Livestock Manure Type Affects Microbial Community Composition and Assembly During Composting

Rice straw co-digestion potential with cow dung and poultry droppings for maximizing biogas production in Bangladesh

Rice is the staple food of the people of Bangladesh. Burning and landfilling of carbon-rich rice straw (RS) causes greenhouse gas emissions. On the other hand, cow dung (CD) and poultry droppings (PD) produced from the livestock sector in Bangladesh could be a potential threat to the environment if the wastes are not properly managed. However, anaerobic co-digestion of RS with CD and PD could be an effective means of biogas generation. Therefore, co-digestion of CD and PD with carbon-rich RS was conducted in batch assay at seven different mixing ratios (100:0, 90:10, 70:30, 50:50, 30:70, 10:90, 0:100) separately. Mesophilic condition (35 °C) was maintained for 92 days of digestion time to investigate biogas production potential and find out optimal mixing ratios of both co-digestion sets. Co-digestion of CD and RS at 70:30 ratio significantly showed maximum biogas yield (441.7 ± 54.1 ml/gVS). Additionally, an increase in biogas yield in this ratio was 212.11 % and 38.10 % compared to mono-digestion of CD and RS, respectively. Another co-digestion set of PD with RS showed highest biogas yield (344.8 ± 22.3 ml/gVS) at 90:10 ratio. The 90:10 ratio of PD and RS improved biogas yield by 173.16 % and 7.8 % as compared to mono-digestion of PD and RS, respectively. Co-digestion of RS with CD and PD had a statistically significant effect (P ≤ 0.05) on biogas production. Furthermore, kinetic modelling outcomes suggested the modified Gompertz model as ideal for forecasting biomethane production over time in both cases. The findings of this study will help in the implementation of ACoD at the field level.

Impact of different continuous fertilizations on the antibiotic resistome associated with a subtropical triple-cropping system over one decade

The prevalence of antibiotic resistance genes (ARGs) in agricultural soils has garnered significant attention. However, the long-term impacts of various nitroge (N)-substitution fertilization regimes on the distribution of soil ARGs and their dominant drivers in a subtropical triple-cropping system remain largely unexplored. This study employed a metagenomic approach to analyze soil ARGs, microbial communities, mobile genetic elements (MGEs), and viruses from a maize-maize-cabbage rotation field experiment with five different fertilization regimes. Soil samples were collected in 2012 and 2021. A total of 615 unique ARG subtypes were identified, with multidrug, bacitracin, and rifamycin resistance genes being the most abundant. Notably, ARG types. the continuous application of fresh chicken manure (CM) over 10 years significantly increased both the count of unique ARG subtypes and the total ARG abundance compared to other fertilization regimes, such as inorganic fertilizer and composted chicken manure. Specifically, the abundance of genes associated with antibiotic target replacement (e.g., sul1 and sul2) in the CM-treated soil rose by 8.83-fold from 2021 to 2012. Our random forest analysis revealed that the abundance of three MGEs (QacEdelta, plasmids, and IstB), two viral families (Myoviridae and Podoviridae), two bacterial phyla (Chloroflexi and Planctomycetes), and two environmental factors (pH and soil organic matter (SOM)) significantly influenced the distribution of ARGs. Furthermore, variance decomposition analysis underscored the critical roles of the three MGEs and the two viral families in the dissemination of ARGs, suggesting that horizontal gene transfer (HGT) may play a key role in ARG spread. These findings enhance our understanding of how different fertilization practices influence ARG dissemination in subtropical triple-cropping agroecosystems over the long term and provide valuable insights for optimizing fertilization management strategies.

Effects of adding corn straw and apple tree branches on antibiotic resistance genes removal during sheep manure composting

The study investigates the effects of composting sheep manure with corn straw (CM) and sheep manure with apple tree branches (AM) on antibiotic resistance genes (ARGs) and microbial communities. The results indicate that AM treatment enables the compost pile to reach the high-temperature phase more quickly. The total phosphorus and total potassium content in AM treatment compost increased compared to the initial stage of composting, while CM treatment effectively enhanced the total nitrogen and total phosphorus content, and CM treatment compost was more conducive to reducing the compost's electrical conductivity. The relative abundance of total ARGs for sulfonamides, tetracyclines, and integrase genes in CM treatment compost were lower than in AM treatment compost. CM treatment was beneficial in reducing the relative abundance of sul1 and tetA-02 by 33.61% and 35.51%, respectively. Both treatments were effective in reducing the relative abundance of sul3 and intI2. The relative abundance of Chloroflexi and Proteobacteria in AM treatment decreased over time, while Bacteroidetes increased, which was opposite to the trend observed in CM treatment. There were significant correlations between the compost's physicochemical properties, bacterial communities, ARGs, and mobile genetic elements (MGEs). ARGs and MGEs can exist in multiple host bacteria, and various ARGs and MGEs can also be hosted in the same bacterium. Mantel analysis showed that the total organic matter, total phosphorus, and total potassium had the greatest contributions to the changes in ARGs and MGEs, while temperature and bacterial communities regulated ARGs by affecting MGEs. Obviously, adding corn straw is more effective in reducing the abundance of ARGs during the sheep manure composting.

The archaeal and bacterial community structure in composted cow manures is defined by the original populations: a shotgun metagenomic approach

Introduction

Organic wastes are composted to increase their plant nutritional value, but little is known about how this might alter the bacterial and archaeal community structure and their genes.

Methods

Cow manure was collected from three local small-scale farmers and composted under controlled conditions, while the bacterial and archaeal communities were determined using shotgun metagenomics at the onset and after 74 days of composting.

Results

The bacterial, archaeal, methanogen, methanotrophs, methylotroph, and nitrifying community structures and their genes were affected by composting for 74 days, but the original composition of these communities determined the changes. Most of these archaeal and bacterial groups showed considerable variation after composting and between the cow manures. However, the differences in the relative abundance of their genes were much smaller compared to those of the archaeal or bacterial groups.

Discussion

It was found that composting of different cow manures did not result in similar bacterial or archaeal communities, and the changes that were found after 74 days were defined by the original populations. However, more research is necessary to determine if other composting conditions will give the same results.

