Increasing the removal efficiency of antibiotic resistance through anaerobic digestion with free nitrous acid pretreatment

Swine manure is a significant reservoir for antibiotic resistance. Anaerobic digestion (AD) is a common biological process used to treat swine manure but still faces low efficiencies in biogas production and antibiotic resistance removal. It is here shown that AD with free nitrous acid pretreatment (FNA) was effective in reducing antibiotic resistance genes (ARGs) in swine manure. FNA pretreatment (nitrite =250 mg N/L, pH=5.0, temperature=20 ± 1 °C) simultaneously reduced antibiotics (Tetracyclines, Quinones and Sulfonamides), inactivated antibiotics resistance bacteria (ARB) by 0.5-3 logs, and decreased ARGs tet, sul and qnr by 1-2, 1-3 and 0.5 logs, respectively. In the following AD step, the total residual ARGs was reduced to ~3.49 × 10⁷ gene copies/g dry total solids (TS), ~1 log lower than that in the AD without pretreatment (3.55 ×10⁸ gene copies/g dry TS). Microbial community and network analyses revealed that the ARG removal was mainly driven by the direct FNA effect on reducing ARGs and antibiotics, not related to ARB. Besides, the FNA pretreatment doubled biochemical methane production potential from swine manure. Together these results demonstrate that AD with FNA pretreatment is a useful process greatly facilitating swine manure management.

Substrate complexity affects the prevalence and interconnections of antibiotic, metal and biocide resistance genes, integron-integrase genes, human pathogens and virulence factors in anaerobic digestion

Anaerobic digestion (AD) is widely used to treat livestock manure that harbors diverse pollutants (resistance genes (ARGs), metal/biocide resistance genes (MBRGs), integron-integrase genes, human pathogens and pathogen virulence factors (VFs)). However, the interplays of these pollutants and the effects of substrate complexity on pollutants in AD are elusive. This study investigated the dynamics of these pollutants and bacterial communities during AD of swine manure, by metatranscriptomic sequencing and amplicon sequencing of 16 S rRNA and 16 S rRNA gene. The pollutant profiles and bacterial communities differed across AD processes, nevertheless with consistent dominance of ARGs of multi-drugs, tetracycline, aminoglycoside and rifamycin, MBRGs of multi-biocides, multi-metals, copper and arsenic, the integron-integrase gene intI1, potential pathogens of Escherichia coli, Streptococcus gallolyticus and Clostridium perfringens, VFs involved in pathogen adherence, and bacterial phyla of Firmicutes, Bacteroidetes and Proteobacteria. Reduced substrate complexity (replacing a part of swine manure, a complex substrate, with a simple substrate, apple waste or fructose) decreased the prevalence and stochastic turnover of ARGs and MBRGs. Network analyses revealed decreased interplays among pollutants under reduced substrate complexity. Our findings provide a mechanical understanding of diverse pollutants dynamics during AD, and reveal the importance of substrate complexity in controlling prevalence and interplays of pollutants.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes

Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.

Improving production of lactic acid and volatile fatty acids from dairy cattle manure and corn straw silage: Effects of mixing ratios and temperature

Anaerobic co-fermentation (AcoF) of dairy cattle manure (DCM) and corn straw silage (CSS) for producing lactic acid (LA) and volatile fatty acids (VFAs) was investigated. Batch experiments were conducted at seven different DCM/CSS ratios and at mesophilic and thermophilic temperatures. Results indicated that the highest concentration of LA was 17.50 ± 0.70 g/L at DCM:CSS ratio of 1:3 and thermophilic temperature, while VFAs was 18.23 ± 2.45 g/L at mono-CSS fermentation and mesophilic temperature. High solubilization of thermophilic conditions contributed to LA accumulation in AcoF process. Presence of the CSS increased the relative abundance of Lactobacillus for LA production at thermophilic. Meanwhile, the abundance of Bifidobacterium was increased when CSS was added at mesophilic, which could conduce to VFAs production. This study provides a new route for enhancing the biotransformation of DCM and CSS into short-chain fatty acids, potentially bringing economic benefits to agricultural waste treatment.

Effect of scleral protein shell amendment on bacterial community succession during the pig manure composting

The impact of scleral protein shell (SPS) amendment on bacterial community succession during pig manure (PM) composting were evaluated in the present work. Five treatments representing different dry weight dosage of SPS [0 % (T1), 2.5 % (T2), 5 % (T3), 7.5 % (T4), 10 % (T5) and 12 % (T6)] were applied with initial mixture of raw materials (Wheat straw along with the PM) and composted for 42 days. Results indicated that the dominant of phyla were Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes. The relative abundance (RA) of genus un-identified, Ruminofilibacter, Thermovum, Longispora and Pseudomonas were greater among the all treatments but interestingly genus Ruminofilibacter was also higher in control treatment. The network analysis was confirmed that T6 treatment with higher dosage of SPS amendment could enhance the bacterial population and rate of organic matter mineralization. Compared with T1, the T5 has greater potential impact to enhance the bacterial population and significant correlation among the pH and temperature.

Magnesite driven the complementary effects of core fungi by optimizing the physicochemical parameters in pig manure composting

The effects of magnesite (MS) on fungi communities and the core fungi complementarity during pig manure (PM) composting were explored. Different dosage of MS [0% (T1), 2.5% (T2), 5% (T3), 7.5% (T4) and 10% (T5)] as amendments mixed with PM for 42 days composting. The results showed the dominant of phyla were Ascomycota (78.87%), Neocallimastigomycota (41.40%), Basidiomycota (30.81%) and Aphelidiomycota (29.44%). From day 7 to 42, the abundance of Ascomycota and Aphelidiomycota were increased from 7.75% to 42.41% to 57.27%-78.87% and 0-0.70% to 11.73%-29.44% among all treatments. Nevertheless, the phyla abundance of Neocallimastigomycota and Basidiomycota decreased from day 7 to 42. The co-occurrence network indicated that the high additive amendment could enhance the core fungi complementarity effects capacity. The 10% MS addition was a promisable candidate to optimum fungal communities, and causing a better compost quality. This study illustrated the potential and fungi communities changing of MS as additives in composting.

