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1.
PLoS One ; 16(9): e0257759, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34555107

RESUMO

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.


Assuntos
Bactérias/classificação , Fluoretos/química , Esterco/microbiologia , Metano/análise , Enxofre/análise , Taninos/química , Poluentes Atmosféricos/análise , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Isótopos de Carbono/análise , DNA Bacteriano/genética , DNA Ribossômico/genética , Sequenciamento de Nucleotídeos em Larga Escala , Esterco/análise , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Suínos , Águas Residuárias/química
2.
PLoS One ; 16(9): e0256969, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34499697

RESUMO

The fertility and productive value of soil are closely related to the physical and chemical properties of the soil as well as its biological activity. This activity is related to the intensity of microbially catalysed processes of transformation of organic and mineral substances contained in the soil. These processes are closely correlated with the abundance and biodiversity of soil microorganisms, especially bacteria, and the activity of enzymes produced by them. In this article we have compared some physicochemical properties of soil derived from conventional and organic farms and microbial communities inhabiting these ecosystems. We aim to investigate whether the soil management regime affects the abundance and diversity of these environments in terms of bacteria. Some differences in microbial communities were observed, but the rhizosphere of plants from organic and conventional soils does not harbour separate microbiomes. Albeit, the method of fertilization influences the diversity of soil microorganisms. A greater diversity of bacteria was observed in soils from farms where organic fertilizers were applied. Soil pH and activity of some soil enzymes were also shown to differ between organic and conventional soil cropping systems.


Assuntos
Bactérias/metabolismo , Fertilização/genética , Rizosfera , Microbiologia do Solo , Bactérias/química , Bactérias/genética , Biodiversidade , Fertilizantes/normas , Variação Genética/genética , Esterco/microbiologia , Microbiota/genética , Oryza/crescimento & desenvolvimento , Oryza/microbiologia , Solo/química
3.
Molecules ; 26(15)2021 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-34361594

RESUMO

Carbon is the crucial source of energy during aerobic composting. There are few studies that explore carbon preservation by inoculation with microbial agents during goat manure composting. Hence, this study inoculated three proportions of microbial agents to investigate the preservation of carbon during goat manure composting. The microbial inoculums were composed of Bacillus subtilis, Bacillus licheniformis, Trichoderma viride, Aspergillus niger, and yeast, and the proportions were B1 treatment (1:1:1:1:2), B2 treatment (2:2:1:1:2), and B3 treatment (3:3:1:1:2). The results showed that the contents of total organic carbon were enriched by 12.21%, 4.87%, and 1.90% in B1 treatment, B2 treatment, and B3 treatment, respectively. The total organic carbon contents of B1 treatment, B2 treatment, and B3 treatment were 402.00 ± 2.65, 366.33 ± 1.53, and 378.33 ± 2.08 g/kg, respectively. B1 treatment significantly increased the content of total organic carbon compared with the other two treatments (p < 0.05). Moreover, the ratio of 1:1:1:1:2 significantly reduced the moisture content, pH value, EC value, hemicellulose, and lignin contents (p < 0.05), and significantly increased the GI value and the content of humic acid carbon (p < 0.05). Consequently, the preservation of carbon might be a result not only of the enrichment of the humic acid carbon and the decomposition of hemicellulose and lignin, but also the increased OTU amount and Lactobacillus abundance. This result provided a ratio of microbial agents to preserve the carbon during goat manure aerobic composting.


Assuntos
Inoculantes Agrícolas/metabolismo , Carbono/metabolismo , Compostagem/métodos , Esterco/microbiologia , Animais , Cabras , Substâncias Húmicas
4.
PLoS One ; 16(8): e0254836, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34432793