Evaluation of the potential horizontal gene transfer ability during chicken manure and pig manure composting

Resistance genes have been identified as emerging pollutants due to their ability to rapidly spread in the environment through horizontal gene transfer (HGT). Microbial community serves as the pivotal factor influencing the frequency of HGT during manure composting. However, the characteristics of HGT in microbial community from different types of manure were unclear. Therefore, this study aimed to evaluate the potential risk of HGT in bacterial community through the co-composting of chicken manure and pig manure in different proportions. The experimental results showed that the abundance of sulfonamide antibiotic resistance genes and integrase genes was higher during pig manure composting than those during chicken manure composting. In addition, the addition of pig manure also increased resistance genes abundance during chicken manure composting. These results suggested that the potential HGT risk was greater during pig manure composting. Furthermore, microbial analysis of co-composting suggested that bacterial community of pig manure was more competitive and adaptable than that of chicken manure. Ultimately, statistical analysis indicated that compared to chicken manure composting, the potential ability of HGT was greater during pig manure composting. This study provided the vital theoretical support and scientific guidance for mitigating the HGT risk during manure composting.

Carbon-mediated modulation pathways of phytotoxicity in chicken manure composting

Compost phytotoxicity affects the safety of organic fertilizers returned to the field, thus hindering the breeding cycle, so it is essential to reduce the compost phytotoxicity. The phytotoxicity of compost was estimated utilizing the germination index (GI) and the aqueous substances (organics and ions) present in compost correlated closely with GI. This study assessed the effect of carbon additives from different plant sources (mushroom substrates (MS), cornstalks (CS) and garden substrates (GS)) on maturity parameters (temperature, pH, EC, C/N), content of aqueous carbon and nitrogen matters, salt ions, heavy metal ions, and microbiome of piles when composting with chicken manure and especially focused on their effect on GI. Results showed that all additives significantly improved GI (85.25%-106.28%). The primary factors influencing seed germination were Mg2+ and SO42- in CM compost, acetic acid and NH4+ in CM + MS compost, humic acid in CM + CS compost, and dissolved total nitrogen in CM + GS compost. During composting, the growth of heavy metal passivating bacteria (Bacillus) and organic matter degrading bacteria (Desemzia and Turicibacter) can be promoted by decreasing aqueous carbon and nitrogen substances (volatile fatty acids, NH4+, dissolved total nitrogen, amino acids) and increasing the content of humic acid, which improved the composting environment and provided favorable conditions for the germination of seeds, thereby increasing GI. Therefore, GS showed the best potential for accelerating degradation of organic matter and improving GI during composting with chicken manure.

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of health-promoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations.

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure

Researchers have extensively studied the effect of oxygen on the growth and survival of bacteria. However, the impact of oxygen on bacterial community structure, particularly its ability to select for taxa within the context of a complex microbial community, is still unclear. In a 21-day microcosm experiment, we investigated the effect of aerobic exposure on the fecal community structure and succession pattern in broiler, calf, and piglet feces (n = 10 for each feces type). Bacterial diversity decreased and community structure changed rapidly in the broiler microbiome (P < 0.001), while the fecal community of calves and piglets, which have higher initial diversity, was stable after initial exposure but decreased in diversity after 3 days (P < 0.001). The response to aerobic exposure was host animal specific, but in all three animals, the change in community structure was driven by a decrease in anaerobic species, primarily belonging to Firmicutes and Bacteroidetes (except in broilers where Bacteroidetes increased), along with an increase in aerobic species belonging to Proteobacteria and Actinobacteria. Using random forest regression, we identified microbial features that predict aerobic exposure. In all three animals, host-beneficial Prevotella-related ASVs decreased after exposure, while ASVs belonging to Acinetobacter, Corynbacterium, and Tissierella were increased. The decrease of Prevotella was rapid in broilers but delayed in calves and piglets. Knowing when these pathobionts increase in abundance after aerobic exposure could inform farm sanitation practices and could be important in designing animal experiments that modulate the microbiome.IMPORTANCEThe fecal microbial community is contained within a dynamic ecosystem of interacting microbes that varies in biotic and abiotic components across different animal species. Although oxygen affects bacterial growth, its specific impact on the structure of complex communities, such as those found in feces, and how these effects vary between different animal species are poorly understood. In this study, we demonstrate that the effect of aerobic exposure on the fecal microbiota was host-animal-specific, primarily driven by a decrease in Firmicutes and Bacteroidetes, but accompanied by an increase in Actinobacteria, Proteobacteria, and other pathobionts. Interestingly, we observed that more complex communities from pig and cattle exhibited initial resilience, while a less diverse community from broilers displayed a rapid response to aerobic exposure. Our findings offer insights that can inform farm sanitation practices, as well as experimental design, sample collection, and processing protocols for microbiome studies across various animal species.

Influence of Compost Amendments on Soil and Human Gastrointestinal Bacterial Communities during a Single Gardening Season

To measure associations between gardening with different compost amendments and the human gut microbiota composition, gardeners (n = 25) were provided with one of three types of compost: chicken manure (CM), dairy manure and plant material (DMP), or plant-based (P). Stool samples were collected before gardening (T1), after compost amendment (T2), and at peak garden harvest (T3). Compost and soil samples were collected. DNA was extracted, 16S rRNA libraries were established, and libraries were sequenced by Illumina MiSeq. Sequences were processed using mothur, and data were analyzed in R software version 4.2.2. Fast expectation-maximization microbial source tracking analysis was used to determine stool bacteria sources. At T2/T3, the gut microbiotas of P participants had the lowest Shannon alpha diversity, which was also the trend at T1. In stool from T2, Ruminococcus 1 were less abundant in the microbiotas of those using P compost as compared to those using CM or DMP. At T2, Prevotella 9 had the highest abundance in the microbiotas of those using CM compost. In participants who used CM compost to amend their gardening plots, a larger proportion of the human stool bacteria were sourced from CM compared to soil. Soil exposure through gardening was associated with a small but detectable change in the gardeners' gut microbiota composition. These results suggest that human interactions with soil through gardening could potentially impact health through alterations to the gut microbiota.

