Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material

Dynamics of bacterial and archaeal communities during horse bedding and green waste composting

Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.

Abundance and composition of airborne archaea during springtime mixed dust and haze periods in Beijing, China

Archaea have an important role in the elemental biogeochemical cycle and human health. However, characteristics of airborne archaea affected by anthropogenic and natural processes are unclear. In this study, we investigated the abundance, structures, influencing factors and assembly processes of the archaeal communities in the air samples collected from Beijing in springtime using quantitative polymerase chain reaction (qPCR), high-throughput sequencing technology and statistical analysis. The concentrations of airborne archaea ranged from 10¹ to 10³ copies m^-3 (455 ± 211 copies m^-3), accounting for 0.67% of the total prokaryote (sum of archaea and bacteria). An increase in airborne archaea was seen when the air quality shifted from clean to slightly polluted conditions. Sandstorm dust imported a large number of archaea to the local atmosphere. Euryarchaeota, Thaumarchaeota and Crenarchaeota were the dominant phyla, revealing the primary role of soil in releasing archaea to the ambient environment. Dispersal-related neutral processes play an important role in shaping the structure of airborne archaeal assembly. Of all phyla, methanogenic Euryarchaeota were most abundant in the air parcels come from the south of Beijing. Air masses from the west of Beijing, which brought sandstorm to Beijing, carried large amounts of ammonia oxidizing archaea Nitrososphaera. The results demonstrate the importance of air mass sources and local weather conditions in shaping the local airborne archaea community.

Biotic and abiotic dynamics of a high solid-state anaerobic digestion box-type container system

A solid-state anaerobic digestion box-type container system for biomethane production was observed in 12 three-week batch fermentations. Reactor performance was monitored using physico-chemical analysis and the methanogenic community was identified using ANAEROCHIP-microarrays and quantitative PCR. A resilient community was found in all batches, despite variations in inoculum to substrate ratio, feedstock quality, and fluctuating reactor conditions. The consortia were dominated by mixotrophic Methanosarcina that were accompanied by hydrogenotrophic Methanobacterium, Methanoculleus, and Methanocorpusculum. The relationship between biotic and abiotic variables was investigated using bivariate correlation analysis and univariate analysis of variance. High amounts of biogas were produced in batches with high copy numbers of Methanosarcina. High copy numbers of Methanocorpusculum and extensive percolation, however, were found to negatively correlate with biogas production. Supporting these findings, a negative correlation was detected between Methanocorpusculum and Methanosarcina. Based on these results, this study suggests Methanosarcina as an indicator for well-functioning reactor performance.

Application of compost for effective bioremediation of organic contaminants and pollutants in soil

Soils contaminated with hazardous chemicals worldwide are awaiting remediation activities; bioremediation is often considered as a cost-effective remediation approach. Potential bioapproaches are biostimulation, e.g. by addition of nutrients, fertiliser and organic substrates, and bioaugmentation by addition of compound-degrading microbes or of organic amendments containing active microorganisms, e.g. activated sludge or compost. In most contaminated soils, the abundance of the intrinsic metabolic potential is too low to be improved by biostimulation alone, since the physical and chemical conditions in these soils are not conducive to biodegradation. In the last few decades, compost or farmyard manure addition as well as composting with various organic supplements have been found to be very efficient for soil bioremediation. In the present minireview, we provide an overview of the composting and compost addition approaches as 'stimulants' of natural attenuation. Laboratory degradation experiments are often biased either by not considering the abiotic factors or by focusing solely on the elimination of the chemicals without taking the biotic factors and processes into account. Therefore, we first systemise the concepts of composting and compost addition, then summarise the relevant physical, chemical and biotic factors and mechanisms for improved contaminant degradation triggered by compost addition. These factors and mechanisms are of particular interest, since they are more relevant and easier to determine than the composition of the degrading community, which is also addressed in this review. Due to the mostly empirical knowledge and the nonstandardised biowaste or compost materials, the field use of these approaches is highly challenging, but also promising. Based on the huge metabolic diversity of microorganisms developing during the composting processes, a highly complex metabolic diversity is established as a 'metabolic memory' within developing and mature compost materials. Compost addition can thus be considered as a 'super-bioaugmentation' with a complex natural mixture of degrading microorganisms, combined with a 'biostimulation' by nutrient containing readily to hardly degradable organic substrates. It also improves the abiotic soil conditions, thus enhancing microbial activity in general. Finally, this minireview also aims at guiding potential users towards full exploitation of the potentials of this approach.

Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments

BACKGROUND

Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments.

METHODOLOGY/PRINCIPAL FINDINGS

Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4(3-)) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively.

CONCLUSIONS/SIGNIFICANCE

This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.

Concentration of bioaerosols in composting plants using different quantification methods

BACKGROUND

Bioaerosols (organic dusts) containing viable and non-viable microorganisms and their metabolic products can lead to adverse health effects in exposed workers. Standard quantification methods of airborne microorganisms are mainly based on cultivation, which often underestimates the microbial burden. The aim of the study was to determine the microbial load in German composting plants with different, mainly cultivation-independent, methods. Second purpose was to evaluate which working areas are associated with higher or lower bioaerosol concentrations.

METHODS

A total of 124 inhalable dust samples were collected at different workplaces in 31 composting plants. Besides the determination of inhalable dust, particles, and total cell numbers, antigen quantification for moulds (Aspergillus fumigatus, Aspergillus versicolor, Penicillium chrysogenum, and Cladosporium spp.) and mites was performed. Concentrations of β-glucans as well as endotoxin and pyrogenic activities were also measured. The number of colony forming units (cfu) was determined by cultivation of moulds and actinomycetes in 36 additional dust samples.

RESULTS

With the exception of particle numbers, concentrations of all determined parameters showed significant correlations (P < 0.0001; r Spearman: 0.40-0.80), indicating a close association between these exposure markers. Colony numbers of mesophilic moulds and actinomycetes correlated also significantly with data of cultivation-independent methods. Exposure levels showed generally large variations. However, all parameters were measured highest in dusty working areas like next to the shredder and during processing with the exception of Cladosporium antigens that were found in the highest concentrations in the delivery area. The lowest concentrations of dust, particles, antigens, and pyrogenic activity were determined in wheel loader cabins (WLCs), which were equipped with an air filtration system.

CONCLUSION

It was possible to assess the microbial load of air in composting plants with different quantification methods. Since allergic and toxic reactions may be also caused by nonliving microorganisms, cultivation-independent methods may provide additional information about bioaerosol composition. In general, air filtration reduced the bioaerosol exposure shown in WLCs. Due to the fact that the mechanical processing of compost material, e.g. by shredding or sieving is associated with the generation of high bioaerosol concentrations, there is still a need of improved risk assessment and state-of-the-art protective measures in composting plants.

Insights into fungal communities in composts revealed by 454-pyrosequencing: implications for human health and safety

Fungal community composition in composts of lignocellulosic wastes was assessed via 454-pyrosequencing of ITS1 libraries derived from the three major composting phases. Ascomycota represented most (93%) of the 27,987 fungal sequences. A total of 102 genera, 120 species, and 222 operational taxonomic units (OTUs; >97% similarity) were identified. Thirty genera predominated (ca. 94% of the sequences), and at the species level, sequences matching Chaetomium funicola and Fusarium oxysporum were the most abundant (26 and 12%, respectively). In all composts, fungal diversity in the mature phase exceeded that of the mesophilic phase, but there was no consistent pattern in diversity changes occurring in the thermophilic phase. Fifteen species of human pathogens were identified, eight of which have not been previously identified in composts. This study demonstrated that deep sequencing can elucidate fungal community diversity in composts, and that this information can have important implications for compost use and human health.

Prokaryotic successions and diversity in composts as revealed by 454-pyrosequencing

In this study, 454-pyrosequencing was applied to analyze prokaryotic patterns in three lignocellulosic composting systems across the three main phases. In all composts, diversity expanded as composting progressed. Communities in the mesophilic- and mature-phases of all composts were distinct, which did not support the concept that organisms present in the mesophilic phase enter dormancy during thermophilic period, and re-colonize the compost at the mature phase. Analysis of similarity revealed compost phase was a significant source of dissimilarity (p=0.011), compost type was not (p=0.401). Analysis of variance also showed significant phase effects on the abundance of (p-value): Archaea (0.001), Planctomycetes (0.002), Chloroflexi (0.016), Deltaproteobacteria (0.027), Bacteria (0.046) and Gammaproteobacteria (0.056). Mature-phase compost was a preferred niche for the Archaea, Planctomycetes, Chloroflexi and Deltaproteobacteria, while Gammaproteobacteria were predominant in earlier phases. Thus, the mature phase pattern could have implications in the development of biomarker assays for compost maturity.

