Studying manure in feedlots and fields shedding light on microbes
Studies at USDA are shedding some light on the microbes that dwell in cattle manure—what they are, where they thrive, where they struggle, and where they can end up.
This research, which is being conducted by Agricultural Research Service (ARS) scientists at the agency’s Agroecosystems Management Research Unit in Lincoln, NE, supports the USDA priority of ensuring food safety. ARS is USDA’s chief intramural scientific research agency.
“When we look at potential pathogens that can cause foodborne illness, we need to look at the whole bacterial ecosystem,” says ARS microbiologist Lisa Durso. “For instance, some people used to think all cattle have the same bacteria in their gastrointestinal [GI] tracts. But we’ve found some big differences; so if we say, ‘Oh, it’s just manure,’ we could miss important factors in pathogen control.”
That’s why Durso headed up a study that provided the first-ever “gold standard” accounting of the fecal bacterial types associated with beef cattle.
The researchers used pyrosequencing, a relatively new method of rapidly analyzing bacterial DNA markers, to classify the bacteria into different taxonomic groups. “People hadn’t looked at doing this type of bacterial census before because some bacteria could be cultured, but other types didn’t grow well,” said Durso, who conducted this investigation while she was working at the ARS U.S. Meat Animal Research Center in Clay Center, NE. “Pyrosequencing let us give every bacterium a name tag ID.”
Using fecal samples from six beef cattle, Durso identified a core set of bovine GI bacterial groups common to both beef and dairy cattle. But she also determined that Prevotella was the most common bacterial genus in the cattle she studied—occurring in 24 percent of the total number of DNA sequences she analyzed.
Another published study had identified Prevotella in only 5.5 percent of the bacterial genes sequenced from 20 dairy cattle. And while another survey had identified Clostridium in 19 percent of the bacterial DNA sequenced from dairy cattle, Durso detected the genus in only 1.5 percent of the DNA sequences in her study.
Durso observed bacteria in the beef cattle that had not been reported in dairy cows. She also identified a diverse assortment of bacteria from the six individual beef cows, even though all six animals consumed the same diet and were the same breed, sex and age. Given her results, Durso believes much more highresolution community sequencing will be needed to identify “core” members of the bovine bacterial community.
The implications of these findings? “The focus on food safety is fecal contamination, and preharvest pathogen control has often been animal-centric—for instance, how to ‘fix’ the problem of E. coli in a cow’s GI tract,” Durso says. “But a bacterium has a different pathway once it’s outside of the gut. So we need to start thinking strategically about how to control pathogens when they are at their weakest—outside the animal, rather than inside it.”
In another study, Durso collaborated with ARS agricultural engineer John Gilley and others to study how livestock diet affected the transport of pathogens in field runoff from manureamended soils.
“Manure applications can help a farmer meet soil nutrient requirements, but it’s more expensive to apply it every year because of the costs of labor, equipment and fuel,” Gilley says.
“A farmer can reduce costs by applying enough manure to meet 2-year or 4-year soil nutrient requirements, but we need to understand more about how these larger applications might be affecting the environment.”
The scientists added two types of manure to experimental conventional-till and no-till fields at 1-, 2-, or 4-year application rates. The manure had been collected from livestock that had consumed either corn or feed with wet distillers grains.
After a series of simulated rain events, the team collected and analyzed samples of field runoff and determined that neither diet nor tillage management significantly affected the transport of fecal indicator bacteria. But they did note that diet affected the transport of bacteriophages—viruses that invade bacteria—in field runoff.
Gilley also conducted an investigation into how standing wheat residues affected water quality in runoff from fields amended with 1-, 2-, or 4-year application rates of manure. The scientists found that runoff loads of dissolved phosphorus, total phosphorus, nitrates, nitrogen, and total nitrogen were much higher from plots with residue cover. The team also observed that runoff from fields amended with 4-year application rates of manure had significantly higher levels of total phosphorus and dissolved phosphorus than fields amended with 1-year or 2-year manure rates.
“Our study—which is one of the first studies on this question—indicates there is a significant difference in how manure application rates affect runoff loads,” Gilley said. “And even though crop residues can be effective in controlling soil erosion, the residues also slow the movement of water across fields. So there’s more time for water to pick up nutrients from the soil.”
In a follow-up study, Gilley’s team found that narrow grass hedges planted at the edge of manure-amended plots reduced mean runoff loads of dissolved phosphorus from 0.69 to 0.08 kilogram per hectare and total phosphorus from 1.05 to 0.13 kilogram per hectare—similar to levels from plots that had not been amended with manure.
“This study shows that if you have hedges you can substantially reduce nutrient loads in runoff,” Gilley says. “Planting grass hedges is a practice that isn’t expensive and can have a substantial impact.” — Ann Perry, Agricultural Research Service Information Staff