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International Journal of Recycling of Organic Waste in Agriculture
https://doi.org/10.1007/s40093-019-0243-0
REVIEW
Agrowaste bioconversion andmicrobial fortication have prospects
forsoil health, crop productivity, andeco‑enterprising
DhananjayaP.Singh1· RatnaPrabha1· ShuklaRenu1· PramodKumarSahu1· VivekSingh1
Received: 11 May 2018 / Accepted: 14 January 2019
© The Author(s) 2019
Abstract
Purpose Agricultural chemicals either used as nutrient inputs for soil fertility or pesticides are creating physicochemical and
biological deterioration of the soils and disturbing the agro-ecosystems worldwide. Alarming concerns towards integrated
agroecology demand for renewed interest in low-external input-based farming practices. These practices comprise strength-
ening of soil biological properties, recycling of inherent soil minerals and reuse of agricultural residual wastes.
Methods We described approaches for the bioconversion of agricultural residual wastes into value-added compost. The
process involves conversion of residual waste into raw compost followed by its fortification with beneficial decomposer
microorganisms to produce quality fortified compost product. Finally, incubation of fortified compost with single or consortia
of beneficial microorganisms like N-fixers, P-solubilizers or K-mobilizers and biocontrol agents further enriches compost
to produce bioorganic products.
Results Bioconversion of agricultural wastes into compost using potential decomposer microorganisms and fortification
of decomposed organic matter with beneficial bacterial and fungal species is of immense importance. Additional enrich-
ment of compost with botanicals, humic acid, amino acids, mineral nutrients, phytohormones etc. may also add value to the
bioinput products.
Conclusion In an integrated way, on-farm production of raw compost using different agricultural residual wastes and its
further fortification with bioorganic farm inputs can help farmers produce value-added compost products for direct appli-
cation in the crop production. Adoption of microbial bioconversion technologies and their field applications may become
eco-enterprising for the rural resource-poor farming communities for enhancing their livelihood along with improving farm
productivity and soil health.
Keywords Microbial technology· Agricultural wastes· Bioconversion· Compost· Microbial inoculants· Bioorganic farm
inputs
Introduction
Agricultural production has always been increasing pace due
to the use of high-yield varieties which were input-intensive
and demanded excessive chemical fertilizers and pesticides
for supporting soil fertility and plant nutrition (Kibble-
white etal. 2008; Lorenz etal. 2013). Indiscriminate use
of chemical inputs into the agricultural system has raised
several problems concerned with the groundwater quality,
soil agroecology and plant health (Power 2010). This has led
to serious deleterious polluting impact on soil fertility, crop
production, irrigation water, nutritional produce quality,
and human health (Popp etal. 2013). Soils are continuously
becoming low in organic carbon content and losing ben-
eficial microbial communities. Agricultural chemicals have
altered traditional cultivation practices and created physical,
chemical, and biological deterioration of cultivable lands
(Pretty and Bharucha 2014). Excessive chemical use has
adversely influenced biodiversity of the soils, caused loss
of nutritional ingredients and accumulation of non-desirable
chemical intermediates in the food chain (Lal 2015). Other
major problem associated with the chemical-dependent
agricultural system is the increasing contamination of sur-
face and groundwater due to residual pesticides, industrial
* Dhananjaya P. Singh
dhananjaya.singh@icar.gov.in; dpsfarm@rediffmail.com
1 ICAR-National Bureau ofAgriculturally Important
Microorganisms, Kushmaur, MaunathBhanjan,
UttarPradesh275101, India
International Journal of Recycling of Organic Waste in Agriculture
1 3
wastes, heavy metals, and organic chemicals (Jaishankar
etal. 2014; Khatri and Tyagi 2015).
Health of agricultural production system is at stake in the
wake of shrinking land resources, increasing industrializa-
tion, expanding urbanization, excessive chemical usage and
diminishing viable bioorganic inputs in the soils (Phalan
etal. 2014). Agricultural sustainability is compromised due
to the reducing biological wealth of farm resources. This
needs to be suitably addressed to sustain long-term agri-
cultural productivity to support food security and rural
livelihood (Frison etal. 2011; Pradhan etal. 2015). There
exists no simple or single way to understand and implicate
such complex ecological, socioeconomic, and technological
aspects of declining sustainability in agricultural systems
(Pretty and Bharucha 2014). However, addressing connec-
tion between a balanced agro-ecosystem and sustainable
crop productivity in a holistic manner could offer better solu-
tion to restore sustainability in agriculture systems.
Public concerns over adverse impacts of external chemi-
cal inputs on the quality of produce, farm soils, water and
environment are rising (Bohlke 2002; Aktar etal. 2009;
Mohanty etal. 2013; Hongsibsong etal. 2017). This has
raised questions as to whether the present agricultural pro-
duction system is able to provide quality food for all-over
longer term (Hossard etal. 2014; Pradhan etal. 2015).
Therefore, many countries are now taking initiatives to
reduce the use of fertilizers and pesticides in the food crop
production system (FAO 2017). Green Revolution wit-
nessed high pace of crop productivity in the past few dec-
ades. However, now this has left with emerging associated
risks of dependence on high external inputs, disturbance of
agroecology and resurgence of pests and diseases (Pingali
2014; Godfray and Garnett 2014). Such threatening con-
cerns have generated renewed interest in the alternative
ways of farming practices that are based on recycling and
reuse of farm wastes as bioorganic inputs to enhance soil
productivity (Schröder etal. 2018). This has also provoked
current thinking on intensified promotion of soil biodiver-
sity and biogeochemical processes that enhance soil car-
bon and microbial communities having specific functional
traits (Gattinger etal. 2012; Lori etal. 2017). Results from
long-term experimental data generated on nitrogen fertiliza-
tion strategies in Italy for limiting environmental risk from
excessive N-application and animal farming created Nitrates
Directives application scheme for more relaxed application
of manure-N. Studies reflected that application of composted
materials with bacterial biofertilizers improved soil micro-
bial community structure and diversity in degraded soils
from croplands (Zhen etal. 2014). Similar practices can
balance bioorganic and microbiological equilibrium of the
soils in the ways that simultaneously favor production and
protection of food crops along with the soil fertility status.