RESUMO

Antibiotic resistance genes (ARGs) are emerging contaminants causing serious global health concern. Interventions to address this concern include improving our understanding of methods for treating waste material of human and animal origin that are known to harbor ARGs. Anaerobic digestion is a commonly used process for treating dairy manure, and although effective in reducing ARGs, its mechanism of action is not clear. In this study, we used three ARGs to conducted a longitudinal bench scale anaerobic digestion experiment with various temperatures (28, 36, 44, and 52°C) in triplicate using fresh dairy manure for 30 days to evaluate the reduction of gene abundance. Three ARGs and two mobile genetic elements (MGEs) were studied: sulfonamide resistance gene (sulII), tetracycline resistance genes (tetW), macrolide-lincosamide-streptogramin B (MLSB) superfamily resistance genes (ermF), class 1 integrase gene (intI1), and transposase gene (tnpA). Genes were quantified by real-time quantitative PCR. Results show that the thermophilic anaerobic digestion (52°C) significantly reduced (p < 0.05) the absolute abundance of sulII (95%), intI1 (95%), tnpA (77%) and 16S rRNA gene (76%) after 30 days of digestion. A modified Collins-Selleck model was used to fit the decay curve, and results suggest that the gene reduction during the startup phase of anaerobic digestion (first 5 days) was faster than the later stage, and reductions in the first five days were more than 50% for most genes.


Assuntos
Indústria de Laticínios , Resistência Microbiana a Medicamentos/genética , Sequências Repetitivas Dispersas/genética , Esterco/microbiologia , Anaerobiose , Reatores Biológicos/microbiologia , Genes Bacterianos , Análise dos Mínimos Quadrados , Dinâmica não Linear , RNA Ribossômico 16S/genética
5.
PLoS One ; 16(8): e0254730, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34343206

RESUMO

Foam accumulation in swine manure deep-pits has been linked to explosions and flash fires that pose devastating threats to humans and livestock. It is clear that methane accumulation within these pits is the fuel for the fire; it is not understood what microbial drivers cause the accumulation and stabilization of methane. Here, we conducted a 13-month field study to survey the physical, chemical, and biological changes of pit-manure across 46 farms in Iowa. Our results showed that an increased methane production rate was associated with less digestible feed ingredients, suggesting that diet influences the storage pit's microbiome. Targeted sequencing of the bacterial 16S rRNA and archaeal mcrA genes was used to identify microbial communities' role and influence. We found that microbial communities in foaming and non-foaming manure were significantly different, and that the bacterial communities of foaming manure were more stable than those of non-foaming manure. Foaming manure methanogen communities were enriched with uncharacterized methanogens whose presence strongly correlated with high methane production rates. We also observed strong correlations between feed ration, manure characteristics, and the relative abundance of specific taxa, suggesting that manure foaming is linked to microbial community assemblage driven by efficient free long-chain fatty acid degradation by hydrogenotrophic methanogenesis.


Assuntos
Esterco/microbiologia , Metano/biossíntese , Microbiota , Ração Animal , Bactérias/metabolismo , Carbono/análise , Dieta , Fermentação , Propriedades de Superfície
6.
Artigo em Inglês | MEDLINE | ID: mdl-34287119

RESUMO

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696T, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696T were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °Ð¡, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696T associated with Devosia chinhatensis (97.9 % sequence identity), Devosia riboflavina (97.3 %) and Devosia indica (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (n=17) compared within the type strains of species of of the genus Devosia. CC-YST696T contained C16:0, C18:0, C18:1ω7c 11-methyl and C18:1ω6c/ C18:1ω7c as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696T is proposed to represent a novel species of the genus Devosia, for which the name Devosia faecipullorum sp. nov. (type strain CC-YST696T=BCRC 81284T=JCM 34167T) is proposed.


Assuntos
Hyphomicrobiaceae/classificação , Esterco/microbiologia , Filogenia , Aves Domésticas/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Glicolipídeos/química , Hyphomicrobiaceae/isolamento & purificação , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Taiwan , Ubiquinona/análogos & derivados , Ubiquinona/química
7.
Ecotoxicol Environ Saf ; 220: 112413, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34139628

RESUMO

Aerobic composting is commonly used to dispose livestock manure and is an efficient way to reduce antibiotic resistance genes (ARGs). Here, the effects of different quality substrates on the fate of ARGs were assessed during manure composting. Results showed that the total relative abundances of ARGs and intI1 in additive treatments were lower than that in control, and high quality treatment with low C/N ratio and lignin significantly decreased the relative abundance of tetW, ermB, ermC, sul1 and sul2 at the end of composting. Additionally, higher quality treatment reduced the relative abundances of some pathogens such as Actinomadura and Pusillimonas, and some thermotolerant degrading-related bacteria comprising Pseudogracilibacillus and Sinibacillus on day 42, probably owing to the change of composting properties in piles. Structural equation models (SEMs) further verified that the physiochemical properties of composting were the dominant contributor to the variations in ARGs and they could also indirectly impact ARGs by influencing bacterial community and the abundance of intI1. Overall, these findings indicated that additives with high quality reduced the reservoir of antibiotic resistance genes of livestock manure compost.


