Succession of a microbial community during stable operation of a semi-continuous garbage-decomposing system

Local environment, surface characteristics and stochastic processes shape the dynamics of urban dustbin surface microbiome

Dustbins function as critical infrastructures for urban sanitation, creating a distinct breeding ground for microbial assemblages. However, there is no information regarding the dynamics of microbial communities and the underlying mechanism for community assembly on dustbin surfaces. Here, surface samples were collected from three sampling zones (business building, commercial street and residential community) with different types (kitchen waste, harmful waste, recyclables, and others) and materials (metallic and plastic); and distribution pattern and assembly of microbial communities were investigated by high-throughput sequencing. Bacterial and fungal communities showed the distinct community variations across sampling zones and waste sorting. Core community and biomarker species were significantly correlated with the spatial distribution of overall community. The detection of pathogens highlighted the potential risk of surface microbiome. Human skin, human feces and soil biomes were the potential source environments of the surface microbiomes. Neutral model prediction suggested that microbial community assembly was significantly driven by stochastic processes. Co-association patterns varied with sampling zones and waste types, and neutral amplicon sequence variants (ASVs) that fall within the 95 % confidence intervals of neutral model were largely involved in the stability of microbial networks. These findings improve our understanding of the distribution pattern and the underlying assembly of microbial community on the dustbin surface, thus enabling prospective prediction and assessment of urban microbiomes and their impacts on human health.

Bacterial community structure transformed after thermophilically composting human waste in Haiti

Recycling human waste for beneficial use has been practiced for millennia. Aerobic (thermophilic) composting of sewage sludge has been shown to reduce populations of opportunistically pathogenic bacteria and to inactivate both Ascaris eggs and culturable Escherichia coli in raw waste, but there is still a question about the fate of most fecal bacteria when raw material is composted directly. This study undertook a comprehensive microbial community analysis of composting material at various stages collected over 6 months at two composting facilities in Haiti. The fecal microbiota signal was monitored using a high-density DNA microarray (PhyloChip). Thermophilic composting altered the bacterial community structure of the starting material. Typical fecal bacteria classified in the following groups were present in at least half the starting material samples, yet were reduced below detection in finished compost: Prevotella and Erysipelotrichaceae (100% reduction of initial presence), Ruminococcaceae (98–99%), Lachnospiraceae (83–94%, primarily unclassified taxa remained), Escherichia and Shigella (100%). Opportunistic pathogens were reduced below the level of detection in the final product with the exception of Clostridium tetani, which could have survived in a spore state or been reintroduced late in the outdoor maturation process. Conversely, thermotolerant or thermophilic Actinomycetes and Firmicutes (e.g., Thermobifida, Bacillus, Geobacillus) typically found in compost increased substantially during the thermophilic stage. This community DNA-based assessment of the fate of human fecal microbiota during thermophilic composting will help optimize this process as a sanitation solution in areas where infrastructure and resources are limited.

Composting of waste algae: a review

Although composting has been successfully used at pilot scale to manage waste algae removed from eutrophied water environments and the compost product applied as a fertiliser, clear guidelines are not available for full scale algae composting. The review reports on the application of composting to stabilize waste algae, which to date has mainly been macro-algae, and identifies the peculiarities of algae as a composting feedstock, these being: relatively low carbon to nitrogen (C/N) ratio, which can result in nitrogen loss as NH3 and even N2O; high moisture content and low porosity, which together make aeration challenging; potentially high salinity, which can have adverse consequence for composting; and potentially have high metals and toxin content, which can affect application of the product as a fertiliser. To overcome the challenges that these peculiarities impose co-compost materials can be employed.

Comparative microbial diversity analyses of modern marine thrombolitic mats by barcoded pyrosequencing

Thrombolites are unlaminated carbonate structures that form as a result of the metabolic interactions of complex microbial mat communities. Thrombolites have a long geological history; however, little is known regarding the microbes associated with modern structures. In this study, we use a barcoded 16S rRNA gene-pyrosequencing approach coupled with morphological analysis to assess the bacterial, cyanobacterial and archaeal diversity associated with actively forming thrombolites found in Highborne Cay, Bahamas. Analyses revealed four distinct microbial mat communities referred to as black, beige, pink and button mats on the surfaces of the thrombolites. At a coarse phylogenetic resolution, the domain bacterial sequence libraries from the four mats were similar, with Proteobacteria and Cyanobacteria being the most abundant. At the finer resolution of the rRNA gene sequences, significant differences in community structure were observed, with dramatically different cyanobacterial communities. Of the four mat types, the button mats contained the highest diversity of Cyanobacteria, and were dominated by two sequence clusters with high similarity to the genus Dichothrix, an organism associated with the deposition of carbonate. Archaeal diversity was low, but varied in all mat types, and the archaeal community was predominately composed of members of the Thaumarchaeota and Euryarchaeota. The morphological and genetic data support the hypothesis that the four mat types are distinctive thrombolitic mat communities.

Microbial population dynamics and changes in main nutrients during the acidification process of pig manures

This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure.

Application of COMPOCHIP microarray to investigate the bacterial communities of different composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.

