Further GRBaV Observations

A number of things we have noticed about red blotch did not really fit into the themes of prior posts but we feel bear mention.

The first, along the lines of Dr. Golino’s finding of a similar virus in a leaf from Sonoma County in 1940 is something we bumped into on the UC Master Gardener website.

Roger's Red

“Roger’s Red” apparently is a prized “cultivar” for horticulturalists. Photo credit houzz.com. A google search will show that this vinifera/californica hybrid first found by Roger Raiche along Palmer Creek Road west of Healdsburg in 1983 has been propagated far and wide as an ornamental.

We sent an email suggesting this be tested for GRBaV to Master Gardeners and were assured the suggestion has been sent to Rhonda Smith.

The second is just an observation we make no attempt to interpret of unusual cane reddening and subsequent abnormal growth in a miniscule subset of symptomatic vines. We have not found it  in any asymptomatic vines, and it seems randomly distributed.

IMG_0742 We first noticed it before overall leaf drop in some symptomatic vines vines that prematurely lost their basal leaves. Early basal leaf drop corresponds with the first year of symptom development to our eyes. In contrast, we find reduced abscission in fully developed gross symptomatic vines similar to that from girdling by breakage or the beetle.

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This photo does not show it very well but in December we found unusual growth from these reddened canes. We could go around the vineyard to a half dozen places where red leaves were still hanging on and find growth like this from reddened canes.

The last is a quick comment on the red blotch state of affairs. Dr. Daane has been unable to get leaf hoppers to transmit blotch even at feeding levels barely sub lethal to the plants even though the virus can be assayed in their guts. The vector  remains at large. In Sonoma county researchers have had difficulty finding GRBaV negative control vines for comparison studies. Most assays performed so far have been to verify symptoms. The cost to systematically assay a vineyard remains staggering. We really have no idea the extent of this disease except as it is revealed through symptoms.

Posted in GRBaV, Red Blotch Disease, Wine | Tagged , , | Leave a comment

Say Watt? Or Why I Just Love Math

Mathematics is one of the many human languages. It is written in very impressive hieroglyphics that can include multitudes of “terms”, many of which are given Greek letters. This language has been very much in fashion since the Enlightenment and in the popular imagination anything written it has an automatic aura of truth.

To decipher this language it is necessary to define the “terms”. Recently I had a go with watts.

A watt is defined as one joule per second. Very nice. We know what “1” is and our clocks tell us what a second is, but what is a joule?

A joule is the energy required to move one kilogram one meter using one newton of force.

Um, if the newton is doing the work, why do we need the joule? A supervisor, perhaps.

Will we ever know what a watt is? They just keep adding new terms.

Ok, a newton is the energy to move one kilogram one meter at the RATE of one meter per second squared.

Hooboy, we ALREADY moved that kilo a meter back when it was a joule. The crowbar we used was a newton. Now they say our crowbar was just the energy to produce a certain (and seemingly arbitrary) rate of movement across a meter. Is a definition circular if the energy to move a kilo a meter is defined by the energy to move a (presumably different) kilo a meter in the square root of a second? Why are we squaring the seconds, anyway?

We delved into this squared thing a while back. Sir Isaac just loved squares and his finding that gravity diminished (crudely) with the square if distance may be the hazy rationale for our definition of a newton. Yet our watt, if we can remember back that far, is already a rate. We are defining a rate with a rate.

So here is our evolved hieroglyphic for a watt:

1w=(1k/m/s2 moving 1k a distance of 1m)/s

w=((k/m/s2)km)/s or some such.

At least it is a precise definition, but somehow I still don’t feel I really know what a watt is, and if that is the precise definition, why didn’t they just say so to begin with?

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GRBaV, Heredity or Environment?

The burning question in the vineyard business these days is whether or not to rip out and replant Red Blotch infected vines. On the one hand, the first variant of the disease has spread at an average of maybe 4% per year at the UCD Oakville station. This might be a rate of spread that is manageable now that we are dialed into the symptoms.

On the other hand, a second variant of the disease has seemingly invaded the Oakville station from a different direction and general symptoms have spread to very nearly 100% of vineyards in Napa, Sonoma, and Mendocino counties within the last few years.