Crop production strategies based on low external input
farming practices that nurtured ecological dynamics have
potentials of minimizing chemical fertilizers, inorganic
inputs and pesticides. This has reliably led to reducing the
cost of production, producing high-quality nutritionally val-
uable and sellable crop produce, ensuring ecological safety
and rural livelihood and most importantly, holistic human
health (Kesavan and Swaminathan 2008). In such a farming
system, crop yield is maintained through greater emphasis
on cultural practices, use of biological inputs, integration of
pest/disease management practices and managed utilization
of on-farm agricultural resources (Gliessman and Rosemeyer
2010; Branca etal. 2011; Osteen etal. 2012). Making the
soils rich in organic carbon support diverse microbial inhab-
itants that in turn promote soil functions (Gougoulias etal.
2014; Trivedi etal. 2016). Global land distribution and soil
quality are compromised due to high pressure to produce
more crops, changing pattern in global food consumption,
insufficient adoption of soil management practices, urbani-
zation, and industrialization and life style of the population
(Blum 2013). The role of organic carbon richness in the
soils in terms of its functional benefits is obvious (Clara
etal. 2017). Usually low-carbon soils fail to support diverse
microbial attributes that naturally drive ecosystem functions
independently (Louis etal. 2016). Therefore, there is a need
to implicate enhanced availability of organic matter in the
soils for sustainable improvement in crop productivity and
tolerance against biotic and abiotic stresses (Zhang etal.
2016). Site-specific organic carbon content in the top-soils
is a major prerequisite for sustainable soil functions indi-
cating a good soil quality and agronomic value (Seremesic
etal. 2011). Decline in soil organic matter due to insufficient
addition of organic manures, low crop rotation and manage-
ment practices (like tillage, fertilization) and on-farm crop
residue burning is widely reported (Bhan and Behera 2014;
Godde etal. 2016). The organic content of the soils can
be improved by increasing organic matter gain of the soils
through the addition of decomposed materials or by reducing
organic matter losses through released respiring carbon by
microorganisms (Carter 2002).
One of the potential sources of organic carbon return to
the soils is the crop residue produced during the cropping
season and post harvest. These residues usually go waste and
create environmental sanitation issues. However, if incor-
porated in the soils it can increase crop yield (Han etal.
2017). Loss of organic carbon from the soil reduces crop
productivity worldwide. Therefore, locally feasible practices
are needed to support farmers to help regain soil organic
matter (Wei etal. 2015). Farmers usually lack knowledge on
the importance of microbial resources in the above-ground
and below-ground soils and benefits of their on-farm impli-
cations. They also lack information on biological manage-
ment of farms using microbial technologies, potentialities of
International Journal of Recycling of Organic Waste in Agriculture
1 3
managed integration of on-farm resources and conversion of
agro-wastes into organic farm inputs to enhance soil capa-
bilities (Han etal. 2017). These issues, if accepted, worked
out and adapted by the resource-poor farmers can help in
minimizing dependency on external chemicals and fertiliz-
ers, reducing cost of crop production and improving ecosys-
tem services in the soils. Therefore, the agricultural residue
decomposition technology using microbial interventions and
fortification of the compost with beneficial microorganisms
has immense scope.
We reviewed significance of microbe-mediated agrowaste
bioconversion practices and their reuse for strengthening
soils. We described how fortification and bioaugmentation
of the raw decomposed products using specific microbial
inoculants that act as decomposers, plant growth promoters
and/or bioagents can help farmers obtain functionally poten-
tial bioorganic farm inputs? The usefulness of such technolo-
gies in producing different crops has also been summarized
with specific examples from the field-scale applications.
Microorganisms are thekey toagrowaste
bioconversion
The ways in which microorganisms have been used to
advance human and animal health, food processing, food
safety and quality, environmental protection, crop produc-
tion, and agricultural biotechnology has made them alterna-
tives for high-input farming practices. Lignocellulose that
consists of cellulose, hemicellulose and lignin represents
major structural component of agricultural crop residues
(Pothiraj etal. 2006). Due to extensive agricultural activi-
ties, huge amounts of agricultural residues contribute sig-
nificantly to the yearly global yield of lignocellulose (Loow
etal. 2015). Various agricultural residues that contain up to
20–30% lignin–hemicellulose–have potential biotechnologi-
cal values because of their bioconversion and/or fermenta-
tion to yield industrially important constituents including
biofuels (Sorek etal. 2014). However, due to the recalcitrant
nature of the lignin, which has resistance against microbial
attack (Loow etal. 2017a), cost-efficient methods to reuti-
lize the lignocellulose components within the biomass effec-
tively have remained challenging (Loow etal. 2017b). Much
of the lignocellulose wastes create environmental pollution
problems if remained in the farm either as biomass or burnt
upon. Huge amount of lignocellulosic wastes if converted to
the value-added products using enzymes such as cellulases,
glucanases, hemicellulases, glycosidase hydrolases, polysac-
charide lyases and carbohydrate esterases or with the help
of microbes (Himmel etal. 2010) can yield chemicals, fuel,
textile, paper, and agricultural inputs (Pothiraj etal. 2006).
Bioconversion, more specifically composting of agri-
cultural residues refers to step-wise biodecomposition
procedures carried out due to the intervention of different
microbial communities under aerobic conditions (Pan etal.