Assuntos
Compostagem/métodos , Resistência Microbiana a Medicamentos/genética , Genes Bacterianos/efeitos dos fármacos , Esterco/análise , Esterco/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Carbono/análise , Carbono/farmacologia , Galinhas/microbiologia , Lignina/análise , Lignina/farmacologia , Microbiota/efeitos dos fármacos , Nitrogênio/análise , Nitrogênio/farmacologia
8.
Ecotoxicol Environ Saf ; 221: 112432, 2021 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-34166937

RESUMO

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.


Assuntos
Atrazina/metabolismo , Biodegradação Ambiental , Esterco/microbiologia , Microbiologia do Solo , Animais , Atrazina/análise , Bactérias/metabolismo , Ecossistema , Cabras , Herbicidas/análise , Herbicidas/metabolismo , Solo/química , Poluentes do Solo/análise , Poluentes do Solo/metabolismo
9.
Appl Environ Microbiol ; 87(16): e0075021, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34085860

RESUMO

Manure storage methods can affect the concentration and prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field-scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles; however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatment during the winter-spring cycle, but a significant reduction of the ARGs erm(B), tet(O), and tet(Q) over time was observed for both the composting pile and stockpile during the summer-fall cycle. Results from this study suggest that (i) bulking agent may be an important source of ARB and ARGs for composting; (ii) during cold months, the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; and (iii) during warm months, both stockpiling and composting can be effective in reducing ARG abundance. IMPORTANCE Proper treatment of manure is essential to reduce the spread of antibiotic resistance and protect human health. Stockpiling and composting are two manure storage methods which can reduce antibiotic-resistant bacteria and resistance genes, although few field-scale studies have examined the relative efficiency of each method. This study examined the ability of both methods in both winter-spring and summer-fall cycles, while also accounting for heterogeneity within field-scale manure piles. This study determined that bulking agents used in composting could contribute antibiotic-resistant bacteria and resistance genes. Additionally, seasonal variation could hinder the efficacy of composting in colder months due to heterogeneity in temperature within the pile; however, in warmer months, either method of manure storage could be effective in reducing the spread of antibiotic resistance.


Assuntos
Bactérias/efeitos dos fármacos , Proteínas de Bactérias/genética , Compostagem/métodos , Farmacorresistência Bacteriana , Esterco/microbiologia , Animais , Antibacterianos/farmacologia , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Bovinos , Solo/química
10.
Appl Environ Microbiol ; 87(16): e0087121, 2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34085862

RESUMO

Comprehensive microbial risk assessment requires high-throughput quantification of diverse microbial risks in the environment. Current metagenomic next-generation sequencing approaches can achieve high-throughput detection of genes indicative of microbial risks but lack quantitative capabilities. This study developed and tested a quantitative metagenomic next-generation sequencing (qmNGS) approach. Numerous xenobiotic synthetic internal DNA standards were used to determine the sequencing yield (Yseq) of the qmNGS approach, which can then be used to calculate absolute concentration of target genes in environmental samples based on metagenomic sequencing results. The qmNGS approach exhibited excellent linearity as indicated by a strong linear correlation (r2 = 0.98) between spiked and detected concentrations of internal standards. High-throughput capability of the qmNGS approach was demonstrated with artificial Escherichia coli mixtures and cattle manure samples, for which 95 ± 3 and 208 ± 4 types of antibiotic resistance genes (ARGs) were detected and quantified simultaneously. The qmNGS approach was further compared with quantitative real-time PCR (qPCR) and demonstrated comparable levels of accuracy and less variation for the quantification of six target genes (16S, tetO, sulI, tetM, ermB, and qnrS). IMPORTANCE Monitoring and comprehensive assessment of microbial risks in the environment require high-throughput gene quantification. The quantitative metagenomic NGS (qmNGS) approach developed in this study incorporated numerous xenobiotic and synthetic DNA internal standard fragments into metagenomic NGS workflow, which are used to determine a new parameter called sequencing yield that relates sequence base reads to absolute concentration of target genes in the environmental samples. The qmNGS approach demonstrated excellent method linearity and comparable performance as the qPCR approach with high-throughput capability. This new qmNGS approach can achieve high-throughput and accurate gene quantification in environmental samples and has the potential to become a useful tool in monitoring and comprehensively assessing microbial risks in the environment.


