Nitrogen transformation processes catalyzed by manure microbiomes in earthen pit and concrete storages on commercial dairy farms

Storing manure is an essential aspect of nutrient management on dairy farms. It presents the opportunity to use manure efficiently as a fertilizer in crop and pasture production. Typically, the manure storages are constructed as earthen, concrete, or steel-based structures. However, storing manure can potentially emit aerial pollutants to the atmosphere, including nitrogen and greenhouse gases, through microbial and physicochemical processes. We have characterized the composition of the microbiome in two manure storage structures, a clay-lined earthen pit and an aboveground concrete storage tank, on commercial dairy farms, to discern the nitrogen transformation processes, and thereby, inform the development of mitigation practices to preserve the value of manure. First, we analyzed the 16S rRNA-V4 amplicons generated from manure samples collected from several locations and depths (0.3, 1.2, and 2.1-2.75 m below the surface) of the storages, identifying a set of Amplicon Sequence Variant (ASVs) and quantifying their abundances. Then, we inferred the respective metabolic capabilities. These results showed that the manure microbiome composition was more complex and exhibited more location-to-location variation in the earthen pit than in the concrete tank. Further, the inlet and a location with hard surface crust in the earthen pit had unique consortia. The microbiomes in both storages had the potential to generate ammonia but lacked the organisms for oxidizing it to gaseous compounds. However, the microbial conversion of nitrate to gaseous N₂, NO, and N₂O via denitrification and to stable ammonia via dissimilatory nitrite reduction seemed possible; minor quantities of nitrate was present in manure, potentially originating from oxidative processes occurring on the barn floor. The nitrate-transformation linked ASVs were more prevalent at the near-surface locations and all depths of the inlet. Anammox bacteria and archaeal or bacterial autotrophic nitrifiers were not detected in either storage. Hydrogenotrophic Methanocorpusculum species were the primary methanogens or methane producers, exhibiting higher abundance in the earthen pit. These findings suggested that microbial activities were not the main drivers for nitrogen loss from manure storage, and commonly reported losses are associated with the physicochemical processes. Finally, the microbiomes of stored manure had the potential to emit greenhouse gases such as NO, N₂O, and methane.

Methane Emission Reduction and Biological Characteristics of Landfill Cover Soil Amended With Hydrophobic Biochar

Biochar-amended landfill cover soil (BLCS) can promote CH₄ and O₂ diffusion, but it increases rainwater entry in the rainy season, which is not conducive to CH₄ emission reduction. Hydrophobic biochar–amended landfill cover soil (HLCS) was prepared to investigate the changes in CH₄ emission reduction and biological characteristics, and BLCS was prepared as control. Results showed that rainwater retention time in HLCS was reduced by half. HLCS had a higher CH₄ reduction potential, achieving 100% CH₄ removal at 25% CH₄ content of landfill gas, and its main contributors to CH₄ reduction were found to be at depths of 10–30 cm (upper layer) and 50–60 cm (lower layer). The relative abundances of methane-oxidizing bacteria (MOB) in the upper and lower layers of HLCS were 55.93% and 46.93%, respectively, higher than those of BLCS (50.80% and 31.40%, respectively). Hydrophobic biochar amended to the landfill cover soil can realize waterproofing, ventilation, MOB growth promotion, and efficient CH₄ reduction.

Enhancing the compost maturation of swine manure and rice straw by applying bioaugmentation

Microorganisms capable of decomposing cellulose, xylan, starch and protein were individually isolated from swine manure compost and soil in this study. The correlations with pH, carbon source concentration, C/N ratio and enzyme activity among these isolated microorganisms were also investigated. Furthermore, the effect of additional inoculation in the compost was studied by measuring variations in the C/N ratio, enzyme activity and compost maturation rate. The inoculated microorganisms used in this study included four bacterial isolates and one commercial microorganism Phanerochaete chrysosporium. The results indicated that the isolated Kitasatospora phosalacinea strain C1, which is a cellulose-degraded microorganism, presented the highest enzyme activity at 31 ℃ and pH 5.5, while the C/N ratio was 0.8%. The isolated xylan-degraded microorganism Paenibacillus glycanilyticus X1 had the highest enzyme activity at 45 ℃ and pH 7.5, while the C/N ratio was 0.5%. The starch-degraded microorganism was identified as Bacillus licheniformis S3, and its highest enzyme activities were estimated to be 31 ℃ and pH 7.5 while the C/N ratio was 0.8%. The highest enzyme activity of the protein-degraded microorganism Brevinacillus agri E4 was obtained at 45 ℃ and pH 8.5, while the C/N ratio was 1.0%. The rate of temperature increase in the compost inoculated with P. chrysosporium was only higher than that of the compost without inoculation, and its compost maturation level was also lower than that of other composts with additional inoculation. The optimal initial C/N ratio of the compost was 27.5 and the final C/N ratio was 18.9. The composting results also indicated that the secondary inoculation would benefit compost maturation, and the lowest final C/N ratio of 17.0 was obtained.