2012). The end product of the aerobic composting yields sta-
bilized organic product, which is beneficial for plant growth
and development. Efforts on microbial intervention for bet-
ter decomposition gained strength from the identification
and characterization of such microbial communities from
the agricultural soils, composts, vermicompost and humus-
rich sites, that prominently catalyzed biodegradation and
decomposition (Eida etal. 2012). Scaling-up of bioconver-
sion processes and large-scale production technologies using
microbial inoculants have resulted in producing mass-scale
composted material that may be bioaugmented with benefi-
cial microorganisms or fortified with organic inputs, bio-
inoculants, and vermicompost (Singh and Sharma 2002;
Nair and Okamitsu 2012; Malusá etal. 2012). Composted
products were reported to act as soil conditioners in low-cost
crop production practices for resource-poor farming com-
munities (Gajalakshmi and Abbasi 2008).
The uniqueness of microorganisms and their functions
have made them potential candidates for decomposing
agricultural residues into valuable products (Kumar and
Sai Gopal 2015). Microbial communities have emerged to
influence litter decomposability and size of nutrient pool in
the soils. They primarily immobilize mineralized nutrients
into microbial biomass and release nutrients from microbial
pool after decomposition (Sahu etal. 2018). This phenom-
enon has major impact on the bioavailability of nutrients
to the plants (Miki etal. 2010). It further regulates cycling
of nutrients into the soils. Various microorganisms possess
enzyme activities directly linked to the decomposition of
organic materials which under improved composting condi-
tions yield better compost products (Eida etal. 2012). There
have been several reports on the isolation and trait charac-
terization of microbial communities that can perform func-
tionally better in combination with the existing rhizosphere
bacteria, beneficial mycorrhizal fungi and biological control
agents (Boulter etal. 2002; Anastasi etal. 2005; Vishan
etal. 2017). The decomposed organic matter when used in
the soils makes native beneficial microorganisms more effec-
tive due to their rich carbon content (Meena etal. 2014;
Rashid etal. 2016). Vermicompost, a composted product
produced by the intervention of earthworm Eisenia fetida is
also known to enhance native soil microbial diversity and
promote plant growth (Lim etal. 2015). Bacterial diversity
from vermicompost exhibiting plant growth promoting traits
has been investigated (Singh and Sharma 2002; Pathma and
Sakthivel 2012). Co-inoculation of beneficial bacterial and
fungal organisms like species of Rhizobium, Azotobacter,
Azospirillum, Pseudomonas, Bacillus, Burkholderia cepa-
cia, Candida oleophila, Coniothyrium minitans, C. scle-
rotiorum, Aspergillus niger, Fusarium oxysporum (non-
pathogenic), Gliocladium spp., Phlebia gigantean, Pythium
International Journal of Recycling of Organic Waste in Agriculture
1 3
oligandrum, Streptomyces griseoviridis and Trichoderma
spp. with organic matter-rich compost can add to the soil
health. Such practices are known to improve crop productiv-
ity through diverse mechanisms through nutrient acquisition,
mineralization, carbon addition and phytohormone produc-
tion (Rashid etal. 2016; Meena etal. 2017). The species
of Rhizobium, Azotobacter, Azospirillum, and phosphate
solubilizing microorganisms that are currently being used
as commercial formulations of biofertilizers, when added
in combination with the compost can also provide major
support to agriculture (Reddy and Saravanan 2013; Sharma
etal. 2013). Use of farm yard manure (FYM), vermicom-
post and other humus-based organic farm inputs also sup-
port agricultural production. Overall, organic and microbi-
ally fortified farm-supplement constituents as termed by the
names biofertilizers, biopesticides, microbial inoculants, soil
conditioners if used in an integrated manner can make soils
more live, healthy, and viable for improved crop production
(Parnell etal. 2016).
Microbial bioconversion of agricultural waste, house-
hold waste or other natural products like leaf litter and non-
decomposed matter into compost products was developed
in the past several years. Various microorganisms were
reported as fast decomposers, biodegraders, and biocon-
verters of non-useful products (Gautam etal. 2012). Fungal
communities develop fast in the arable soils in straw residue
degradation conditions (Ma etal. 2013). Rapid changes have
also been observed in primary decomposer fungal communi-
ties suggesting that litter decomposition is a highly complex
process mediated by diverse taxa (Voříšková and Baldrian
2013). Bacterial succession on plant residual biomass
decomposition also exhibits specific pattern of bacteria and
fungus communities. Results on bacterial succession sug-
gested early-stage (2–4months), mid-stage (6–8months)
and later-stage (10–24months) prominent changes in
decomposer communities (Tláskal etal. 2016).
The role of microorganisms as bioconversion agents is
important due to their fast ability to convert cellulosic and
lignocellulosic wastes into organic materials (de Souza
2013). Mature compost in combination with microbial con-
sortia more prominently helps bioremediation of environ-
mental pollutants (petroleum hydrocarbons) (Gomez and
Sartaj 2014). It also improves microbial interaction with root
rhizosphere to promote plant growth and develop top-soil
structure (Sinha etal. 2009; Abhilash etal. 2016; Marcela
etal. 2017). Composting process usually involves three
phases in which diverse microbial organisms like bacteria,
actinomycetes and fungi act on the lignocellulosic compo-
nents of the residue biomass. This converts waste into humus
under mesophilic (Streptomyces rectus) and thermophilic
(Actinobifida chromogena, Thermomonospora fusca, Micro-
bispora bispora) conditions (Pan etal. 2012; Zeng etal.
