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Onion is a high value specialty crop in the United States. Here in the Columbian basin of Washington and Oregon, growers produce onions on about 25,000 acres. This is just one of seven major onion production regions around the US, each growing different varieties of onions at different times in the year, to meet market demand.
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Bacterial diseases cause around 60 million dollars in losses each year, mostly due to rots that may not be evident in growing plants, but often develop in mature onion bulbs after harvest. If an onion blub is rotten when it gets to the customer, whether that’s the retailer, restaurant or domestic consumer, it’s way too late for the farmer to treat and manage the disease. In this short video, you’ll hear more about how pathogenic bacteria cause diseases in onion and new research that’s aimed at finding more effective ways to manage these diseases.
So one of the problems is that there may not be any symptoms in the bulbs when they are harvested from the field and go into the packing shed or into storage. Growers may actually cut some open and look for rot and if there’s no rot, that doesn’t necessarily mean that the bulbs don’t have bacteria in them. And the development of those symptoms might happen in storage and the longer growers store bulbs, the higher the risk that those bulb rots will develop.
Stop the Rot is a four year research project on onion bacterial disease in the United States, with two main objectives. First, to develop effective, rapid molecular diagnostic tools based on the genetics of the bacteria that cause disease in onions. Second, to provide recommendations that can help growers reduce losses, by optimizing their production practices, managing environmental factors and minimizing inoculum sources.
Symptoms of bacterial disease of onions can be very difficult to diagnose and this is because a number of bacteria cause bacterial disease of onions, as well as fungal pathogens and abiotic problems such as stressful weather conditions or chemical damage or mechanical injury to plants. They can result in symptoms that look very similar to bacterial disease. So for example, in a very hot summer growers can experience a problem in onions called leaf tip dieback, so the stress from heat stress, the heat stress basically cause the leaf tip to dieback. An onion bacterial leaf blight can cause very similar dieback of the leaf tip. Another example where growers can be confused about whether a problem is bacterial or it might be something else is some of the fungal diseases that attack the roots of onions. They’re expressed above ground by dieback of the foliage and that can look very similar to some of the bacterial disease. But if you know it’s a fungal disease, you’re going to manage it very differently than if you think it’s a bacterial disease. So it’s really important for growers to understand accurately what’s causing the problem. So there are at least 19 species of bacteria that we know can cause diseases of onion and that’s a large spectrum of pathogens to have to try and manage. Some of these bacteria occur very naturally in the environments in which we grow onions. Some for example, persist naturally in soil. Here in the Columbia Basin, the most common bacteria we find causing rots on onions are two, one is burkholderia gladioli and the other one is pantoea agglomerans. And these are the two we most commonly find when I receive a sample of onions, plants or bulbs that are rotten. So, what do these bacterial diseases look like in general? Well, earlier on when you still have green leaves, if the bacteria land on injured tissue or they have the right conditions with heat or moisture or if they cool [inaudible] bacteria and you’re producing bulbs in Georgia, in the south, in the winter and the conditions are right, when they land on the tissue and colonize that tissue, they start to break down things so you get these lesions on the leaves that look very water soaked. And that can move all the way down into the neck and so the neck can start to get very soft and mushy and wet and it can progress down into the bulb. And in our lab what we’ve done is if we take these bacteria and we grow them in pure culture and we inject them into the bulb and then we incubate those bulbs at a temperature we know those bacteria like. So 86, 90 degrees, we can speed up the progression of the symptoms in those bulbs.
Two of the pathogens that we most commonly find here in the Columbia Basin, are burkholderia gladioli and pantoea agglomerans. pantoea agglomerans. Here in these cut open onions you can see the rotten, fleshy scale tissue, extending down into the onion bulb, which is typical of how these bacteria act. Both burkholderia and pantoea are quite aggressive pathogens. Here on this tray, onions in the top row show symptoms just a week after injection with burkholderia gladioli. In the bottom row of onions, by four weeks after injection, the symptoms have progressed rapidly and the rot has become severe. Similar symptoms of rot occurred when bulbs are injected with pantoea agglomerans and pantoea ananatis as you can see here. The challenge for growers as well as for pathologists, is that the symptoms of infections caused by these two different pathogens, burkholderia and pantoea, are very similar. Two other bacterial pathogens found in the Colombia Basin are enterobacter cloacae and pseudomonas viridiflava. These tend to be less aggressive. Here you can see that when these pathogens were injected into onion bulbs, they caused relatively mild symptoms, which progressed more slowly over time. Compared to the symptoms caused by the burkholderia and pantoea pathogens. Fungal pathogens can cause rot symptoms that are similar to those of bacterial disease. botrytis neck rot is caused by a fungus which enters the bulb through the neck, in much the same way that bacteria do. Water collects in the neck of the onion bulb. The fungal spores land in the neck, start growing there because of the moisture and then move down into the fleshy scales of the bulb. In fungal disease like botrytis neck rot, the rot tends to be drier. We sometimes see a fluffy type of mold or these dark resting structures called sclerotia, associated with the rot. These are easier to diagnose and identify, helping the pathologist to distinguish fungal from bacterial diseases. Mold on onion bulbs is a sign of a fungal infection, as you can see in these onions, that have been injected at the base with a fungal pathogen fusarium oxysporum forma specialis cb which causes fusarium basal rot. And near the top of these bulbs at were injected through the neck with the fungus aspergillus niger which causes black mold. One of the simple tests we do in the lab to see whether a particular bacterial strain is pathogenic on onion, is to inject inoculum of that bacterial strain, into healthy red onion scales. After four days, pathogenic bacteria causes clear patches at the inoculation site, where the red onion scale tissue dies. This is called, red scale increases assay. Sometimes, the hardest part of diagnosing the problem is communicating clearly.