The best estimates of the latency period between infection and symptoms is 1-2 years. The average rate of vineyard replanting in Napa and Sonoma is on the order of 5%. In the seven years since GRBaV was first noticed, we might expect that 35% of the vineyards have been replanted.

All of these vineyards could potentially have been replanted infected. An equal number of additional vineyards infected by transmission from neighboring vineyards at the internal vineyard rate might bring the expected total to an aggregate 70% of vineyards possibly infected by planting and transmission since 2008. Yet if we accept the two year latency, no vines planted or vector infected this last year should be symptomatic yet. This would reduce the expected aggregate infection since 2008 to 60%.

Turning this analysis on it’s head, to reach the 100% infection of vineyards observed, it would be necessary to postulate that for four years prior to 2008 beginning in 2004 the same rates of infected planting and transmission to an aggregate infection of 40% of vineyards by 2008 went unnoticed.

Maybe.

Oakville station is a very small sample size and it is possible that internal rate of spread there is not representative. Yet this low rate is roughly consistent with the rate observed in a completely isolated vineyard an order of magnitude larger.

An alternate possibility is that the virus spreads more efficiently between vineyards than within. This possibility could explain edge/road effects. The vector would prefer the dust and turbulence of frequently travelled roads to the intermittent passage of machinery and workers within the rows. Then again, it could prefer ambient vegetation to vines and be a reluctant invader.

The edge/road effect is pretty ironclad, but what does it really mean?

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If it means that a vector is established in ambient vegetation or an adjacent vineyard or block and efficiently colonizes the edge of a new vineyard or another block, why would it spread less efficiently within the new vineyard or block? The Napa valley is essentially grape monoculture, one giant vineyard. The areas of ambient vegetation are limited to the perimeter of the valley, a few creeks and volcanic knobs, and landscaping.  If this is what is meant by edge we should see a pattern of infection emanating from theses areas. This is not what we see. We see a pattern of infection along roads throughout the monoculture.

The very existence of this road pattern within individual vineyards and within the monoculture as a whole suggests that there is more going on than a monotonic internal rate of spread.

The following is the pattern of grossly infected vines in autumn 2014 in an isolated vineyard. An isolated vineyard can be thought of as a microcosm for Napa or Sonoma valley monoculture.

2014 Blotch

 

The red vines are defined as grossly symptomatic with more than 50% red canopy. The blue vines are missing in action and undoubtedly victims of trunk diseases and landslides. There are a few yellow vines shown that are really red but convey misinformation because they were transplanted or budded over.

There are three rootstocks. The light grey is 44-53, the darker grey is 99R, and the black is 1103P. A quick take is that the 44-53 is wildly symptomatic. I have written this but I hereby repent. A more careful analysis reveals that the combination of 44-53 rootstock and the CS337 clone best explains the disparity in distribution.

The vineyard provides a way to separate the variables. Most of the 44-53 rootstock was  grafted with CS337, but not all.

By Rootstock

When the data is sorted by rootstock it becomes clear that when the 44-53 is paired with CS 4 there is a drastically reduced rate of gross symptoms.

By Clone

When the data is sorted by clone it is apparent that it is not just the clone either because when the 337 clone is paired with 1103P rootstock the gross symptom rate also drops off dramatically. The 44-53 and 337 seems an unhappy pairing.

Heredity plays a role.

Environment seemingly as well.

4453 337

The image above is cropped to highlight the extent of the 44-53/337 in the vineyard. There are two areas divided by a heavily forested area and a 300′ ravine. To our eyes they are different animals. In the tradition of phylogenetics and population biology we conclude that the upper area with 34% average gross symptoms is the original source of infection. This area also shows far less edge concentration. In contrast, the lower area shows striking edge concentration.

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The image above is of the upper portion in 2009, the image below of the lower portion swung around to a similar view attitude on the same date.

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While the reservoir side clearly shows red leaf symptoms in October 2009, the other side does not. It should be noted that the 28 qPCR assays we have  done so far of symptomatic vines have all been positive for GRBaV and RSPaV but negative for all other viruses tested. We also performed two phytoplasma assays which were negative.

We know so little about this virus that is premature to jump to grand conclusions, but our evidence suggests that the virus spread from the reservoir side to the other side of the ravine along the roads. The notion of road dispersal is further reinforced by observations of roadside infection of wild grapes and even cultivated grapes overhanging St Helena/Spring Mountain Road.