2016). The first phase initiates with the rise in temperature
and reduces substrate by degradation action of mesophiles
(Zeng etal. 2016). This is followed by the increase in the
temperature up to 70°C due to the abundant activities of
thermophilic microorganisms (Schloss etal. 2003). Ben-
efits of the thermophilic phase lie in terms of the loss of
pathogenic bacteria and fungi which are degraded due to
high temperature. Afterwards, the compost pile temperature
returns to normal stage (Novinscak etal. 2008). The process
of decomposition of crop residues involves differentially var-
iable conditions (pH, temperature, moisture, nutrient avail-
ability) for the microbial communities involved during the
period of degradation. Certain organisms like Coprinus spe-
cies belonging to Basidiomycota grow well in alkaline con-
ditions while other fungi, e.g., Trichoderma, Mucor, Nocar-
dia, and Phanerochaete chrysosporium need optimum pH
(5.5–8.0) for attaining high population that could help rapid
biodegradation (Varma etal. 2017). The decomposition abil-
ity of the microbial communities is largely influenced by the
conditions of the residual waste products being decomposed
like pH (< 7.0), moisture content (~ 60%), volatile ammonia
emission (30–70%), temperature (30–60°C) and different
organic mixtures (polysaccharides, cellulose, hemicellu-
lose, amino acids, and fatty acids) (Urbanová etal. 2015).
Conventional processes were reported in the past but rapid
composting using microbial consortia is more advanced and
advantageous concept due to the ease of controlled environ-
ment, identified ingredients for fast degradation and timely
composting (Chen etal. 2016; Patchaye etal. 2018).
The enteric fermentation of the ruminants from the live-
stock, especially of the cattle used at large scale in agricul-
tural practices leads to the production of green house gases
(GHGs). One such gas methane (CH4) contributes to almost
1/3rd of the total emissions of GHGs from agricultural sec-
tor (https ://www.epa.gov/ghgem issio ns/sourc es-green house
-gas-emiss ions#agric ultur e). The other gaseous emission in
agricultural sector that largely contributes to GHGs in the
environment includes nitrous oxide and carbon dioxide, the
mitigation of which needs specific technologies associated
to irrigation type and nitrogen use status (Sanz-Cobena etal.
2017). Improper manure management, burning crop residues
in the fields, application of synthetic nitrogenous fertilizers
and high nitrogen crops are the major factors that contribute
to the GHGs in the environment (http://www.ipcc.ch/ipccr
eport s/tar/wg3/index .php?idp=115). Agricultural residues
or animal wastes, when left in the fields for months have
possibilities of uncontrolled decomposition by undesirable
bacteria or fungi and therefore, are liable to produce more
amount of GHGs (Patra and Babu 2017). Associated with
this, there always remains risk of polluting air and water
with nitrogen and microbial pathogens (Venglovsky etal.
2009). For this reason, safety concerns for the use of animal
manures in the soils by spreading onto the land is challeng-
ing and needs various treatment methods for the deactivation
International Journal of Recycling of Organic Waste in Agriculture
1 3
of pathogenic microbial species (Martens and Böhm 2009).
However, the controlled composting such as conversion of
pig slurry into pellets help farmers improve soil properties
due to reduction in ammonia volatilization and mitigate
GHG emissions (Pampuro etal. 2017a, b). Microbe-medi-
ated controlled composting yields composted products from
livestock wastes also in a time-lined manner with the use of
known microbial degraders and specific ingredients. This
becomes helpful in obtaining decomposed products of spe-
cific C:N ratio having beneficial microbial communities for
direct field utilization (Ng etal. 2016).
Technological aspects ofmicrobial
bioconversion ofagricultural wastes
One of the major identified reasons for declining agriculture
sustainability is poor soil condition due to reduced applica-
tion of organic matter into the farms and non-conservational
practices that majorly disturb top soils (Kibblewhite etal.
2008; Hobbs etal. 2008). Huge volume of agricultural
wastes in farmer’s fields has economic and environmental
benefits as suggested by the studies on pyrolysis and biochar
of rice straw, corn stover, orchard, and animal wastes (Kung
etal. 2015). Crop wastes blended with the cow dung for
biogas production after anaerobic digestion using anaerobic
bacteria (acidogenic and acetogenic bacteria) generate elec-
tricity through potential technologies (Muthu etal. 2017).
The product of anaerobic digestion after waste treatment or
the digestate remains can add value through decomposition.
Prominent microbial community dynamics was observed
when the anaerobic digestate from the municipal food resi-
dues, and green and kitchen wastes were composted under
natural composting conditions (Franke-Whittle etal. 2014).
Understanding on microbial dynamics during different
phases of composting helped better control of bio-oxidative
processes followed by stabilization and maturation phases
that use specific technology in static reactor of high capac-
ity (up to 600L or more) (Villar etal. 2016). Studies have
opened new avenues for better utilization of anaerobic diges-
tate after improved composting using beneficial microorgan-
isms, the products of which could be directly utilized in the
farms for improving soil organic content (Zeng etal. 2016).
Such composts proved to be good alternatives of farmyard
manures for field application.
Composting technologies are farmer-friendly, reproduc-
ible, easy to adopt and yield productive inputs for the farms
to sustain agricultural productivity beside generating biogas
for bioenergy (Achinas etal. 2017). Agricultural residues
have remained tremendous sources of bioenergy world-
wide. Crop dry matter and oil-rich residual biomass have
attained the attention due to their huge yearly quantitative
volume of ~ 11.33 million tons that could be converted to
3.84 giga-liters (GI) of bioethanol, 1.07 GI biobutanol, 3.15
billion Cu-Meter (BCM) biogas and ~ 1.0 BCM of biohy-
drogen (Karimi and Yaghmaei 2016). Under methanogenic
condition, hydrogen, carbon dioxide, and methane are gener-
ated due to the action of degrading enzymes on residual crop
biomass. Another important aspect of crop residual resource
management lies with the characterization and thermal
conditioning of bio-oils into fuel production (Bertero etal.
2012). These technologies, based on the microbial role in
waste bioconversion have also been developed for the pro-
duction of ethanol, biofuels, platform chemicals, and biore-
finary products (Mielenz 2001; Prassad etal. 2007; Weber
etal. 2010; Msangi 2012). In India, nearly 700 million tons
of organic residual wastes are generated annually (Nagaval-
lemma etal. 2004). One of the most prominent ways of the
safe disposal of the majority of waste is composting which is
an environmentally sound bioprocess of converting organic
residual wastes into valuable products for farms (Pan etal.
