Article

Microbial Diversity and Nitrogen-metabolizing Gene Abundance in Backyard Food Waste Composting Systems

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Abstract

Aims The microbial diversity of backyard compost piles is poorly understood compared to large‐scale, highly regulated composting systems. The purpose of this study is the identification of the microbial community composition and associated change over time among three different backyard composting styles. Methods and Results Food waste was composted in a household backyard compost bin, a small‐scale aerated windrow or a semi‐aerated static pile. Samples were obtained from each sequential phase of the composting process for 16s rRNA sequencing and relationships between temperature, moisture and microbial communities were examined. The Bacilli dominated in the early phases of composting then transitioned to Proteobacteria in the later stages. Different bacterial species increased and decreased dramatically in different composting systems and at different phases of the composting process. We performed qPCR to quantify gene abundance of nirS to profile the nitrogen‐metabolizing bacteria present in each composting system. Gene abundance of nirS varied with temperature, but peaked during the cooling phase in the aerated windrow. Conclusions Although the phases of decomposition were not as distinct as large‐scale regulated piles, the microbial diversity mirrored the appropriate phases. Interestingly, different backyard composting styles were marked by the predominance of certain bacterial species. In particular, nitrogen‐metabolizing bacterial communities peaked in the later stages of decomposition. Significance and Impact of the Study A profile of the compost microbiome yields important clues about how differences in backyard food waste composting systems influence bacterial species that may facilitate or hinder nitrogen metabolism. This article is protected by copyright. All rights reserved.

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... Historically, composting has been used to recycle agricultural wastes and return the composted organic matter into the soil to maintain soil fertility and crop productivity with minimum application of synthetic chemical fertilizers [9]. During composting, the diversity and structure of microbial communities, as well as chemical and physical properties of the composting substrates change dramatically in the course of several weeks [10][11][12][13]. ...
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... A similar result was obtained by Galitskaya et al. (2017) for the microbiota of composted wastewater sludge. However, some works on composting reported predominance of this genus Weglarz al., 2018). Moreover, high diversity of bacterial taxa was found at each stage, with no significant predominance of a specific genus throughout compost maturation: the share of predominant genera at each stage of composting varied within the range of 10-38%. ...
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We analyzed succession of the bacterial communities during composting of animal manure in three individual facilities. Polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) targeting for the bacterial 16S rRNA gene were used to clarify the changes of bacterial community throughout each composting process. Our study revealed that the bacterial community structures differed during the composting process. The bacterial community in composting of facility A showed little change throughout the process. In the compost sample from facility B, its community had a small shift as the temperature increased. In compost from facility C, the temperature dynamically changed; it was shown that various bacterial communities appeared and disappeared as follows: in the initial phase, the members of phylum Bacteroidetes dominated; in the thermophilic phase, some bacteria belonging to phylum Firmicutes increased; towards the end, the community structure consisted of three phyla, Bacteroidetes, Firmicutes, and Proteobacteria. This study provides some information about the bacterial community actually present in field-scale composting with animal manure.
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Many companies, restaurants, colleges, as well as individual homeowners, have initiated green marketing campaigns, and the composting of food and yard wastes has become commonplace. Thus, it is essential to obtain a more complete understanding of the microbial populations present in such composting processes. The focus of this study was to identify bacterial populations in a static windrow compost pile initiated on a college campus containing food trim and tree debris. Given that the compost pile was initiated during the winter it was uniquely characterized by a pre-mesophilic stage in addition to the characteristic mesophilic, thermophilic, and cooling/maturation stages. Bacteria were cultured from each stage and were identified by sequencing the 16S rRNA gene. Dominating the numbers throughout the study were bacteria within the Bacillus and Bacillus-like genera. Actinobacteria were found primarily within the pre-mesophilic stage. The mesophilic and beginning thermophilic stages displayed the most diversity, characterized by several different genera within the Proteobacteria phylum. In contrast, during the late thermophilic stage, only bacteria within the Bacillus and Brevibacillus genera were cultured. Overall, 49 different species within 27 different genera, 13 families, and 4 phyla, were identified and several genera that have not been commonly associated with household compost. Thus, this study supports a role for the continuation of culture-dependent studies to more completely define the bacterial flora involved in various composting processes.
