A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

Diversity and composition of rare bacterial community in gut and vermicompost of Eudrilus eugeniae fed with multiple substrates during vermicomposting

Vermicomposting has been recognized as a sustainable solution for the managing of organic waste, primarily because of the bacterial communities that drive microbial decomposition. However, while the roles of abundant bacteria in composting processes are well-documented, the contributions of rare bacteria remain underexplored. In this study, we investigated the diversity and composition of abundant and rare bacterial communities in gut of Eudrilus eugeniae and resulting vermicompost, comparing okara as a single substrate compared to a combination of more substrates, such as kitchen waste or okara and kitchen waste. Amplicon sequencing revealed a total of 3085 operational taxonomic units (OTUs), comprising 188 abundant OTUs and 2127 rare OTUs. Significant differences in bacterial community composition were observed between vermicompost and the earthworm gut, particularly in the rare bacterial communities, with distinct abundances of Gemmatimonadota, Desulfobacteria, Myxococcota, Acidobacteria, and Firmicutes. Interestingly, no significant differences were found between treatments in the abundant bacterial communities, suggesting that okara alone can sustain a bacterial community comparable to mixed substrates. However, rare bacterial communities were more sensitive to substrate variation, with okara fostering distinct rare microbial populations in the vermicompost and earthworm gut. Our results indicate okara can support both abundant and rare bacteria, producing compost with similar physico-chemical properties to those derived from mixed substrates. The study highlights the importance of rare bacterial communities in vermicomposting and demonstrates the potential of okara as a valuable resource for sustainable waste management and soil improvement.

Microbiome multi-omics can accelerate human excrement composting research

In this editorial, we discuss the need for a new, long-term strategy for managing human excrement (feces and urine) to facilitate health equity and promote environmental sustainability. Human excrement composting (HEC), a human-directed process driven by highly variable and diverse microbiomes, provides a means to advance this need and we discuss how microbiome science can help to advance HEC research. We argue that the technological advancements that have driven the growth of microbiome science, including microbiome and untargeted metabolome profiling, can be leveraged to enhance our understanding of safe and efficient HEC. We conclude by presenting our perspective on how we can begin applying these technologies to develop accessible procedures for safe HEC. Video Abstract.

Microbiome science of human excrement composting

Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of human excrement (human feces and urine) stands as a significant concern. Over two billion people do not have access to adequate sanitation, signifying a global public health crisis. Composting is the microbial biotechnology aimed at cycling organic waste, including human excrement, for improved public health, agricultural productivity and safety, and environmental sustainability. Applications of modern microbiome omics and related technologies have the capacity to support continued advances in composting science and praxis. In this article, we review literature focused on applications of microbiome technologies to study composting systems and reactions. The studies we survey generally fall into the categories of animal manure composting, biosolids composting, and human excrement composting. We review experiments utilizing microbiome technologies to investigate strategies for enhancing pathogen suppression and accelerating the biodegradation of organic matter. Additionally, we explore studies focused on the bioengineering potential of microbes as inoculants to facilitate degradation of toxins, such as pharmaceuticals or per- and polyfluoroalkyl substances. The findings from these studies underscore the importance of advancing our understanding of composting processes through the integration of emerging microbiome omics technologies. We conclude that work to-date has demonstrated exciting basic and applied science potential from studying compost microbiomes, with promising implications for enhancing global environmental sustainability and public health.

Characterization of physicochemical parameters and bacterial diversity of composted organic food wastes in Dubai

Composting favours recycling organic waste and producing an end product with high bioenergy potential and significant nutritional value for the soil. Analysing composted organic waste prepared in Dubai, a region with a desertic climate and a unique environment is essential since environmental conditions can greatly affect the physicochemical and biological soil properties and no studies in the Gulf region have been published yet on that process. This study analysed twelve different compost samples prepared in well ventilated wooden chambers, using home-generated organic wastes following the hot aerobic composting method for a duration of three months. The physicochemical parameters, measured at the end of the study, revealed that organic matter, electrical conductivity and pH were within the standard ranges while moisture content was low. Concerning macronutrients, most of the samples were within the standard range for carbon, potassium and sodium, while they were poor in phosphorous and nitrogen. Metagenomic analysis with Illumina MiSeq revealed the abundance of Firmicutes (30.35%), followed by Bacteroidota (26.69%), Proteobacteria (21.47%), and Actinobacteriota (11.17%). The phylum Planctomycetota, solely detected in compost and known to have a significant impact on soil ecosystem and decomposition of organic matter, was reported at a relatively significant level (2.35%). The Clostridia class, efficient in degrading cellulose, was described at high levels compared to other studies. The composting project succeeded in generating a healthy soil but lengthening the duration will allow the samples to fully decompose and therefore increase the total available nitrogen and phosphorus to meet the criteria of a typical mature compost. Various microbial consortia helped in the decomposition process. The qualitative information collected in this study will help in improving the composting technology to favour its utilization by a larger public in the Gulf region.

Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks

BACKGROUND

Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined.

METHODS

Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases.

RESULTS

Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis.

CONCLUSION

Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.

Effects of hydrolyzed polymaleic anhydride addition combined with vermicomposting on maturity and bacterial diversity in the final vermicompost from the biochemical residue of kitchen waste

A large amount of kitchen waste is produced all over the world. Biochemical disposal is an effective method for the reduction and safe utilization of kitchen waste. However, high salinity, low maturity and poor biocompatibility were encountered when utilizing the biochemical residue of kitchen waste (BRKW) as a kind of soil amendment. To reduce the high salinity, accelerate the maturity and improve the biocompatibility in the BRKW, this study used the BRKW as the main feedstock for earthworms after hydrolyzed polymaleic anhydride (HPMA) was added and focused on revealing the effect of HPMA addition combined with the vermicomposting process on the growth of earthworms and on the basic physicochemical properties and the microbial diversity of the derived vermicompost. The results showed that HPMA addition can promote earthworm growth and reproduction. The pH, electric conductivity, organic matter content, C/N and NH₄⁺-N/NO₃^--N were decreased in the final vermicompost, while total nitrogen, total phosphorus and total potassium contents, and the seed germination index were increased. Scanning electron microscopy analysis showed that there was more disintegration in the final vermicompost. Meanwhile, adding the HPMA also helped to decrease the total number of fungi while increasing the populations of nitrogen-fixing bacteria, phosphorus-solubilizing bacteria and potassium-solubilizing bacteria as well as amount of total bacteria and actinomycetes. The vermicomposting process increased the bacterial phyla that promote the degradation of OM, such as Actinobacteria, Firmicutes and Acidobacteria, decreased the pathogenic Enterobacter and increased the bacterial genera that promote the maturity and quality, such as Cellvibrio and Pseudomonas. Thus, HPMA addition combined with vermicomposting can promote the growth of beneficial bacteria that promote the degradation of lignocelluloses and accelerate maturity while inhibiting some potential bacterial pathogens, which helps guarantee the safety of vermicomposting products from BRKW. Hence, employing HPMA to promote BRKW vermicomposting can possibly reduce salt content and improve the maturity and biocompatibility of the final vermicompost. This approach may help realize the safe utilization of BRKW and further promote the biochemical disposal of kitchen waste.

A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird's nest on Sumatera Island, Indonesia

Background and Aim:

Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird’s nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island.

Materials and Methods:

In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software.

Results:

Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were Aeromonas, Escherichia, Acinetobacter, Arcobacter, and Acetoanaerobium. Those in Group B (nitrite levels <30 ppm) were Aeromonas, Pseudomonas, Shewanella, Escherichia, and Acinetobacter. There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively.

Conclusion:

This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. Aeromonas was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs.

Fate of Functional Bacterial and Eukaryotic Community Regulated by Earthworms during Vermicomposting of Dewatered Sludge, Studies Based on the 16S rDNA and 18S rDNA Sequencing of Active Cells

DNA sequencing of active cells involved in vermicomposting can clarify the roles of earthworms in regulating functional microorganisms. This study aimed to investigate the effect of earthworms on functional microbial communities in sludge by comparing biodegradation treatments with and without earthworms. PCR and high throughput sequencing based on pretreatment of propidium monoazide (PMA) were used to detect the changes in active bacterial 16S rDNA and eukaryotic 18S rDNA during vermicomposting. The results showed that the nitrate in sludge vermicomposting and control were significantly different from day 10, with a more stable product at day 30 of vermicomposting. Compared with the control, the Shannon indexes of active bacteria and eukaryotes decreased by 1.9% and 31.1%, respectively, in sludge vermicompost. Moreover, Proteobacteria (36.2%), Actinobacteria (25.6%), and eukaryotic Cryptomycota (80.3%) were activated in the sludge vermicompost. In contrast, the control had Proteobacteria (44.8%), Bacteroidetes (14.2%), Cryptomycota (50.00%), and Arthropoda (36.59%). Network analysis showed that environmental factors had different correlations between active bacterial and eukaryotic community structures. This study suggests that earthworms can decrease the diversity of bacterial and eukaryotic communities, forming a specific-functional microbial community and thus accelerating organic matter decomposition during vermicomposting of dewatered sludge.