Effect of inoculation with newly isolated thermotolerant ammonia-oxidizing bacteria on nitrogen conversion and microbial community during cattle manure composting

Nitrogen loss during composting is closely related to NH₄⁺-N conversion, and ammonia-oxidizing bacteria (AOB) are important microorganisms that promote NH₄⁺-N conversion. Since the biological activity of conventional AOB agents used for compost inoculation declines rapidly during the thermophilic phase of composting, new compound inoculants should be developed that are active during that phase. In the current study, the effects of inoculating cattle manure compost with newly isolated AOB (5%, v/w) [thermotolerant AOB X-2 strain (T-AOB-2), mesophilic AOB X-4 strain (M-AOB-4), and AOB X-2 combined with AOB X-4 (MT-AOB-2-4)] on the conversion of nitrogen, compost maturity, and the resident microbial community were studied. During 35 days of composting, compared with the control, AOB inoculation reduced NH₃ emissions by 29.98-46.94%, accelerated the conversion of NH₄⁺-N to NO₂^--N, increased seed germination values by 13.00-25.90%, and increased the abundance of the microbial community at the thermophilic phase (16.38-68.81%). Network analysis revealed that Bacillaceae play a crucial role in the composting process, with the correlation coefficients: 0.83 (p < 0.05) with NH₃, 0.64 (p < 0.05) with NH₄⁺-N, and 0.81 (p < 0.05) with NO₂^--N. In addition, inoculation with MT-AOB-2-4 notably increased the total nitrogen content of compost, prolonged the sanitation stage, and promoted compost maturity. Hence, MT-AOB-2-4 may be used to increase the microbial community abundance and improve the efficiency of cattle manure composting.

The effects of ammonia acclimation on biogas recovery and the microbial population in continuous anaerobic digestion of swine manure

This study investigated the ammonia toxicity and the acclimation of anaerobic microbiome in continuous anaerobic digestion of swine manure using unacclimated inoculum. When the total ammonia nitrogen concentration (TAN) reached 2.5 g N/L, the methane yield decreased from 254.1 ± 9.6 to 154.6 ± 9.9 mL/g COD. The free ammonia nitrogen concentration of the inhibited condition was 190 mg N/L. The methane yield was eventually recovered as 269.6 ± 3.6 mL/g COD with a further operation. Anaerobic toxicity assay (ATA) showed that mixed liquor from the recovered phase possessed enhanced tolerance to ammonia, not only within the exposed level in continuous operation (<2.5 g NH₃/L) but also over the range (>2.5 g NH₃/L). Microbial analysis revealed that continuous operation under ammonia stress resulted in the change of both bacterial and archaeal populations. The ammonia adaptation was concurrent with the archaeal population shift from Methanosaeta to Methanosarcina and Methanobacterium. The dominancy of Clostridia in bacterial population was found in the recovered phase. It is highly recommended to use an inoculum acclimated to a target ammonia level which can be pre-checked by ATA and to secure a start-up period for ammonia adaptation in the field application of anaerobic digestion for swine manure.

Migration and toxicity of toltrazuril and its main metabolites in the environment

Veterinary drugs heavily used in livestock are passed into the environment through different ways, resulting in risks to terrestrial environments and humans. The migration of toltrazuril (TOL), an important anticoccidial drug used intensively in livestock, and its main metabolites between the chicken manure compost, soil and vegetables was investigated, and then the impacts of TOL on the soil bacterial community and ARGs, soil enzyme activities and phytotoxicity were detected. In the process of aerobic composting for 80 days, except for toltrazuril sulfoxide (the degradation half-life was 59.74 d), TOL and ponazuril (PON) were not significantly degraded. However, TOL and its metabolites were significantly degraded in fertilized soil, and the degradation half-life was 28.17-346.50 d. Among the three drugs, only PON could migrate from soil to vegetables, and the residual concentrations of PON in lettuce and radish were 2.64-70.02 μg kg-1 and 0-2.80 μg kg-1, respectively. Moreover, TOL and its main metabolisms had no significant effect on the bacterial community structure and the abundance of antibiotic resistance genes during composting, but affected the microbial activity in the soil. The presence of TOL and its main metabolites reduced soil urease activity, increased catalase activity, and decreased alkaline phosphatase activity at the beginning and then increased slightly. They had negative effects on plant growth. Compared with the control group, the inhibition rates of TOL and its metabolites on lettuce and radish seed germination were 8.33% and 26.74% respectively, and the inhibition rates of root elongation length were 25.88% and 34.45% respectively. These results showed that TOL and its main metabolites were ineffectively removed by aerobic composting, and could be migrated from composting to soil and vegetables, which had adverse effects on soil enzyme activity and plant growth. Therefore, its environmental ecological risk and human health risk needs to be further evaluated.

Biochar induced inhibitory effects on intracellular and extracellular antibiotic resistance genes in anaerobic digestion of swine manure

Distribution of intracellular (iARGs) and extracellular ARGs (eARGs) in manure anaerobic digestion (AD) process coupled with two types of biochar (BC and BP) were investigated. And the effects of biochar on the conjugation transfer of ARGs were explored by deciphering the interaction of biochar with bacterial stress responses, physiological metabolism and antibiotic resistances. Results showed that AD process could effectively remove all the detected eARGs with efficiency of 47.4-98.2%. The modified biochar (BP) with larger specific surface area (SSA) was propitious to decrease the absolute copy number of extracellular resistance genes. AD process could effectively remove iARGs by inhibiting the growth of host bacteria. The results of structural equation models (SEM) indicated that biochar put indirect influences on the fate of ARGs (λ = -0.23, P > 0.05). Analysis on oxidative stress levels, antioxidant capacity, DNA damage-induced response (SOS) response and energy generation process demonstrated that biochar induced the oxidative stress response of microorganisms and enhanced the antioxidant capacity of bacteria. The elevated antioxidant capacity negatively affected SOS response, amplified cell membrane damage and further weakened the energy generation process, resulted in the inhibition of horizontal transfer of ARGs.

What role does organic fertilizer actually play in the fate of antibiotic resistome and pathogenic bacteria in planting soil?

Organic fertilizer increase antibiotic resistance genes (ARGs) and bacterial pathogens have widely documented. However, how organic fertilizer is involved in changing soil ARGs and pathogenic bacteria after long-term (≥5 years) application remains unclear. Herein, the ARGs and pathogenic bacteria were compared in organic fertilized soils (AF) and non-fertilized soils (NF), and the contribution of input sources (organic fertilizer, irrigation water, air and background soil) on soil ARGs also was determined in this study. Results showed that the abundances of some ARGs, such as vanR and aac(6')-I in AF, were significantly higher than these of NF (p < 0.05). And a relatively higher abundance of potential pathogens, especially, Salmonella enterica and Stenotrophomonas maltophilia, in AF was observed. This indicated that organic fertilizer application can maintain a high level of some soil ARGs and pathogenic bacteria for at least 5 years. Traceability analysis unearthed that organic fertilizer application mainly increased its own contribution to soil ARGs from 1.16% to 9.05%, as well reduced the contribution of background soil, suggesting that the increase in soil ARGs may be partly attributable to organic fertilizer inputs. Notably, organic fertilizer application did not significantly alter the contribution ratio of input sources to microorganisms, but there was a clear change in the composition of soil microorganisms, which meant that the effect of the input source on the microorganism may emanate from other factors, rather than direct inputs. Subsequent structural equation demonstrated that organic fertilizer application significantly enhanced the effect of environmental factors on ARGs, and also indirectly increased the influence of communities on ARGs. Collectively, under the long-term fertilization, the role of organic fertilizers on soil ARGs not just stems from its own input, and also dominates the influence of environmental factors on ARGs. This study elucidates main causes for the difference in ARGs in AF vs. NF and enlightens actual role of organic fertilizer in them.