Archaeal community composition affects the function of anaerobic co-digesters in response to organic overload

Microbial community diversity in two thermophilic laboratory-scale and three full-scale anaerobic co-digesters was analysed by genetic profiling based on PCR-amplified partial 16S rRNA genes. In parallel operated laboratory reactors a stepwise increase of the organic loading rate (OLR) resulted in a decrease of methane production and an accumulation of volatile fatty acids (VFAs). However, almost threefold different OLRs were necessary to inhibit the gas production in the reactors. During stable reactor performance, no significant differences in the bacterial community structures were detected, except for in the archaeal communities. Sequencing of archaeal PCR products revealed a dominance of the acetoclastic methanogen Methanosarcina thermophila, while hydrogenotrophic methanogens were of minor importance and differed additionally in their abundance between reactors. As a consequence of the perturbation, changes in bacterial and archaeal populations were observed. After organic overload, hydrogenotrophic methanogens (Methanospirillum hungatei and Methanoculleus receptaculi) became more dominant, especially in the reactor attributed by a higher OLR capacity. In addition, aggregates composed of mineral and organic layers formed during organic overload and indicated tight spatial relationships between minerals and microbial processes that may support de-acidification processes in over-acidified sludge. Comparative analyses of mesophilic stationary phase full-scale reactors additionally indicated a correlation between the diversity of methanogens and the VFA concentration combined with the methane yield. This study demonstrates that the coexistence of two types of methanogens, i.e. hydrogenotrophic and acetoclastic methanogens is necessary to respond successfully to perturbation and leads to stable process performance.

Nitrogen conservation in simulated food waste aerobic composting process with different Mg and P salt mixtures

To assess the effects of three types of Mg and P salt mixtures (potassium phosphate [K3PO4]/magnesium sulfate [MgSO4], potassium dihydrogen phosphate [K2HPO4]/MgSO4, KH2PO4/MgSO4) on the conservation of N and the biodegradation of organic materials in an aerobic food waste composting process, batch experiments were undertaken in four reactors (each with an effective volume of 30 L). The synthetic food waste was composted of potatoes, rice, carrots, leaves, meat, soybeans, and seed soil, and the ratio of C and N was 17:1. Runs R1-R3 were conducted with the addition of K3PO4/ MgSO4, K2HPO4/MgSO4, and KH2PO4/MgSO4 mixtures, respectively; run R0 was a blank performed without the addition of Mg and P salts. After composting for 25 days, the degrees of degradation of the organic materials in runs R0-R3 were 53.87, 62.58, 59.14, and 49.13%, respectively. X-ray diffraction indicated that struvite crystals were formed in runs R1-R3 but not in run R0; the gaseous ammonia nitrogen (NH3-N) losses in runs R0-R3 were 21.2, 32.8, 12.6, and 3.5% of the initial total N, respectively. Of the tested Mg/P salt mixtures, the K2HPO4/ MgSO4 system provided the best combination of conservation of N and biodegradation of organic materials in this food waste composting process.

Anaerobic digestion of renewable biomass: thermophilic temperature governs methanogen population dynamics

Beet silage and beet juice were digested continuously as representative energy crops in a thermophilic biogas fermentor for more than 7 years. Fluorescence microscopy of 15 samples covering a period of 650 days revealed that a decrease in temperature from 60 degrees C to 55 degrees C converted a morphologically uniform archaeal population (rods) into a population of methanogens exhibiting different cellular morphologies (rods and coccoid cells). A subsequent temperature increase back to 60 degrees C reestablished the uniform morphology of methanogens observed in the previous 60 degrees C period. In order to verify these observations, representative samples were investigated by amplified rRNA gene restriction analysis (ARDRA) and fluorescence in situ hybridization (FISH). Both methods confirmed the temperature-dependent population shift observed by fluorescence microscopy. Moreover, all samples investigated demonstrated that hydrogenotrophic Methanobacteriales dominated in the fermentor, as 29 of 34 identified operational taxonomic units (OTUs) were assigned to this order. This apparent discrimination of acetoclastic methanogens contradicts common models for anaerobic digestion processes, such as anaerobic digestion model 1 (ADM1), which describes the acetotrophic Euryarchaeota as predominant organisms.