Antimicrobial sensitivity profiling of bacterial communities recovered from effluents of municipal solid waste dumping site

The diversity of antibiotic-resistance bacteria (ARB) from the effluents of Aizawl city municipal waste dumping site was studied using a culture-dependent method. The present study molecularly identified 73 isolates that were differentiated into three phyla (Proteobacteria, Actinobacteria, and Firmicutes) belonging to 17 family and 22 genera. Bacillus constitutes the most dominant genus comprising 16% of the total isolates. The topology of the phylogenetic tree differentiates them into five major clades. Corynebacterium and Rhodococcus which are morphologically alike were clustered together and the Gram-positive bacteria such as Staphylococcus, Bacillus, and Lysinibacillus formed a separate cluster. Antibiotic resistance of the identified bacterial isolates was performed using 19 different antibiotics. Among the isolates, 70 of them found resistant to polymixin B and nalidixic acid and 10 isolates exhibited resistance to 15 tested antibiotics. The present study revealed that bacteria with antibiotic resistance are extensively distributed in the effluents of the dumping site and may serve as a significant reservoir for the spreading of antibiotic resistance to opportunistic pathogens.

Evaluating changes in microbial population and earthworms weight during vermicomposting of cow manure containing co-trimoxazole

BACKGROUND

Transmission of pathogens such as fecal coliforms is regarded as a significant concern about using livestock manure in agricultural applications.

PURPOSE

The aim of this study was to evaluate the effects of vermicomposting on fecal coliforms in cow manure containing co-trimoxazole as a widely used drug for cow diseases in animal husbandry.

METHODS

Adaptation process of earthworms was carried out in two phases for 6 weeks; then, the main process was fulfilled in 9 weeks. The final weight of cow manure per reactor was 3.5 kg. 120 g of earthworms added to each reactor (approximately 280-300 numbers in the reactor). Co-trimoxazole was also prepared with a purity of 99% from Pakdarou Co., Iran, and added to the reactors at concentrations of 10, 20, 50, and100mg/kg. Organic carbon, total Kjeldahl nitrogen (TKN), carbon-to-nitrogen (C:N) ratio, as well as phosphorus content of the reactors were measured. Fecal coliforms and parasite eggs were counted using standard laboratory methods (i.e. the Iranian Compost Standard) for 8 weeks.

RESULTS

The results revealed a decrease in organic carbon, C:N ratio, and co-trimoxazole content but a rising trend in TKN and phosphorus levels. The weight of earthworms also increased at the end of the process in all reactors, except for one case. A significant reduction was observed in fecal coliforms and parasite eggs at the end of the vermicomposting.

CONCLUSIONS

According to the results, earthworms could be active in cow manure vermicomposting including 10-100 mg/kg concentration of co-trimoxazole antibiotic. The vermicomposting seems to be an effective method for reducing fecal coliforms and parasites in cow manure. As well, co-trimoxazole in common concentration could not have any effects on the ability of earthworms. At the end of the vermicomposting, all parameters were placed within the ICS (National) - Grade 1.

Amplicon sequencing and imputed metagenomic analysis of waste soil and sediment microbiome reveals unique bacterial communities and their functional attributes

The discharge of solid and liquid waste from domestic, municipal, and hospital premises pollutes the soil and river ecosystems. However, the diversity and functions of the microbial communities present in these polluted environments are not well understood and may contain harmful microbial communities with specialized metabolic potential. In this present study, we adapted the Illumina sequencing technology to analyze microbial communities and their metabolic capabilities in polluted environments. A total of 1113884 sequences of v3-v4 hypervariable region of the 16S rRNA were obtained using Illumina sequencing and assigned to the corresponding taxonomical ranks using Greengenes databases. Proteobacteria and Bacteroidetes were dominantly present in all the four studied sites (solid waste dumping site (SWD); Chite river site (CHR), Turial river site (TUR), and Tuikual river site (TUKR)). It was found that the SWD was dominated by Firmicutes, Actinobacteria; CHR by Acidobacteria, Verrucomicrobia, Planctomycetes; TUR by Verrucomicrobia, Acidobacteria; and TUKR by Verrucomicrobia and Firmicutes, respectively. The dominant bacterial genus present in all samples was Acinetobacter, Flavobacterium, Prevotella, Corynebacterium, Comamonas, Bacteroides, Wautersiella, Cloacibacterium, Stenotrophomonas, Sphingobacterium, and Pseudomonas. Twenty-seven putative bacterial pathogens were identified from the contaminated sites belonging to Salmonella enterica, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus. Functional analysis showed a high representation of genes in the KEGG pathway involved in the metabolism of amino acids and carbohydrates and identified several genes associated with antibiotic resistance and xenobiotic degradation in these environments, which can be a serious problem for human health and environment. The results from this research will provide a new understanding of the possible management practices to minimize the spread of pathogenic microorganisms in the environment.