Article
A comprehensive understanding of the microbial community is necessary to ensure a significant reduction in pathogens during the composting process. Two biosecure, static composting systems containing cattle mortalities were constructed at sub-zero temperatures. Temperature at each sampling site was measured continuously and samples were grouped as either ≤ 50°C or ≥ 55°C, based on temperature exposure required for effective pathogen inactivation during composting. High-throughput 454-sequencing was used to characterize the bacterial communities within each sample. Clustering of bacterial communities was observed according to temperature. However, neither richness nor diversity differed between temperature groups. Firmicutes was the most abundant phylum within both temperature groups, but was more pronounced (63.6%) in samples ≥ 55°C (p < 0.05). Similarly, members of Clostridia, Clostridium sensu stricto (3.64%), Clostridium XI (0.59%), UF (Clostridiaceae 1) (5.29%), and UF (Clostridiales Incertae Sedis XI) (6.20%), were prominent at ≥ 55°C (p < 0.05), likely a reflection of spore survival and / or anaerobic microenvironments within passively aerated compost piles. Members of Thermobifida (3.54%), UO (Actinomycetales) (12.29%) and UO (Bacillales) (19.49%) were also prominent at ≥ 55°C (p < 0.05). Substantial spatial diversity exists within bacterial communities in field- scale compost piles. Localized temperature at the site of sampling may be one of the factors contributing to this phenomenon. This is the first study to describe the microbial community profile with the use of targeted 16S rRNA high-throughput sequencing in passively aerated composted livestock mortalities. This article is protected by copyright. All rights reserved.
Article
The purpose of this study was to investigate the diversity of denitrifier community during agricultural waste composting. The diversity and dynamics of the denitrifying genes (nirK and nirS) were determined using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Relationships between physico-chemical parameters and denitrifying genes structures were simultaneously evaluated by redundancy analysis (RDA). Phylogenetic analysis indicated that nirK clones grouped into six clusters and nirS clones into two major clusters, respectively. The results showed a very high diversity of nir gene sequences within composting samples. RDA showed that the nirK and nirS gene structures were significantly related to pH and pile temperature (P < 0.05). Significant amounts of the variation (49.2 and 38.3 % for nirK and nirS genes, respectively) were explained by pH and pile temperature, suggesting that those two parameters were the most likely ones to influence, or be influenced by the denitrifiers harboring nirK and nirS genes.
Article
Denitrification is a microbial respiratory process during which soluble nitrogen oxides are used as an alternative electron acceptor when oxygen is limiting. It results in considerable loss of nitrogen, which is the most limiting nutrient for crop production in agriculture. Denitrification is also of environmental concern, since it is the main biological process responsible for emissions of nitrous oxide, one of the six greenhouse gases considered by the Kyoto protocol. In addition to natural variations, agroecosystems are characterized by the use of numerous practices, such as fertilization and pesticide application, which can influence denitrification rates. This has been widely documented in the literature, illustrating the complexity of the underlying mechanisms regulating this process. In the last decade, however, application of molecular biology approaches has given the opportunity to look behind denitrification rates and to describe genes, transcripts, and enzymes responsible for the process. In order to reduce denitrification in arable soil, it is important to understand how different factors influence denitrification and how the denitrifier community structure is related to in situ activity. This chapter focuses on the impact of natural events as well as agricultural practices on denitrifying microorganisms.
Article
To evaluate the NH3, N2O, and CH4 emissions from composting of livestock waste without forced aeration in turned piles, and to investigate the possible relationship between the scale of the compost pile and gas emission rates, we conducted swine manure composting experiments in parallel on small- and large-scale compost piles. Continuous measurements of gas emissions during composting were carried out using a chamber system, and detailed gas emission patterns were obtained. The total amount of each gas emission was computed from the amount of ventilation and gas concentration. NH3 emission was observed in the early period of composting when the material was at a high temperature. Sharp peaks in CH4 emission occurred immediately after swine manure was piled up, although a high emissions level continued after the first turning only in the large-scale pile. N2O emissions started around the middle stage of the composting period when NH3 emissions and the temperature of the compost material began to decline. The emission rates of each gas in the small and large piles were 112.8 and 127.4 g NH3-N/kg T-N, 37.2 and 46.5 g N2O-N/kg T-N, and 1.0 and 1.9 g CH4/kg OM, respectively. It was found that changing the piling scale of the compost material was a major factor in gas emission rates.