While this road effect is by no means certain, the possibility that it is real is a very important factor in any decision to replant a vineyard. If the new vineyard cannot be protected from reinfection, the effort is pointless.

As much as we would love to believe that the distribution of GRBaV follows from grafted heredity, our information suggests that the environment is a very important factor as well.

 

Posted in Biology, GRBaV, Red Blotch Disease, Wine | Tagged | Leave a comment

The State of the Onion

Let’s say the way this planet works is an onion. There are many layers and they interact in ways far more complex than onion rings. Yet we have to start somewhere, and peeling back the layers of this onion can at least help us grasp the huge holes in our understanding.

Let’s start around the middle of the onion at the surface of the earth. A very significant transition takes place here between land and water on one side and air on the other. The water is confounding because it fills in low areas we might be inclined to call land if there were no water there. These low areas get quite deep and are so extensive that 70% of the planet is covered by ocean.

The ocean and the atmosphere have mirror image onion layers beginning with a mixed layer and progressing to stratified layers.

Atnosphere and Ocean

The lower image above is the ocean and the upper the atmosphere.

The Aristotelian elements, air and water have different properties, but at the interface and extending up ten kilometers in the atmosphere and down somewhat less than a kilometer down in the ocean are turbulent mixed layers. These mixed layers both transition, up and down respectively, to stratified layers that make our onion proud. The atmosphere has more layers and is more complex because gravity assures that cold materials go nowhere but down and warm materials go nowhere but up. The ocean below the “clines” is simple and incredibly stable because there is nowhere for it to go. It is constrained at the bottom by another Aristotelian element, earth.

There are generally two sorts of earth, continents and ocean basins.

fig5crosssection

This graphic by NASA shows the general layers of oceanic crust.

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This graphic (credit unavailable) is a good general representation of the onion rings of sediments overlying the different sorts of igneous rocks (ocean and continental and their relative densities) and the mantle layer below. The oceanic crust is to the right and continental crust to the left.

Since we are downward bound from the middle of the onion, lets head for the center of the earth.

 picture21

This graphic (credit Geopangea Research Group) is a good representation of the earth’s internal onion rings. Each layer is known from a change in velocity of seismic waves from earthquakes.

Problems with our understanding of the onion begin at the core. It has long been posited that convection within the outer core creates the earth’s magnetic field. A nice, easy answer, but it happens that Iron melts above its magnetic Curie point. Above the Curie point a material loses its magnetic properties.

Let’s just say we have no idea how the earth’s magnetic field is generated.

The seismic waves from earthquakes show us amazing things. Above the core/mantle boundary there are two very interesting extrusions.

 

Doughboys

To me they are doughboys. Credit Ritsema. One can think of them as Atlas holding up the earth. The important thing is they flatten out at the 660 km discontinuity like thunderheads hitting the stratosphere.

We have long been told that mantle convection causes the continents to move.

Dashed Conceptions

Childish conceptions like this. Credit unavailable.

The very same seismic waves that illuminate the doughboys show us this simply isn’t true.

Ritsema

The mantle is substantially stratified. Nothing anywhere near mid-ocean convection driving ocean floor spreading is in evidence.

Kustowski et al 2008

These sections from Kutowski et al (2008) show that the ocean ridge system is in fact a shallow feature. It is readily apparent down to 100km but vanishes as a linear feature before the 660 discontinuity and is unrecognizable in the Perovskite at 1000 km in the lower mantle. At the core/mantle boundary at 2800 km all that remains is the doughboys.

If the doughboys are feeding the ridge system at all they are doing it through tiny venturi in the Perovskite and then spreading out as massive sills. Other offset venturi through the intervening layers and the Mohorovicic (MOHO) discontinuity would then need to feed the sinuous dead end rivers of the ocean ridge system.

Doesn’t really work for me but  the raw edge of human understanding does not bear waxing pedantic. Another very serious problem is that the MOHO just below the crust marks the beginning of a low velocity ductile zone generally referred to as the “asthenosphere”. It is on this layer that crustal “plates” are supposed to be moving. Trouble is, seismic waves appear to show that continents have roots far deeper than this.

ngeo1982-f2

Credit NatureGeo. Continents appear to have roots that extend to 400 km near the base of the Olivine layer and the ductile material that allows their movement may be more a result of local pressure from movement forces than from a continuous ductile layer.

