16S rRNA analysis of diversity of manure microbial community in dairy farm environment

Pramod Pandey, Colleen Chiu, Max Miao, Yi Wang, Matthew Settles, Noelia Silva Del Rio, Alejandro Castillo, Alex Souza, Richard Van Vleck Pereira, Richard Jeannotte

Research output: Contribution to journalArticle

Abstract

Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.

LanguageEnglish (US)
Article numbere0190126
JournalPLoS One
Volume13
Issue number1
DOIs
StatePublished - Jan 1 2018

Fingerprint

Manure
Dairies
Manures
dairy farming
Farms
animal manures
microbial communities
ribosomal RNA
Fertilizers
manure handling
fertilizers
liquids
Liquids
sampling
Bacteria
Animals
Population
Microbiota
bacteria
Central Valley of California

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Pandey, P., Chiu, C., Miao, M., Wang, Y., Settles, M., Del Rio, N. S., ... Jeannotte, R. (2018). 16S rRNA analysis of diversity of manure microbial community in dairy farm environment. PLoS One, 13(1), [e0190126]. https://doi.org/10.1371/journal.pone.0190126

16S rRNA analysis of diversity of manure microbial community in dairy farm environment. / Pandey, Pramod; Chiu, Colleen; Miao, Max; Wang, Yi; Settles, Matthew; Del Rio, Noelia Silva; Castillo, Alejandro; Souza, Alex; Pereira, Richard Van Vleck; Jeannotte, Richard.

In: PLoS One, Vol. 13, No. 1, e0190126, 01.01.2018.

Research output: Contribution to journalArticle

Pandey, P, Chiu, C, Miao, M, Wang, Y, Settles, M, Del Rio, NS, Castillo, A, Souza, A, Pereira, RVV & Jeannotte, R 2018, '16S rRNA analysis of diversity of manure microbial community in dairy farm environment' PLoS One, vol. 13, no. 1, e0190126. https://doi.org/10.1371/journal.pone.0190126
Pandey, Pramod ; Chiu, Colleen ; Miao, Max ; Wang, Yi ; Settles, Matthew ; Del Rio, Noelia Silva ; Castillo, Alejandro ; Souza, Alex ; Pereira, Richard Van Vleck ; Jeannotte, Richard. / 16S rRNA analysis of diversity of manure microbial community in dairy farm environment. In: PLoS One. 2018 ; Vol. 13, No. 1.
@article{7e9e72a70a284ac8a69468f2ce8fb20f,
title = "16S rRNA analysis of diversity of manure microbial community in dairy farm environment",
abstract = "Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.",
author = "Pramod Pandey and Colleen Chiu and Max Miao and Yi Wang and Matthew Settles and {Del Rio}, {Noelia Silva} and Alejandro Castillo and Alex Souza and Pereira, {Richard Van Vleck} and Richard Jeannotte",
year = "2018",
month = "1",
day = "1",
doi = "10.1371/journal.pone.0190126",
language = "English (US)",
volume = "13",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "1",

}

TY - JOUR

T1 - 16S rRNA analysis of diversity of manure microbial community in dairy farm environment

AU - Pandey, Pramod

AU - Chiu, Colleen

AU - Miao, Max

AU - Wang, Yi

AU - Settles, Matthew

AU - Del Rio, Noelia Silva

AU - Castillo, Alejandro

AU - Souza, Alex

AU - Pereira, Richard Van Vleck

AU - Jeannotte, Richard

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.

AB - Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers.

UR - http://www.scopus.com/inward/record.url?scp=85040127474&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040127474&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0190126

DO - 10.1371/journal.pone.0190126

M3 - Article

VL - 13

JO - PLoS One

T2 - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 1

M1 - e0190126

ER -