Assuntos
Antibacterianos/farmacologia , Escherichia coli/efeitos dos fármacos , Escherichia coli/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Animais , Bovinos , Escherichia coli/isolamento & purificação , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Esterco/microbiologia , Metagenômica
11.
PLoS One ; 16(6): e0252881, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34111183

RESUMO

Liquid manure (slurry) from livestock releases methane (CH4) that contributes significantly to global warming. Existing models for slurry CH4 production-used for mitigation and inventories-include effects of organic matter loading, temperature, and retention time but cannot predict important effects of management, or adequately capture essential temperature-driven dynamics. Here we present a new model that includes multiple methanogenic groups whose relative abundance shifts in response to changes in temperature or other environmental conditions. By default, the temperature responses of five groups correspond to those of four methanogenic species and one uncultured methanogen, although any number of groups could be defined. We argue that this simple mechanistic approach is able to describe both short- and long-term responses to temperature where other existing approaches fall short. The model is available in the open-source R package ABM (https://github.com/sashahafner/ABM) as a single flexible function that can include effects of slurry management (e.g., removal frequency and treatment methods) and changes in environmental conditions over time. Model simulations suggest that the reduction of CH4 emission by frequent emptying of slurry pits is due to washout of active methanogens. Application of the model to represent a full-scale slurry storage tank showed it can reproduce important trends, including a delayed response to temperature changes. However, the magnitude of predicted emission is uncertain, primarily as a result of sensitivity to the hydrolysis rate constant, due to a wide range in reported values. Results indicated that with additional work-particularly on the magnitude of hydrolysis rate-the model could be a tool for estimation of CH4 emissions for inventories.


Assuntos
Monitoramento Ambiental/métodos , Esterco/microbiologia , Metano/análise , Animais , Aquecimento Global , Gado , Modelos Biológicos , Eliminação de Resíduos Líquidos
12.
Appl Environ Microbiol ; 87(14): e0298020, 2021 06 25.
Artigo em Inglês | MEDLINE | ID: mdl-33931422

RESUMO

The present study investigated the impact of on-farm anaerobic digestion on the abundance of enteric bacteria, antibiotic resistance-associated gene targets, and the horizontal transfer potential of extended-spectrum ß-lactamase (ESBL) genes. Samples of raw and digested manure were obtained from six commercial dairy farms in Ontario, Canada. Digestion significantly abated populations of viable coliforms in all six farms. Conjugative transfer of plasmids carrying ß-lactamase genes from manure bacteria enriched overnight with buffered peptone containing 4 mg/liter cefotaxime into a ß-lactam-sensitive green fluorescent protein (GFP)-labeled Escherichia coli recipient strain was evaluated in patch matings. Digestion significantly decreased the frequency of the horizontal transfer of ESBL genes. Twenty-five transconjugants were sequenced, revealing six distinct plasmids, ranging in size from 40 to 180 kb. A variety of ESBL genes were identified: blaCTX-M-1, blaCTX-M-14, blaCTX-M-15, blaCTX-M-27, blaCTX-M-55, and blaPER-1. blaCTX-M-15 was the most prevalent ESBL gene detected on plasmids harbored by transconjugants. Various mobile genetic elements were found located proximal to resistance genes. Ten gene targets, including sul1, str(A), str(B), erm(B), erm(F), intI1, aadA, incW, blaPSE, and blaOXA-20, were quantified by quantitative PCR on a subset of 18 raw and 18 digested samples. Most targets were significantly more abundant in raw manure; however, erm(B) and erm(F) targets were more abundant in digested samples. Overall, on-farm digestion of dairy manure abated coliform bacteria, a number of antibiotic resistance-associated gene targets, and the potential for in vitro conjugation of plasmids conferring resistance to extended-spectrum ß-lactams and other classes of antibiotics into E. coli CV601. IMPORTANCE Using livestock manure for fertilization can entrain antibiotic-resistant bacteria into soil. Manure on some dairy farms is anaerobically digested before being land applied. Recommending the widespread implementation of the practice should be founded on understanding the impact of this treatment on various endpoints of human health concern. Although lab-scale anaerobic treatments have shown potential for reducing the abundance of antibiotic resistance genes, there are very few data from commercial farms. Anaerobic digestion of manure on six dairy farms efficiently abated coliform bacteria, E. coli, and a majority of antibiotic resistance-associated gene targets. In addition, the conjugation potential of plasmids carrying ESBL genes into introduced E. coli strain CV601 was reduced. Overall, anaerobic digestion abated coliform bacteria, the genes that they carry, and the potential for ESBL-carrying plasmid transfer.