2012). Besides, if scaled up and industrialized, these prod-
ucts can also meet alternative fuel needs through sustainable
waste management practices (Weiland etal. 2009). Various
microorganisms, their potential constituents that help in fast
decomposition, biodegradation and bioconversion of crop
residues and other valuable products are listed in Table1.
Microorganisms are the major key players in maintain-
ing nutrient flow from residues to the farm soils (Erickson
etal. 2009). Plant materials, especially the crop residues
are rich in lignocellulosic biomass but have crystalline
structures embedded with silica, lignin, suberin, and other
polymeric constituents that hinder the process of smooth
microbial degradation for composting (Huber and Praznik
2004). Therefore, pretreatment of lignocellulosic biomass
with the help of acid, alkali, steam, urea, and hydrolytic
enzymes is recommended for substantial breakdown of
hard constituents to smoothen the process of composting
(Mosier etal. 2005; Table1). Lignolytic enzymes produced
by some potential microbial isolates can also be a source of
rapid biodegradation module for large-scale and effective
lignin degradation (Table1) (Fenga etal. 2011). The role of
gut microorganisms like Coptotermes formosanus isolated
from termites is also important in changing physicochemi-
cal properties of the crop residues. Cellulose and lignins can
be made readily available for the existing microbial com-
munities for degradation (Harazano etal. 2003). Potential
microorganisms with impressive enzymatic capabilities for
fast degradation of recalcitrant lignin are discussed (Table1)
(Perez etal. 2014; Varma etal. 2017). Since these organic
compounds possess complex interlinked fractions, their bio-
mass valorization is tough and highly resistant to hydroly-
sis and solubilization (Kumar and Sharma 2017). There-
fore, instead of a single process for pretreatment, multiple
physical, chemical, and biological steps are required in an
integrated way to minimize undesirable inhibitors (Masran
International Journal of Recycling of Organic Waste in Agriculture
1 3
Table 1 Various bacteria and fungi have been isolated, identified, and their products, especially enzymes were used for enhanced decomposition
and degradation of agricultural residues into compost
S. no. Microorganisms Biodegradation activity Nature of organic matter References
Fungi
1. Pleurotus sajor-caju Exocellular lignocellulose
degradation
Multiple matters Singh (2000)
2. Pleurotus flabellatus Exocellular lignocellulose
degradation
Rice straw, sisal leaves Mshandete and Cuff (2008)
3. Pleurotus eryngii Lignocellulose degradation, lac-
case enzyme activity (degrada-
tion of phenolics)
Agricultural wastes Yildirim etal. (2015)
4. Aspergillus niger Cellulase, xyalanase production Pre-decomposition of organic
matter, sugarcane bagasse
Singh and Sharma (2002);
Romero etal. (2007)
5. Trichoderma harzianum Hemicellulose degradation
(hemicellulase production)
Pre-decomposition of organic
matter
Singh and Sharma (2002);
Jorgensen etal. (2003)
6. Trichoderma reesei Cellulase and hemicellulase
production
Commercial production of
enzyme for degradation
Nieves etal. (1998)
7. Penicillium brasilianum Cellulases and xylanases produc-
tion
Commercial production of
enzyme for degradation
Jorgensen etal. (2003)
8. Phanerochaete chrysosporium Lignin peroxydases, glyoxal oxi-
dase, manganese peroxydases
(lignin degradation enzymes)
Lignin-containing biomass like
wood shavings, agro wastes
Martinez (2002), Kersten and
Cullen (2007) and Zhang
etal. (2013)
9. Xylaria hypoxylon Xylanase, laccase, glucosidase,
esterase
Woody materials Liers etal. (2006)
10. Pycnoporus cinnabarinus Lignin peroxidases, manganese
peroxidases, laccase
Woody materials Alves etal. (2004)
11. Trametes versicolor Laccase Agro wastes and woody sub-
strates
Cabuk etal. (2006)
12. Aspergillus awamori Cellulases Agro wastes Gaind and Nain (2007) and
Pleissner etal. (2013)
13. Paecilomyces marquandii Keratinase Poultry waste (feather waste) Veselá and Friedrich (2009)
14. Phanerochaete chrysosporium Increases the humification
degree of humic acid
Agro waste Huang etal. (2009)
Bacteria and actinomycetes
15. Bacillus sp. Lignin degradation Degradation of pulp paper waste Chandra etal. (2007)
16. Paenibacillus sp. Lignin degradation Degradation of pulp paper waste Chandra etal. (2007)
17. Aneurinibacillus aneurinilyticus Lignin degradation Degradation of pulp paper waste Raj etal. (2007)
18. Pseudomonas putida Manganese peroxydases and
laccase
Agro waste Ahmad etal. (2010)
19. Pseudomonas aeruginosa Manganese peroxidases, lipid
peroxidase and laccase
Agro waste Bholay etal. (2012)
20. Serratia marcescens Manganese peroxidases, lipid
peroxidase and laccase
Agro waste Chandra etal. (2012)
21. Citrobacter freundii Manganese peroxidases, lignin
degradation
Agro waste, saw dust Ali etal. (2017)
22. Streptomyces spp. Cellulases, xylosidase, acety-
lesterase, xylanases
Agro waste Benimelia etal. (2007)
23. Bacillus licheniformis and a
Streptomyces sp.
Keratin degradation by Kerati-
nases
Poultry waste Ichida etal. (2001)
24. Mono and co-cultures of B.
subtilis and P. ostreatus Cellulase Apple and plum wastes mixed
with cereal wastes.