Let’s just say we have no idea why the continents are moving.

We are working our way backwards from the core of the onion and listing the problems with our understanding. We have reached the surface where we live and where we started. Take a deep breath of the atmosphere.

The atmospheric mixed layer, called the troposphere, is thought to have varied in average temperature within a range of six degrees for all of geological time. We happen to live in one of half a dozen glacial periods known in geological time so it is comparatively chilly out. Furthermore, the last three glacial periods including our own have been characterized by oscillations between glacial and interglacial episodes. We live towards the end of an interglacial.

We have no idea what causes glacial/interglacial fibrillations nor what causes the macro scale glacial periods to come along every few hundred million years.

Iceindex

This is what the descent into our current ice age, the Pleistocene, looked like.

Let’s just say we have no idea why the mixed layers of the lower atmosphere and ocean warm and cool.

The next layer of the atmosphere is the stratosphere. It’s a long way back to the first graphic so it is reiterated here.

1000px-Comparison_US_standard_atmosphere_1962_svg

Temperature declines steadily through the mixed layer or troposphere for a bit over 10 km and suddenly flatlines up to about 20 km  where it starts warming again and this warming accelerates through the ozone layer in the mid stratosphere. The warming continues well above the ozone to the top of the stratosphere at about 50 km where cooling resumes throughout the mesosphere to about 80 km where it flatlines and then warms in the thermosphere.

One weird onion. Strange how the speed of sound follows temperature rather than density. We ain’t done yet. There is at least another 100 km “sphere of influence” above the thermosphere.

2004-van-allen-belts

This is a NASA image of the Van Allen ring currents, more a donut than onion rings.

mbs1

In this graphic from the Chinese Academy of Sciences we reach the outer skin of our onion. Beyond the onion we get into the rest of the universe, 95% of which seems comprised of dark energy and dark matter of which we have no understanding.

So what is the state of the onion? It is just a silly metaphor to attempt to reduce head spinning complexity to something we can get our heads around, yet even at this dumbed down level our understanding utterly fails.

1. We have no idea how or even if the planet’s core produces the earth’s magnetic field evident in the “bow shock”, the flakey outer skin of our onion above. We further have no idea why it periodically and erratically switches polarity.

2. We have no idea what is causing the crust to move.

3. We have no idea what is causing changes in oceanic and atmospheric temperature nor why these changes seem limited to a range of 6 degrees  over geological time.

Generally, we are missing a lot of energy, both inside the onion and out.

Posted in Climate, Geology, LLSVP's are Doughboys, Magnetic Reversals, Moho, Oceanography, Seismic Tomography | Tagged | Leave a comment

Pope Misguided the XXXXXXXXIX Preaches Crusade Against Carbon

In an action that betrays all the more clearly the religious roots of the Carbon crusade, the Pope continues a long and sorry tradition of involving the church in matters best left to science and individual conscience. From Galileo a harmless gas the church has an unimaginably dismal record in matters of science. Even flipping a coin on each issue would have produced a better result. After all this time he might have learned…

Posted in Anthropology, Carbon Theology, Climate, Ethics | Tagged , | Leave a comment

Lamarc Col, Muir Pass, Mt. solomons, Charybdis, Mt. Goddard, Echo Col, December, 1976

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We had fallen in love with the moonscape of Muir Pass and the improbable hut there while hiking the John Muir Trail in 1966. No vegetation besides hardy buckwheats and lichen can be seen in any direction from this 11,955′ pass that divides the San Joaquin and Kings rivers. We resolved then and there that we simply must see this surreal place in the winter and made three attempts to ski in during the early 70’s college Christmas vacations that were thwarted by inadequate equipment and planning, bad weather, and deep snow with companions unequal to the raw wild in roughly that order.

74-12.18 Humphries Basin Camp

We set up this camp in Humphries Basin in December, 1974 with a notion to follow the “Bishop Loop” route to Muir Pass.

