Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

Abstract

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Physico-chemical and biological characteristics of compost from decentralised composting programmes

“…The presence of the genera Comamona and Serratia in compost samples was also reported by Chandna et al (2013). Recent application of next generation sequencing of rRNA gene phylogenetic markers (bacterial 16S and fungal ITS1) has provided novel insight into total bacterial and fungal community dynamics in commercial composting (Neher et al, 2013) that needs to be extended to decentralised composting such as described in this study. Table 6 summarises information on number of invertebrate individuals identified to taxa/species in the different compost samples.…”

“…Bacteria and fungi are key groups of microbes present in both compost and soil and have a direct influence on the composting process through driving both carbon and nitrogen cycles (e.g. Neher et al, 2013). Soil bacteria and fungi promote soil fertility, stimulate plant growth and plant defence mechanisms against patogens (Harman, 2006;Contreras-Cornejo et al, 2009).…”

Bacterial Groups Concerned with Maturing Process in Manure Production Analyzed by a Method Based on Restriction Fragment Length Polymorphism Analysis

“…As composting is a biological aerobic decomposition process consisted from different phases, microbial groups concerned with this process have intensively been investigated by using a variety of culture-based [2]- [5] and unculture-based techniques [6]- [14]. Because application of organic fertilizer, prepared under suitable composting process, has found to maintain soil fertility by amending physical, chemical and biological properties of field soil.…”

“…Although unculture-based technique, such as denaturing gradient gel electrophoresis (DGGE) [7] [8] [10] [11] [13] or clone library sequencing [6] [9] [11] [12] [14], targets the both cultured and uncultured microorganisms, the method only reveals variations of relative abundance of each microbial groups and a change of the microbial numbers remains unclear.…”

Stable isotope analysis (δ13C andδ15N) of soil nematodes from four feeding groups

“…Feeding response of nematode trophic groups may not be represented fully, without testing finer resolution taxonomic groups (Neher & Weicht, 2013; Cesarz et al, 2013) and certain groups (i.e., omnivores) may shift trophic level feeding as a result of life stage development (Moens, Traunspurger & Bergtold, 2006). Omnivorous nematodes are taken as generalist feeders and less so as ‘true’ omnivores (Moens, Yeates & De Ley, 2004), however, ‘true’ omnivory (i.e., feeding across different trophic levels) may be more widespread than once assumed in soil food webs (Scheu, 2002), and nematode communities are no exception to this theory (Moens, Traunspurger & Bergtold, 2006).…”