Petre etal. (2014)
25. Geobacillus strains Boost the total bacterial count Vegetable waste Pal etal. (2010)
26. Stenotrophomonas maltophilia,
Scedosporium apiospermium Biodegradation of asphaltens Asphaltens from Prestige oil
spill
Martín-Gil etal. (2008)
27. Bacillus cereus, Bacillus mega-
terium Breakdown of cellulose and
hemicelluloses
Organic substrate Ribeiro etal. (2017)
International Journal of Recycling of Organic Waste in Agriculture
1 3
etal. 2016; Shrestha etal. 2017). Maintenance of proper
pH, temperature, air (oxygen) and moisture conditions and
softening of the surface layer of residual biomass with the
help of surfactant or urea is helpful. Likewise, fungal treat-
ments in which fungi and actinomycetes directly colonize
with the residues or enzymatic treatments using lignolytic
enzymes help improving biodelignification process (Ilyin
etal. 2004; Moreno etal. 2015). It further needs exposure
of suitable mesophilic and thermophilic conditions that may
include combined organic and inorganic complexes like
CuSO4-gallic acid supplement for aggravating high func-
tional bioconversion activities (Mishra and Jana 2017).
The bioconversion process can be fastened with the use
of such functionally characterized microbial inoculants that
possess high enzymatic activities for lignocellulosic degra-
dation (Choudhary etal. 2016). Industrial composting for
mushroom production is an established biological proce-
dure to produce Agaricus bisporus (Jurak etal. 2014). Mush-
rooms are among the most fascinating fungal organisms to
be used as pretreatment degraders of the lignocellulose con-
stituents of crop residues and perform improved enzymatic
release of monosaccharides for biofuels. It also helps to
convert residual biomass into valuable protein-rich edible
fruits of high nutritional importance (Jurak etal. 2015).
Compost preparation for mushroom production involves
microorganisms that decompose natural lignocellulose into
simple mineral components, on which mushroom mycelial
mass grows and produces fruiting bodies (Mouthier etal.
2017). Therefore, besides obtaining high-value protein-rich
functional food product from the bioconversion of crop resi-
dues by mushroom fungi (Chang 2008), farmers can also get
value-added compost for their farms to enhance crop pro-
duction and soil fertility. Fortification of raw compost with
plant growth-promoting bacteria and biocontrol agents like
Trichoderma harzianum potentially enhance suppressiveness
of soil-borne diseases and efficacy of compost microbiota
against pathogenic diseases (Pugliese etal. 2011; Ros etal.
2017). Mushroom production is of high economic signifi-
cance in many parts of the world (Marshall and Nair 2009;
Zhang etal. 2014) and compost fortified with beneficial
microorganisms also has potentials of enterprising (Awad
and Khaled 2012; Sarkar and Chourasia 2017).
Direct composting of agricultural crop residues using
large windrows allows thermophilic conditions to convert
high volume of lignocellulosic wastes into stable compost
with specific ingredients of definite C:N ratio (Vigneswaran
etal. 2016). The whole process is biochemically sound and
mediated by microbial metabolic activities that produce
heat, water, CO2 and results in mineralization, transforma-
tion, and humification (Shilev etal. 2007). The technol-
ogy is cheaper and sustainable in terms of its requirements
for ingredients, manpower, energy, water, time, resource
integration, and reproducibility. As far as the agricultural
benefits are concerned, in controlled and defined condi-
tions, the process can yield organic matter disinfected by
high temperature. It is also a mineral-rich nutritional sub-
stance that improves structural components of the soil by
degrading large complex molecules into simple ones for soil
fertility (Sonesson etal. 2000). After production of good-
quality compost using windrows, biofortification of the raw
product can be done with the use of beneficial microbial
inoculants (plant growth-promoting bacteria, mycorrhiza,
and biocontrol fungi) (Muttalib etal. 2016). Enrichment of
raw compost material with organic inputs like humic acid,
amino acids, phytohormones, mineral nutrients (zinc, iron,
boron), phytonutrients, botanicals and vermicompost can
further add value to the products that can help in organic
farming (Mohler and Johnson 2009).
Large-scale livestock production systems are the source
of huge amount of agricultural residual biomass of manures
and slurries that can be applied to the land for fertility
improvement (Bernal etal. 2009). Pig slurries and poultry
manures have remained a common source of composting
ingredient (Pampuro etal. 2016). Co-composting of wastes
from winery distilleries with animal and poultry manure
under static pile composting system was assessed on dif-
ferent parameters such as pH, electrical conductivity (EC),
organic matter, soluble carbon, polyphenolics content,
humification characteristics, and plant germination index
(Bustamante etal. 2008). Agricultural food wastes are also
attractive composting materials for their conversion into
decomposed manures to be used for producing high-value
crops (Rubio etal. 2013). It was largely considered that
composting processes that ensure nutrient-rich conditions,
appropriate carbon rating, organic matter humification and
adequate bulking for reducing N-losses are required to over-
come production cost (Bernal etal. 2009). Results confirm
that composting helped in detoxification and degradation of
phytotoxic compounds in the residual matter and therefore,
offers a favorable way to recycle wastes into value-added
products (Pampuro etal. 2016).
Potential benets ofmicrobe‑mediated
compost asfarm inputs
The role of microorganisms as bioconversion agents and
their ability to convert cellulosic and lignocellulosic wastes
into organic materials, bioremediate environmental pol-
lutants and interact with root rhizosphere to promote plant
growth and soil structure were defined (Sánchez 2009;
Huang etal. 2010). They are inevitable for the natural
resource management in the farmers’ fields. Controlled
composting guided by microbial interventions dependent
on defined microbiological processes to decompose agri-
cultural residues properly and timely and produce high-value
International Journal of Recycling of Organic Waste in Agriculture
1 3
low-cost bioorganic farm inputs (Ahmad etal. 2007; Singh
and Nain 2015; Singh and Prabha 2017; Sudharmaidevi
etal. 2017). This is how rapid composting processes can
help farmers in timely production of compost and forti-
fied bioorganic farm inputs of desired quality for organic
farming needs and high-value commercial crops like veg-
etables, fruits, flowers, and organic crops (Hoornweg etal.
