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

Thuy, Thi; Nolan, Stephen; Hayes, Nicky; O’Flaherty, Vincent; Burgess, Catherine M.; Brennan, Fiona; Walsh, Fiona

doi:10.1016/j.envpol.2022.119271

Cited by 21 publications

(20 citation statements)

References 69 publications

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“…Firmicutes has a high tolerance to high temperatures, and hence is more abundant during the thermophilic phase, while Bacteroidetes prefers lower temperatures and is more abundant during the cooling phase (Liu et al, 2020). Similar results were obtained by Do et al (Do et al, 2022), but in liquid pig slurry rather than solid manure; however, other researchers have also confirmed these observations for solid pig manure (Lei et al, 2021; Li et al, 2019; Liu et al, 2021). Although storage is the most commonly applied manure management technology, few studies have examined its effect on the bacterial community.…”

Section: Discussionsupporting

confidence: 88%

“…Our study detected an elevated ARG and MGE abundance after all applied manure treatment strategies; however, the smallest increase was observed for samples collected after 10 weeks of composting. Similar increases in resistance gene prevalence has been previously noted by Cao et al (Cao et al, 2020) and recently by Do et al (Do et al, 2022). Moreover, in the PCoA plot of ARGs, the cluster assigned to the initial untreated samples was clearly separate from those assigned to treated manure; however, the two clusters belonging to stored and composted samples overlap.…”

Section: Discussionsupporting

confidence: 88%

“…These results only partially agree with ours. Although we found an increase in MGE abundance, as reported previously (Do et al, 2022), this increase was smaller after composting than after storage.…”

Section: Discussionsupporting

confidence: 88%

“…Firmicutes , Actinobacteria , and Bacteroidetes have been found to be the most prevalent bacterial phyla in pig manure during storage under diverse conditions (Lim et al, 2018), which is in agreement with our present findings. Do et al (Do et al, 2022) also report that these phyla dominate in stored manure at different time points.…”

Section: Discussionmentioning

confidence: 95%

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Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Zalewska

Błażejewska

Czapko

et al. 2022

Preprint

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One of the most important public health challenges facing the world today is that posed by antibiotic resistance. Many pathogenic antibiotic-resistant bacteria and their antibiotic resistance genes, usually located on mobile genetic elements, are frequently present in the faeces of farm animals. To prevent the possibility of antimicrobial resistance transfer to the environment, these faeces should undergo treatment before being used as natural fertilizer. The two strategies for processing pig manure proposed in this study, viz. storage (most commonly used for livestock manure today) and composting, are cheap and do not require special tools or technologies. The present study examines the changes in the physicochemical properties of treated manure, in the microbiome, through metagenomic sequencing, and in the resistome, using the SmartChip Real-time PCR system compared to raw manure. This is the first such comprehensive analysis performed on the same batch of manure. Our results suggest that while none of the processes completely eliminates the environmental risk, composting results in a faster and more pronounced reduction of mobile genetic elements harbouring antibiotic resistance genes, including those responsible for multi-drug resistance. The physicochemical parameters of the treated manure are comparable after both processes; however, composting resulted in significantly higher organic matter. Overall, it appears that the composting process can be an efficient strategy for mitigating the spread of antibiotic resistance in the environment and reducing the risk of its transfer to agricultural crops and hence, the food chain. It also provides the organic matter necessary for humus formation, and increases the sorption properties of the soil and the micro and macro elements necessary for plant growth, which in turn translates into increased soil productivity.HighlightsThe changes in microbial population composition correlate with changes in specific antibiotic-resistance genes and mobile genetic elements in the studied populations.Positive correlations have been demonstrated between microbial phyla and genes coding the multi-drug resistance mechanismCo-occurrence networks showed positive correlations between antibiotic-resistance genes and mobile genetic elementsThe composting strategy was most efficient at reducing microbial loads, antibiotic resistance genes and mobile genetic elements.Composted manure can be part of a natural, safe soil fertilization strategy.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 95%

See 2 more Smart Citations

Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Zalewska

Błażejewska

Czapko

et al. 2022

Preprint

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“…Despite modern technologies and substantial removal of resistant bacteria from the water fraction, digested sludge or treated wastewater still contain heightened levels of ARB and ARGs ( Parsley et al, 2010 ; Gatica and Cytryn, 2013 ; Rizzo et al, 2013 ; Balcazar, 2014 ; Calero-Cáceres et al, 2014 ). Using this material as biofertilizer on agricultural fields, causes AMR spread in the soil and aqueous systems ( Finley et al, 2013 ; Yang et al, 2014 ; Ross and Topp, 2015 ; Qiao et al, 2018 ; Pérez-Valera et al, 2019 ; Krzemiński and Popowska, 2020 ; Do et al, 2022 ). Many researchers showed also that direct application of animal manure to agricultural land, introduces ARB and ARGs to the environment ( Kyselková et al, 2015 ; Wei et al, 2016 ; Muziasari et al, 2017 ; Berendsen et al, 2018 ; Guo et al, 2018 ; Pérez-Valera et al, 2019 ; Do et al, 2022 ).…”

Section: Factors Promoting Antimicrobial Resistance Disseminationmentioning

confidence: 99%

Factors promoting and limiting antimicrobial resistance in the environment – Existing knowledge gaps

Goryluk-Salmonowicz

Popowska²

2022

Front. Microbiol.

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The dissemination of multidrug-resistant bacteria strains and genes carrying antibiotic resistance is currently considered to be one of the most important global problem. The WHO calls for the need to contain the spread of Antimicrobial Resistance (AMR) from all possible sources. There have been many international actions grouping scientists studying this phenomenon, and quite a lot of scientific projects devoted to this problem have already been carried out. As well, so far several strategies have been developed that can inhibit the AMR spread. In this mini-review, we highlight overlooked aspects that seem to be crucial for creating a comprehensive picture of AMR, especially in the context of One Health approach.

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Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Zalewska,

Błażejewska,

Szadziul

et al. 2024

Environ Sci Pollut Res

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Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3–V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

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

Cited by 21 publications

References 69 publications

Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Pig manure treatment strategies for mitigating the spread of antibiotic resistance

Factors promoting and limiting antimicrobial resistance in the environment – Existing knowledge gaps

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

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