Does Dna From a Banana, Bacteria, Beef All Look the Same

Studying Manure in Cows, in Feedlots, in Fields

At Lincoln, Nebraska, microbiologist Lisa Durso examines the results of a test to quantify bacteria in cattle fecal specimens and runoff from manure-amended soils. The number of yellow and glowing wells helps determine the number of bacteria present.
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Agronomical Enquiry Service scientists at the Agroecosystems Direction Enquiry Unit in Lincoln, Nebraska, take been conducting some very thorough investigations on the microbes that dwell in cattle manure—what they are, where they thrive, where they struggle, and where they may end up.

"When we expect at potential pathogens that can crusade foodborne affliction, we demand to look at the whole bacterial ecosystem," says ARS microbiologist Lisa Durso. "For example, some people used to recall all cattle have the same bacteria in their gastrointestinal [GI] tracts. But we've found some large differences; so if we say, 'Oh, it's merely manure,' we could miss important factors in pathogen command."

That's why Durso headed upwards a report that provided the offset-always "gold standard" accounting of the fecal bacterial types associated with beef cattle.

The researcher used pyrosequencing, a relatively new method of rapidly analyzing bacterial DNA markers, to allocate the bacteria into different taxonomic groups. "People hadn't looked at doing this type of bacterial demography earlier, because some bacteria could be cultured, but other types didn't grow well," says Durso, who conducted this investigation while she was working at the ARS U.S. Meat Creature Inquiry Center in Clay Center, Nebraska. "Pyrosequencing permit u.s.a. requite every bacterium a name tag ID."

Using fecal samples from 6 beef cattle, Durso identified a core set of bovine GI bacterial groups common to both beef and dairy cattle. Only 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 percentage of the bacterial DNA sequenced from dairy cattle, Durso detected the genus in only 1.v percent of the DNA sequences in her report.

In Lincoln, Nebraska, technicians Jaime LaBrie (left) and Jennifer McGhee process samples for enumerating manure-associated bacteria. (D2751-1)

Durso observed bacteria in the beef cattle that had not been reported in dairy cows. She also identified a various assortment of bacteria from the six individual beefiness cows, fifty-fifty though all six animals consumed the same diet and were the same breed, gender, and age. Given her results, Durso believes much more high-resolution customs sequencing will exist needed to identify "core" members of the bovine bacterial community.

Durso also compared her results to a survey of bacterial types she collected from beef cattle feedlot surfaces. Of a total of 139 different bacterial genera from both groups, 25 were detected in both fecal samples and feedlot floor samples, 21 were establish only in the fecal samples, and 93 were institute only in samples from the feedlot surfaces. She attributes the distribution differences to choice pressures bacteria face in feedlot pens that aren't nowadays in the oxygen-costless, night, moist cattle GI tract.

The implications of these findings? "The focus on food safety is fecal contagion, and preharvest pathogen control has often been animal-centric—for instance, how to 'fix' the trouble of East. coli in a cow's GI tract," Durso says. "Only a bacterium has a different pathway once information technology's outside of the gut. Then nosotros demand to start thinking strategically almost how to control pathogens when they are at their weakest—outside the animal, rather than within it."

Durso also partnered with Lincoln agricultural engineer John Gilley and others to study how livestock diet affected pathogen transport in field runoff from manure-amended soils. "Manure applications tin can help a farmer meet soil food requirements, but information technology'due south more expensive to apply it every year considering of the costs of labor, equipment, and fuel," Gilley says. "A farmer can reduce costs by applying plenty manure to come across 2-year or 4-year soil nutrient requirements, simply we need to understand more near how these larger applications might be affecting the environment."

Beefiness cattle in a feedlot at Clay Eye, Nebraska.
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Gilley's squad amended conventional-till and no-till fields at 1-, two-, or 4-year awarding rates of manure from livestock that had consumed either corn or feed containing forty percent wet distillers grains. After a series of simulated pelting events, they analyzed runoff samples from the fields. They establish that neither diet nor cultivation management significantly affected transport of fecal indicator leaner, merely that diet did bear upon send of bacteriophages—viruses that invade leaner—in the runoff.

Gilley as well conducted an investigation into how wheat residues affected water quality in runoff from plots amended with 1-, 2-, or 4-year application rates of manure. Some of the plots were covered with postharvest wheat residue, and others were bare.

The scientists found that runoff loads of dissolved phosphorus, total phosphorus, nitrate nitrogen, and total nitrogen were much higher from plots with residue cover. In addition, they observed that runoff from fields amended with 4-year application rates of manure had significantly college levels of dissolved phosphorus and total phosphorus than fields amended with 1-year or 2-twelvemonth manure rates.

"Our study—which is one of the beginning studies on this question—indicates there is a significant divergence in how manure awarding rates bear upon runoff loads," Gilley says. "And fifty-fifty though crop residues can be effective in controlling soil erosion, the residues also tedious the movement of water across fields. Then at that place's more time for h2o to pick up nutrients from the soil."

Technician Sandy Fryda-Bradley (left) and microbiologist Lisa Durso collect fecal pats from a feedlot pen. Samples are taken back to the lab to exist cultured for bacteria, including E. coli.
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In a follow-up study, Gilley's squad institute that narrow grass hedges planted at the edge of manure-amended plots reduced hateful runoff loads of dissolved phosphorus from 0.69 to 0.08 kilogram per hectare and total phosphorus from 1.05 to 0.thirteen kilogram per hectare—similar to levels from plots that had not been amended with manure.

"This study shows that if you take hedges you lot 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."

Results from these studies have been published in Foodborne Pathogens and Affliction, Applied and Ecology Microbiology, and Transactions of the ASABE.—By Ann Perry, Agronomical Enquiry Service Information Staff.

This research is office of Food Safety (#108), Climate Change, Soils, and Emissions (#212), and Agronomical and Industrial Byproducts (#214), three ARS national programs described at world wide web.nps.ars.usda.gov.

Lisa Durso and John Gilley are in the USDA-ARS Agroecosystems Management Inquiry Unit, University of Nebraska, Lincoln, NE 68583; (402) 472-9622 [Durso], (402) 472-2975 [Gilley].

"Studying Manure in Cows, in Feedlots, in Fields" was published in the February 2013 effect of Agricultural Research mag.

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Source: https://agresearchmag.ars.usda.gov/2013/feb/cows/

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