Scott Lambert and I were bad assed Orinda kids and we planned another try in December, 1976, but this was the apex of the drought and there was little snow. We carried our skis over Lamarc Col, stayed several days at the Muir Hut and climbed Mt. Solomons, Charybdis, and Mt. Goddard before carrying our skis out over Echo Col. It would have been very foolish to venture out there without skis.

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The first night we camped high on Bishop Creek.

76-12_2 Sunrise on the Ice Bishop Creek

We reached Muir Pass mid-day our second day and I climbed Mt. Solomons behind the hut the first evening we were there.

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I was rewarded with this view to the south and Charybdis.

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And this view to the north of Wanda Lake and the upper San Joaquin drainage we had followed up.

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Back down at the hut…

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The moonscape, Wanda Lake, and Mt. McGee were very much the experience we had first imagined a decade earlier. The next morning we set out across the Ionian Basin to climb Mt. Goddard.

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The ice was two feet thick but it boomed like cannon under our weight.

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South from Mt. Goddard.

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North.

The next day I climbed Charybdis and found this view of Mt. Goddard to the north.

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Approaching the metamorphic weakness that allows Echo Col on the way out.

Ultimately this trip was about the ice, the lessons of cold with little snow.

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The culmination of a decade long dream nearly forty years ago, and an unforgettable lesson in the beauty and complexity of the planet we live on.

 

 

 

 

 

 

 

 

 

 

 

 

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GRBaV, The Vector, Which Mite It Be?

At a recent UC extension course, “Current Issues in Vineyard Health”, an impressive group of researchers presented their work. Dr. Brian Bahder revealed evidence of a second variant of GRBaV, commonly called red blotch virus, that seems to have invaded a block at the UC Oakville Station from a different direction. He also reported finding both variants in wild blackberry, adding that prolific bush to wild grape as natural reservoirs of the disease. Perhaps poison oak will be next?

The tone of the presenters at this course was very skeptical of a paper by Dr. Bahder’s old colleague and fellow doctoral candidate at Washington State, Dr. Poojari, (et. al 3013) which reported evidence that the Virginia Leafhopper could transmit the virus. What Dr. Poojari did was let Virginia hoppers feed on infected plants and then move them to uninfected plants. His result was that an identical virus was transmitted to the uninfected plant. Seems pretty solid, but I have heard suspicions of contamination of the supposedly uninfected sample. Dr. Bahder found at a Davis increase block that was fairly crawling with Virginia hoppers that little or no transmission seemed to be taking place, but at the Oakville Station where the Virginian has not yet arrived significant transmission is well documented. Even in Washington the Virginia hoppers seem not to be transmitting the virus in the field.

Obviously  transmission of blotch is taking place out of the range of the Virginia hopper. Still, Dr. Bahder’s picture of  blackberry looked pretty well hopper chewed to my eye. Unless  Dr. Poojari’s receptor vines were contaminated, his work shows at very least that hoppers are biochemically capable of transmitting the virus.

Vector relationships are complex and usually specific. They involve interactions between the viral coat proteins and proteins in the vector’s digestive tract. The virus must survive in the vector at least long enough for the vector to move to another plant. Relationships seem to range from short-term persistence in the mouth of the vector to “circulative” virulence where the virus takes a ride through the insect and into its salivary to long-term arrangements where the virus reproduces in the vector .

We don’t even have the first clue about much of this stuff in the case of blotch, but those of us with more than an academic interest get an automatic license to think. We live and bleed with the enormous financial consequences of this disease, and so can be forgiven an abductive thought experiment.

Let’s list the few things we think we know about the disease in rough order of certainty:

1. There are at least two variants and one may be more recent.

2. A substantially similar virus has been documented in a grape leaf collected in Sonoma  County in 1940.

3. Blackberry and wild grape harbor the virus, possibly by transmission from vineyards.

4. Koch’s postulates seem to have been fulfilled.

5. One or two year latency has been reported between detectable titers and symptoms.

6. Symptoms appear to have increased exponentially in the last season.

7. There appears to be an edge effect resulting from transmission from neighboring vineyards and woodlands.

8. There appears (to me anyway) to be a road effect of transmission by machinery, dust, or tissue.

What sort of vector could do all of this?