Effects of exogenous cellulose-degrading bacteria on humus formation and bacterial community stability during composting

This study aimed to reveal the potential mechanism of influence exogenous cellulose-degrading bacteria (ECDB) exerted on humus synthesis during the co-composting of corn straw and cattle manure. By measuring the changes in physicochemical factors and bacterial communities, it was revealed that inoculation with ECDB enhanced the driving force of cellulose degradation and humus synthesis. ECDB not only directly participated in cellulose degradation as degrading bacteria, but also changed the bacterial community succession, and increased the abundance of bacterial communities associated with cellulose degradation. The results showed that ECDB stimulated the potential functions and interactions of bacterial communities. Structural equation modeling confirmed that ECDB acted mainly as a bioactivator to promote humus formation in co-composting of corn straw and cattle manure. Taken together, these findings offered new strategies which can be effectively utilized to increase the efficiency and quality of corn straw composting.

Bioaugmentation with methanogenic culture to improve methane production from chicken manure in batch anaerobic digestion

This study sought to investigate the effect of bioaugmentation on batch anaerobic digestion of chicken manure. The digestion performance with and without bioaugmentation and bioaugmented efficiency under different dosages were compared. The results demonstrated that bioaugmentation increased the methane yield and shortened the methane production time in batch reactors. Compared to the un-bioaugmented control, the methane yield of bioaugmented digesters was increased by 1.2-, 1.7-, 2.2-, 3.4-, and 3.6-fold at addition ratios of 0.07, 0.14, 0.21, 0.27, and 0.34 g VS _{bioaugmentation seed (BS)}/g VS_CM, respectively. However, higher bioaugmentation doses (0.34 g VS_BS/g VS_CM) did not exhibit significantly improved bioaugmentation efficiency, thus, the recommended dose is 0.27 g VS_BS/g VS_CM for biomethane conversion of CM. Moreover, whole genome pyrosequencing revealed that Methanoculleus and Methanobrevibacter predominated the non-bioaugmentation digesters, whereas Methanothrix, Methanobacterium, and Methanomassiliicoccus were the dominant methanogens in bioaugmentation digesters. The increased methane may be explained by an increase in the Methanothrix population, which accelerated acetic acid degradation. With bioaugmentation the mainly methanogenic pathways have become more diverse. From gene function perspective, bioaugmentation enhanced metabolic activities in digestor which function better in metabolism.

Tourmaline enhanced methane yield via regulating microbial metabolic balance during anaerobic co-digestion of corn stover and cow manure

This work performed a pilot-scale study on the effects of the substrate ratio, the concentration of tourmaline (Tur), and its high-temperature thermally modified (HTM) material on the anaerobic co-digestion of corn stover (CS) and cow manure (CM). The experimental results showed that the CH₄ yield was higher at a corn stover -to- cow manure feeding ratio of 2:1. The cumulative CH₄ yield increased by 22.76% and 8.31% at a concentration of tourmaline of 2.0 g/L and a tourmaline treatment temperature of 400 °C respectively. Microbial diversity analysis revealed that adding low doses of tourmaline regulated the distribution of microorganisms and that Methanobacteria became the dominant methanogenic archaea in the fermentation broth. This work clarified the effect of the concentration of tourmaline on gas production by anaerobic co-digestion from the perspective of the microbial metabolic balance and suggested the possibility of its application on a larger scale.

Particle size effects in microbial characteristics in thermophilic anaerobic digestion of cattle manure containing copper oxide

Roles of bulk-, micron-, and nano-copper oxide (CuO) on methane production, microbial diversity, functions during thermophilic anaerobic digestion (AD) were investigated in this study. Results showed that bulk-, micron-, and nano-CuO promoted methane production by 27.8%, 47.6%. and 83.1% compared to the control group, respectively. Microbial community analysis demonstrated that different particle sizes could cause various shifts on bacteria community, while had little effect on archaeal diversity. Thereinto, bacteria belonging to phylum Firmicutes and Coprothermobacterota dominated in enhanced hydrolysis process in groups with nano-CuO and bulk-CuO, respectively, while micron-CuO had stronger promotion on the abundances of hydrolytic and fermentative bacteria belonging to families Peptostreptococcaceae, Caloramatoraceae, Erysipelotrichaceae, and Clostridiaceae, than other two CuO sizes. Metabolic pathways revealed that energy-related metabolism and material transformation in bacteria were only boosted by micron-CuO, and nano-CuO and bulk-CuO were important to methanogenic activity, stimulating energy consumption and methane metabolism, respectively.

Horizontal Gene Transfer of an IncP1 Plasmid to Soil Bacterial Community Introduced by Escherichia coli through Manure Amendment in Soil Microcosms

The quantification and identification of new plasmid-acquiring bacteria in representative mating conditions is critical to characterize the risk of horizontal gene transfer in the environment. This study aimed to quantify conjugation events resulting from manure application to soils and identify the transconjugants resulting from these events. Conjugation was quantified at multiple time points by plating and flow cytometry, and the transconjugants were recovered by fluorescence-activated cell sorting and identified by 16S rRNA sequencing. Overall, transconjugants were only observed within the first 4 days after manure application and at values close to the detection limits of this experimental system (1.00-2.49 log CFU/g of manured soil, ranging between 10^-5 and 10^-4 transconjugants-to-donor ratios). In the pool of recovered transconjugants, we found amplicon sequence variants (ASVs) of genera whose origin was traced to soils (Bacillus and Nocardioides) and manure (Comamonas and Rahnella). This work showed that gene transfer from fecal to soil bacteria occurred despite the less-than-optimal conditions faced by manure bacteria when transferred to soils, but these events were rare, mainly happened shortly after manure application, and the plasmid did not colonize the soil community. This study provides important information to determine the risks of AMR spread via manure application.