Article
Strain 78-123T was isolated from a sample of a bird's nest situated on the bank of Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain in the Xin-jiang Uygur Autonomous Region in north-western China. Phylogenetic analysis based on 16S rRNA gene sequence similarity showed that strain 78-123T was related to members of the genus Pseudomonas. 16S rRNA gene sequence similarity between strain 78-123T and Pseudomonas mendocina ATCC 25411T, Pseudomonas pseudoalcaligenes JCM 5968T and Pseudomonas alcaliphila AL15-21T was 97.1, 97.4 and 97.5 %, respectively. The major cellular fatty acids were C(16 : 0), C(16 : 1)omega7c and/or iso-C(15 : 0) 2-OH, C(18 : 1)omega7c and C(12 : 0). The G+C content was 60.4 mol%. On the basis of the phenotypic characteristics, phylogenetic analysis and DNA-DNA relatedness data, the novel species Pseudomonas tuomuerensis sp. nov. is proposed, with the type strain 78-123T (=CGMCC 1.1365T =JCM 14085T).
Article
Two contrasting compost windrows were monitored for various physical, chemical and microbiological parameters for a period of 106 days. The different input materials and management practises gave rise to different temperature, moisture, and oxygen consumption profiles as composting proceeded. However, despite the different composting conditions, the specific respiratory activity, as determined by oxygen consumption per bacterial cell, was remarkably similar for both windrows. Further investigations into diversity dynamics were done through DGGE and cloning and sequencing of bacterial 16S rDNA PCR products. Although sequence analysis showed differing bacterial communities across time and between the different windrows, similarities in the progression were noted. The majority of sequences recovered from the first sampling period (day 1) were highly similar to previously isolated organisms. The clone libraries from the last sampling period (day 106) contained organisms that showed lower homology to their closest relatives, often with other uncultured organisms, and in phyla that contain few cultured representatives. These data suggest that specific respiratory activity may be an important driver of bacterial diversity in composting environments.
Article
Publisher Summary This chapter focuses on the components of municipal waste which are compostable. Composting is the microbial degradation of organic solid material that involves aerobic respiration and passes through a thermophilic stage. It yields the stabilized end-product compost. Various solid waste management objectives can be achieved through composting, including sanitation, mass and bulk reduction, and resource recovery. Compost plays a unique role in certain specialized practices, including hotbed gardening, which requires self-heating organic matter, and as a substrate for edible-mushroom cultivation. For these purposes compost derived from municipal solid waste can substitute for the traditional horse manure preparation. Compost can be an economic soil conditioner for high-value crops, such as vegetables and flowers grown out of season. The chapter reveals that there are many proprietary processes for the treatment of municipal solid waste by composting, which offer a variety of mechanical and structural approaches to the problems of aerating and mixing the composting mass. From a microbiological viewpoint, only two major process variants are evident: batch and continuous composting.
Article
Phenotypic and phylogenetic studies were performed on seven unidentified gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).
Article
To evaluate the NH(3), N(2)O, and CH(4) emissions from composting of livestock waste without forced aeration in turned piles, and to investigate the possible relationship between the scale of the compost pile and gas emission rates, we conducted swine manure composting experiments in parallel on small- and large-scale compost piles. Continuous measurements of gas emissions during composting were carried out using a chamber system, and detailed gas emission patterns were obtained. The total amount of each gas emission was computed from the amount of ventilation and gas concentration. NH(3) emission was observed in the early period of composting when the material was at a high temperature. Sharp peaks in CH(4) emission occurred immediately after swine manure was piled up, although a high emissions level continued after the first turning only in the large-scale pile. N(2)O emissions started around the middle stage of the composting period when NH(3) emissions and the temperature of the compost material began to decline. The emission rates of each gas in the small and large piles were 112.8 and 127.4 g NH(3)-N/kg T-N, 37.2 and 46.5 g N(2)O-N/kg T-N, and 1.0 and 1.9 g CH(4)/kg OM, respectively. It was found that changing the piling scale of the compost material was a major factor in gas emission rates.