Let’s start out with the known vectors of Geminiviridae. Not that this list should be exclusive, but vector relationships are often conserved.

drawing.png

One can see from this after Hogenhout et al 2008 that the list of suspects is rather small and that whiteflies and leafhoppers do all the known damage with the lone exception of one case of a treehopper, a similar insect in the same family as the leafhopper. But there is a problem  because GRBaV coat proteins are very different from the four genera above and may eventually become its own genus.

Blotchcoat vector

This graphic by Dr. Fuchs shows that GRBaV coat proteins hark back to the family of all Gemini virus genera. This family is believed to have evolved in Africa from algal plasmids before the breakup of Pangea and New World Geminiviridae seem to lost the Old World retinue of “satellite” molecules by evolution in isolation.

Begomovirus Proteins Flourescing in a Whitefly

These images by Dr. Monica Gotz show Begomovirid proteins fluorescing in the gut of a whitefly.

All things considered, what little we know of Geminivirid vectors is not much help. I have heard verbally from someone who ought to know that white flies have been considered and rejected as GRBaV vectors, and the UC groups seem not at all salubrious about leafhoppers, in spite of having vacuumed them up for testing last season. Furthermore, most plant virus vector specificity is at the genus level. As Dr. Fuchs has shown, GRBaV coat proteins hark back to the family level. This may well mean all bets are off regarding potential blotch vectors.

The known vectors (hoppers and whiteflies), besides being contradicted by some research and current opinion, seem unable to explain “road effects”. They are both leaf feeders that tend to be in population decline at harvest. Furthermore, they are both adapted to dispersal by flight. They are readily visible and produce choking clouds when disturbed. One simply does not see them on harvested grapes or grape trucks. Whiteflies have sluggish instars and hoppers do not even undergo true metamorphosis with the larval stages looking remarkably like an adult.

WFlifestages

Trilobite looking whitefly instars credit Shetlar at Oregon State University.

grape leafhopper instarLeafhopper%20grape%20adult

Grape leafhopper instars and an adult by Martin Rice at Iowa State.

Although sluggish instars of mealy bugs which vector leafroll virus  are known to become unlikely aviators by climbing shoot tips to launch into the wind, mealy bug adults have no ability to fly. For whiteflies and hoppers flight by adults is a vastly more efficient means of dispersal.

If not whiteflies or hoppers, what?

Sharpshooters are in the same family as leafhoppers and they have long feeding tubes able to reach into the xylem of plants. They are known vectors of bacteria, but not of viruses, and they have been shown to “hand off” Pierce’s Disease bacteria to common leafhoppers in grapes. Word has it they are being looked at, but sharpshooters are big and obvious, and absent a “hand off” to a more ubiquitous insect, they just don’t seem do have the population density or distribution in Sanapanoma to explain the rapid spread of bloch symptoms.

Blue Green Sharpshooter

Blue Green Sharpshooter UC IPM online.

Cixids are another bunch of hoppy little guys in the Cicade family with leafhoppers and sharpshooters. They are known to vector the “bois noir” phytoplasma disease of grapes in Europe and a proteobacterium disease of beets. Rhonda Smith of UC extension in Sonoma County reportedly pulled in the EGVM traps to look at Cixids. Cixids are also leaf feeders which tend to spike in population early in the season.

Cixiid

Cixiid by Ian Boyd

Speaking of phytoplasmas, a leafhopper is known to vector the phytoplasma responsible for “flavescence dore” which is spreading across Europe. The symptoms of this disease are remarkably similar to blotch. We ran broad spectrum phytoplasma qPCR assays on some blotch positive vines and they came back negative.

What about mites? They are about the only vectors left unless you want to get into fungi or pollen.

Nobody seems to be considering the Acari. There are three (barely) visible web spinning mites, Pacific, Two Spotted, and Willamette that are grapevine nuisances. None of them is a known vector of anything. Pacific and Willamette seem somewhat antagonistic since sulfur sprays commonly used in the early season to control fungus, and to which all mites seem susceptible to some degree, skew their relative populations, and generally delay their population spikes until after sulfur is discontinued. Even with the sulfur delay, populations of these mites fall to very low levels by harvest.

There is a parallel universe of biological dark matter in the form of invisible mites.