Managing Fenton-treated sediment with biochar and sheep manure compost: Effects on the evolutionary characteristics of bacterial community

Fenton oxidation is a widely used method for the fast and efficient treatment of contaminated sediment, but few studies have investigated the management of Fenton-treated sediment for resource utilization. In this study, the evolutionary characteristics of bacterial community composition in Fenton-treated riverine sediment were investigated using 16S rRNA gene sequencing after the incorporation of rice straw biochar and sheep manure compost. The Fenton treatment caused a decline in the relative abundance of Bacteroidetes from 39% to 8% on the 7th day, and using biochar and compost rapidly increased the relative abundance of Firmicutes from 13% to 61% and 57%, respectively. Applying 1.25 wt% biochar after the Fenton treatment contributed to high Shannon diversity indices of 4.80, 4.69, and 4.76 on the 7th, 28th, and 56th day, respectively. The reduced differences of Shannon indexes on the 56th day indicated that the bacterial diversity among different treatments tended to be similar over time. The genera Flavisolibacter and Bacillus were representatively detected on the 7th day in the untreated sediment and Fenton/biochar-treated sediment, respectively. The number of feature bacteria decreased significantly from 88 on the 7th day to 29 on the 56th day. The community functions for the carbon, nitrogen, and sulfur cycles were sensitive to the Fenton-treatment and the subsequent treatment with biochar and compost. This study may provide a useful reference for follow-up work on the remediation of contaminated sediment using advanced oxidation processes, and promote the development of resource utilization of amended sediment.

Effects of soil protists on the antibiotic resistome under long term fertilization

Soil protists are key in regulating soil microbial communities. However, our understanding on the role of soil protists in shaping antibiotic resistome is limited. Here, we considered the diversity and composition of bacteria, fungi and protists in arable soils collected from a long-term field experiment with multiple fertilization treatments. We explored the effects of soil protists on antibiotic resistome using high-throughput qPCR. Our results showed that long term fertilization had stronger effect on the composition of protists than those of bacteria and fungi. The detected number and relative abundance of antibiotic resistance genes (ARGs) were elevated in soils amended with organic fertilizer. Co-occurrence network analysis revealed that changes in protists may contribute to the changes in ARGs composition, and the application of different fertilizers altered the communities of protistan consumers, suggesting that effects of protistan communities on ARGs might be altered by the top-down impact on bacterial composition. This study demonstrates soil protists as promising agents in monitoring and regulating ecological risk of antibiotic resistome associated with organic fertilizers.

Enrichment and balancing of nutrients for improved methane production using three compositionally different agro-livestock wastes: Process performance and microbial community analysis

Balanced nutrition is important for maximizing anaerobic digestion (AD) performance. Herein, the strategy of balancing sugar-fiber-nitrogen nutrients was first established for improved methane production by co-digesting two agricultural and one livestock wastes with complementary compositional properties, such as banana pseudo-stem (BPS), sugarcane baggage (SCB), and chicken manure (CM) having high sugar, fiber and nitrogen contents, respectively. The maximum methane yield was 186.5 mL/g VS_added with a mixture of 45.7% BPS, 26.2% SCB and 28.1% CM (with 1: 11.3: 0.3 of sugar to fiber to nitrogen ratio), increasing by 16.1%, 53.3%, 122.6% than those of mono- BPS, SCB, and CM, respectively. The co-digestion process remained stable under an organic load of 4 g VS/(L·day), which was attributed to the predominant presence of Bacteroidetes, Proteobacteria, Thauera, uncultured_bacterium_p_Aegiribacteria, and hydrogenotrophic methanogens. This study provides a deeper understanding of the co-digestion with agricultural and livestock wastes from the perspective of nutrient balance.

Co-composting with cow dung and subsequent vermicomposting improve compost quality of spent mushroom

In order to determine a feasible degrading process for spent mushroom (SMS) with high lignin content, the present work used cow dung (CD), SMS, and a mixture of CD and SMS as substrates and evaluated the effects of vermicomposting on the microflora and the quality of composting products. Bacterial (R² = 0.548, P = 0.001) and fungal (R² = 0.314, P = 0.005) community both were different between composting and vermicomposting. Vermicomposting and substrates affected enzyme activities indirectly by affecting ammonium, pH, total carbon, richness, and bacterial community composition. These results suggested that appropriate regulation of environmental factors may increase microbial activity. An increase in ion-exchange capacity (up to 139.8%), pH (6.9%), and nitrate (71.1%) and a decrease in total carbon (31.2%) and carbon/nitrogen ratio (32.1%) in vermicomposting indicated that earthworms could further improve product quality. Co-composting with CD and integrated subsequent vermicomposting efficiently promoted the maturity of SMS.

Effects of composting on the fate of doxycycline, microbial community, and antibiotic resistance genes in swine manure and broiler manure

Aerobic composting is an economical and effective technology that is widely used to treat animal manure. To study the fate of doxycycline (DOX), the microbial community, and antibiotic resistance genes (ARGs) during composting, aerobic composting of broiler manure and swine manure was carried out under natural environmental conditions. Aerobic composting effectively removed DOX (with a removal rate > 97%) and most ARGs from animal manure. The microbial diversity and the numbers of ARGs were higher in composted swine manure compared with composted broiler manure. The microbial community structure changed during composting, and the dominant phyla of broiler manure and swine manure changed from Firmicutes to Bacteroidetes and Proteobacteria, respectively. DOX changed the structure and relative abundance of the microbial community during composting, and the relative abundance of multidrug resistance genes and mobile genetic elements (MGEs) increased, which might lead to the risk of transmission of resistance in the environment. The C / N ratio, DOX concentration, Firmicutes, intl1, and intl2 were the key factors driving the change in ARGs during composting. These results help to reveal the effects of DOX on microbial communities, ARGs, and MGEs during composting and clarify the possible ways to reduce the risk of resistance gene transmission in the environment.

Research on the electrochemistry synergied cellulase enzymes strengthens the anaerobic fermentation of cow dung

Lignocellulose degradation (LCD) was the key factor limiting the development of anaerobic fermentation (AF) by the cow dung (CD). In the research, the effects of cellulase pretreatment (CP) and microvoltage (MV) alone and combination on the gas production and LCD during the AF were investigated. The results showed that both CP and MV had an significant effect on the AF, though the synergistic reaction was more pronounced. The total biogas yield (TBY) could reach 11521 mL, and the highest methane production rate was 73% in the synergistic reactions, which was increased by 18.7% and 10.0% compared to CP and MV alone respectively. Meanwhile, the degradation rates of cellulose and lignin could be increased by 33.44% and 22.23%, respectively. The results of SEM, FT-IR and excitation emission matrix demonstrated that CP and MV played an important role in improving the fermentation efficiency. The microbial biomass change results indicated that the synergistic effect of CP and 0.8 V MV on the LCD was achieved by promoting the growth of lignocellulose-degrading bacteria. Moreover, the electricity could not only accelerate the movement of microorganisms and enzymes, but also promoted and enhanced the activity of enzymes, which provided an important reference for further development of the AF technology and the biogas industry.

