Abstract:Bacterial community structure and biochemical changes during the composting of lignocellulosic oil palm empty bunch (EFB) and palm oil mill effluent (POME) anaerobic sludge were studied by examining the succession of the bacterial community and its association with changes in lignocellulosic components by denaturing gradient gel electrophoresis (DGGE) and the 16S rRNA gene clone library. During composting, a major reduction in cellulose after 10 days from 50% to 19% and the carbon content from 44% to 27% towar… Show more
“…Analysis of the bacterial community structure at the levels of phylum and order by shotgun DNA as well as by 16S rRNA gene amplicon sequencing yields two main results: 1) shotgun DNA and 16S amplicon results by and large agree with each other; 2) the phyla and orders that are most abundant agree with those found in previous studies14789101112. The four most abundant phyla throughout the composting process are Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria (Supplementary Fig.…”
Section: Resultssupporting
confidence: 80%
“…The biological decomposition of organic matter is performed by mesophilic and thermophilic microbial consortia with distinct physiological requirements and tolerances, consistent with the continuously changing environment throughout composting34567. Bacterial phyla including Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are routinely found in composting, being more or less abundant depending on the starting materials and the composting procedure14789101112. Generally, fungi are not detected in composting piles above 65 °C, suggesting that their degradative activities during the thermophilic stages of composting are minor compared to that of bacteria1314.…”
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
“…Analysis of the bacterial community structure at the levels of phylum and order by shotgun DNA as well as by 16S rRNA gene amplicon sequencing yields two main results: 1) shotgun DNA and 16S amplicon results by and large agree with each other; 2) the phyla and orders that are most abundant agree with those found in previous studies14789101112. The four most abundant phyla throughout the composting process are Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria (Supplementary Fig.…”
Section: Resultssupporting
confidence: 80%
“…The biological decomposition of organic matter is performed by mesophilic and thermophilic microbial consortia with distinct physiological requirements and tolerances, consistent with the continuously changing environment throughout composting34567. Bacterial phyla including Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are routinely found in composting, being more or less abundant depending on the starting materials and the composting procedure14789101112. Generally, fungi are not detected in composting piles above 65 °C, suggesting that their degradative activities during the thermophilic stages of composting are minor compared to that of bacteria1314.…”
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem. The time-series data showed that the turning procedure has a strong impact on the compost microbiota, restoring to a certain extent the population profile seen at the beginning of the process; and that lignocellulosic biomass deconstruction occurs synergistically and sequentially, with hemicellulose being degraded preferentially to cellulose and lignin. Moreover, our sequencing data allowed near-complete genome reconstruction of five bacterial species previously found in biomass-degrading environments and of a novel biodegrading bacterial species, likely a new genus in the order Bacillales. The data and analyses provided are a rich source for additional investigations of thermophilic composting microbiology.
“…The results suggested that the highest value for degradation rate, OM loss and lowest final C/N were obtained by using periodic addition of sludge compared to the addition of only water and no addition at all regardless of the initial C/N ratio of the different experiments. The results obtained agreed with those of the previous work carried out by Mohd Zainudin et al (2014) and Wan Razali et al (2012). Clearly, as expected, periodic addition of sludge allowed the organic matter loss increase to justify addition not only for moisture content regulator but supporting nutrient needs for microbial to grow.…”
The main objective of this work was to investigate the effects of the controlled periodic addition of anaerobic sludge during composting to increase amount of microbial DNA, which appears to be correlated to soluble sugar content which may relate to rate of lignocellulosic degradation. In this study, the composting of pressed-shredded oil palm empty fruit bunch with the periodic addition of palm oil mill effluent anaerobic sludge for moisture control in a newly designed in-vessel type composter was carried out. A control experiment was also conducted over the same period but with the periodic addition of water for moisture control instead of the anaerobic sludge. The lignocellulosic composition and the reducing sugar content were determined via fibre analysis and the spectrophotometric method respectively. The bacterial profile throughout the composting process was quantified by using qPCR. The growth of bacteria reached its peak at 48°C and the degradation of lignocellulose was highest during the thermophilic stage. The highest content of reducing sugar coincided with the highest degradation rate of lignocellulose and the highest DNA copy number during the thermophilic stage. Under the controlled experimental condition of increasing the microbial community, the composting was accelerated to 2.07% OM degradation per day compared to the water addition control at 0.60% OM per day.
“…In spite of all this potential, knowledge on how to control and explore those microbes and their functions remains encrypted within their genomes and the multiple combinations of metabolic pathways that they can activate [7][8][9]. So far, research on composting microbes has focused mainly on enriched cultures [9][10][11] or taxonomic biodiversity assessments based on 16S rRNA gene amplicon sequencing data [12,13]. Enriched cultures have lower diversity richness due to cultivation bias and the limited number ecological niches [9].…”
Background: Thermophilic composting is a semi-engineered process carried out by diverse microbial communities. Composting is an environment friendly way of degrading biomass; its study may help uncover important biomass-degrading organisms and key enzymes. DNA sequence-based previous studies have presented a general description of the microbial-molecular features of composting, but they have lacked more specific information on the key organisms that are active during the process and their genomes. Methods: We present an analysis of metagenome-assembled genomes (MAGs) obtained from time-series samples of a thermophilic composting process in the São Paulo Zoological Park (Brazil). Our results are based on a careful analysis of MAG gene content and on metabolic modeling of their interactions. Results: We recovered 60 MAGs from sequencing datasets from two separate composting cells. Phylogenetic analysis shows that 47 of these MAGs represent novel taxa at the genus or higher levels. We have analyzed the gene repertoire of these MAGs in terms of lignocellulose degradation, secondary metabolite production, antibiotic resistance genes, denitrification genes, sulfur metabolism, hydrogen metabolism, and oxygen metabolism. For one of the composting cells we also had metatranscriptome data, which allowed a deeper analysis of 49 MAGs. This analysis showed the presence of three distinct clusters of MAGs with varying activity during the 99-day composting process. The interaction model pointed to Sphaerobacter thermophilus and Thermobispora bispora as key players in the process, as well as other bacteria that are novel. Our results also show the importance of coadjuvant bacteria and of microbial functions related to efficient bioenergetic processes during biomass conversion, such as N2O reduction and hydrogenases. A novel acidobacteria MAG encodes N2O reductase hallmark genes (nosZD). Strong metabolic dependencies predicted between MAGs revealed that cross-feeding in composting can be determined by complementary functions found in the genomes of producers and consumers, supporting the Black Queen hypothesis for co-evolutionary interactions. Conclusions: This study reveals for the first time the key bacterial players in thermophilic composting and provides a model of their dynamic metabolic interactions. These findings pave the way for more rational composting procedures and provide information that could help the development of novel biomass-degrading technologies.
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