We have the pathogen names, which are Latin names and kind of complicated to remember for growers, but we also have the names of the diseases and those names sometimes are pretty accurate in describing what’s there and sometimes they’re pretty arbitrary. And so we may use one common name as a pathologist and the grower may use a different common name. And when we are talking on the phone or even in person, but not interest field, we may not realize we’re not talking about the same thing. So one really classic example is a fungal disease on onions called botrytis neck rot. So often we’ll talk about neck rot without necessarily saying botrytis before that. And neck rot to a pathologist means it’s caused by the fungus botrytis and if I think a grower had botrytis neck rot I’m going to make fungicide recommendations, recommendations for that specific fungus. So if a grower has a neck rot problem because the necks are rotting and as a pathologist it’s my responsibility to make sure we’re talking the same language. So the grower should either have the pathologist come out to the field and look and collect samples or submit samples to a lab that has experience with diagnosing these onion diseases, so that we can actually get an accurate identification and give the correct management recommendations.
There’s a lot that can influence bacterial diseases of onion, one important factor is irrigation. This includes the type of irrigation system used, such as overhead versus drip irrigation, as well as the timing and amount of irrigation applied and when and how rapidly irrigation is terminated at the end of the season. We do know that irrigation practices can be optimized to reduce the severity of onion crop losses due to pathogenic bacteria, without necessarily compromising the yield. Because these bacteria are splashed dispersed and favored by moisture, it is important to provide for the water needs of the crop while not favoring bacterial pathogens. Fertility practices can affect bacterial diseases too. This includes the amount of fertilizer and when fertilizer is applied to the crop. Particularly important is when the grower stops applying fertilizer. Other factors to consider in managing bacterial diseases are when onion bulbs are undercut and topped before harvest. How long they are dried in the field and how the bulbs are cured and stored after harvest.
There are things that also are very difficult for growers to control, such as in the Colombia Basin, the high summer temperatures. So we typically see the bacteria that cause rots in onion bulb crops here are ones that like heat, these thermophilic bacteria. We’ve just had about three weeks in the Colombia Basin this season of temperatures over 100. We can’t control that, that’s the environment in which we’re growing. It’s an advantage in terms of helping onions dry down really well when they’re ready to finish in the field, but those high temperatures combined with overhead irrigation mean we have higher risk. Other aspects that are difficult to control for example, damage from storms that might come through or from insect pests like thrips that feed, they create these wounds on the leaves that allow bacteria to colonize the leaves more easily. And those are things that are difficult to manage or can be more difficult to manage. So soil, we have to grow onions in soil and soil can even be a source of inoculum. Some of these bacteria are also pathogens of other crops. So the crops that a grower choses to rotate with onions, might act as a reservoir of inoculum buildup of inoculum to then infect the onion crops. We also know that there’s inoculum from sources like weeds. Some weeds that grow in fields can be hosts, even though they may not show symptoms. We can have these weeds potentially serve as what we call as asymptomatic hosts. And so we want to figure out how important are some of these weeds, as contributors of inoculum to outbreaks of these bacterial diseases in the field. We also know that a few of these bacteria can be carried on seed. So when growers purchase seed, it’s important to purchase from repeatable companies. Many of these companies test the seeds to try and minimize the risk that the bacteria would come on the seed. We also know that growers that produce crops from transplants, are getting their transplants from another farm and potentially those transplants could bring in inoculum. So trying to assure that you’re getting a source of planting material, whether it’s seed or transplants, that doesn’t have these bacteria is a very important part of managing these diseases. The two very key drivers behind these bacterial diseases are moisture and the right temperature for that organism and many of the bacteria that cause bulb rots are heat loving. And so, if you’ve got moisture and you’ve got heat, you’ve got risk of bacterial diseases. So when onions are harvested from the field and go into storage, the key thing is to try and take away those variable conditions and when onions go into storage, growers want to make sure those onions are dried down really well so the neck tissue is completely dried down, there’s no moisture that allows the bacteria to keep progressing down into the bulb. If there’s a concern about how much moisture there is and how long it’s going to take to dry out, growers will use heat to add — speed up that curing process, that post-harvest curing process. The danger with heat is that most of this bacteria that rot onions like heat. So if we’re starting to add heat and we still have moisture, we haven’t quite gotten rid of it, you can actually increase the problem. So heat should only be used to the extent to speed up drying and heat shouldn’t be used too long or for too high a temperature because it will actually favor the bacteria. But you first need to dry out those necks and so a really critical part of storage of onions is to remove that moisture with wind, with air. And so all the storage units either have slots in the ground where the air is pumped through the pile of onions or you have a plantar that blasts air through the stacks of onions so that you can remove that moisture. To reduce losses from onion bacterial diseases, growers need tools to diagnose bacterial diseases rapidly and to manage them effectively in the field. The Stop the Rot project team includes scientists and extension staff, from all seven onion production regions in the US who are combining their knowledge and expertise to help growers around the country. The projects advisory panel of onion growers, consultants, seed company personnel and pathologists, helps guide the team, ensuring that this cutting edge research is grounded in the real world of onion production.
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