Potential of biochar integrated manganese sulfate for promoting pig manure compost humification and its biological mechanism

This study aimed to clarify the effect of the integrated addition of different proportions of biochar (0 and 5%) and MnSO₄ (0, 0.25%, and 0.50%) to pig manure compost. The results indicated the integrated use of biochar (BC) and Mn²⁺ advanced the compost humification. In particular, the integrated use of 0.50% Mn²⁺ and 5% BC showed higher total organic carbon degradation (20.67%) and humic acid production (81.26 g kg^-1) than other treatments. Microbial community analysis showed the integrated use of BC and Mn²⁺ regulated the diversity and community structure of organic matter-mineralizing microbes by maintaining the relative abundance of bacteria Firmicutes (54.62%) and Proteobacteria (38.05%) at high levels during the thermophilic period and boosting those of the fungi of Ascomycota (58.91%) and Actinobacteria (15.60%) during the maturity period of composting. This study illustrated the potential and biological mechanisms of integrating BC and Mn²⁺ as additives in compost humification.

Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation

Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of mcr-4 in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.

Industrial aerobic composting and the addition of microbial agents largely reduce the risks of heavy metal and ARG transfer through livestock manure

Composting is an effective and necessary modality in the recycling of agricultural wastes such as livestock manure, furfural, and straw. However, the risks of heavy metals (HMs) and antibiotic resistance genes (ARGs) during industrial-scale composting process have not been adequately assessed, especially with the addition of bacterial agents. In this study, changes in HMs toxicity, ARGs propagation and microbial community structure during industrial-scale aerobic composting of livestock manure were firstly investigated with various substrates addition. Moreover, the effect of the addition of bacterial agents (Bacillus strains) was evaluated. The results showed that industrial aerobic composting process could immobilize various HMs with different extents and significantly reduce the levels of ARGs such as intl1 and oqxB genes. The addition of Bacillus strains could further reduce the levels of most detected ARGs and the bioavailability of Cu and Cr, and the relative abundance of ereA and tetA was undetectable in some materials. After composting, the main bacterial community structures were similar among different substrates irrespective of bacterial agents and indicated that the composting process was the main driver for their change. This study provides a scientific reference for the safe reuse of livestock manure.

Impact of surface-applied liquid manure on the drainage resistance profile of an agricultural tile-drained clay till field

Dissemination of antibiotic resistance genes (ARGs) in aquatic environments is a concern due to human and animal health. Application of liquid manure on agricultural land is an important source of ARGs, where pathogens, antibiotic-resistant bacteria, and selective agents are released. To improve our understanding of ARGs spreading through soils, our main objective was to evaluate the effectiveness of the soil as a barrier protecting water resources. Over the course of a year, profiles and abundances of ARGs and mobile genetic elements in soil and drainage from an agricultural tile-drained clay till field were investigated upon liquid pig manure application by applying high-throughput quantitative polymerase chain reaction targeting 143 genes. The findings were as follows: (a) 97 genes were detected, where only the transposon gene tnpA-03/ IS6 was shared between the genes detected in drainage and those in acidified liquid manure or fertilized soils, indicating that liquid manure application had a limited impact on the drainage resistance profile; (b) intI1 gene was present in ∼60% of drainage samples in concentrations up to 1,634 intI1 ml^-1 ; and (c) evapotranspiration from barley (Hordeum vulgare L., 'KWS Irina') and a low groundwater table appeared to reduce preferential transport to drainage during the first 3 mo of liquid manure application. Interestingly, the first preferential transport to drainage was observed immediately after the harvest of spring barley. Overall, during the monitoring year we found the soil to be an effective barrier against the spread of fecal ARGs even though the occurrence of the intI1 gene questions the barrier effect from previous years.

Dynamics and key drivers of antibiotic resistance genes during aerobic composting amended with plant-derived and animal manure-derived biochars

Plant-derived and animal manure-derived biochars have been used to improve the quality of compost but the differences in their effects on antibiotic resistance genes (ARGs) during composting are unclear. This study selected two types of biochar (RB and PB) produced from abundant agricultural waste to be added to the compost. Adding plant-derived RB performed better in ARGs, mobile genetic elements, and human pathogenic bacteria removal during aerobic composting, whereas adding manure-derived PB even increased ARGs abundance. Vertical gene transfer was possibly the key mechanism for persistent ARGs, and easily removed ARGs were regulated by horizontal and vertical gene transfer. Adding plant-derived RB reduced the abundances of persistent ARG hosts (e.g., Pseudomonas and Longispora) and ARG-related metabolic pathways and genes. The higher nitrogen content of manure-derived PB may have promoted the proliferation of ARG hosts. Overall, adding manure-derived biochar during composting may not be the optimal option for eliminating ARGs.

Profiles of antibiotic- and heavy metal-related resistance genes in animal manure revealed using a metagenomic analysis

Farmed animals produce excrement containing excessive amounts of toxic heavy metals as a result of consuming compound feed as well as receiving medical treatments, and the presence of these heavy metals may aggravate the risk of spreading drug-resistance genes through co-selection during manure treatment and application processes. However, research on the association between heavy metals and antimicrobial resistance is still lacking. In this study, metagenomic sequencing was used to explore the effects of the co-selection of environmentally toxic heavy metals on the resistome in manure. A relevance network analysis showed that metal-resistance genes (MRGs), especially for copper (Cu) and zinc (Zn), were positively correlated with multiple types of antibiotic-resistance genes (ARGs) and formed a complex network. Most bacteria that co-occurred with both MRGs and ARGs simultaneously are members of Proteobacteria and accounted for 54.7% of the total microbial species in the relevance network. The remaining bacteria belonged to Firmicutes, Bacteroidetes and Actinobacteria. Among the four phyla, Cu- and Zn-resistance genes had more complex correlations with ARGs than other MRG types, reflecting the occurrence of ARG co-selection under the selective pressure of high Cu and Zn levels. In addition, approximately 64.8%, 59.1% and 68.4% of MRGs that correlated with the presence of plasmids, viruses and prophages, respectively, are Cu- or Zn-resistant, and they co-occurred with various ARGs, indicating that mobile genetic elements participate in mediating ARG co-selection in response to Cu and Zn pressure. The results indicated that the use of heavy-metal additives in feed induces the increases of drug resistance genes in manure through co-selection, aggravating the risk of antimicrobial resistance diffusion from animal farm to manure land applications.

