have undergone many
years of scientific evaluation. These commercial inocula are now used routinely but require several
inoculation steps in each crop cycle that span from soaking setts in the inoculum to injection of soil,
and their formulation accommodates particular sugarcane varieties and soil types to ensure efficacy
(Schultz et al., 2014).
Globally, R&D into PGPR is expanding, and substantial progress is foreseeable. Scientific
investigations are enabling the manufacture of inocula that are effective for specific crop varieties,
soils and climates as formulation, storage and application techniques are being optimised.
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In markets such as Europe, where companies selling microbial inoculum are required to
prove efficacy to government regulators, robust science is underway and PGPR are increasingly
part of horticultural and broad acre crop production.
Bacteria may also act as biological control agents. For example, the bacterium Pasteuria
penetrans parasitises nematodes and reduces the ability of crop-damaging nematodes to reproduce
(Stirling, 2014). While Pasteuria penetrans is relatively common in cane soils in Australia, it rarely
occurs at high population densities, presumably because tillage disrupts the intimate relationship
between the parasite and its nematode host (Stirling et al., 2016). It would be highly desirable for
the industry if populations of Pasteuria penetrans can be increased to provide effective biological
control of parasitic nematodes, and research is ongoing (Anderson et al., unpublished results).
Bacteria may be pathogens where there is a specific host pathogen relationship (Agrios,
2005) in addition to deleterious rhizosphere bacteria, which negatively affect plant growth and
vigour through the production of toxins and hormones, competition for nutrients and inhibiting
beneficial mycorrhizal fungi (Lehman et al., 2015). How much there is yet to learn about soil
bacteria (and their prokaryotic counterparts Archaea) is highlighted in the recent Biomes of
Australian Soil Environments (BASE) project (Bissett et al., 2011). While similar higher-order
bacterial and Archaea groupings occur across land uses, including sugarcane soil, bacterial
communities have yet to be characterised in depth. The BASE project provides genetic sequences,
contextual data as well as search tools that allow researchers to interrogate Australia’s first soil
microbial diversity database for numerous applications.
Fungi
Fungi are recognised key players in soil function, as their hyphae structures span large
distances in soil, decompose recalcitrant substrates and contribute to soil carbon sequestration
(Fontaine et al., 2011; Frey et al., 2003). Fungi are particularly sensitive to disturbance such as
tillage, as they tend to be comparatively slow growing with mycelial networks regenerating slowly
after disturbance (Beare et al., 1997). Agronomic practices such as nitrogen fertiliser rate can affect
fungal community composition in sugarcane fields, with higher N rates resulting in a decreased
proportion of Basidiomycota (filamentous hyphae-based fungi, which include lignin decomposers)
and increases in Ascomycota and putative crop pathogenic fungi (Paungfoo-Lonhienne et al.,
2015).
A range of fungal organisms are associated with sugarcane roots some are pathogenic but
the majority are beneficial (Rutherford et al., 2002). Beneficial fungi such as Trichoderma species
are common rhizosphere inhabitants. Trichoderma species have been widely studied for their
capacity to produce antibiotics, parasitise other fungi and compete with deleterious plant
microorganisms such as Rhizoctonia and Fusarium (Contreras-Cornejo et al., 2016).
In sugarcane fields treated with filter cake (mill-mud), Trichoderma species are among the
first fungal colonisers of mill-mud and are suppressive to Pythium and nematodes (Roth, 1971;
Sharon et al., 2001). Other potentially beneficial fungi that are abundant in sugarcane soil include
non-pathogenic Fusarium, nematode trapping fungi (Arthrobotrys species, Dectylella spp,
Beauveria spp, and Metarhizium (Rutherford et al., 2002; Stirling, 2014).
Fungal organisms that form association with plants, and that live entirely or for part of their
life cycle in plants, but cause no apparent harm, are known as endophytes. These endophytic fungi
form symbiotic relationships with the host plant, provide a range of beneficial services such as
enhanced nutrient uptake, drought tolerance and disease resistance (Stirling, 2014).
Fusarium sacchari and Epicoccum nigrum are effective in controlling several fungal
pathogens and insect pest African sugarcane borer, Eldana saccharina (de Lima Favaro et al. 2012;
Mahlanza et al., 2015). Mycorrhizal fungi are a particular example of endophytes and benefits in
assisting in phosphorus uptake, stress tolerance and nematode suppression have been documented in
sugarcane, including in Australia (Kelly et al., 1997; Sankaranarayanan and Hari, 2016). Overall,
there is surprisingly little known about the presence and effects of mycorrhizal endophytes in
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Australian sugarcane crops, and a recent study found that endomycorrhizal fungi (Glomeromycota)
were absent from soil and roots of two commercial sugarcane fields (Paungfoo-Lonhienne et al.,
2015). Whether this observation reflects the situation in the industry as a whole is unknown. It also
remains to be investigated whether commercial mycorrhizal inoculum can successfully re-introduce
endomycorrhizal species if these are indeed scarce or missing from Australian sugarcane soils.