Devitalization of Bacteria in Composted Cattle Manure with Natural Additives and Risk for Environment

Nowadays, there is an effort to improve the effectiveness of the composting process, supported by the addition of various supplements to reduce soil nutrition losses and increase soil remediation. The aim of this study was to examine the devitalization effect of natural additives like zeolite-clinoptilolite and its combination with hydrated lime in composted cattle manure on indicator and pathogen bacteria. The composting process was running in three static piles of cattle manure mixed with wheat straw (control, zeolite-lime, and zeolite) for 126 days. Composted manure substrates were determined for physicochemical (temperature, pH, nitrogen and phosphorus content, C/N, organic matter, and moisture) and microbiological analyses (Salmonella spp., indicator bacteria). The effects of additives were reflected in changes in physicochemical factors, e.g., an increase in temperature (<53 °C) or pH (<9.3). According to Pearson correlation, these changes (pH, Nt, Pt) resulted in a significant decrease (p < 0.001) of indicator bacteria (two or three orders) in zeolite pile or zeolite-lime pile. Die-off of Salmonella spp. in the zeolite-lime pile was indicated within 41 days; in other piles, this occurred on day 63. Our results can aid in further optimizing the composting of cattle manure in order to lower environmental pollution and the risk of human infection.

Investigating fungal community characteristics in co-composted cotton stalk and various livestock manure products

Agricultural wastes, comprising cotton straw and livestock manure, can be effectively managed through aerobic co-composting. Nevertheless, the quality and microbial characteristics of co-composting products from different sources remain unclear. Therefore, this study utilized livestock manure from various sources in Xinjiang, China, including herbivorous sheep manure (G), omnivorous pigeon manure (Y), and pigeon-sheep mixture (GY) alongside cotton stalks, for a 40-day co-composting process. We monitored physicochemical changes, assessed compost characteristics, and investigated fungal community. The results indicate that all three composts met established composting criteria, with compost G exhibiting the fastest microbial growth and achieving the highest quality. Ascomycota emerged as the predominant taxon in three compost products. Remarkably, at the genus level, the biomarker species for G, Y, and GY are Petromyces and Cordyceps, Neurospora, and Neosartorya, respectively. Microorganisms play a pivotal role in organic matter degradation, impacting nutrient composition, demonstrating significant potential for the decomposition and transformation of compost components. Redundancy analysis indicates that potassium, total organic carbon, and C:N are key factors influencing fungal communities. This study elucidates organic matter degradation in co-composting straw and livestock manure diverse sources, optimizing treatment for efficient agricultural waste utilization and sustainable practices.

Dynamics of microbial functional guilds involved in the humification process during aerobic composting of chicken manure on an industrial scale

Proper composting treatment of poultry manure waste is recommended before its use as a fertilizer. This involves many bioprocesses driven by microorganisms. Therefore, it is important to understand microbial mechanisms behind these bioprocesses in manure composting systems. Many efforts have been made to study the microbial community structure and diversity in these systems using high-throughput sequencing techniques. However, the dynamics of microbial interaction and functionality, especially for key microbial functional guilds, are not yet fully understood. To address these knowledge gaps, we collected samples from a 150-day industrial chicken manure composting system and performed the microbial network analysis based on the sequencing data. We found that the family Bacillaceae and genus Bacillus might play important roles in organic matter biodegradation at the mesophilic/thermophilic phases. Genera Virgibacillus, Gracilibacillus, Nocardiopsis, Novibacillus, and Bacillaceae_BM62 were identified as the key ones for humic acid synthesis at the mature phases. These findings improve our understanding about the fundamental mechanisms behind manure composting and can aid the development of microbial agents to promote manure composting performance.

Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment

The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.

Continuous thermophilic composting of distilled grain waste improved organic matter stability and succession of bacterial community

Continuous thermophilic composting (CTC) is potentially helpful in shortening the composting cycle. However, its universal effectiveness and the microbiological mechanisms involved are unclear. Here, the physicochemical properties and bacterial community dynamics during composting of distilled grain waste in conventional and CTC models were compared. CTC accelerated the organic matter degradation rate (0.2 vs. 0.1 d-1) and shortened the composting cycle (24 vs. 65 d), mainly driven by the synergism of bacterial genera. Microbial analysis revealed that the abundance of Firmicutes was remarkably improved compared to that in conventional composting, and Firmicutes became the primary bacterial phylum (relative abundance >70 %) during the entire CTC process. Moreover, correlation analysis demonstrated that bacterial composition had a remarkable effect on the seed germination index. Therefore, controlling the composting process under continuous thermophilic conditions is beneficial for enhancing composting efficiency and strengthening the cooperation between bacterial genera.

A review on the effects of discharging conventionally treated livestock waste to the environmental resistome

Globally, animal production has developed rapidly as a consequence of the ongoing population growth, to support food security. This has consequently led to an extensive use of antibiotics to promote growth and prevent diseases in animals. However, most antibiotics are not fully metabolized by these animals, leading to their excretion within urine and faeces, thus making these wastes a major reservoir of antibiotics residues, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) in the environment. Farmers normally depend on conventional treatment methods to mitigate the environmental impact of animal waste; however, these methods are not fully efficient to remove the environmental resistome. The present study reviewed the variability of residual antibiotics, ARB, as well as ARGs in the conventionally treated waste and assessed how discharging it could increase resistome in the receiving environments. Wherein, considering the efficiency and environmental safety, an addition of pre-treatments steps with these conventional treatment methods could enhance the removal of antibiotic resistance agents from livestock waste.

Effect of the addition of biochar and wood vinegar on the morphology of heavy metals in composts

In the experiment, the morphology of heavy metals (Pb, Cr, Cd, and Ni, HMs) was characterized using flame atomic absorption spectroscopy. In addition, Fourier transform infrared spectroscopy (FTIR) and three-dimensional excitation-emission matrix fluorescence spectroscopy (3D-EEM) were used to characterize the correlation between environmental factors and metal morphology in the rotting compost from several angles. The results showed that the humus treated with wood vinegar solution had a high degree of humification and rich aromatic structure. FTIR spectroscopy confirmed that the degree of humus aromatization gradually increased during the composting process, which enhanced the complexation of humus (HS) with HMs but had less effect on Ni. In addition, the optimum concentration of wood vinegar (WV) was determined to be 1.75%. The results of the study showed that in the Pb passivation treatment group, the proportion of soluble (Red) and exchangeable states (Exc) converted to oxidized (Oxi) and residual states (Res) was 8%, 14%, 6%, 1%, and 12% in the CK, T1, T2, T3, and T4 treatment groups, respectively; in the Cr passivation treatment group, the proportion of Cr-Red and Cr-Exc converted to oxidized and residual states was 31%, 33%, 25%, 29%, and 25%; in the Cd passivation treatment group, the proportions of Cd-Red and Cd-Exc converted to oxidized and residual states were 5%, 15%, 4%, 9%, and 11%, respectively; whereas the Ni treatment group did not show any significant passivation effect. The proportion of Pb-Oxi was relatively stable, Cr-Oxi was converted to Cr-Res, whereas Cd showed the conversion of Cd-Oxi to Cd-Exc. SUVA254 and SUVA280 showed significant positive correlations with Pb-Res, Cr-Res and Ni-Res, and significant positive correlations with moisture content (MC); whereas MC was significantly negatively correlated with each form of HMs. Total potassium (TK), total nitrogen (TN), and both carbon (TOC) were negatively correlated with Pb-Res and Pb-Exc. Structural equation modeling verified the relationship between environmental factors and HMs, and the composting results showed that the addition of biochar (BC) and a higher percentage of WV could increase compost decomposition and passivate HMs to improve its agronomic function.