Composting temperature directly affects the removal of antibiotic resistance genes and mobile genetic elements in livestock manure

The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Clarifying the beneficial effects of plant growth-promoting rhizobacteria for reducing abundances of antibiotic resistance genes during swine manure composting

This study investigated the effects on antibiotic resistance genes (ARGs) and the related mechanisms of different plant growth-promoting rhizobacteria (PGPR) inoculation strategies during composting: no inoculation (CK), inoculation in initial phase (T1), inoculation in cooling phase (T2), and inoculation in both initial and cooling phases (T3). After composting, the total relative abundances (RAs) of ARGs decreased by 0.26 and 0.03 logs under T3 and T2, respectively, but increased by 0.05 and 0.22 logs under T1 and CK. The abundances of eight ARGs were lowest under T3, including some high risk ARGs with clinical importance. Bioavailable Cu significantly affected the readily removed ARGs, and PGPR inoculation decreased the bioavailability of Cu. T3 reduced the abundances of potential pathogen hosts, inhibited horizontal gene transfer by reducing the RAs of mobile gene elements (0.48 logs), and downregulated the expression of genes related to ARG propagation, thereby decreasing the ecological risk of ARGs.

Resource utilization of mink manure: Functional microbial inoculation to elevate the bioavailability of organic nitrogen during composting

Mink manure is one of the high nitrogenous wastes, which can easily cause nitrogen mineralization during composting, resulting in low resource reutilization. However, there are few studies on the resource utilization of mink manure. Therefore, this study investigated the effects of functional microbial (bacterial and actinomycetes agents) inoculation on nitrogen mineralization during mink manure composting. Results suggested that the inoculum, especially actinomycetes agents, could increase organic nitrogen and bioavailable organic nitrogen (BON) content. Principal component analysis and Random Forest model demonstrated that the inoculants increase the abundance of microorganisms that positively correlated with BON, decrease the microorganisms that negatively correlated with BON. Consequently, the inoculation of functional microbial agents could effectively reduce nitrogen mineralization and improve composting quality. Therefore, this study provided theoretical and technical support for optimizing mink manure composting, promoting the resource utilization of high nitrogen wastes.

Elucidating the beneficial effects of diatomite for reducing abundances of antibiotic resistance genes during swine manure composting

Diatomite (DE) has been used for nitrogen conservation during the composting of feces but its effects on antibiotic resistance genes (ARGs) and the associated mechanisms are still unclear. In this study, DE was added at three different proportions (0%, 4%, and 8%) to swine manure during composting. The results showed that adding DE helped to reduce the abundances of ARGs and the maximum decrease (88.99%) occurred with the highest dose. DE amendment promoted the transformation of reducible copper into a more stable form, i.e., the residual fraction, which reduced the selective pressure imposed by copper and further decreased the abundances of ARGs. Tn916/1545 and intI1 were critical genetic components related to ARGs, and thus the reductions in the abundances of ARGs may be attributed to the suppression of horizontal transfer due to the decreased abundances of mobile genetic elements (MGEs). The microbial community structure (bacterial abundance and diversity) played key role in the evolution of ARGs. DE could enhance the competition between hosts and non-hosts of ARGs by increasing the bacterial community diversity. Compared with CK, DE amendment optimized the bacterial community by reducing the abundances of the potential hosts of ARGs and pathogens such as Corynebacterium, thereby improving the safety of the compost product. In addition, KEGG function predictions revealed that adding DE inhibited the metabolic pathway and genes related to ARGs. Thus, composting with 8% DE can reduce the risk of ARG transmission and improve the practical value for agronomic applications.

Dry anaerobic digestion of ammoniated straw: Performance and microbial characteristics

This paper explores the influence of the mixing ratio of ammoniated straw to biogas residue on the stability and methane yield of dry anaerobic digestion and analyzes the structure of the microbial community with digestion time. Five reactors containing ammoniated straw and swine manure biogas residue at ratios of 5:1, 4:2, 3:3, 2:4 and 1:5 (total solids) were constructed, and neither total ammonia nitrogen nor free ammonia nitrogen was inhibited. Three reactors produced gas successfully. The reactor with a ratio of 3:3 (R3-3) yielded the best methane production, with a cumulative methane production of 115.13 mL/(g·VS_added). Analysis of the R3-3 microbial community showed that bacteria were dominant species. Archaea, mainly Methanosarcina, played an important role in anaerobic digestion and methane production. Methanobacterium, with high acid tolerance, was positively related to total volatile fatty acids (TVFA), playing a key role in preventing the acidification of the anaerobic digestion system.

Exploring the impact of biochar on antibiotics and antibiotics resistance genes in pig manure aerobic composting through untargeted metabolomics and metagenomics

This study investigated the effect of biochar on antibiotics and antibiotic resistance genes (ARGs) during aerobic composting of pig manure. First, the composition and content of antibiotics in the manure were determined qualitatively and quantitatively. Biochar promoted the degradation of these antibiotics (oxytetracycline, chlortetracycline, and tetracycline). The relative abundance (RA) of antibiotic-resistant bacteria carrying ARGs accounted for about 29.32% of the total bacteria. Firmicutes and Actinomycetes were dominant phylum-level bacteria at the early and late stages of composting, respectively. Biochar decreased the total RA of ARGs by 16.83%±4.10%. tetW and tetL, closely related to tetracycline resistance, were significantly diminished during aerobic composting, and biochar was able to promote this removal. Biochar enhanced RAs of Mycobacterium tuberculosis kasA mutant. RAs of ARGs related to antibiotic efflux pumps, such as baeS and arlS, remained at a high level. Conclusively, biochar promotes degradation of antibiotics and removal of ARGs.

Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting

Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.

Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species

The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.

Biochar-based solid acid accelerated carbon conversion by increasing the abundance of thermophilic bacteria in the cow manure composting process

This study investigated the effects of biochar-based solid acids (SAs) on carbon conversion, alpha diversity and bacterial community succession during cow manure composting with the goal of providing a new strategy for rapid carbon conversion during composting. The addition of SA prolonged the thermophilic phase and accelerated the degradation of lignocellulose; in particular, the degradation time of cellulose was shortened by 50% and the humus content was increased by 22.56% compared with the control group (CK). In addition, high-throughput sequencing results showed that SA improved the alpha diversity and the relative abundance of thermophilic bacteria, mainly Actinobacteria, increased by 12.955% compared with CK. A redundancy analysis (RDA) showed that Actinobacteria was positively correlated with the transformation of carbon.

Bacteria in (vermi)composted organic wastes mostly survive when applied to an arable soil cultivated with wheat (Triticum sp. L.)