Assuntos
Resistência Microbiana a Medicamentos/genética , Esterco , Anaerobiose , Animais , Bactérias/genética , Bovinos , DNA Bacteriano/genética , Fazendas , Feminino , Transferência Genética Horizontal , Genes Bacterianos , Genótipo , Esterco/microbiologia , Fenótipo , Plasmídeos
13.
mBio ; 12(3)2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33975936

RESUMO

In agricultural settings, microbes and antimicrobial resistance genes (ARGs) have the potential to be transferred across diverse environments and ecosystems. The consequences of these microbial transfers are unclear and understudied. On dairy farms, the storage of cow manure in manure pits and subsequent application to field soil as a fertilizer may facilitate the spread of the mammalian gut microbiome and its associated ARGs to the environment. To determine the extent of both taxonomic and resistance similarity during these transitions, we collected fresh manure, manure from pits, and field soil across 15 different dairy farms for three consecutive seasons. We used a combination of shotgun metagenomic sequencing and functional metagenomics to quantitatively interrogate taxonomic and ARG compositional variation on farms. We found that as the microbiome transitions from fresh dairy cow manure to manure pits, microbial taxonomic compositions and resistance profiles experience distinct restructuring, including decreases in alpha diversity and shifts in specific ARG abundances that potentially correspond to fresh manure going from a gut-structured community to an environment-structured community. Further, we did not find evidence of shared microbial community or a transfer of ARGs between manure and field soil microbiomes. Our results suggest that fresh manure experiences a compositional change in manure pits during storage and that the storage of manure in manure pits does not result in a depletion of ARGs. We did not find evidence of taxonomic or ARG restructuring of soil microbiota with the application of manure to field soils, as soil communities remained resilient to manure-induced perturbation.IMPORTANCE The addition of dairy cow manure-stored in manure pits-to field soil has the potential to introduce not only organic nutrients but also mammalian microbial communities and antimicrobial resistance genes (ARGs) to soil communities. Using shotgun sequencing paired with functional metagenomics, we showed that microbial community composition changed between fresh manure and manure pit samples with a decrease in gut-associated pathobionts, while ARG abundance and diversity remained high. However, field soil communities were distinct from those in manure in both microbial taxonomic and ARG composition. These results broaden our understanding of the transfer of microbial communities in agricultural settings and suggest that field soil microbial communities are resilient against the deposition of ARGs or microbial communities from manure.


Assuntos
Antibacterianos/farmacologia , Esterco/microbiologia , Metagenômica , Microbiota/efeitos dos fármacos , Microbiota/genética , Microbiologia do Solo , Agricultura , Animais , Bovinos , Indústria de Laticínios , Resistência Microbiana a Medicamentos/genética , Fazendas , Feminino , Genes Bacterianos , Metagenoma , Estações do Ano
14.
Microbes Environ ; 36(2)2021.
Artigo em Inglês | MEDLINE | ID: mdl-33907062