Relating bacterial dynamics and functions to greenhouse gas and odor emissions during facultative heap composting of four kinds of livestock manure

Although facultative heap composting is widely used in small and medium-sized livestock farms in China, there are few studies on greenhouse gas (GHG) and odor emissions from this composting system. This study focused on GHG and odor emissions from facultative heap composting of four types of livestock manure and revealed the relationship between the gaseous emissions and microbial communities. Results showed that pig, sheep, and cow manure reached high compost maturity (germination index (GI) > 70%), whereas chicken manure had higher phytotoxicity (GI = 0.02%) with higher electrical conductivity and a lower carbon/nitrogen ratio. The four manure types significantly differed in the total GHG emission, with the following pattern: pig manure (308 g CO2-eq·kg-1) > cow manure (146 g CO2-eq·kg-1) > chicken manure (136 g CO2-eq·kg-1) > sheep manure (95 g CO2-eq·kg-1). Bacterium with Fermentative, Methanotrophy and Nitrite respiratory functions (e.g. Pseudomonas and Lactobacillus) are enriched within the pile so that more than 90% of the GHGs are produced in the early (days 0-15) and late (days 36-49) composting periods. CO2 contributed more than 90% in the first 35 d, N2O contributed 40-75% in the late composting period, and CH4 contributed less than 8.0%. NH3 and H2S emissions from chicken and pig manure were 4.8 times those from sheep and cow manure. Overall, the gas emissions from facultative heap composting significantly differed among the four manure types due to the significant differences in their physicochemical properties and microbial communities.

Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem

IMPORTANCE

Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.

Effects of compost as a soil amendment on bacterial community diversity in saline-alkali soil

Introduction

Soil salinization poses a worldwide challenge that hampers agricultural productivity.

Methods

Employing high-throughput sequencing technology, we conducted an investigation to examine the impact of compost on the diversity of bacterial communities in saline soils. Our study focused on exploring the diversity of bacterial communities in the inter-root soil of plants following composting and the subsequent addition of compost to saline soils.

Results

Compared to the initial composting stage, Alpha diversity results showed a greater diversity of bacteria during the rot stage. The germination index reaches 90% and the compost reaches maturity. The main bacterial genera in compost maturation stage are Flavobacterium, Saccharomonospora, Luteimonas and Streptomyces. Proteobacteria, Firmicutes, and Actinobacteria were the dominant phyla in the soil after the addition of compost. The application of compost has increased the abundance of Actinobacteria and Chloroflexi by 7.6 and 6.6%, respectively, but decreased the abundance of Firmicutes from 25.12 to 18.77%. Redundancy analysis revealed that soil factors pH, solid urease, organic matter, and total nitrogen were closely related to bacterial communities.

Discussion

The addition of compost effectively reduced soil pH and increased soil enzyme activity and organic matter content. An analysis of this study provides theoretical support for compost's use as a saline soil amendment.

Comparison of bacterial and fungal communities structure and dynamics during chicken manure and pig manure composting

Composting is a sustainable and eco-friendly technology that turns animal waste into organic fertilizers. It remains unclear whether differences exist in the structure of microbial communities during different livestock manure composting. This study analyzed the dynamic change of bacterial and fungal communities, metabolic function, and trophic mode during chicken manure (CM) and pig manure (PM) composting based on 16S rRNA and ITS sequencing. Environmental factors were investigated for their impact on microbial communities. During composting, bacterial diversity decreased and then increased, while fungal diversity slightly increased and then decreased. Saccharomonospora and Aspergillus were the dominant genera and key microorganisms in CM and PM, respectively, which played crucial roles in sustaining the stability of the ecological network structure in the microbial ecology and participating in metabolism. Saccharomonospora gradually increased, while Aspergillus increased at first and then decreased. PM had better microbial community stability and more keystone taxa than CM. In CM and PM, the primary function of bacterial communities was metabolism, while saprotroph was the primary trophic mode of fungal communities. Dissolved organic carbon (DOC) was the primary factor influencing the structure and function of microbial communities in CM and PM. In addition to DOC, pH and moisture were important factors affecting the fungal communities in CM and PM, respectively. These results show that the succession of bacteria and fungi in CM and PM proceeded in a similar pattern, but there are still some differences in the dominant genus and their responses to environmental factors.

Large-scale production of house fly, Musca domestica (Diptera: Muscidae), larvae fed 3 manure types

House flies, Musca domestica, L., (Diptera: Muscidae) are well-known pests at animal facilities; however, they can be used for manure biodegradation. Utilizing house flies to process animal manure offers a means to recycle nutrients and reduce contaminants (e.g., pathogens and heavy metals), while also producing multiple revenue streams (e.g., protein for feed, fat for biodiesel, frass as a soil amendment). This study determined house fly larval performance on a larger scale (kilogram of wastes; thousands of larvae; single feeding) as a follow-up to a previous experiment performed at a bench-top scale (g of wastes; hundreds of larvae; incremental feeding). Four thousand larvae were fed 1 kg of swine, dairy, or poultry manure, or a control (Gainesville diet: 50% wheat bran, 30% alfalfa meal, and 20% corn meal). Peak larval weight occurred 4 days after inoculation and no significant difference in development time to first pupariation occurred across diets. However, percent survivorship to pupariation varied, with the highest occurring in Gainesville (74%), swine (73%), and poultry (67%) manure, whereas 50% survived when fed dairy manure. The highest pupal weight was found for those fed Gainesville (27 mg), and similar weights were found for those fed swine (21 mg), dairy (24 mg), and poultry (25 mg) manure. Although using house flies to manage manure has received little consideration in Western countries, other regions have this practice in place. Results may provide insight on differences between small- and large-scale studies, which is valuable for industrialization of this species for waste management and creating a more circular economy.