Article
Bacterial communities are important catalysts in the production of composts. Here, it was analysed whether the diversity of bacteria in finished composts is stable and specific for the production process. Single-strand conformation polymorphism (SSCP) based on polymerase chain reaction amplified partial 16S rRNA genes was used to profile and analyse bacterial communities found in total DNA extracted from finished composts. Different batches of compost samples stored over a period of 12 years and a 1-year-old vermicompost were compared to each other. According to digital image analysis, clear differences could be detected between the profiles from compost and vermicompost. Differences between three different periods of compost storage and between replicate vermicompost windrows were only minor. A total of 41 different 16S rRNA genes were identified from the SSCP profiles by DNA sequencing, with the vast majority related to yet-uncultivated bacteria. Sequences retrieved from compost mainly belonged to the phyla Actinobacteria and Firmicutes. In contrast, vermicompost was dominated by bacteria related to uncultured Chloroflexi, Acidobacteria, Bacteroidetes and Gemmatimonadetes. The differences were underscored with specific gene probes and Southern blot hybridizations. The results confirmed that different substrates and composting processes selected for specific bacterial communities in the finished products. The specificity and consistency of the bacterial communities inhabiting the compost materials suggest that cultivation-independent bacterial community analysis is a potentially useful indicator to characterize the quality of finished composts in regard to production processes and effects of storage conditions.
Article
Gene sequence analysis of nirS and nirK, both encoding nitrite reductases, was performed on cultivated denitrifiers to assess their incidence in different bacterial taxa and their taxonomical value. Almost half of the 227 investigated denitrifying strains did not render an nir amplicon with any of five previously described primers. NirK and nirS were found to be prevalent in Alphaproteobacteria and Betaproteobacteria, respectively, nirK was detected in the Firmicutes and Bacteroidetes and nirS and nirK with equal frequency in the Gammaproteobacteria. These observations deviated from the hitherto reported incidence of nir genes in bacterial taxa. NirS gene phylogeny was congruent with the 16S rRNA gene phylogeny on family or genus level, although some strains did group within clusters of other bacterial classes. Phylogenetic nirK gene sequence analysis was incongruent with the 16S rRNA gene phylogeny. NirK sequences were also found to be significantly more similar to nirK sequences from the same habitat than to nirK sequences retrieved from highly related taxa. This study supports the hypothesis that horizontal gene transfer events of denitrification genes have occurred and underlines that denitrification genes should not be linked with organism diversity of denitrifiers in cultivation-independent studies.
Article
To determine the microbial succession of the dominating taxa and functional groups of microorganisms and the total microbial activity during the composting of biowaste in a monitored process. Biowaste (vegetable, fruit and garden waste) was composted in a monitored composting bin system. During the process, taxonomic and functional subpopulations of microorganisms were enumerated, and dominating colonies were isolated and identified. All counts decreased during the thermophilic phase of the composting, but increased again when the temperature declined. Total microbial activity, measured with an enzyme activity assay, decreased during the thermophilic phase, increased substantially thereafter, and decreased again during maturation. Bacteria dominated during the thermophilic phase while fungi, streptomycetes and yeasts were below the detection limit. Different bacterial populations were found in the thermophilic and mesophilic phases. In fresh wastes and during the peak-heating phase, all bacterial isolates were bacilli. During the cooling and maturation phase the bacterial diversity increased, including also other Gram-positive and Gram-negative bacteria. Among the fungi, Aspergillus spp. and Mucor spp. were predominant after the thermophilic phase. The microbial abundance, composition and activity changed substantially during composting and compost maturity was correlated with high microbial diversity and low activity. A more complete overview of the whole composting process of biowaste, based on microbial counts, species diversity and functional groups and abiotic parameters is presented, and the potential of a simple enzyme assay to measure total microbial activity was demonstrated.
Article
To investigate microbial diversity of swine manure composts in the initial stage and the spatial distribution due to gradient effect. Samples in different locations of a composting pile were taken and analysed by using a culture-independent approach. Total community DNA was extracted and bacterial 16S rRNA genes were subsequently amplified, cloned, restriction fragment length polymorphism-screened and sequenced. Thirty-three unique sequence types were found among the 110 analysed positive clones from superstratum sample; 56 among 122 from middle-level sample and 32 among 114 from substrate sample, respectively. The sequences related to Clostridium sp. were most common in the composts. One hundred and thirteen out of 121 16S rDNA sequence types displayed homology with those in the GenBank database. Seven 16S rDNA sequence types were not closely related to any known species. The middle-level sample had the highest microbial diversity, containing unique sequences related to Lactosphaera pasteurii, Firmicutes sp., Aerococcus sp., Megasphaera sp. and Stenotrophomonas sp. Pile temperature significantly affected microbial community in the initial stage of the composting. Microbial community in different locations is quite different resulting from gradient effect. Results of this study reveal high bacterial diversity in manure composts, and provide molecular evidence to support gradient effect on microbial diversity in initial stage as well.
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