Extracellular enzyme profiles during co-composting of poultry manure and yard trimmings

Rapid decomposition of rice straw by application of a novel microbial consortium and study its microbial community dynamics

Rice straw decomposition is an attractive solution to open-field burning but the traditional method has slow kinetics and takes 60-90 days to obtain mature compost. In this study, we propose to boost up the decomposition process by addition of a novel microbial consortium rich in lignocellulolytic microbes. C: N ratio of the compost reached 11.69% and degradation efficiency of cellulose and hemicellulose was found to be 64 and 87% respectively within 25 days. Lignocellulolytic activity of the microbial consortium was confirmed by plate and activity assay. These parameters clearly indicated that a mature compost was obtained in 25 days. The 16S rRNA gene amplicon sequencing and functional analysis of predicted genes indicated amino acid and carbohydrate metabolism as the major metabolic pathway during composting. The tertiary level of functional analysis revealed the major metabolic pathways in the bacterial communities as pentose phosphate pathway, glycolysis and tricarboxylic acid cycle.

Isolation and Characterization of Urease-Producing Soil Bacteria

Urease is an enzyme produced by ureolytic microorganisms which hydrolyzes urea into ammonia and carbon dioxide. Microbial urease has wide applications in biotechnology, agriculture, medicine, construction, and geotechnical engineering. Urease-producing microbes can be isolated from different ecosystems such as soil, oceans, and various geological formations. The aim of this study was to isolate and characterize rapid urease-producing bacteria from Ethiopian soils. Using qualitative urease activity assay, twenty urease-producing bacterial isolates were screened and selected. Among these, three expressed urease at high rates as determined by a conductivity assay. The isolates were further characterized with respect to their biochemical, morphological, molecular, and exoenzyme profile characteristics. The active urease-producing bacterial isolates were found to be nonhalophilic to slightly halophilic neutrophiles and aerobic mesophiles with a range of tolerance towards pH (4.0-10.0), NaCl (0.25-5%), and temperature (20-40°C). According to the API ZYM assays, all three isolates were positive for alkaline phosphatase, leucine aryl amidase, acid phosphatase, and naphthol_AS_BI_phosphohydrolase. The closest described relatives of the selected three isolates (Isolate_3, Isolate_7, and Isolate_11) were Bacillus paramycoides, Citrobacter sedlakii, and Enterobacter bugandensis with 16S rRNA gene sequence identity of 99.0, 99.2, and 98.9%, respectively. From the study, it was concluded that the three strains appear to have a relatively higher potential for urease production and be able to grow under a wider range of growth conditions.

Development of a Soil Quality Index for Soils under Different Agricultural Management Conditions in the Central Lowlands of Mexico: Physicochemical, Biological and Ecophysiological Indicators

The Bajío—Mexico’s central lowlands—is a region of economic importance because of its agricultural industry. Over time, agricultural practices have led to soil deterioration, loss of fertility, and abandonment. In this study, six agricultural soils were analyzed: AGQ, CTH, CTJ, JRM, CRC, and CYI, and used to develop a soil quality index (SQI) that includes the use of physicochemical, biological, and ecophysiological indicators to differentiate soil quality. Principal component analysis (PCA) was used, reducing the indicators from 46 to 4, which represents 80.4% of data variability. It was implemented the equation of additive weights using the variance of the principal components as a weight factor for the SQI. The developed SQI was according to the indicators WHC, SLT, N-NO3−, and qCO2, differentiating the quality of soils from the agricultural management in low quality (JRM < CYI < AGQ) and moderate quality (CTJ < CRC < CTH). The use of biological and ecophysiological indicators added to the PCA and the equation of additive weights allowed establishing an SQI with a minimum of indicators, sensitive to agricultural management, facilitating its interpretation and implementation for the Mexican Bajío region and soils in similar conditions around the world.

