processes Review Food Waste Composting and Microbial Community Structure Profiling Kishneth Palaniveloo 1,* , Muhammad Azri Amran 1, Nur Azeyanti Norhashim 1 , Nuradilla Mohamad-Fauzi 1,2, Fang Peng-Hui 3, Low Hui-Wen 3, Yap Kai-Lin 3, Looi Jiale 3, Melissa Goh Chian-Yee 3, Lai Jing-Yi 3, Baskaran Gunasekaran 3,* and Shariza Abdul Razak 4,* 1 Institute of Ocean and Earth Sciences, Institute for Advanced Studies Building, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] (M.A.A.); [email protected] (N.A.N.) 2 Institute of Biological Sciences, Faculty of Science, University of Malaya, Wilayah Persekutuan Kuala Lumpur 50603, Malaysia; [email protected] 3 Faculty of Applied Science, UCSI University (South Wing), Cheras, Wilayah Persekutuan Kuala Lumpur 56000, Malaysia; [email protected] (F.P.-H.); [email protected] (L.H.-W.); [email protected] (Y.K.-L.); [email protected] (L.J.); [email protected] (M.G.C.-Y.); [email protected] (L.J.-Y.) 4 Nutrition and Dietetics Program, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia * Correspondence: [email protected] (K.P.); [email protected] (B.G.); [email protected] (S.A.R.); Tel.: +60-3-7967-4640 (K.P.); +60-16-323-4159 (B.G.); +60-19-964-4043 (S.A.R.) Received: 20 May 2020; Accepted: 16 June 2020; Published: 22 June 2020 Abstract: Over the last decade, food waste has been one of the major issues globally as it brings a negative impact on the environment and health. Rotting discharges methane, causing greenhouse effect and adverse health effects due to pathogenic microorganisms or toxic leachates that reach agricultural land and water system. As a solution, composting is implemented to manage and reduce food waste in line with global sustainable development goals (SDGs). This review compiles input on the types of organic composting, its characteristics, physico-chemical properties involved, role of microbes and tools available in determining the microbial community structure. Composting types: vermi-composting, windrow composting, aerated static pile composting and in-vessel composting are discussed. The diversity of microorganisms in each of the three stages in composting is highlighted and the techniques used to determine the microbial community structure during composting such as biochemical identification, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE), terminal restriction fragment length polymorphism (T-RFLP) and single strand-conformation polymorphism (SSCP), microarray analysis and next-generation sequencing (NGS) are discussed. Overall, a good compost, not only reduces waste issues, but also contributes substantially to the economic and social sectors of a nation. Keywords: organic food waste; sustainability; composting; microbial community structure 1. Introduction The need for food has its impacts on the environment in ways we never expected, from emissions of greenhouse gasses, water and air pollution, abstraction of water, loss of biodiversity, land-use change, eventually risking food security and sustainability. Statistics from Food and Agriculture Organization (FAO) and United Nation (UN) projects food demand to rise meeting the global population estimated at approximately 10 billion in 2050 [1]. Since the demand for food is resource-dependent, food loss and Processes 2020, 8, 723; doi:10.3390/pr8060723 www.mdpi.com/journal/processes Processes 2020, 8, 723 2 of 30 waste accumulation are generated. Approximately one-third of the food produced which is equivalent to 1.3 billion tons of food is being wasted in the world each year and private households represent the largest contributor to food wastes [2]. Based on the latest United Nations report, approximately 821 million people suffer from hunger and over 150 million children are stunted due to malnutrition in 2017. Food loss and wastage is a constant problem at all stages from production to consumption. Waste is generated at the processing stage from transporting of material to processing and up to distribution. Even at the retailing stage, wastage has been recorded. Eventually, as much as 40% is lost at the consumption stage in households and commercial sector [3]. Such magnitude of food wastage results in huge economic losses and a lot of needless hunger, in addition to climate and environmental issues. In line with the Sustainable Development Goal 12 (SDGs) of Responsible Consumption and Production to substantially reduce waste generation through prevention, reduction, recycling and reuse by 2030, composting is seen as a solution to properly manage waste to promote good health and well being through sustainable practices [4]. Food waste impacts the environment as discarded food waste would rot in the landfill discharging methane gas, a very potent gas that causes the greenhouse effect [5]. As environmental, health and social implication became concerning, from a managerial perspective, authorities started shifting from prevention and control to introducing frameworks such as the ‘3Rs’ (Reduce, Re-use, Recycle), polluter pays principle and Sustainable Consumption and Production (SCP). Observation shows that awareness is highest when legislation is enforced, such as taxed bin bags which is trending nowadays. Most food-based sectors resort to building collaborations with other stakeholders such as suppliers, associations, local authorities and waste management companies. Under sustainable resource management, the concept of waste is wealth takes form, thus organic food waste composting is aggressively promoted in which food waste such as fruits, vegetables, grains, eggshells and dairy products are broken down into smaller particles and decomposed naturally [6]. Organic food waste composting minimizes the impact on many sectors. For instance, reduction of methane gas production from landfills directly minimizes the greenhouse effect, production of compost material reduces the dependability on pesticides and synthetic fertilizers resulting in the natural balance of pH level of the soil [7]. Various types of organic food waste composting systems are implemented worldwide with techniques such as vermi-composting, windrow composting, aerated static pile composting and in-vessel composting and are of considerable interest. Organic food waste composting is only possible with the involvement of function-specific microbial community [8]. Microbial community comprises of a variety of microbial species ranging from culturable and non-culturable strains that can interact with each other in the environment they co-exists in [9]. During food waste composting, these microorganisms would break down the food waste into smaller particles before composting. The microbial community structure is crucial in determining the compost maturity as it will modify and evolve during the composting process. Several methods are used to determine microbial community structure in composting such as the conventional biochemical tests, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) [10], terminal restriction fragment length polymorphism (T-RFLP) [11] and single strand-conformation polymorphism (SSCP) [12], microarray analysis [13] and next-generation sequencing (NGS) based 16S ribosomal ribonucleic acid (rRNA) sequencing [14]. 1.1. Organic Food Waste Composting Organic food waste composting is a type of natural food waste decomposition process under controlled aerobic conditions whereby food wastes are being broken down into their simplest components by microorganisms [8]. Composting eventually will be able to improve soil structure, texture and aeration and improve the water retention capacity of the soil [15]. The simplest components would then be formed into humus which is known as compost [7]. During composting the volume of the accumulated waste reduces over time to produce a stable product that has high nutrient level that resulted from the transformation of raw organic materials through microbiological transformation. Processes 2020, 8, 723 3 of 30 This organic matter rich compost is used as a natural fertilizer in the agriculture sector as it has a positive effect on soil and the environment since it is rich with fiber and inorganic nutrients. Stable compost product has higher nutrient level compare to raw organic materials and does not produce metabolites intermediate that can interfere with the growth of plants [16]. This high nutrient compost improves soil fertility and is able to meet crop nutrient demand resulting in improved crop production. Composting process requires a few essential elements which are humus, rich compost, organic waste and oxygen [17]. During the composting process, microorganisms play an important role in converting organic material into stable material through the various biochemical processes, producing fiber-rich carbon containing humus rich in inorganics such as nitrogen, phosphorus. The final output of composting can be utilized as fertilizers and soil amendments, which are rich in humic substances [18]. There are two stages in composting; 1) characterization by microbial activity and 2) conversion of organic material. During the first stage the microbiome initiates the composting process by increasing temperature through the oxidation of organic material, decomposing majority of the biodegradable material and increases the stability of the organic residue. The microbiome during composting includes bacteria,