Trends in the management of organic swine farm waste by composting: A systematic review

Pig farming contributes to the economic development of nations and supplies human food demand; however, it generates a large amount of organic waste which, if not managed properly, becomes a risk to the environment and human and animal health. Considering the relevance of composting and its usefulness for the use of waste, this study aimed to determine the global trends in the management of composting manure, mortality and other organic waste produced on pig farms over the last five years (2017-2022). Systematic search involved four databases: ISI Web of Science, Scopus, Ebsco and Scielo. Of the total findings, 56 articles were included in the review, further classified into 14 categories for their respective analysis: co-substrates/additives, microbial communities, antibiotic resistance, heavy metals, polycyclic aromatic hydrocarbons, microbiological/parasitological quality, phytopathogens, nitrogen transformation, bioinoculants, comparison/combination with other waste management techniques, factors affecting composting, swine mortality and plant growth promotion/phytotoxicity. The review exemplified the importance of swine mortality composting as an alternative for organic matter management in pig farms, considering that the process also includes manure, vegetable waste and wood chips, among others. Controlled factors throughout the process are a requirement to obtain a stable product with physicochemical and microbiological quality that complies with national and international regulations and that will be useful and safe for application on crops, ensuring environmental, animal, and human health.

Microbial Risks Caused by Livestock Excrement: Current Research Status and Prospects

Livestock excrement is a major pollutant yielded from husbandry and it has been constantly imported into various related environments. Livestock excrement comprises a variety of microorganisms including certain units with health risks and these microorganisms are transferred synchronically during the management and utilization processes of livestock excrement. The livestock excrement microbiome is extensively affecting the microbiome of humans and the relevant environments and it could be altered by related environmental factors as well. The zoonotic microorganisms, extremely zoonotic pathogens, and antibiotic-resistant microorganisms are posing threats to human health and environmental safety. In this review, we highlight the main feature of the microbiome of livestock excrement and elucidate the composition and structure of the repertoire of microbes, how these microbes transfer from different spots, and they then affect the microbiomes of related habitants as a whole. Overall, the environmental problems caused by the microbiome of livestock excrement and the potential risks it may cause are summarized from the microbial perspective and the strategies for prediction, prevention, and management are discussed so as to provide a reference for further studies regarding potential microbial risks of livestock excrement microbes.

Hyperthermophilic pretreatment composting can reduce ammonia emissions by controlling proteolytic bacterial community and the physicochemical properties

Proteolysis is the rate-limiting step in the mineralization of organic nitrogen into ammonium (NH4+) and thereby the ammonia (NH3) released during the composting. However, the dynamics of bacterial proteolytic communities related to NH3 emissions during the composting systems are mostly unknown. This study aimed to examine and compare the effects of hyperthermophilic pretreatment composting (HPC) and traditional composting (TC) methods on (i) the difference of NH3 loss and nitrogenous compounds; (ii) the dynamics of the proteolytic bacterial community involved in the proteolysis and (iii) the correlation between the proteolytic bacterial community, biophysiochemical characteristics and NH3 loss. Results revealed that the HPC decreased NH3 loss by 42% as compared to TC during 60-day composting period. This was accompanied with an inhibitory effect on protease activity in the HPC where the relative abundances of the proteolytic bacteria (Bacillus megaterium and Staphylococcus cohnii) were reduced significantly as compared to TC. Partial least-squares path modeling suggested that various physicochemical properties such as higher temperature as well as lower C/N ratio during composting played a dominant role in affecting the abundance of proteolytic bacteria, which may have been an important factor contributing to the lower NH3 loss in HPC. All these findings lead us to conclude that the HPC can significantly reduce NH3 loss by inhibiting the proteolytic bacteria and protease activity responsible for NH3 release.

Impacts of adding FeSO4 and biochar on nitrogen loss, bacterial community and related functional genes during cattle manure composting

This study investigated the impacts of adding FeSO₄ and biochar to cattle manure and rice straw composts on functional genes controlling nitrogen loss, bacterial community, nitrification, and denitrification. Four treatments were established, including a control group (CP), and CP mixtures that included 4% biochar (TG1), 4% FeSO₄ (TG2), or 2% FeSO₄ and 2% biochar (TG3). Compared to CP, TG1-3 had a lower total nitrogen loss rate, and TG3 resulted in reduced NH₃ (52.4%) and N₂O (35.6%) emissions to mitigate nitrogen loss. The abundance of amoA and narG gene in TG3 was higher than in the other groups, and TG3 was beneficial to the growth of Proteobacteria and Actinobacteria. According to redundancy and Pearson analysis, TG3 had a positive effect on the nitrification process by increasing the abundance of amoA and narG. Thus, biochar and FeSO₄ addition mitigate nitrogen loss by regulating the nitrification processes.

Abiotic and Biotic Drivers of Soil Fungal Communities in Response to Dairy Manure Amendment

Modern agriculture often relies on large inputs of synthetic fertilizers to maximize crop yield potential, yet their intensive use has led to nutrient losses and impaired soil health. Alternatively, manure amendments provide plant available nutrients, build organic carbon, and enhance soil health. However, we lack a clear understanding of how consistently manure impacts fungal communities, the mechanisms via which manure impacts soil fungi, and the fate of manure-borne fungi in soils. We assembled soil microcosms using five soils to investigate how manure amendments impact fungal communities over a 60-day incubation. Further, we used autoclaving treatments of soils and manure to determine if observed changes in soil fungal communities were due to abiotic or biotic properties, and if indigenous soil communities constrained colonization of manure-borne fungi. We found that manure amended soil fungal communities diverged from nonamended communities over time, often in concert with a reduction in diversity. Fungal communities responded to live and autoclaved manure in a similar manner, suggesting that abiotic forces are primarily responsible for the observed dynamics. Finally, manure-borne fungi declined quickly in both live and autoclaved soil, indicating that the soil environment is unsuitable for their survival. IMPORTANCE Manure amendments in agricultural systems can impact soil microbial communities via supplying growth substrates for indigenous microbes or by introducing manure-borne taxa. This study explores the consistency of these impacts on soil fungal communities and the relative importance of abiotic and biotic drivers across distinct soils. Different fungal taxa responded to manure among distinct soils, and shifts in soil fungal communities were driven largely by abiotic factors, rather than introduced microbes. This work demonstrates that manure may have inconsistent impacts on indigenous soil fungi, and that abiotic properties of soils render them largely resistant to invasion by manure-borne fungi.

Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land

Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.

Physicochemical and bacterial changes during composting of vegetable and animal-derived agro-industrial wastes

This study investigates the impact of different agro-industrial organic wastes (i.e., sugarcane filter cake, poultry litter, and chicken manure) on the bacterial community and their relationship with physicochemical attributes during composting. Integrative analysis was performed by combining high-throughput sequencing and environmental data to decipher changes in the waste microbiome. The results revealed that animal-derived compost stabilized more carbon and mineralized a more organic nitrogen than vegetable-derived compost. Composting enhanced bacterial diversity and turned the bacterial community structure similar among all wastes, reducing Firmicutes abundance in animal-derived wastes. Potential biomarkers indicating compost maturation were Proteobacteria and Bacteroidota phyla, Chryseolinea genus and Rhizobiales order. The waste source influenced the final physicochemical attributes, whereas composting enhanced the complexity of the microbial community in the order of poultry litter > filter cake > chicken manure. Therefore, composted wastes, mainly the animal-derived ones, seem to present more sustainable attributes for agricultural use, despite their losses of C, N, and S.

Distinctive community assembly enhances the adaptation to extreme environments during hyperthermophilic composting

Hyperthermophilic composting (hTC) is a promising technique for solid waste treatment due to its distinctive microbiomes. However, the assembly process of the hTC microbial community remains unclear. We investigated the assembly process of hTC and explored the underlying drivers influencing community assembly in this work by employing conventional thermophilic composting (cTC) as a comparison group. Our results showed that the two composting treatments have different community assembly processes. Especially for the initial and thermophilic phases, hTC is affected by homogeneous dispersal (48%) and homogeneous selection (44%), respectively, while cTC is controlled by undominant (38%) and homogeneous selection (92%), respectively. Furthermore, random forest models and network results suggested that different factors govern the community assembly in these two composting methods. Specifically, the hTC community increases the stability of the thermophilic community via enhancing the interactions of low-abundance taxa with other operational taxonomic units (OTUs) in community assembly. Our results suggested that the distinctive nature of hTC community assembly may be responsible for its adaptation to extreme environments.

Impacts of utilizing swine lagoon sludge as a composting ingredient

Lagoon sludge, a byproduct of swine operations in the Southeast United States, poses a management challenge due to its high mineral and metal content. Composting is a low-cost, scalable technology for manure management. However, limited information is available on composting swine lagoon sludge in terms of recipes, greenhouse gas emissions and end-product quality. Moreover, due to its high Zn and Cu content, high inclusion of sludge in composting recipes can potentially inhibit the process. To address these knowledge gaps, in-vessel aerated composting (0.4 m3each) was carried out to evaluate impacts of sludge inclusion, at 10% (Low Sludge, LS-Recipe) and 20% (High sludge, HS-Recipe) wet mass-basis, on composting process and end-product quality. Comparable maximum temperatures (74 ± 2.7 °C, 74.9 ± 2.9 °C), and organic matter loss were observed in both recipes. Similarly, sludge inclusion ratio had no significant impact on cumulative GHG emissions. The global warming potential (20-year GWP) for swine lagoon sludge composting using LS and HS recipes was observed to be 241.9 (±13.3) and 229.9 (±8.7) kg CO2-e/tDM respectively. Both recipes lost 24-28% of initial carbon (C) and 4-15% of nitrogen (N) respectively. Composting and curing did not change water-extractable (WE) phosphorus (P) concentrations while WE Zn and Cu concentrations decreased by 67-74% and 55-59% respectively in both recipes. End compost was stable (respiration rates <2 mgCO2-C/g OM/day) with germination index >93 for both recipes.

An evaluation of homeostatic plasticity for ecosystems using an analytical data science approach

The natural world is constantly changing, and planetary boundaries are issuing severe warnings about biodiversity and cycles of carbon, nitrogen, and phosphorus. In other views, social problems such as global warming and food shortages are spreading to various fields. These seemingly unrelated issues are closely related, but it can be said that understanding them in an integrated manner is still a step away. However, progress in analytical technologies has been recognized in various fields and, from a microscopic perspective, with the development of instruments including next-generation sequencers (NGS), nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC/MS), and liquid chromatography-mass spectrometry (LC/MS), various forms of molecular information such as genome data, microflora structure, metabolome, proteome, and lipidome can be obtained. The development of new technology has made it possible to obtain molecular information in a variety of forms. From a macroscopic perspective, the development of environmental analytical instruments and environmental measurement facilities such as satellites, drones, observation ships, and semiconductor censors has increased the data availability for various environmental factors. Based on these background, the role of computational science is to provide a mechanism for integrating and understanding these seemingly disparate data sets. This review describes machine learning and the need for structural equations and statistical causal inference of these data to solve these problems. In addition to introducing actual examples of how these technologies can be utilized, we will discuss how to use these technologies to implement environmentally friendly technologies in society.

Effects of different microbial agents on bedding treatment of ectopic fermentation of buffalo manure

Introduction

The rapid development of the farming industry has increased the amount of manure produced by livestock and poultry, causing increasingly prominent environmental pollution problems. In recent years, due to the increase in conventional bedding material costs, an increasing number of farmers choose to use harmless recycled manure as bedding. Manure bedding treatment of farms can not only solve the problem of manure pollution, but also resource utilization of manure and cost savings.

Methods

This study compared the effects of five microbial agents (Microbial agents A, B, C, E, F) on buffalo manure bedding treatment by testing the temperature, moisture content, pH, microbial bacteria distribution of buffalo manure ectopic fermentation, and screened the lowest cost and most effective agent. The changes of microbial bacteria distribution in different periods of bedding treatment were also detected.