Applicability of API ZYM to capture seasonal and spatial variabilities in lake and river sediments

Waters draining into a lake carry with them much of the suspended sediment that is transported by rivers and streams from the local drainage basin. The organic matter processing in the sediments is executed by heterotrophic microbial communities, whose activities may vary spatially and temporally. Thus, to capture and evaluate some of these variabilities in the sediments, we sampled six sites: three from the St. Clair River and three from Lake St. Clair in spring, summer, fall, and winter of 2016. At all sites and dates, we investigated the spatial and temporal variations in 19 extracellular enzyme activities using API ZYM. Our results indicated that a broad range of enzymes were found to be active in the sediments. Phosphatases, lipases, and esterases were synthesized most intensively by the sediment microbial communities. No consistent difference was found between the lake and sediment samples. Differences were more obvious between sites and seasons. Sites with the highest metabolic (enzyme) diversity reflected the capacity of the sediment microbial communities to breakdown a broader range of substrates and may be linked to differences in river and lake water quality. The seasonal variability of the enzymes activities was governed by the variations of environmental factors caused by anthropogenic and terrestrial inputs, and provides information for a better understanding of the dynamics of sediment organic matter of the river and lake ecosystems. The experimental results suggest that API ZYM is a simple and rapid enzyme assay procedure to evaluate natural processes in ecosystems and their changes.

Biochemical and microbial changes reveal how aerobic pre-treatment impacts anaerobic biodegradability of food waste

Aerobic pre-treatment of food waste (FW) was performed at different oxygen concentrations (0%, 5%, 10% and 21%O₂) and different durations (1, 2, 3 and 4 days) to investigate its impact on biochemical and microbial community characteristics of the waste and its ability to improve anaerobic biodegradability. Whatever the duration, the highest effect of pre-treatment was observed at full aerobic pre-treatment (21%O₂) while 5%O₂ and 10%O₂ showed lower transformation performances. Biochemical variations at 21%O₂ were mainly a decrease of simple carbohydrates, volatile fatty acids (VFA) and low molecular weight water soluble compounds and an increase of high weight water soluble compounds. Microbial community analysis showed a clear modification of populations after 21%O₂ aerobic pre-treatment, changing from an initial dominance of lactic acid bacteria to a final dominance of VFA consumers (like Acetobacter) and a higher presence of Fungi. Enzymatic tests showed an increase of exoenzymes content and a higher presence of protein and carbohydrates degrading enzymes. Finally, the aerobic pre-treatment did not negatively impact methane potential of FW (496 NLCH₄·kgVS^-1) which remained unchanged after two days of pre-treatment at 21%O₂. These latter optimal pre-treatment conditions are proposed to be tested in future investigation of anaerobic digestion (AD) process with low inoculum to substrate ratio in order to assess their ability to avoid acidification risk during AD of FW.

Assessing and monitoring the effects of filter material amendments on the biophysicochemical properties during composting of solid winery waste under open field and varying climatic conditions

Waste management in winery and distillery industries faces numerous disposal challenges as large volumes of both liquid and solid waste by-products are generated yearly during cellar practices. Composting has been suggested as a feasible option to beneficiate solid organic waste. This incentivized the quest for efficient composting protocols to be put in place. The objective of this study was to experiment with different composting strategies for spent winery solid waste. Compost materials consisting of chopped pruning grape stalks, skins, seed and spent wine filter material consisting of a mixture of organic and inorganic expend ingredients were mixed in compost heaps. The filter material component varied (in percentage) among five treatments: T1 (40%) lined, T2 (20%) lined, T3 (0%) lined, T4 (40%) ground material, lined and T5 (40%) unlined. Composting was allowed to proceed under open field conditions over 12months, from autumn to summer. Indicators such as temperature, moisture, enzyme activities, microbial counts, pH, and C/N ratio, were recorded. Generally, season (df=3, 16, P<0.05) had significant effects (df=1, 3, P<0.05) on heap temperature and moisture in all treatments. Similarly, microorganisms (actinobacteria and heterotrophs) varied significantly in all treatments in response to seasonal change (df=3, 16; P<0.05). Enzyme activities fluctuated in accordance with seasonal factors and compost maturity stages, with phosphatases, esterases, amino-peptidases, proteases and glycosyl-hydrolases being most prominent. Compared to treatments T2 and T3, compost treatments with higher percentage waste filter materials (T1, T4 and T5) had higher N (16,100-21,300mg/kg), P (1500-2300mg/kg), K (19,800-28,200mg/kg), neutral pH, and lower C/N ratios (13:1-10:1), which were also comparable with commercially produced composts. Filter materials therefore, appears to be a vital ingredient for composting of winery solid waste.

Screening for novel bacteria from the bioenergy feedstock switchgrass (Panicum virgatum L.)