RESUMO

Malodorous emissions are a crucial and inevitable issue during the decomposition of biological waste and contain a high concentration of ammonia. Biofiltration technology is a feasible, low-cost, energy-saving method that reduces and eliminates malodors without environmental impact. In the present study, we evaluated the effectiveness of compost from cattle manure and food waste as deodorizing media based on their removal of ammonia and the expression of ammonia-oxidizing genes, and identified the bacterial and archaeal communities in these media. Ammonia was removed by cattle manure compost, but not by food waste compost. The next-generation sequencing of 16S ribosomal RNA obtained from cattle manure compost revealed the presence of ammonia-oxidizing bacteria (AOB), including Cytophagia, Alphaproteobacteria, and Gammaproteobacteria, and ammonia-oxidizing archaea (AOA), such as Thaumarchaeota. In cattle manure compost, the bacterial and archaeal ammonia monooxygenase A (amoA) genes were both up-regulated after exposure to ammonia (fold ratio of 14.2±11.8 after/before), and the bacterial and archaeal communities were more homologous after than before exposure to ammonia, which indicates the adaptation of these communities to ammonia. These results suggest the potential of cattle manure compost as an efficient biological deodorization medium due to the activation of ammonia-oxidizing microbes, such as AOB and AOA, and the up-regulation of their amoA genes.


Assuntos
Archaea/enzimologia , Proteínas Arqueais/metabolismo , Bactérias/enzimologia , Proteínas de Bactérias/metabolismo , Esterco/microbiologia , Oxirredutases/metabolismo , Amônia/metabolismo , Animais , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Proteínas Arqueais/genética , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Bovinos , Compostagem , Filtração , Esterco/análise , Oxirredução , Oxirredutases/genética , Filogenia
15.
PLoS One ; 16(4): e0249884, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33886593

RESUMO

Excessive use of chemical fertilizers in agricultural practices have demonstrated a significant impact on microbial diversity and community in soil by altering soil physical and chemical properties, thereby leading to a certain degree of soil salinization and nutritional imbalances. As an organic amendment, maize straw has been widely used to improve soil quality; however, its effect on the soil bacterial community remains limited in Calcarie-Fluvie Cambisols soil in semi-humid arid plateau of North China. In the present experiment, we investigated the effects of continuous straw utilization and fertilization on bacterial communities in Shouyang, Shanxi province, China. Soil samples were collected from 5 different straw utilization and fertilization modes in the following ways: straw mulching (SM), straw crushing (SC), cattle manure (CM), in which way straw is firstly used as silage and then organic fertilizer, control with no straw return (NSR), and control without fertilizers (CK), same amount of N+P fertilizer was applied to the regimes except CK. High-throughput sequencing approaches were applied to the V3-V4 regions of the 16S ribosomal RNA for analysis of the bacterial abundance and community structures. Different long-term straw returning regimes significantly altered the physicochemical properties and bacterial communities of soil, among which CM had the most significant effects on soil fertility and bacterial diversity. Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were consistently dominant in all soil samples, and Redundancy analysis (RDA) showed significant association of total nitrogen (TN), total phosphorus (TP) and available potassium (AK) with alternation of the bacterial community. Cattle manure had the most beneficial effects on soil fertility and bacterial diversity among different straw utilization and fertilization modes.


Assuntos
Bactérias/genética , Esterco/microbiologia , Microbiota , Microbiologia do Solo , Solo/química , Zea mays/química , Animais , Bactérias/isolamento & purificação , Bovinos , China , Cinnamomum zeylanicum/crescimento & desenvolvimento , Análise por Conglomerados , Fertilizantes/análise , Sequenciamento de Nucleotídeos em Larga Escala , Concentração de Íons de Hidrogênio , Nitrogênio/análise , Fósforo/análise , Potássio/análise , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , RNA Ribossômico 16S/metabolismo , Análise de Sequência de RNA , Zea mays/metabolismo
16.
Genes (Basel) ; 12(4)2021 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-33917127

RESUMO

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.


Assuntos
Quimiotaxia , Fertilizantes/análise , Metagenômica , Doenças das Plantas/genética , Microbiologia do Solo , Solo/química , Zea mays/genética , Esterco/microbiologia , Doenças das Plantas/microbiologia , Rizosfera , Zea mays/efeitos dos fármacos , Zea mays/crescimento & desenvolvimento , Zea mays/microbiologia
17.
Sci Rep ; 11(1): 6103, 2021 03 17.
Artigo em Inglês | MEDLINE | ID: mdl-33731751

RESUMO

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


Assuntos
Bactérias/crescimento & desenvolvimento , Compostagem , Esterco/microbiologia , Oryza/microbiologia , Phanerochaete/crescimento & desenvolvimento , Animais , Suínos
18.
Ecotoxicol Environ Saf ; 213: 111981, 2021 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-33592372

RESUMO

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.