Results

Agent A was eliminated because of poor fermentation effect and low fermentation temperature, which could not achieve the effect of harmless treatment. The other four agents of bacteria achieved a harmless effect, but the bedding treatment effect of agent F was significantly better than agent E, B, and C. In terms of the cost of agents: the cost of agent F required for fermenting 100m^³ buffalo manure was the lowest, 1000yuan, followed by E (1200yuan), C (1750yuan), and B (1980yuan). In the process of ectopic fermentation bedding treatment of buffalo manure, Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Chloroflexi were the major bacteria used. The process was divided into three periods; the heating period - high temperature period - cooling period, the high temperature period could reach more than 75°C, and a large number of pathogenic bacteria and harmful bacteria, and other miscellaneous bacteria in the pile were degraded, their species diversity was reduced, and the structure of bacterial flora had significant differences in different treatment periods. In conclusion, this study has provided a guide for the resource utilization of manure in cattle farms and the reduction of manure pollution to the environment.

Phytotoxicity of farm livestock manures in facultative heap composting using the seed germination index as indicator

Static facultative heap composting of animal manure is widely used in China, but there is almost no systematic research on the phytotoxicity of the produced compost. Here, we evaluated the phytotoxic variation in compost produced by facultative heap composting of four types of animal manure (chicken manure, pig manure, sheep manure, and cattle manure) using different plant seeds (cucumber, radish, Chinese cabbage, and oilseed rape) to determine germination index (GI). The key factors that affected GI values were identified, including the dynamics of the phytotoxicity and microbial community during heap composting. Sensitivity to toxicity differed depending on the type of plant seed used. Phytotoxicity during facultative heap composting, evaluated by the GI, was in the order: chicken manure (0-6.6 %) < pig manure (14.4-90.5 %) < sheep manure (46.0-93.0 %) < cattle manure (50.2-105.8 %). Network analysis showed that the volatile fatty acid (VFA) concentration was positively correlated with Firmicutes abundance, and NH₄⁺-N was correlated with Actinobacteria, Proteobacteria, and Bacteroidetes. More bacteria were stimulated to participate in conversions of dissolved organic carbon, dissolved nitrogen, VFA, and ammonia-nitrogen (NH₄⁺-N) in sheep manure heap composting than that in other manure. The GI was most affected by VFA in chicken manure and cattle manure heap composting, while NH₄⁺-N was the main factor affecting the GI in pig manure and sheep manure compost. The dissolved carbon and nitrogen content and composition, as well as the core and proprietary microbial communities, were the primary factors that affected the succession of phytotoxic substances in facultative heap composting, which in turn affected GI values. In this study, the key pathways of livestock manure composting that affected GI and phytotoxicity were found and evaluated, which provided new insights and theoretical support for the safe use of organic fertilizer.

Thermophilic semi-continuous composting of kitchen waste: Performance evaluation and microbial community characteristics

This study evaluated the feasibility, system stability, and microbial community succession of thermophilic semi-continuous composting of kitchen waste (KW). The results revealed that treatment performance was stable at a 10 % feeding ratio, with an organic matter (OM) degradation efficiency of 81.5 % and seed germination index (GI) of 50.0 %. Moreover, the OM degradation efficiency and GI were improved to 83.4 % and 70.0 %, respectively, by maintaining an optimal compost moisture content (50-60 %). However, feeding ratios of ≥ 20 % caused deterioration of the composter system owing to OM overloading. Microbial community analysis revealed that Firmicutes, Actinobacteria, Chloroflexi, Proteobacteria, and Gemmatimonadetes were dominant. Additionally, moisture regulation significantly increased the Proteobacteria abundance by 57.1 % and reduced the Actinobacteria abundance by 57.8 %. Moreover, network analysis indicated that the bacterial community stability and positive interactions between genera were enhanced by moisture regulation. This information provides a useful reference for practical KW composting treatment in the semi-continuous mode.

Functional keystone drive nitrogen conversion during different animal manures composting

In this study, nitrogen transformation of chicken manure (CM) and cattle dung (CD) during composting was analyzed and its related functional keystones were identified. The results showed that chicken manure showed more severe nitrogen conversion during composting. The main N conversion factors in cattle dung were nitrite nitrogen (NO₂^--N) and ammonium nitrogen (NH₄⁺-N), while the main N conversion factors in chicken manure were NH₄⁺-N and nitrate nitrogen (NO₃^--N). The nitrogen-transforming bacterial community in chicken manure was more diverse. Variations in functional keystone abundances in cattle dung tended to be confined to the cooling and maturation periods, whereas changes in chicken manure persisted throughout the composting process. Environmental factors affected the functional keystones of nitrogen transformation. This study may provide directions for regulating nitrogen conversion in animal manure composting.

Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes

Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.

Effects of salinomycin and ethanamizuril on the three microbial communities in vivo and in vitro

The fate of a drug is not only the process of drug metabolism in vivo and in vitro but also the homeostasis of drug-exposed microbial communities may be disturbed. Anticoccidial drugs are widely used to combat the detrimental effects of protozoan parasites in the poultry industry. Salinomycin and ethanamizuril belong to two different classes of anticoccidial drugs. The effect of salinomycin and ethanamizuril on the microbiota of cecal content, manure compost, and soil remains unknown. Our results showed that although both salinomycin and ethanamizuril treatments suppressed some opportunistic pathogens, they failed to repair the great changes in chicken cecal microbial compositions caused by coccidia infection. Subsequently, the metabolite5 profiling of cecal content by LC-MS/MS analyses confirmed the great impact of coccidia infection on chicken cecum and showed that histidine metabolism may be the main action pathway of salinomycin, and aminoacyl tRNA biosynthesis may be the major regulatory mechanism of ethanamizuril. The microbial community of manure compost showed a mild response to ethanamizuril treatment, but ethanamizuril in soil could promote Actinobacteria reproduction, which may inhibit other taxonomic bacteria. When the soil and manure were exposed to salinomycin, the Proteobacteria abundance of microbial communities showed a significant increase, which suggested that salinomycin may improve the ability of the microbiota to utilize carbon sources. This hypothesis was confirmed by a BIOLOG ECO microplate analysis. In the animal model of coccidia infection, the treatment of salinomycin and ethanamizuril may reconstruct a new equilibrium of the intestinal microbiota. In an in vitro environment, the effect of ethanamizuril on composting and soil microbiota seems to be slight. However, salinomycin has a great impact on the microbial communities of manure composting and soil. In particular, the promoting effect of salinomycin on Proteobacteria phylum should be further concerned. In general, salinomycin and ethanamizuril have diverse effects on various microbial communities.