A small number of pathogenic soil fungi can impact substantially on sugarcane yield.
Pachymetra root rot (Pachymetra chounorhiza) is widely spread across Australian sugarcane
growing regions and can cause significant yield loss if susceptible sugarcane varieties are planted,
and no other known control measures are effective against this pathogen (Croft and Magarey,
2000). Pineapple sett rot (Ceratocystis paradoxa) can cause considerable damage at emergence of
sugarcane in favourable conditions (Girard and Rott, 2000).
Various species of Trichoderma and Gliocladium fungi were found to be effective in
controlling pineapple sett rots under controlled growth conditions, but their effectiveness under
field conditions has yet to be proven (Girard and Rott, 2000). Pythium root rot (Pythium spp.) is
only a problem in wet temperate climates and the severity of Pythium root rot is controlled by
interaction with soil organisms and organic matter (Hoy, 2000).
Magarey (1996) identified a range of pathogens (sub-clinical pathogens) which were
affecting root surfaces and leading to poor root growth and yield decline of sugarcane. It is likely
that conventional farming systems provide conditions favouring sub-clinical pathogens with soil
compaction, lack of organic matter, anoxia and crop monoculture as potential contributing factors.
Magarey (1996) recommended research on further identification of these sub-clinical
pathogens and on the management practices that influence this group of pathogens; however this
has not yet occurred.
Nematodes
Sugarcane is largely grown as a constant monoculture with only a few months of break
every three to 10 years, resulting in favourable conditions for the development of large nematode
communities. More than 310 species of 48 genera of endo- and ectoparasitic nematodes have been
recorded from sugarcane roots and/or rhizosphere (Cadet and Spaull, 2005).
The most common plant parasitic nematodes that are widespread in sugarcane fields are
Pratylenchus and Meloidogyne species (Stirling and Blair 2000).
Other genera that are particularly widespread in sugarcane fields include, Helicotylenchus
(35 species), Tylenchorhynchus (36 spp.), Xiphinema (52 spp.), Hoplolaimus (11 spp.),
Paratrichodorus and Trichodorus (nine spp.) (Cadet and Spaull, 2005).
Nematodes associated with sugarcane do not occur alone in the soil but are present in
communities comprising a number of species. Surveys from various parts of the world show that
the number of nematode genera present in a single soil sample ranges from one to 12 with an
average of between 3.2 and 7.9 (Cadet and Spaull, 2005). These show the wide diversity and
complexity of plant parasitic nematodes associated with sugarcane roots and rhizosphere.
Free-living nematodes that are often regarded as beneficial form part of the sugarcane
rhizosphere community. In most sugarcane soils free-living nematodes are present in lower
numbers compared with plant parasitic nematodes, representing 30–70% of total nematode
population (Cadet and Spaull, 2005; Stirling et al., 2001; Stirling et al., 2002).
Some free-living nematodes are predacious and others are a food source for fungal predators
of nematodes, and this may have been one of the reasons why populations of plant parasitic
nematodes were suppressed when numbers of free-living nematodes were increased by adding
organic matter to soil (Stirling and Eden, 2008).
An inverse relationship between nitrogen fertiliser and beneficial nematodes was observed
with a lower presence of beneficial nematodes in soil receiving 160 kg N per hectare than soil
fertilised with only 40 kg N/ha (Stirling et al., 2015).
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Microarthropods
Microarthropods, a size-based class variously defined but generally recognised as being
composed of mites, springtails, and very small insects, arachnids and myriapods, are considered
significant indicators of soil health because of their abundance (typically hundreds of thousands in
the upper 10 cm of a square metre of healthy soil), diversity (typically hundreds of species), and
diversity of function. Perhaps their most important function is maintaining and stoking the
microbial decomposer engine by penetration and comminution of litter, stimulatory grazing of
microbes, and dispersal of microbial propagules.
Another important function is the regulation of grazer populations by predators and, of
special interest to agricultural systems, the suppression of root pathogens including nematodes
(Stirling et al. 2016). In sugarcane soils, microarthropods have barely been studied, but see Stirling
et al. (2016) and Walter and Proctor (2013) for recent overviews of their function and importance in
other systems. Manwaring et al. (2015) show preliminary results from Australian sugarcane fields
and conclude that sugarcane soils contain a microarthropod community with potential to contribute
to the suppression of nematode pests.