Performance and molecular evaluation of an anaerobic system with suspended biomass for treating wastewater with high fat content after enzymatic hydrolysis

The effect of a lipase-rich fungal enzymatic preparation, produced by a Penicillium sp. during solid-state fermentation, was evaluated in an anaerobic digester treating dairy wastewater with 1200 mg of oil and grease/L. The oil and grease hydrolysis step was carried out with 0.1% (w/v) of solid enzymatic preparation at 30 degrees C for 24 h, and resulted in a final free acid concentration eight times higher than the initial value. The digester operated in sequential batches of 48 h at 30 degrees C for 245 days, and had high chemical oxygen demand (COD) removal efficiencies (around 90%) when fed with pre-hydrolyzed wastewater. However, when the pre-hydrolysis step was removed, the anaerobic digester performed poorly (with an average COD removal of 32%), as the oil and grease accumulated in the biomass and effluent oil and grease concentration increased throughout the operational period. PCR-DGGE analysis of the Bacteria and Archaea domains revealed remarkable differences in the microbial profiles in trials conducted with and without the pre-hydrolysis step, indicating that differences observed in overall parameters were intrinsically related to the microbial diversity of the anaerobic sludge.

Effect of pre-aeration and inoculum on the start-up of batch thermophilic anaerobic digestion of municipal solid waste

In this study, a short pre-aeration step was investigated as pre-treatment for thermophilic anaerobic digestion of the organic fraction of municipal solid waste (OFMSW). It was found that pre-aeration of 48 h generated enough biological heat to increase the temperature of bulk OFMSW to 60 degrees C. This was sufficient self-heating of the bulk OFMSW for the start-up of thermophilic anaerobic digestion without the need for an external heat source. Pre-aeration also reduced excess easily degradable organic compounds in OFMSW, which were the common cause of acidification during the start-up of the batch system. Careful consideration however must be taken to avoid over aeration as this consumes substrate, which would otherwise be available to methanogens to produce biogas. To accelerate methane production and volatile solids destruction, the anaerobic digestion in this study was operated as a wet process with the anaerobic liquid recycled through the OFMSW. Appropriate anaerobic liquid inoculum was found to be particularly beneficial. It provided high buffer capacity as well as suitable microbial inoculum. As a result, acidification during start-up was kept to a minimum. With volatile fatty acids (VFAs-acetate in particular) and H2 accumulation typical of hydrolysis and fermentation of the easily degradable substrates during start-up, inoculum with high numbers of hydrogenotrophic methanogens was critical to not only maximise CH4 production but also reduce H2 partial pressure in the system to allow VFAs degradation. In a lab-scale bioreactor, the combined pre-aeration and wet thermophilic anaerobic digestion was able to stabilise the OFMSW within a period of only 12 days. The stabilised inert residual material can be used as a soil amendment product.

Recommendations for study design and sampling strategies for airborne microorganisms, MVOC and odours in the surrounding of composting facilities

Microorganisms and odour emissions from composting plants often lead to complaints by residents, especially by people living close to such plants. Both parameters were studied in a systematic approach under specific local meteorological conditions at nine different composting plants in Germany with emphasis on dispersal of microorganisms. Measurements were done at emission points and at sampling sites in the downwind and upwind directions of the facilities under 'normal case' (i.e. weather conditions typical for the location in combination with working activities at the plants) and 'real worst case' conditions (dispersal of bioaerosols into the surroundings expected to occur with high probability). Airborne microorganisms were sampled using filtration and impingement. Subsequent cultivation on four different culture media allowed quantification and identification of the culturable microflora. It turned out that a general assessment of emissions and dispersal of bioaerosols from composting plants is not possible because of the coherences of various factors influencing the dispersal. The site-specific meteorological situations must be considered carefully, whenever sampling locations are selected and need to be recorded in any sampling protocol. Air inversions in particular can lead to high concentrations of microorganisms (>10(4)-10(5)cfu m(-3) of thermophilic actinomycetes and thermotolerant fungi) in the surroundings of composting plants. Finally, it was shown that both thermotolerant fungi and thermophilic actinomycetes can serve as indicator organisms.