Composting and vermicomposting are an environmentally friendly way to reduce pathogens in organic wastes and generate a valuable product that provides nutrients for crops. However, how the bacterial community structure changes during these different processes and if the bacteria applied with the (vermi)composted products survive in an arable cultivated soil is still largely unknown. In this study, we monitored how the bacterial community structure changed during conditioning, composting with and without Eisenia fetida, and when the end-product was applied to arable soil cultivated with wheat Triticum sp. L. The organic wastes used were biosolid, cow manure, and a mixture of both. Large changes occurred in the relative abundance of some of the most abundant bacterial genera during conditioning, but the changes were much smaller during composting or vermicomposting. The bacterial community structure was significantly different in the organic wastes during conditioning and (vermi)composting but adding E. fetida had no significant effect on it. Changes in the relative abundance of the bacterial groups in the (vermi)composted waste applied to the arable soil cultivated with wheat were small, suggesting that most survived even after 140 days. As such, applying (vermi)composted organic wastes not only adds nutrients to a crop but also contributes to the survival of plant growth-promoting bacteria found in the (vermi)compost. However, putative human pathogens found in the biosolid also survived in the arable soil, and their relative abundance remained high but mixing the biosolid with cow manure reduced that risk. It was found that applying (vermi)composted organic wastes to an arable soil not only provides plant nutrients and adds bacteria with plant growth-promoting capacities, but some putative pathogens also survived.

Microecological insight to fungal structure and key fungal communities regulating nitrogen transformation based on spatial heterogeneity during cow manure composting by multi-angle and multi-aspect analyses

Composting is the mainstream technology for the treatment of agricultural solid waste, but limited efforts were made to investigate fungal composition and its contributions to nitrogen transformation in different depths of compost. In this study, spatial distributions of fungi were analyzed using high throughput sequencing by multi-angle analyses, and the key fungal communities determining nitrogen transformation were quantified and identified by multi-aspect analyses during cow manure composting. Multi-angle analyses showed that fungal structure, biomarkers and trophic mode composition varied in different layers, revealing that spatial heterogeneity is the distinctive attribute of composting system. Ascomycota and Basidiomycota were dominant phyla during composting, the two phyla peaked in top and bottom layer respectively. At mesophilic stage, Tremellales, and unclassified Ascomycota (order) were biomarkers in top and middle layer respectively, and so were Remersonia, Pyrenochaetopsis, and Wallemia in bottom layer by LEfSe analysis. Based on multi-aspect analyses, Unclassified Dothideomycetes mainly affected NH₄⁺-N transformation both in top (1.2816***) and middle layers (1.1726*). Trichocladium asperum (0.9536***) and Zopfiella (-0.9484***) mainly affected TN transformation in top layer. Guehomyces pullulans (-0.9684**) and Preussia (-1.0508**) regulated NO₃^--N transformation in middle layer. Thermomyces lanuginosus (0.7127***) and Typhula sp. UW973129 (0.7298***) were the key species promoting TN and C/N transformation in bottom layer, respectively. Interestingly, different fungal communities showed a complex network interaction driving nitrogen transformation, and the abundance of microbial community could be conducive to characterizing nitrogen transformation in the vertical space of composting.

Mechanism that allows manno-oligosaccharide to promote cellulose degradation by the bacterial community and the composting of cow manure with straw

The new sugar source manno-oligosaccharide can regulate the structure of the microbial community. This study investigated the effects of adding manno-oligosaccharide at four different levels (0, 0.1%, 0.5%, and 1% w/w compost) to composting cow manure and straw on lignocellulose degradation and the bacterial community. Adding 0.5% manno-oligosaccharide had the greatest effects on accelerating the composting process, reducing its toxicity, and improving the stability of the product. After composting for 25 days, adding 0.5% manno-oligosaccharide decreased the hemicellulose, cellulose, and lignin contents to 2.25%, 11.25%, and 7.07%, respectively, compared with those under CK. Manno-oligosaccharide promoted the degradation of lignocellulose by increasing the abundances of Thermobifida, Streptomyces, and Luteimonas. In addition, manno-oligosaccharide inhibited pathogenic bacteria and increased the abundances of functional genes related to metabolism. Finally, adding 0.5% manno-oligosaccharide mainly affected the degradation of lignocellulose by enhancing the C/N ratio and the abundances of Streptomyces and the secretion system during composting according to redundancy analysis.

Prairie strips' effect on transport of antimicrobial resistance indicators in poultry litter

Poultry litter is a valuable nutrient resource for agricultural production but is also a potential source for introducing antibiotic resistance genes (ARGs) and litter-associated bacteria (LAB) to the environment. Prairie strips have been demonstrated as an effective conservation practice to improve environmental quality in agroecosystems. This research aims to assess prairie strips' potential for reducing the transport of LAB and ARGs in runoff after litter application. Plot-scale rainfall simulations were performed using a replicated block design, with soil and surface runoff samples taken during the rainfall event. Microbial taxa and ARGs were characterized in the litter, soil, and water samples. In plots with litter application, LAB and ARGs were mainly detected in runoff, with very low detection in soils. Detection of ARGs in runoff, irrespective of strip installations, is consistent with previous observations of litter as a source of antimicrobial resistance (AMR) risks. The effectiveness of prairie strips to remove LAB and ARGs varied. In two of the three prairie strip plots, fewer AMR indicators were detected relative to control plots, suggesting that the prairie strips can potentially reduce these risks. In one plot, which was also associated with increased flow rate, we observed increased AMR indicators despite the installation of a prairie strip. Our observations highlight the need to prioritize understanding of soil properties even within the same site. Although we show that prairie strips can potentially reduce AMR risks, further research is needed to better understand the influence of rainfall timing, soil, and litter characteristics.

Culturable antibiotic-resistant fecal coliform bacteria in soil and surface runoff after liquid dairy manure surface application and subsurface injection

Land application of manure, while beneficial to soil health and plant growth, can lead to an overabundance of nutrients and introduction of emerging contaminants into agricultural fields. Compared with surface application of manure, subsurface injection has been shown to reduce nutrients and antibiotics in surface runoff. However, less is known about the influence of subsurface injection on the transport and persistence of antibiotic-resistant microorganisms. We simulated rainfall to field plots at two sites (one in Virginia and one in Pennsylvania) 1 or 7 d after liquid dairy manure surface and subsurface application (56 Mg ha^-1 ) and monitored the abundance of culturable antibiotic-resistant fecal coliform bacteria (ARFCB) in surface runoff and soils for 45 d. We performed these tests at both sites in spring 2018 and repeated the test at the Virginia site in fall 2019. Manure subsurface injection, compared with surface application, resulted in less ARFCB in surface runoff, and this reduction was greater at Day 1 after application compared with Day 7. The reductions of ARFCB in surface runoff because of manure subsurface injection were 2.5-593 times at the Virginia site in spring 2018 and fall 2019 and 4-5 times at the Pennsylvania site in spring 2018. The ARFCB were only detectable in the 0-to-5-cm soil depth within 14 d of manure surface application but remained detectable in the injection slits of manure subsurface-injected plots even at Day 45. This study demonstrated that subsurface injection can significantly reduce surface runoff of ARFCB from manure-applied fields.