Assuntos
Resistência Microbiana a Medicamentos/genética , Fermentação/fisiologia , Genes Bacterianos , Esterco/microbiologia , Metais Pesados/análise , Animais , Antibacterianos/análise , Bactérias/efeitos dos fármacos , Cobre , Integrons , Gado , Esterco/análise , Suínos , Tetraciclina/farmacologia
19.
Sci Rep ; 11(1): 102, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33420281

RESUMO

Northeastern Thailand relies on agriculture as a major economic activity, and has used high levels of agrochemicals due to low facility, and salty sandy soil. To support soil recovery and sustainable agriculture, local farmers have used organic fertilizers from farmed animal feces. However, knowledge about these animal fecal manures remains minimal restricting their optimal use. Specifically, while bacteria are important for soil and plant growth, an abundance and a diversity of bacterial composition in these animal fecal manures have not been reported to allow selection and adjustment for a more effective organic fertilizer. This study thereby utilized metagenomics combined with 16S rRNA gene quantitative PCR (qPCR) and sequencing to analyze quantitative microbiota profiles in association with nutrients (N, P, K), organic matters, and the other physiochemical properties, of the commonly used earthworm manure and other manures from livestock animals (including breed and feeding diet variations) in the region. Unlike the other manures, the earthworm manure demonstrated more favorable nutrient profiles and physiochemical properties for forming fertile soil. Despite low total microbial biomass, the microbiota were enriched with maximal OTUs and Chao richness, and no plant pathogenic bacteria were found based on the VFDB database. The microbial metabolic potentials supported functions to promote crop growth, such as C, N and P cyclings, xenobiotic degradation, and synthesis of bioactive compounds. Pearson's correlation analyses indicated that the quantitative microbiota of the earthworm manure were clustered in the same direction as N, and conductivity, salinity, and water content were essential to control the microbiota of animal manures.


Assuntos
Bactérias/isolamento & purificação , Fertilizantes/microbiologia , Esterco/microbiologia , Microbiota , Animais , Bactérias/classificação , Bactérias/genética , Fezes/microbiologia , Fertilizantes/parasitologia , Gado , Esterco/parasitologia , Oligoquetos/classificação , Oligoquetos/genética , Solo/química , Tailândia
20.
Ecotoxicol Environ Saf ; 208: 111724, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33396055

RESUMO

In recent years, in order to promote animal growth and reduce the risk of disease, a variety of antibiotics are frequently added to the animal feed of livestock and poultry. However, these antibiotics can not be fully digested by animals and most of them are excreted with feces, consequently causing the enrichment of antibiotic resistance genes (ARGs) and huge environmental risks. Nowadays, composting is a better option to solve these problems. Accordingly, this study explored the effects of co-composting swine manure with different inoculants dominated by Phanerochaete chrysosporium (p), Aspergillus niger (a), and Bacillus licheniformis (b) on the simultaneous removal of multiple antibiotics and resistance genes and evolution of the bacterial community. The results showed that the highest removal extent of tetracycline and oxytetracycline occurred in pile D (p:b:a=1:5:5, biomass) reaching 89.2% and 87.8%, respectively, while the highest removal extent of doxycycline and enrofloxacin occurred in pile A (p:b:a=1:0:0, biomass) reaching 98.6% and 89%, respectively. Compared with the levels in pile B (control check), in pile D, ARGs, except those for sulfonamides, decreased by 1.059 × 10-3-6.68 × 10-2 gene copies/16S rRNA copies. Inoculation with p alone effectively reduced intI1 and intI2. Canonical correspondence analysis (CCA) that microbial community structure evolution had a greater influence on ARGs than environmental factors. In summary, this study provided a feasible way to efficiently remove the antibiotics and antibiotic resistance genes in pig manure.


Assuntos
Antibacterianos/análise , Resistência Microbiana a Medicamentos/genética , Esterco/microbiologia , Ração Animal/análise , Animais , Antibacterianos/metabolismo , Bactérias/efeitos dos fármacos , Compostagem/métodos , Genes Bacterianos , Gado , Microbiota/efeitos dos fármacos , Oxitetraciclina/farmacologia , RNA Ribossômico 16S , Suínos , Tetraciclina/farmacologia
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