Metagenomic and HT-qPCR analysis reveal the microbiome and resistome in pig slurry under storage, composting, and anaerobic digestion

Direct application of pig slurry to agricultural land, as a means of nutrient recycling, introduces pathogens, antibiotic resistant bacteria, or genes, to the environment. With global environmental sustainability policies mandating a reduction in synthetic fertilisation and a commitment to a circular economy it is imperative to find effective on-farm treatments of slurry that maximises its fertilisation value and minimises risk to health and the environment. We assessed and compared the effect of storage, composting, and anaerobic digestion (AD) on pig slurry microbiome, resistome and nutrient content. Shotgun metagenomic sequencing and HT-qPCR arrays were implemented to understand the dynamics across the treatments. Our results identified that each treatment methods have advantages and disadvantages in removal pollutants or increasing nutrients. The data suggests that storage and composting are optimal for the removal of human pathogens and anaerobic digestion for the reduction in antibiotic resistance (AMR) genes and mobile genetic elements. The nitrogen content is increased in storage and AD, while reduced in composting. Thus, depending on the requirement for increased or reduced nitrogen the optimum treatment varies. Combining the results indicates that composting provides the greatest gain by reducing risk to human health and the environment. Network analysis revealed reducing Proteobacteria and Bacteroidetes while increasing Firmicutes will reduce the AMR content. KEGG analysis identified no significant change in the pathways across all treatments. This novel study provides a data driven decision tree to determine the optimal treatment for best practice to minimise pathogen, AMR and excess or increasing nutrient transfer from slurry to environment.

Effect of distillery sewage sludge addition on performance and bacterial community dynamics during distilled grain waste composting

This study evaluated the dynamics of physicochemical characteristics and bacterial communities during the co-composting of distilled grain waste (DGW) and distillery sewage sludge (SS), with DGW mono-composting as a control. Results showed that co-composting with SS significantly improved DGW degradation efficiency (61.38% vs. 54.13%) and end-product quality (seed germination index: 129.82% vs. 113.61%; N + P₂O₅ + K₂O: 9.08% vs. 5.28%), compared to DGW mono-composting. Microbial community analysis revealed that co-composting accelerated the bacterial community succession rate and enhanced the abundance of the phyla Proteobacteria, Firmicutes, Chloroflexi, and Deinococcota by 45.86%, 4.38%, 37.49%, and 15.29%, respectively. Network analysis showed that DGW-SS co-composting altered the interactions among the bacterial genera and improved bacterial community stability. Spearman correlation analysis indicated that the correlation between bacterial genera and environmental factors was more significant in DGW-SS co-composting. Therefore, co-composting of DGW and SS is a suitable strategy for the treatment of solid byproducts from spirit distilleries.

Effects of Turning Frequency on Ammonia Emission during the Composting of Chicken Manure and Soybean Straw

Here, we investigated the impact of different turning frequency (TF) on dynamic changes of N fractions, NH3 emission and bacterial/archaeal community during chicken manure composting. Compared to higher TF (i.e., turning every 1 or 3 days in CMS1 or CMS3 treatments, respectively), lower TF (i.e., turning every 5 or 7 days in CMS5 or CMS7 treatments, respectively) decreased NH3 emission by 11.42-18.95%. Compared with CMS1, CMS3 and CMS7 treatments, the total nitrogen loss of CMS5 decreased by 38.03%, 17.06% and 24.76%, respectively. Ammonia oxidizing bacterial/archaeal (AOB/AOA) communities analysis revealed that the relative abundance of Nitrosospira and Nitrososphaera was higher in lower TF treatment during the thermophilic and cooling stages, which could contribute to the reduction of NH3 emission. Thus, different TF had a great influence on NH3 emission and microbial community during composting. It is practically feasible to increase the abundance of AOB/AOA through adjusting TF and reduce NH3 emission the loss of nitrogen during chicken manure composting.

Key factors affecting seed germination in phytotoxicity tests during sheep manure composting with carbon additives

The germination index (GI) was widely applied to evaluate the phytotoxicity of compost. This study investigated the key phytotoxicity factors affecting seed germination in compost by using aqueous extracts in seed germination tests. The relationship between water-soluble substances in compost and seed germination, and their association with the microbial community were identified. In this study, sheep manure (SM) composted along or with three carbon additives (mushroom substrate, MS; cornstalks, CS; garden substrate, GS) for 49 days and, during this time, changes in multiple physical-chemical parameters, carbon and nitrogen matters, germination indexes (GI) and the compost microbiome were monitored. The results showed that all additives decreased water-soluble total nitrogen (TN), ammonium nitrogen (NH₄⁺-N) and low molecular weight organic acids, and significantly improved the seed germination indexes (seed germination rate, radical length and GI). The GI was correlated with water-soluble carbon degradation products (TOC, butyric acid, humic acid) and certain bacteria (Planifilum, Oceanobacillus, Ruminococcaceae_UCG_005 and Saccharomonospora). A structural equation model revealed that the main factors affecting seed germination were TOC (SM compost), acetic acid (SM+MS compost), humic acid (SM+CS compost), and pH (SM+GS compost). Low TOC and low molecular weight organic acids contents and higher humic acid content promoted GI. The research results could provide theoretical basis and measures for directional regulation of compost maturity.

Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste

In our study, we used 16SrRNA and ITS to investigate the microbial community composition and the effect of compound bacterial agent on the microbial community composition in the aerobic composting process of food waste (FW). At the bacterial level, the main phyla of Group A (compost naturally) were Proteobacteria and Firmicutes, and the main species were Pseudomonas_sp._GR7, Bacillus licheniformis and Pediococcus acidilactici. The main phyla of Group B (compost with compound bacterial agent) were Proteobacteria, Firmicutes and Streptophyta, and the main species were Klebsiella pneumoniae, Cronobacter sakazakii, Macrococcus caseolyticus, Enterococcus faecalis, Citrobacter freundii and Bacillus velezensis. It is worth noting that M. caseolyticus may be able to improve the effect of odour which is an important sensory index during aerobic composting. At the fungal level, the main phylum of both Groups A and B was Ascomycota, and the main species of Group A were Paecilomyces variotii, Byssochlamys spectabilis and Aspergillus fumigatus. The main species of Group B were Ogataea polymorpha and Millerozyma farinosa. Finally, the degradation rate of Group B was 81% that was about 15% higher than that of Group A, indicating that the compound bacterial agent could effectively improve the degradation rate and the composting process, while the low abundance of the compound bacterial agent in the composting process might be due to the small initial addition or the inhibition of other bacteria or fungi in the composting process.