Switchgrass is considered as a good candidate for biofuel, especially ethanol production due to its huge biomass output and high cellulose content. In a search for novel microorganisms capable of using and degrading switchgrass to produce sugars and ethanol, enrichment experiments were established to screen for microorganisms from soil samples obtained at the University of Tennessee Agricultural Research Station, Jackson, Tennessee. Three enrichments were prepared and incubated at different pH and temperatures: (1) 30 degrees C, pH 5, (2) 30 degrees C, pH 8 and (3) 60 degrees C, pH5. Bulk community DNA was directly extracted from the enrichments. Microbial community structures were determined by phylogenetic analysis of 16S rRNA gene sequences retrieved from the enrichment cultures containing switchgrass as the carbon source. The mesophilic enrichments were dominated by Sarcina, Anaerobacter, and Clostrium, which were not found in the thermophilic enrichment. The thermophilic enrichment selected for two types of bacteria belonging to the class Bacilli (Geobacillus and Saccharococcus). The thermophilic enrichments were dominated by the Geobacillus spp. (Firmicutes, class Bacilli), and Saccharococcus (Firmicutes, class Bacilli); both containing thermophilic microorganisms with some cellulolytic members. Enzymatic assays detected the presence of enzymes involved in cellulose (beta-glucosidase and cellobiohydrolase) and hemicellulose degradations (beta-xylosidase); and the activity tends to be higher in the enrichments incubated at 30 degrees C.

Molecular analyses of the functional microbial community in composting by PCR-DGGE targeting the genes of the β-glucosidase

The study investigated the β-glucosidase-producing microbial communities and the enzymatic dynamics of CMCase and β-glucosidase during the process of cattle manure-rice straw composting. In order to analyze the succession of functional community by PCR-denaturing gradient gel electrophoresis (DGGEs), three sets of PCR primers were designed to amplify the family 1 and 3 β-glucosidase genes from both bacteria and fungi. The results showed in general that the stable functional community composition as well as for the high level enzymatic activities of both cellulase and β-glucosidase occurred during the last phase (days 14-31) of composting. In the process of composting, that functional groups were determined by the stable bands (GH1-F, GH1-H, GH1-G, GH3E-D and GH3E-E) may significantly contribute to the increase of β-glucosidase activities in the later phase. Especially, the bands from the family 1 β-glucosidase genes were appeared before that from the family 3 β-glucosidase genes from fungi, then the former was substituted for the latter gradually in the cooling phase. We found significant correlations between the β-glucosidase activity and the communities of the functional bacteria and fungi. The results indicated that different β-glucosidase-producing microbe release different amounts or activities of β-glucosidase, and that the composition of microbial communities may play a major role in determining overall β-glucosidase activity during the composting process.

Composting of rice straw with effective microorganisms (EM) and its influence on compost quality

This study aims to assess the effect of EM application on the composting process of rice straw with goat manure and green waste and to evaluate the quality of both compost treatments. There are two treatment piles in this study, in which one pile was applied with EM and another pile without EM. Each treatment was replicated three times with 90 days of composting duration. The parameters for the temperature, pH, TOC and C/N ratio, show that decomposition of organic matter occurs during the 90-day period. The t-test conducted shows that there is a significant difference between compost with EM and compost without EM. The application of EM in compost increases the macro and micronutrient content. The following parameters support this conclusion: compost applied with EM has more N, P and K content (P < 0.05) compared to compost without EM. Although the Fe in compost with EM is much higher (P < 0.05) than in the compost without EM, for Zn and Cu, there is no significant difference between treatments. This study suggests that the application of EM is suitable to increase the mineralization in the composting process. The final resultant compost indicated that it was in the range of the matured level and can be used without any restriction.

Extracellular hydrolytic enzyme activities of the heterotrophic microbial communities of the Rouge River: an approach to evaluate ecosystem response to urbanization

The potential effects of urbanization on the bioavailability of dissolved organic carbon (DOC) were tested by determining the extracellular enzyme activities of the heterotrophic microbial communities of the Rouge River. The activities of 19 enzymes were monitored across two water samples (river water and groundwater) at different spatial and temporal scales. High phosphatase, esterase, and aminopeptidase activities was observed in site 9 (site most exposed to anthropogenic sources) showed higher concentrations of DOC compared to sites 1 and 8 (sites exposed to less anthropogenic sources), where moderate activities of diverse range of enzymes were observed. High relative contributions of phosphatase, esterase, and aminopeptidase activities to the overall enzyme activity as observed in site 9 stressed the increased importance of peptides as C source for heterotrophic communities and high in-stream carbon processing, which account for high nonspecific extracellular enzyme activities. In contrast, high contribution of glycosyl hydrolases occurred consistently across all sites, which highlights the significance of microbial detrital and plant biomass as carbon sources. Majority of the enzymes showed evidence of activity at various extents during spring and summer. However, higher activities of leucine aminopeptidase, valine aminopeptidase, β-glucosidase, and α-mannosidase were observed in the summer; and alkaline phosphatase and α-glucosidase in the spring. The results presented here suggest a shift in organic carbon bioavailability across all sites of contrasting urbanization, despite similarities in DOC concentrations. Hence, API ZYM technique can be used as an effective indicator of river water and groundwater system health across an urban gradient.