Deciphering the dominant components and functions of bacterial communities for lignocellulose degradation at the composting thermophilic phase

The decomposition and transformation of organic matters during composting process are performed by various microorganisms. However, the bacterial communities and their functions usually vary with composting materials. Here the dominant bacterial genera and their functions were identified at the thermophilic phase during composting of mulberry branches with silkworm excrement (MSE), pig manure (MPM) and cow manure (MCD). The activities of β-glucosidase and endoglucanase were highest for MCD (1.31 and 17.15 µg g^-1 min^-1) and lowest for MPM (0.92 and 14.22 µg g^-1 min^-1). Random Forest model and correlation analysis revealed that Stenotrophomonas, Bacillus, and Sinibacillus were the dominant bacterial genera involved in lignocellulose degradation regardless of composting materials. Carbohydrate metabolism, amino acid metabolism, and DNA replication and repair were primary functions of the bacterial communities for the three types of composting. The quantification of lignocellulose degradation genes further verified the dominant functions of the bacterial communities.

A global meta-analysis of animal manure application and soil microbial ecology based on random control treatments

The processes involved in soil domestication have altered the soil microbial ecology. We examined the question of whether animal manure application affects the soil microbial ecology of farmlands. The effects of global animal manure application on soil microorganisms were subjected to a meta-analysis based on randomized controlled treatments. A total of 2303 studies conducted in the last 30 years were incorporated into the analysis, and an additional 45 soil samples were collected and sequenced to obtain 16S rRNA and 18S rRNA data. The results revealed that manure application increased soil microbial biomass. Manure application alone increased bacterial diversity (M-Z: 7.546 and M-I: 8.68) and inhibited and reduced fungal diversity (M-Z: -1.15 and M-I: -1.03). Inorganic fertilizer replaced cattle and swine manure and provided nutrients to soil microorganisms. The soil samples of the experimental base were analyzed, and the relative abundances of bacteria and fungi were altered compared with no manure application. Manure increased bacterial diversity and reduced fungal diversity. Mrakia frigida and Betaproteobacteriales, which inhibit other microorganisms, increased significantly in the domesticated soil. Moreover, farm sewage treatments resulted in a bottleneck in the manure recovery rate that should be the focus of future research. Our results suggest that the potential risks of restructuring the microbial ecology of cultivated land must be considered.

Microbial community structures and antibiotic biodegradation characteristics during anaerobic digestion of chicken manure containing residual enrofloxacin

To explore the interaction between the residual antibiotic in animal manure and biological treatment, the effect of enrofloxacin (ENR) on the anaerobic digestion of chicken manure, and biodegradation rate of ENR was studied under the condition of actual residual ENR content of 0, 8, 16 and 32 mg/kg·TS. The results showed that the addition of ENR increased the total biogas production, especially 8 mg/kg·TS promoted the anaerobic reaction obviously, and the corresponding cumulative biogas production was increased by 15.33%. However, in the presence of 32 mg/kg·TS, the biogas production rate was reduced and the peak period of biogas production was delayed. The results of enzyme activities determination and 16S rRNA sequencing showed that ENR had different effects on archaea and bacteria. The residual ENR could promote hydrolysis reactions in the anaerobic system, but could inhibit acetoclastic methanogens, and the relative abundance of Methanosaeta declined by 7.22‒12.41%. The first-order kinetic model showed that the half-life period of ENR in the anaerobic digestion system was 9.16‒10.83 days, and the biodegradation rate exceeded 80% after the treatment. This study can bring important information for the management of animal manure in the future.

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.

Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production

An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.

Effects of combined tannic acid/fluoride on sulfur transformations and methanogenic pathways in swine manure

Livestock manure emits reduced sulfur compounds and methane, which affect nature and the climate. These gases are efficiently mitigated by addition of a tannic acid-sodium fluoride combination inhibitor (TA-NaF), and to some extent by acidification. In this paper, TA-NaF treatment was performed on swine manure to study the treatment influence on methanogenic pathways and sulfur transformation pathways in various laboratory experiments. Stable carbon isotope labeling revealed that both untreated and TA-NaF treated swine manures were dominated by hydrogenotrophic methanogenesis. However, in supplementary experiments in wastewater sludge, TA-NaF clearly inhibited acetoclastic methanogenesis, whereas acidification inhibited hydrogenotrophic methanogenesis. In swine manure, TA-NaF inhibited s-amino acid catabolism to a larger extent than sulfate reduction. Conversely, acidification reduced sulfate reduction activity more than s-amino acid degradation. TA-NaF treatment had no significant effect on methanogenic community structure, which was surprising considering clear effects on isotope ratios of methane and carbon dioxide. Halophile sulfate reducers adapted well to TA-NaF treatment, but the community change also depended on temperature. The combined experimental work resulted in a proposed inhibition scheme for sulfur transformations and methanogenic pathways as affected by TA-NaF and acidification in swine manure and in other inocula.

Accelerated atrazine degradation and altered metabolic pathways in goat manure assisted soil bioremediation

The intensive and long-term use of atrazine in agriculture has resulted in serious environmental pollution and consequently endangered ecosystem and human health. Soil microorganisms play an important role in atrazine degradation. However, their degradation efficiencies are relatively low due to their slow growth and low abundance, and manure amendment as a practice to improve soil nutrients and microbial activities can solve these problems. This study investigated the roles of goat manure in atrazine degradation performance, metabolites and bacterial community structure. Our results showed that atrazine degradation efficiencies in un-amended soils were 26.9-35.7% and increased to 60.9-84.3% in goat manure amended treatments. Hydroxyatrazine pathway was not significantly altered, whereas deethylatrazine and deisopropylatrazine pathways were remarkably enhanced in treatments amended with manure by encouraging the N-dealkylation of atrazine side chains. In addition, goat manure significantly increased soil pH and contents of organic matters and humus, explaining the change of atrazine metabolic pathway. Nocardioides, Sphingomonas and Massilia were positively correlated with atrazine degradation efficiency and three metabolites, suggesting their preference in atrazine contaminated soils and potential roles in atrazine degradation. Our findings suggested that goat manure acts as both bacterial inoculum and nutrients to improve soil microenvironment, and its amendment is a potential practice in accelerating atrazine degradation at contaminated sites, offering an efficient, cheap, and eco-friendly strategy for herbicide polluted soil remediation.