11Chuck images

This amazing micrograph by D. Walter shows microscopic broad mites catching a ride on a white fly. Microscopic mites also infest bee colonies.

The Eriophid mites are present in our grapevines and are known virus vectors. Erineum mites, “strains” of which attack buds and cause leaf curl in addition to the well known “fools phylloxera” erinea galls on leaves, are microscopic but are very sensitive to sulfur. Dr. Monica Cooper of UC Extension Napa and Dr. Vaughn Walton at OSU have studied these by putting double sided scotch tape around canes to catch them. At least in Oregon there is also a microscopic “rust” mite, Calepitrimerus, which joins the three “strains” of Colomerus Erineum mites and likely a host of microscopic predatory mites as invisible armies marching up and down our vines.

Eriophid.png

This from Dr. Walton shows a micrograph of an Eriophid mite and an illustration of where they winter over in the buds and scales. Eriophid mites are known to vector Secovirus in black currents and peaches, and Potyvirus in wheat etc., and in figs.

There is another microscopic Acarid, Brevipalpus, which may be among us. This notorious mite with worldwide tropical and subtropical distribution is an infamous vector of Rhabdovirus. This plant version of rabies affects eggplant, coffee, passion fruit, and Orchids among commercial plants. Brevipalpus is also known to vector Bromovirus in cucumber,  Potyvirus in dasheen, and so many unknown viruses that en entire category, Brevipalpus Transmitted Viruses or BTV has been proposed. The most well known BTV is Citrus Leprosis Virus. Dr. Childers (personal communication) has found Brevipalpus californicus  on grape vines in the Central Valley.

Brevipalpus

Micrograph from Kitajima et al 2010. Microscopic mites as vectors can explain all of the known and supposed features of the spread of GRBaV. They are readily airborne and easily spread by wind and mechanical turbulence. They are spread by larger insects, birds, deer, and human workers. They explain both edge effects and road effects. They peak in population at harvest. They can explain how a truckload of grapes could infect a wild grape along a road miles from any vineyard. They have both the population and distribution to explain the rapid spread of symptoms.

In the end we are left with a virus whose coat proteins hark back to the Permian. A virus which has existed in Sonoma County since at least 1940, yet whose current symptoms have exploded in the last six years to nearly every vineyard in Napa and Sonoma counties. A virus whose current symptoms may result from the work of vectors two years ago.

A new vector relationship seems very likely. This new vector need not necessarily be a known Geminivirid vector, and in fact the known vectors and their ilk have been marginalized as suspects by recent research. The large, easy to see suspects are being exhausted. We may need to look to the microscopic dark matter of the Acari, they just mite be it.

 

 

 

Posted in Biology, Ecology, GRBaV, Red Blotch Disease, Wine | 1 Comment

Hold and Haul, The Surprising Result of a Careful Analysis of Sustainability

The purpose of this investigation is to evaluate the “sustainability” in terms of fossil energy use between localized wastewater treatment at a sewage treatment facility and “hold and haul” trucking to the EBMUD cogeneration facility in Oakland for a new American Canyon winery.

According to the EPA typical wastewater treatment energy consumption is 1200 KWh/million gallons or .0012KWh/gallon. There are 40.7 KWh in a gallon of diesel when the two are equilibrated in joules. We therefore multiply to find that a wastewater facility typically uses .04884 (let’s just say .05) equivalent gallons of diesel to treat a gallon of wastewater

The 64 mile round trip to EBMUD from American Canyon @ 5 mpg uses 13 gallons of diesel. Divided by the 5000 gallons in the truck this yields .0026 gallons diesel/gallon wastewater delivered to EBMUD.

Right away it is clear that local wastewater treatment requires nearly twenty times more diesel equivalent energy than hauling to EBMUD.

The comparison is not quite fair because only about half of California electricity is produced by burning fossil fuels. The other half is more sustainable, although “unspecified” sources and the question of nuclear sustainability might make this a substantial exaggeration.

California Energy.png

In an abundance of generosity we will just say that half of California’s electricity is sustainable and divide the .05 gallon diesel to gallon wastewater at a treatment plant in half. At .025 gallons diesel per treated gallon local wastewater treatment uses only about ten times more fossil energy than hauling to EBMUD.

