Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Chhedi Lal Gupta; Ran Avidov; Karuppasamy Kattusamy; Ibrahim Saadi; Vempalli Sudharsan Varma; Shlomo E. Blum; Yong‑Guan Zhu; Xin‑Yuan Zhou; Jian‑Qiang Su; Yael Laor; Eddie Cytryn

Computational and Structural Biotechnology Journal (Jan 2021)

Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles

Chhedi Lal Gupta,
Ran Avidov,
Karuppasamy Kattusamy,
Ibrahim Saadi,
Vempalli Sudharsan Varma,
Shlomo E. Blum,
Yong‑Guan Zhu,
Xin‑Yuan Zhou,
Jian‑Qiang Su,
Yael Laor,
Eddie Cytryn

Affiliations

Chhedi Lal Gupta: Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
Ran Avidov: Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishai, 30095, Israel
Karuppasamy Kattusamy: Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
Ibrahim Saadi: Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishai, 30095, Israel
Vempalli Sudharsan Varma: Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishai, 30095, Israel
Shlomo E. Blum: Department of Bacteriology, Kimron Veterinary Institute, 50250 Beit Dagan, Israel
Yong‑Guan Zhu: Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
Xin‑Yuan Zhou: Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
Jian‑Qiang Su: Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
Yael Laor: Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya’ar Research Center, Ramat Yishai, 30095, Israel
Eddie Cytryn: Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel; Corresponding author at: Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, Rishon Lezion 7528809, Israel.

Journal volume & issue: Vol. 19
pp. 6201 – 6211

Abstract

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Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.

Published in Computational and Structural Biotechnology Journal

ISSN: 2001-0370 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Technology: Chemical technology: Biotechnology
Website: https://www.journals.elsevier.com/computational-and-structural-biotechnology-journal

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