Co-composting of poultry manure with low quantities of carbon-rich materials

To study the feasibility of co-composting poultry manure with low quantities of high-value, carbon-rich materials experiments to characterize three pilot-scale piles were carried out. The piles comprised poultry manure (pile 1), poultry manure and straw (pile 2) and poultry manure and sawdust (pile 3), using wood chips as bulking agent. Pile 1 presented the highest losses of organic matter and nitrogen contents (> or = 92.9% and 92.0%, respectively). Although a thermophilic phase (temperature > 40 degrees C) was not verified for this pile, the final compost was stable (class IV) and free of pathogen indicator micro-organisms but it was the most phytotoxic, and presented a humic and fulvic acids ratio (HA/FA) that was less than 1. In contrast, piles 2 and 3 sustained thermophilic phases and produced stable (class V) and mature (HA/FA > 1) composts. Pile 2 showed the lowest loss in nitrogen content (88.9%) and produced the final compost with the highest C/N ratio (14.7) and the lowest value of electrical conductivity (3.9 mS cm(-1)). This study showed that it is possible to reduce the costs of poultry manure composting, namely the costs associated with the use of carbon-rich materials, given that the final co-composts presented parameters within the range of those recommended by the Second Draft Proposal for compost quality.

Calibration of chemical and biological changes in cocomposting of biowastes using near-infrared spectroscopy

Cocomposting of green wastes and sewage sludges is a complex process involving rapid biological and chemical changes. The objective of the study was to assess the usefulness of near-infrared reflectance spectroscopy (NIRS) to characterize these changes, as an alternative to standard procedures which are often time-consuming and laborious. Samples obtained during 146 days of composting were analyzed by 14 conventional methods and NIRS. Results from conventional methods demonstrated a noticeable separation into two distinct phases. An initial phase from 4 to 50-60 days was characterized by intensive degradation. A second phase up to 146 days was characterized by a decrease in all biological activities. NIRS calibrations allowed accurate predictions of nitrogen (N), carbon (C), C/N, humic acid (HA), pH, respiration, cellulase, phenoloxidase, and composting time successfully. Results were less accurate for organic matter (OM), protease, acid, and alkaline phosphatases and unsatisfactory for fulvic acid. NIRS calibration allows composting time/state of progress of maturation to be predicted accurately to within 10 days. A global index of composting evolution (GICE), resulting from the 14 parameters studied, is proposed. It is precisely predicted and shows that since NIRS is able to predict essential parameters of compost maturity, it could prove invaluable for monitoring biowastes cocomposting.

Effect of bioaugmentation and nitrogen supplementation on composting of paddy straw

A composting experiment was conducted to evaluate the effect of a hyperlignocellulolytic fungal consortium and different nitrogen amendments on paddy straw composting in terms of changes in physicochemical and biological parameters. A fungal consortium comprising four lignocellulolytic mesophilic fungal cultures was used as inoculum for bioaugmentation of paddy straw in perforated pits. The comparative effect of farmyard manure (FYM), soybean trash, poultry litter and urea on the composting process was evaluated at monthly intervals in terms of physicochemical (pH, EC, available P, C:N ratio and humus content) and biological (enzymatic and microbial activity) parameters. The compost prepared from bioaugmented paddy straw composting mixture, with poultry manure as nitrogen supplement attained desirable C:N ratio in 1 month and displayed least phytotoxicity levels along with higher production of beta-1,4-Exoglucanase. The combined activity of the autochthonous composting microbiota as well as the externally applied fungal inoculum accelerated the composting process of paddy straw. Supplementation of paddy straw with poultry manure in 8:1 ratio was identified as the best treatment to hasten the composting process. This study highlights the importance of application of fungal inoculum and an appropriate N-amendment such as poultry manure for preparation of compost using a substrate having high C:N ratio, such as paddy straw.