2000; Seyedbagheri 2010). If farmers need biopesticide-rich
compost material for the control of soil-, seed- or seedling-
borne fungal pathogens in the field, they can biofortify the
raw compost with bioagents (Siddiqui etal. 2008; Ng etal.
2016). Similarly, consortium of microorganisms fixing
nitrogen, solubilizing phosphorus and zinc and mobilizing
potassium can be utilized to fortify raw compost material for
desired quality under suitable enriching conditions of tem-
perature and moisture. This can yield potential bioorganic
inputs enriched with N, P, K and Zn-harvesting and recy-
cling microbial population (Pugliese etal. 2011; Baig etal.
2012; Kamran etal. 2017; Pallavi etal. 2017). The whole
process remains at the ease of the farmer’s need, expertise,
indigenous resource availability, local conditions, and exist-
ing human resources.
Microbe-mediated activities that favor efficient compost-
ing processes, technological aspects of agrowaste bioconver-
sion, microorganisms involved, benefits of microbial forti-
fied and enriched compost and options for adopting such
microbial technologies as models of eco-enterprising are
discussed. All these steps are simple and easily adaptable
by the farming communities. Also, the ingredient resources
are usually available with the farmers at their homes. The
method is helpful in reintroducing organic matter to the soils
along with the beneficial microorganisms that help soils to
improve nutrient status for plant growth and development.
Adoption of such practices in farmers can not only increase
rural sanitation at ground level and support cleanliness
drives of the governments worldwide, but can improve soil
fertility status also. The method yields value-added low-cost
farm inputs from the agricultural farm residues that would
otherwise go waste. When burnt at farmer’s fields, it cre-
ates obnoxious green house gases (GHGs), fog, and smog.
These products are enriched with microbial consortia of
plant growth promoting and biological control microorgan-
isms. These organically rich bio-farm inputs have functional
benefits of microorganisms.
Agrowaste bioconversion
aseco‑enterprising model
Proper utilization of agricultural crop residues can benefit
farms and farming communities. When developed in the
form of an eco-enterprising model, microbe-based bio-
conversion of crop residues can be of immense help of
rural communities to generate rural livelihood through the
products of commercial utility (Naresh 2013). Mushroom
production in rural parts of many countries has gained
the shape of eco-business because of prominent reasons.
Firstly, it has rooted in locally available farm residual
resources, which usually go waste. Secondly, it can be
performed with practical skills, which may be inculcated
in the farming communities through learn-by-doing meth-
ods and thirdly, it can yield high-value food for family
use and/or additional income, if commercialized (Mar-
shall and Nair 2009; Valverde etal. 2015). Looking into
the potential benefits of mushroom production in terms of
high-value food, waste utilization and spent management
(as enzymes, proteins or microbe-fortified compost) (Phan
and Sabaratnam 2012; Kumar etal. 2014), prospective
eco-enterprising model for rural farming communities or
agro-industries can be developed (Celik and Peker 2009).
A workable and integrated eco-enterprising model of
agrowaste bioconversion and fortification with the help of
beneficial microorganisms is presented (Fig.1). The model
can be promoted into the farming communities to attract
resource-poor farmers towards various biological, tech-
nological and commercial aspects of on-farm bioconver-
sion agro-waste management. This may also be helpful in
strengthening the rural economy at a developmental stage
by introducing diversified business and income generation
opportunities for the rural people (Singh etal. 2010).
It has been demonstrated that the bioconversion of crop
residues like straw, husk, corn cobs, bagasse and vegeta-
tive materials coming from regularly grown field crops can
be converted into raw compost using windrows at farmer’s
fields (Singh and Prabha 2017). The raw compost was fur-
ther fortified with the plant growth promoting microor-
ganisms or biocontrol agents like Trichoderma and Pseu-
domonas to scale up the efficiency of microbial formulations
(Galitskaya etal. 2016). The strength of raw compost can
also be improved by the addition of poultry wastes and deg-
radation with the help of microbial enzymes (Brandelli etal.
2015). In the very simple steps, bioconversion processes of
agricultural wastes can be disseminated among rural popu-
lation for adoption of such microbe-based models of bio-
business. The impact of pelletizing pressure for developing
solid state compost from different composting materials like
pig solid fraction, bulking agents, e.g., biochar and wood
chips, swine manure solid fractions and organic co-formu-
lates was assessed for standardizing physical and mechani-
cal properties of the composted material (Romano etal.
2014; Pampuro etal. 2017a, b). These studies resulted in
developing farmer-friendly and easily adaptable composted
products with quality standards for commercialization and
enterprising. These models are supposed to be developed for
introducing multi-enterprising support for smart agriculture
system (Pramanik etal. 2013).
International Journal of Recycling of Organic Waste in Agriculture
1 3
High input-based farming systems, in which chemical
inputs play a major role, are becoming problematic owing
to the loss of diversity of native phyto-, micro- and zoo-
biota and non-responsiveness of the soils (Shennan 2008).
Excessive chemical usage has also led to serious imbalances
in natural ecosystem of the soils and created threat to the
fertility, structure and function of soils, crop intoxication,
productivity losses and damaged harmony of crop–soil inter-
actions (Aktar etal. 2009). Therefore, a farming system that
promotes better utilization of farm residual resources and
usage of low external inputs is the need of the time. Such a
system will engage locally available sources with the farm-
ers and make better use of their own field resources to obtain
better results while minimizing dependency on high external
costs on inputs. This is why, microbial technological inter-
ventions essentially need to be propagated into the farming
communities to obtain better functional food, enhance soil
organic matter by applying self-produced low-cost composts
and microbiologically enriched farm inputs for strengthen-
ing field soils.