Changes in bacterial communities accompanied by aggregation in a fed-batch composting reactor

The contents of fed-batch composting (FBC) reactors often aggregate after prolonged operation. This process leads to irreversible breakdown of the decomposition reaction and possible alteration of the bacterial communities. We compared the structures of bacterial communities in reactors under aggregate and optimal conditions. The results of 16S rRNA gene clone analysis showed that populations of the family Bacillaceae (such as Bacillus spp., Cerasibacillus spp., Gracilibacillus spp.), which dominate (98%) under optimal condition, were significantly decreased under aggregate condition. In contrast, populations of the family Staphylococcaceae considerably increased after aggregation and accounted for 53% of the total. Phylogenetic analysis also showed that anaerobes or facultative anaerobes related to Tetragenococcus halophilus, Atopostipes suicloacalis, Jeotgalicoccus pinnipedialis, and Staphylococcus spp. were dominant in the aggregates. These results suggested that aerobic Gram-positive bacteria mainly contributed to organic degradation and that aggregation created some anaerobic environment, which promoted the growth of bacterial communities usually not found in well-functioning FBC reactors.

Degradation of corn stalk by the composite microbial system of MC1

The composite microbial system of MC1 was used to degrade corn stalk in order to determine properties of the degraded products as well as bacterial composition of MC1. Results indicated that the pH of the fermentation broth was typical of lignocellulose degradation by MC1, decreasing in the early phase and increasing in later stages of the degradation. The microbial biomass peaked on the day 3 after degradation. The MC1 efficiently degraded the corn stalk by nearly 70% during which its cellulose content decreased by 71.2%, hemicellulose by 76.5% and lignin by 24.6%. The content of water-soluble carbohydrates (WSC) in the fermentation broth increased progressively during the first three days, and decreased thereafter, suggesting an accumulation of WSC in the early phase of the degradation process. Total levels of various volatile products peaked in the third day after degradation, and 7 types of volatile products were detected in the fermentation broth. These were ethanol, acetic acid, 1,2-ethanediol, propanoic acid, butanoic acid, 3-methyl-butanoic acid and glycerine. Six major compounds were quantitatively analysed and the contents of each compound were ethanol (0.584 g/L), acetic acid (0.735 g/L), 1,2-ethanediol (0.772 g/L), propanoic acid (0.026 g/L), butanoic acid (0.018 g/L) and glycerine (4.203 g/L). Characterization of bacterial cells collected from the culture solution, based on 16S rDNA PCR-DGGE analysis of DNAs, showed that the composition of bacterial community in MC1 coincided basically with observations from previous studies. This indicated that the structure of MC1 is very stable during degradation of different lignocellulose materials.

Effects of cultivation conditions on the diversity of microbes involved in the conversion of rice straw to fodder

To confirm the optimum cultivation conditions for analyzing lactic acid bacterial communities and to provide the cultivation foundation for lactic acid bacterial communities that were used to convert straw into fodder, fermented rice straw was inoculated into 13 different broths. After 48 h of cultivation, pH values, volatile products, and microbial diversity were analyzed. Except for LAB broth, the pH values of the other broths could decrease to approximately 4.5. GC/MS analysis showed that lactic acid in Tomato MRS broth, MRS broth, LAB broth, and Tomato juice broth was higher than that in the other broths. DNA concentration analysis showed that the counts of microbes in Tomato MRS broth were 2.5 times of those in other broths and that tomato juice favored the reproduction of the microbes. Denaturing gradient gel electrophoresis (DGGE) analysis showed that the number of lactic acid bacterial species in HYA broth, Tomato juice broth, and Tomato MRS broth were higher than those in the other broths.

Effects of water-soluble carbohydrate content on silage fermentation of wheat straw

To determine a suitable initial water-soluble carbohydrate (WSC) content to make wheat straw natural fermentation successful and to study fermentation characteristics, glucose was used to adjust the initial WSC content to 1.4%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, and 10.0% dry matter (DM) in the wheat straw. At 30 d of fermentation, there were three pHs: when the initial WSC content was 1.4%, the pH was 5.5; when the initial WSC contents were 4.0%, 5.0% and 6.0%, the pHs were near 5.1; and when the initial WSC contents were 7.0%, 8.0%, 9.0% and 10.0%, the pHs were near 4.0. The pattern of changes in WSC content during the fermentation was similar to that in pH. At 30 d of fermentation, there existed a dividing line in WSC remnants between the initial 6.0% WSC treatment and the initial 7.0% WSC treatment. When the initial WSC content was more than 7.0%, the remaining WSC content was more than 23.7 g/kg DM. When the initial WSC content was less than 6.0%, the remaining WSC content was less than 13.6 g/kg DM. Particularly for the 1.4% WSC treatment, the remaining WSC content was 2.1 g/kg DM. The results of the microbiological enumeration showed that with the increase in initial WSC content, the numbers of lactic acid bacteria (LAB) and other bacteria generally decreased. Denaturing gradient gel electrophoresis (DGGE) results showed that when the initial WSC content was beyond 7.0%, the LAB of the fermentation system were detected.

Microbial diversity in biodegradation and reutilization processes of garbage

With particular focus on the microbial diversity in garbage treatment, the current status of garbage treatment in Japan and microbial ecological studies on various bioprocesses for garbage treatment are described in detail. The future direction of research in this field is also discussed.