Changes in the composition and function of bacterial communities during vermicomposting may explain beneficial properties of vermicompost

Vermicomposting is the process by which organic waste is broken down through the synergistic actions of earthworms and microbial communities. Although vermicomposting has been shown to effectively reduce organic biomass and generate high-quality fertilizer for plants, little is known about the bacterial communities that are involved in this decomposition process. Since optimization of vermicomposting for commercial use necessitates additional knowledge of the underlying biological processes, this study sought to characterize the bacterial succession involved in the vermicomposting of Scotch broom (Cytisus scoparius), a leguminous shrub that has become invasive around the world with consequences for the dynamics and productivity of the ecosystems they occupy. Scotch broom was processed in a pilot-scale vermireactor for 91 days with the earthworm species Eisenia andrei. Samples were taken at the initiation of vermicomposting, and days 14, 42 and 91, representing both active and mature stages of vermicomposting. Significant changes (P < 0.0001) in the bacterial community composition (richness and evenness) were observed throughout the process. Increases in taxonomic diversity were accompanied by increases in functional diversity of the bacterial community, including metabolic capacity, streptomycin and salicylic acid synthesis, and nitrification. These results highlight the role of bacterial succession during the vermicomposting process and provide evidence of microbial functions that may explain the beneficial effects of vermicompost on soil and plants.

Bacterial succession and functional diversity during vermicomposting of the white grape marc Vitis vinifera v. Albariño

Winemaking produces millions of tons of grape marc, a byproduct of grape pressing, each year. Grape marc is made up of the skins, stalks, and seeds remaining after pressing. Raw grape marc can be hazardous to the environment due to its low pH and high polyphenol content, but previous work has shown that grape marc can be stabilized via vermicomposting to produce organic fertilizer. Here, we utilize 16S rRNA high-throughput sequencing to characterize the bacterial community composition, diversity and metabolic function during vermicomposting of the white grape marc Vitis vinifera v. Albariño for 91 days. Large, significant changes in the bacterial community composition of grape marc vermicompost were observed by day 7 of vermicomposting and throughout the duration of the experiment until day 91. Similarly, taxonomic and phylogenetic α-diversity increased throughout the experiment and estimates of β-diversity differed significantly between time points. Functional diversity also changed during vermicomposting, including increases in cellulose metabolism, plant hormone synthesis, and antibiotic synthesis. Thus, vermicomposting of white grape marc resulted in a rich, stable bacterial community with functional properties that may aid plant growth. These results support the use of grape marc vermicompost for sustainable agricultural practices in the wine industry.

Speciation of heavy metals and bacteria in cow dung after vermicomposting by the earthworm, Eisenia fetida

This work was conducted to evaluate the total concentration and speciation of heavy metals (Cd, Pb and Cr) in vermicompost product (EFCD) by Eisenia fetida (EF) with cow dung (FCD). Meanwhile, the bacterial community and diversity of the three were compared by high-throughput sequencing. Results showed that heavy metal concentrations were declined significantly in EFCD. Sequential extraction indicated that the exchangeable fraction of Cd and Pb decreased markedly and the residual fractions increased in EFCD. Though the exchangeable fraction of Cr increased, the total concentration reduced greatly. Furthermore, the speciation of Cd, Pb and Cr bioaccumulated in EF were different. Besides, the bacterial diversity was highest in EFCD, and twelve genera with species having heavy metal resistance/tolerance were found from the genus of different abundance of the three. Vermicomposting effectively reduced the total concentration and toxicity for heavy metals, and the bacterial composition and diversity were changed greatly during vermicomposting.