Earthworms
Earthworms are often considered indicators of soil health, and are regarded as ‘ecosystem
engineers’ due to their ability to maintain soil structure and improve aeration and water infiltration
(Kibblewhite et al., 2008; Stork and Eggleton, 1992). Earthworm numbers are increased in
abandoned or reforested sugarcane fields compared with managed fields (Zou and Bashkin, 1998),
and numbers tend to decrease in fields after tilling due to soil disruption and drying (Kibblewhite et
al., 2008; Stork and Eggleton, 1992).
Conversely, there are indications that earthworm numbers are correlated at least as strongly
with soil moisture than with land management (Carnovale et al., 2015), and thus may not always be
reliable indicators. In Indonesian sugarcane fields receiving different qualities and quantities of
organic matter, earthworm numbers varied in response to inputs, with higher numbers of
earthworms observed with larger amounts and lower quality litter (Nurhidayati et al., 2012). The
importance of earthworms as soil engineers is not reflected by current research efforts in Australia
and there is much scope to expand knowledge with targeted comparisons across soil types and
agronomies and in context with other soil biology indicators.
Improving soil biology
All of the organisms described above and others (e.g. beetles, protozoa) that have not been
outlined here, interact to form a soil food web (Figure 2). While soil structure, soil water content,
pH and soil temperature play roles in the structure of the food web, the primary driver of activity
within the soil food web is organic matter, in which carbon is an energy source for the remainder of
the food web (Stirling, 2014).
While crop residues (especially sugarcane trash) are the major contributor to organic matter
input, living plants continuously contribute a substantial amount of labile organic matter through
root exudates and root turnover; around 11% of the net fixed carbon produced by plants is on
average deposited by roots into the soil (Jones et al., 2009). This is why it is important to not only
return crop residues to the soil, but also to maintain both crop and rotation species cover to maintain
organic matter inputs to soil and improve soil biology.
The Yield Decline Joint Venture recommended that growers adopt green cane trash
blanketing and legume rotations, minimum tillage, wider (1.8 m) row spacing and GPS guidance to
restrict the area subject to soil compaction. While green cane trash blanketing is now widely
adopted (except in the Burdekin growing region) (Pankhurst et al., 2003; Salter et al., 2010;
Schroeder et al., 2009), the proportion of growers using rotations to other crops remains a minority
(Bell et al., 2007). While trash blanketing is considered to positively affect soil health, field studies
(Robertson and Thorburn, 2007; Salter et al., 2010) have shown no changes in soil carbon levels
over an 18 year period of trash blanketing (Page et al., 2013), and the fate of trash blanket derived C
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and N remain a matter of debate. Very few sugarcane growers have adopted the recommendations
of the Yield Decline Joint Venture in their totality, and, in many cases, a partial adoption may have
little effect (i.e. if trash blanketing is adopted, conventional tillage may still be used). Increasing soil
carbon remains a challenge in most systems worldwide and the drivers of soil carbon sequestration
are not yet fully understood. However, it is becoming increasingly apparent that the soil microbial
community – and particularly fungi has a major influence on the ultimate fate of carbon entering
the soil (Cotrufo et al., 2013; Fontaine et al., 2011; Stockmann et al., 2013).
A large number of tests for biological activity in soil and biodiversity have been developed,
including microbial biomass, fungal biomass, fungal-bacterial ratios, microbial and fungal diversity,
number and diversity of earthworms, free-living nematode counts, CO2 respiration, total organic
carbon, labile carbon, biochemical tests of microbial activity, the ratio of bacterial feeding
nematodes to fungal feeding nematodes, and tests for mycorrhizal fungi (Obriot et al., 2016; Ritz et
al., 2009).
For non-experts, the nuances of these assays are often lost and they are often
interchangeably considered as measures of ‘biology’. However, if the tests are grouped and overlaid
on the soil food web (Figure 2) then the relevance of the various tests becomes clearer. For
example, a nematode community analysis, where omnivorous and predatory nematodes are
dominant to plant parasitic nematodes, indicates a healthy soil food web. A nematode community
analysis that has a dominance of certain groups of bacterial-feeding nematodes is evidence of a soil
that has been recently disturbed or where there have been recent large inputs of organic matter
(Stirling, 2014). Similarly, ratios of fungal:bacterial biomass are more strongly skewed towards
bacteria in disturbed systems, as fungi are more strongly impacted (Bardgett and McAlister, 1999).