Evaluation of calcium cyanamide addition during co-composting of manure and maize straw in a forced-aeration static-pile system

BACKGROUND

Composting is one of the most environmentally friendly treatments to inactivate pathogenic organisms or reduce them to acceptable levels. However, even under thermal conditions, some pathogenic organisms such as E. coli could exist for a long time in composting. Such great persistence may increase the possibility of outbreaks of these organisms and further increase the environmental load. Calcium cyanamide (CaCN₂) has recently been recognized to have the fungicidal effect on the pathogens of the soilborne diseases. So, the present study determined the effect of CaCN₂ addition on composting progress as an antimicrobial agent and an amendment during forced-aeration static-pile composting of cow manure, which was mainly aimed to inhibit the pathogens that had not been inactivated by heat during composting.

METHODS

The mixtures of dairy cow manure and maize straw with addition of 2 % CaCN₂ or no addition were composted for 63 days. The physical, chemical and biological changes in compost mixtures were examined during composting. The data were statistically analyzed using ANOVA procedure from SAS software (version 9.0).

RESULTS

The results showed that the addition of CaCN₂ significantly increased the maximum temperature and lengthened the duration of the thermophilic phase, and increased the percent T-N but decreased C/N ratio. For microbiological test, the addition of CaCN₂ shortened the time to inactivate E. coli, and increased the total average population of thermophilic bacteria but did not significantly influence that of mesophilic bacteria.

CONCLUSION

The results indicated that the addition of CaCN₂, at least at the additive content of 2 % could benefit the thermophilic phase and the composting could quickly reach the sanitary standard during the composting of manure with maize straw in a forced-aeration static-pile system. This finding will contribute to solve the feces disposal problems.

Cultural, Transcriptomic, and Proteomic Analyses of Water-Stressed Cells of Actinobacterial Strains Isolated from Compost: Ecological Implications in the Fed-Batch Composting Process

This study was undertaken to examine the effects of water activity (aw) on the viability of actinobacterial isolates from a fed-batch composting (FBC) process by comparing culturability and stainability with 5-cyano-2,3-ditoryl tetrazolium chloride (CTC). The FBC reactor as the source of these bacteria was operated with the daily loading of household biowaste for 70 d. During this period of composting, aw in the reactor decreased linearly with time and reached approximately 0.95 at the end of operation. The plate counts of aerobic chemoorganotrophic bacteria were 3.2-fold higher than CTC-positive (CTC+) counts on average at the fully acclimated stage (after 7 weeks of operation), in which Actinobacteria predominated, as shown by lipoquinone profiling and cultivation methods. When the actinobacterial isolates from the FBC process were grown under aw stress, no significant differences were observed in culturability among the cultures, whereas CTC stainability decreased with reductions in aw levels. A cDNA microarray-based transcriptomic analysis of a representative isolate showed that many of the genes involved in cellular metabolism and genetic information processing were down-regulated by aw stress. This result was fully supported by a proteomic analysis. The results of the present study suggest that, in low aw mature compost, the metabolic activity of the community with Actinobacteria predominating is temporarily reduced to a level that hardly reacts with CTC; however, these bacteria are easily recoverable by exposure to a high aw culture medium. This may be a plausible reason why acclimated FBC reactors in which Actinobacteria predominate yields higher plate counts than CTC+ counts.

The combination of functional metagenomics and an oil-fed enrichment strategy revealed the phylogenetic diversity of lipolytic bacteria overlooked by the cultivation-based method

Metagenomic screening and conventional cultivation have been used to exploit microbial lipolytic enzymes in nature. We used an indigenous forest soil (NS) and oil-fed enriched soil (OS) as microbial and genetic resources. Thirty-four strains (17 each) of lipolytic bacteria were isolated from the NS and OS microcosms. These isolates were classified into the (sub)phyla Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria, all of which are known to be the main microbial resources of commercially available lipolytic enzymes. Seven and 39 lipolytic enzymes were successfully retrieved from the metagenomic libraries of the NS and OS microcosms, respectively. The screening efficiency (a ratio of positive lipolytic clones to the total number of environmental clones) was markedly higher in the OS microcosm than in the NS microcosm. Moreover, metagenomic clones encoding the lipolytic enzymes associated with Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Armatimonadetes, and Planctomycetes and hitherto-uncultivated microbes were recovered from these libraries. The results of the present study indicate that functional metagenomics can be effectively used to capture as yet undiscovered lipolytic enzymes that have eluded the cultivation-based method, and these combined approaches may be able to provide an overview of lipolytic organisms potentially present in nature.

Bacterial community in the personal-use composting reactor revealed by isolation and cultivation-independent method

Composting is an efficient and cost-effective process for organic waste treatment. In order to expand our knowledge regarding microorganisms and their roles in the composting process, bacterial community structures in the personal-use composting reactor were examined by isolation and 16S rDNA clone analysis (cultivation-independent method). The results of 16S rDNA clone analysis showed that populations of the Bacillaceae family (such as Bacillus spp., Cerasibacillus spp., Gracilibacillus spp.), dominate (98%). By using cultivation method, a total of four species including one novel species (Ureibacillus thermosphaericus, Geobacillus thermoglucosidasius, G. toebii and Thermobacillus composti) were isolated, and were classified into the order Bacillales corresponding to the result of 16S rDNA clone analysis. However, most species detected by clone analysis have not been cultivated, and may be viable but non-culturable VBNC species implying symbiotic interactions among the microorganisms.

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.