Linking farmers withagrowaste
bioconversion
Adoption and adaptation of farmer-friendly microbe-medi-
ated agrowaste bioconversion technology for composting
among the grass-root stakeholders is a matter of perception
and preference. Less awareness on soil and plant characters,
lack of perception for linking up agricultural foods with
human health, low tendency to adopt new technologies,
short-sightedness towards long-term benefits and weak
chain of awareness managers are the key factors that restrict
direct penetration of valuable technologies among farmers.
Awareness on these technologies and penetration into the
farming communities either through ICT tools or by videos,
learning materials or by technical demonstration kits may
enhance technological adaptation (Karubanga etal. 2017).
Some case studies on adaptation of pelletized compost from
animal manure in the farming groups in Italy (Pampuro etal.
2018) and promotion of bioconversion technology in Indian
farmers demanded targeted information campaigns, train-
ings, live product demonstrations and on-farm production
applications to generate hands-on-experience. These efforts
can yield desirable impacts on promotion of integrated farm
management practices and soil fertility level to bring back
countable changes among farming communities (Muller
2009). The outcome can be witnessed in terms of reducing
dependency on high-cost chemical fertilizers, minimizing
risk of pollutants due to residual effects of pesticides, lower-
ing production cost of the crops, enhancing yield quality of
production of commercial crops, ensuring increased fertility
of farm soils and generating income after sale of the compost
products (Aktar etal. 2009; Settle etal. 2012; Yadav etal.
2013). The concerns of direct farmer’s benefits in reducing
the input cost for crop production, improving soil and plant
quality, creating wealth from waste through eco-enterprising
of composted products and applying microbe-rich compost
Fig. 1 Agrowaste bioconversion
model based on crop residues
as primary composting resource
in three steps (1) agricultural
waste (wheat, paddy straw, and
crop leaves) is converted into
raw compost in 30–35days
using different kinds of ingre-
dients (C:N ratio 17:1); (2) raw
compost is further decomposed
in next 30days using decom-
poser microbial consortia to
produce bioorganic farm inputs
with C:N ratio of 30:1 and (3)
fortification with beneficial
microorganisms like nitrogen
fixers, phosphate solubilizers,
biocontrol agent(s), humic acid,
micronutrients for 15days to
obtain microbe-enriched prod-
ucts for direct farm applications
International Journal of Recycling of Organic Waste in Agriculture
1 3
in organic farming practices are important. Therefore, the
Indian government has shown keen interest in promoting
adaptation of such environment- and agriculture-friendly
practices in farmers through various developmental schemes
and funding projects (https ://nmsa.dac.gov.in/; http://midh.
gov.in/; http://agric oop.nic.in/sites /defau lt/files /OPG19
22016 .pdf).
Conclusion
A reductionist approach towards the use of chemical fertiliz-
ers and pesticides is the need of the day across the world.
Minimizing farm chemicals can solve various problems
of the present-day agriculture, especially those which are
directly linked with the soils, plants and human health and
raise negative ecological impacts. Available post harvest
crop residues create sanitation problems in the rural areas
due to uncontrolled anaerobic degradation. While using
excessive chemical fertilizers, farmers have almost forgot-
ten to add organic carbon to the soils and this has resulted
in lowering the carbon content of the soils over a time scale.
Low organic carbon content soils usually become non-
responsive to support life of microorganisms, microflora,
and fauna and thus lose biological functions. Live soil sys-
tems are the integrated part of the crop ecosystem to perform
major ecological functions, which majorly include nutrient
recycling, carbon sequestration, mineralization, availabil-
ity of organic substances and volatiles. If crop residues are
burnt in the farms, they disturb microbiota of the productive
top-soil layers on one hand and pollute air quality on the
other. With the help of microbial interventions and devel-
oping skills among the rural population, the raw residues
can be transformed firstly into mushrooms of high nutrition
value for nourishing food and subsequently, the spent waste
can further be biologically converted into microbe-enriched
compost having specific functional trait. The second option
for the on-farm utilization of the crop residue is the need-
base production of raw compost from the available residual
resources. Its further bioconversion and fortification into
bioorganic farm inputs with the help of potential microor-
ganisms with multifunction can be of immense importance
for the farming communities. One of the major benefits of
using bioconversion technology for agrowaste bioconversion
is to making feasible the availability of ready-to-use organic
input in the soils. Secondly, this can also help to add desired
microbial communities with specific functions, which,
if added without any support of organic matter, may not
flourish in the low-carbon soils. Thirdly, proper availability
of bioorganic materials in the soil supports and enhances
nutrient use efficiency of the soils and ensures proper avail-
ability of micronutrients for longer time durations. Apart
from these direct benefits, there are furthermore benefits
associated with application of compost and biofortified farm
inputs. Presence of beneficial microbial communities in the
soils makes their interactions feasible with the roots of the
plants and thus, strengthens rhizosphere. This will help in
the plant immunization and making crops resistant against
pests and diseases and tolerance against abiotic stresses. In
an integrated way, these microbe-mediated processes help
improve ecological services around the plant roots and sup-
port soil fertility.
Acknowledgements DPS is thankful to the Rashtriya Krishi Vikas
Yojna (RKVY) (Grant no. 2017-18), Government of Uttar Pradesh,
India for funding support for the dissemination of agrowaste bio-
conversion technology. Funding support as a Grant no. DST/SSTP/
UP/38/2017-18(G) from the Department of Science and Technol-
ogy, GOI, New Delhi for promotion of microbe-mediated prac-
tices in the fields in farmers of Eastern Uttar Pradesh is gratefully
acknowledged. RP is thankful to DST for financial support under
DST-Women Scientist Scheme-B (KIRAN Program) (Grant no. DST/
WOS-B/2017/67-AAS).
Open Access This article is distributed under the terms of the Crea-
tive Commons Attribution 4.0 International License (http://creat iveco
mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribu-
tion, and reproduction in any medium, provided you give appropriate
credit to the original author(s) and the source, provide a link to the
Creative Commons license, and indicate if changes were made.
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