Microbes produce enzymes to decompose organic substrates, and the range of enzyme
activities of fungi and bacteria present can be informative about both the current factors limiting
microbial growth, and the availabilities of various chemicals in soils (Brackin et al., 2013). For
example, if many microbes are present that degrade plant cell walls, then then an assay for the
enzyme cellulase will return high values. Other assays (such as fluorescein diacetate hydrolysis)
measure the sum activity of a broad range of enzymes and can be useful general indicators of
microbial activity.
Healthy soils in general have larger microbial populations, higher fungal:bacterial ratios and
higher levels of production of a range of enzymes. CO2 production is frequently used as a measure
of soil microbial activity and of other processes, such as decomposition, mineralisation, and even as
a microbial biomass estimate. In reality, CO2 production is the integrated end result of almost all
soil activity by the entirety of living organisms in soil, including respiration from plant roots. It can
be a useful general indicator of overall soil activity, as it is relatively easy to measure, but, like all
soil biological measurements, is highly dependent on soil moisture. Connecting the various
measures of soil biological composition and function requires greater data integration and
contextualisation.
Future vision and recommendations
While overall soil biological populations decline quickly and community structure changes
rapidly under intensive agricultural land use (Dominy et al., 2002; Holt and Mayer, 1998), re-
establishing a healthy soil biological community in degraded soils can be an extremely slow process
(Fichtner et al., 2014).
Many growers understandably look towards ‘quick fix’ commercial products; however these
are largely unproven and are unlikely to produce positive results, particularly if introduced into an
adverse soil environment that challenges the crop with physical and chemical constraints. There is
also currently not a one-stop-shop for sugarcane growers to measure indicators of soil biology and a
lack of cane-specific recommendations for growers to be able to benchmark their progress. The
grain industry’s Soil Quality project offered tests for total organic carbon, labile carbon, microbial
biomass carbon, soil nitrogen supply, and specific tests for take-all and rhizoctonia diseases, as
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well as tests for cereal cyst and root lesion nematodes. A traffic light system was developed to help
growers identify what they should address in the first instance (Murphy, 2012). To advance the
understanding of soil biology in sugarcane, assessment is required of various agronomic measures
together with considerable numbers of soil samples from different regions and soil types. Sampling
and benchmarking also has to reflect the transition from traditional to modern farming systems in
context of yield and agronomies to be of use for growers.
Fig. 2—The soil food web with various indicators of soil health overlaid (black boxes).
Recommendations include:
1. Collect and assess a range of soils and set benchmarks – ideally, a large collection of
samples of different soil types from different production regions from traditional and
new farming systems assessed collectively with a large range of physical, chemical
and biological indicator tests. These data allow us to identify which measures are the
most suited to sugarcane systems (easy to use and interpret, economical). They will
also provide benchmarks for the various soil types and districts. Such a
comprehensive data set would be combined with yield data and provide information
on the best practices for growers to implement to improve soil biology.
2. Expand research on cover crops research on cover crops should be expanded to
understand the role that legume break crops have in providing nitrogen to subsequent
cane crops, determine suitable cover crops to break pest and disease cycles and
examine the impact of cover crops on increasing soil biological diversity.
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3. Expand research on interactions within the soil food web there is need to better
understand how components of the soil food web interact, for example, there is some
evidence that plant parasitic nematodes increase the susceptibility of sugarcane roots
to sub-clinical pathogens (Stirling, 2008).
In summary, sugarcane soils have diverse communities that contribute to the overall health
of the soil through functions such as nutrient cycling, and pest and disease suppression. Growers
can undertake practices to improve their soils’ biology, but they need the tools to effectively direct
changes and identify which practices will have the biggest benefit.
The quest for not only improving resource use in cropping for farm economic and
environmental benefits, but also consider ecosystem services as a whole (i.e. carbon sequestration
into soils, greenhouse gas fluxes, water infiltrations, nutrient cycling) is increasingly providing a
new framework, where growers are connected to the global community including earth system
processes.
With problems identified and articulated, next steps can now capitalise on powerful
molecular and data analysis tools to characterise soil biological communities to advance the tool kit
for growers.
Acknowledgments
Dr Graham Stirling is thanked for his very helpful comments on drafts of this paper. Sugar
Research Australia is acknowledged for funding project 2014/004, on which David Walter, Shamsul
Bhuiyan and Jay Anderson collaborated with Graham Stirling. Scott Buckley is funded by SRA
project 2014/108.
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