Cattle generate waste, including manure and liquid runoff, which must be managed as part of cattle production systems. Runoff may be collected in holding ponds designed to store waste and allow solids to separate and settle. Managing waste properly is essential for keeping cattle healthy and preventing the spread of harmful bacteria into the environment. An area requiring further investigation is how active, or metabolically alive, bacteria are in the feedlot environment. Most research has focused on the genetic potential of microbes (using DNA), but little work has been done on RNA, which indicates which bacteria are actively doing harm. This study looked at both DNA and RNA to give a clearer picture of how bacteria, especially Salmonella, behave in feedlot waste.
The objectives of this study were: 1. Determine if cattle feedlot holding ponds contain viable Salmonella 2. Characterize the diversity and composition of Salmonella populations in holding ponds and feces from nearby cattle pens 3. Identify correlations between Salmonella ecology and overall microbial populations 4. Compare the profile of metabolically active microbial community members in holding pond water and cattle feces with their overall genetic potential.
Water samples were collected from 13 feedlot holding ponds, along with fecal samples from the pens of cattle nearest to the holding ponds across five feedlots in the Texas Panhandle. The water was collected just below the surface using sterile bottles, while fecal samples were gathered by collecting feces from 20 fecal parts within each pen. Both sample types were immediately placed on ice to preserve them for further analysis. The samples were processed to detect Salmonella using both culture-based methods and PCR (a molecular technique that amplifies DNA for detection). The composition of Salmonella serotypes (a way to group closely related bacteria based on small differences in their surface structures) within each sample was determined with CRISPR-SeroSeq sequencing. Additionally, meta-nomic sequencing methods were then used to quantify Salmonella in the samples and provide detailed insight into the entire microbial community present, including identifying specific antimicrobial resistance genes (ARGs). Additionally, meta-nomic sequencing allowed for the comparison of the overall genetic potential (DNA) of the microbial communities with the metabolically active members (RNA), giving a clearer picture of which microbes were actively contributing to different microbial processes the feedlot environment. This approach helped assess the diversity and function of both passive and active microbial populations in the holding ponds and cattle feces.
The study found Salmonella to be prevalent in both feedlot holding ponds and nearby cattle feces, with 46% of ponds and 40% of fecal samples testing positive. No consistent correlation was observed between Salmonella-positive ponds and feces, and only subtle differences in microbial community structure between Salmonella-positive and Salmonella-negative samples were observed. The study also identified 12 different Salmonella serovars across the samples, with Montevideo (52%), Anatum (44%), and Mbandaka/Lubbock (20%) being the most common. Notably, several serovars were detected, including Anatum, Montevideo, Muenchen, and Newport, with 88% of the samples containing at least one of these serovars. Microbial community profiles differed between pond water and fecal samples, with fecal samples showing a higher abundance of antimicrobial resistance genes (ARGs), reflecting the presence of drug-resistant bacteria. Significant differences were also found between the genetic potential (DNA) and metabolically active members (RNA) of the microbial communities. In 21 fecal samples, only a subset of microbes were actively contributing to ongoing microbial activity. These findings underscore the need to examine both DNA and RNA to gain an understanding of microbial behavior, Salmonella persistence, and the spread of antimicrobial resistance in feedlot environments.
This study highlights the persistence of Salmonella in feedlot waste management systems, particularly in aquatic environments like holding ponds. These findings underscore the potential impact on both cattle health and food safety, as these Salmonella populations can pose significant risks to both animal and human health. Importantly, the study reveals that the metabolically active members in fecal and holding pond microbial populations may not be accurately captured by the sum of their genetic potential. Conversely, little difference was noted between the metabolically active and genetic potential profile of antimicrobial resistance genes (ARGs), suggesting that most ARGs present in the environment are being actively expressed. For industry partners, these results emphasize the need to continually improve aquatic waste management practices and surveillance, especially of holding ponds, where runoff can act as a reservoir for pathogens. By addressing these issues, the presence of pathogens can be monitored, but so can the active microbial populations that drive disease risks.