Conversion Efficiency.png

Nothing is simple. California produces most of the unsustainable half of its electricity from natural gas. To make this equivalent to the diesel burned in the truck to EBMUD this natural gas must be adjusted first by the conversion efficiency to KWh and second for the relative joule content (.67) of natural gas to diesel.

We accomplish this by first dividing the .025 gallons first by the relative energy content .67 to yield .037 and this result by the conversion efficiency .32 to yield .117 diesel equivalent gallons to treat a gallon of wastewater at a typical local plant.

The analysis thus far has compared local treatment with just the transportation to EBMUD as if there were no energy used to treat it at EBMUD. Surprisingly, not only is this justified, but EBMUD actually produces 20% more energy from the wastewater by cogeneration than the processing consumes.

Thus we must take our .117 adjusted diesel gallons to process a gallon of wastewater at a local plant and multiply it by 1.2 to yield EBMUD equivalent gallons, yielding .14 gallons.

We conclude that the .14 equivalent gallons of diesel to process wastewater locally compared to the .0026 gallons used to haul it to EBMUD reveals that local processing would require fifty times more fossil fuel that Hauling to EBMUD. We therefore further conclude that hold and haul is fifty times more sustainable in terms of fossil energy use.

 

 

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The end of the Hollowscene

The concept of the Holocene epoch is a 19th century notion developed when the preceding “ice age” was thought of as a monolithic block of ice extending back to the end of the Pliocene. In this context it made sense to classify the current warmer condition as a new epoch. We have since learned that rather than being a solid block of ice the Pleistocene has been a period of wild swings between glacial periods and interglacial periods like our own, and that several prior interglacial periods have been warmer than our current interglacial so far.

Iceindex

One can easily see from the graphic above that to classify our current interglacial as an epoch in a league with the Pliocene, which began near the left edge of the graphic as the warmer yet Miocene ended, is simply absurd. The absurdity is further exponentially compounded by the recent suggestion of an “Anthropocene”, presumably beginning in 1850. This notion is propounded by zealots who ascribe far more influence to human activity than any evidence supports. We therefore declare the “Misanthroposcene” and the “Hollowscene” null and void.

Sorry y’all, but we are still very much in the Pleistocene. Tell you what, since our interglacial has not been properly named, we propose the Anthropic interglacial, and will refer to it thus henceforth.

Posted in Anthropic interglacial, Anthropocene, Climate, Geology, Holocene, Paleoclimate | Tagged , , | Leave a comment

GRBaV, A Null Hypothesis

As one contemplates the panoramas of red vineyards and walks rows to find disturbingly few completely asymptomatic plants, it is easy to consider a null hypothesis suggested by early notions that red blotch has been around a long time masked by similar symptoms in other viruses, and Dr. Golino’s recent finding that a substantially similar virus existed in Sonoma County in 1940.

A null hypothesis could be that the virus has been here latent in every plant forever and the near universal expression of symptoms this year is the result of unknown cyclic or environmental factors.

This possibility cannot be completely ruled out, but a number of observations about the current outbreak argue against it.

1. Dr. Sudarshana has documented the spread of the virus to plants that previously tested negative at the U.C. Oakville field station.

2. The pronounced edge effect. There is no reason to expect an edge effect unless a new strain or vector relationship has developed.

3. The existence of “one armed” symptoms on cordoned vines. One would expect a widely distributed latent infection to be evenly expressed in the plant.

We present here possible evidence of symptom evolution in an isolated mountain vineyard block. If our interpretation is correct, this evidence would further argue against the null hypothesis.

Google Earth imagery lacked the resolution for any detailed analysis until about 2008 when a significant resolution upgrade seems to have occurred. The usefulness of this imagery is also limited because the photography needs to happen during the symptomatic stages of red blotch which in most vineyards is from September to November. Such photography took place on October 24, 2009.

The resolution is still far less than ideal. Close examination reveals pixelation on the order of ten feet which represents two vines in this vineyard. Additional uncertainty of one position is introduced by the way AutoCAD allocates points along a polyline that extends around corners as this block was counted. In the strictest sense this data could be written off as statistically meaningless. Nevertheless, photons tell no lies. When an otherwise green vineyard registers red and purple areas and appropriate margins of error are incorporated, it may well be possible to derive significant results. In our opinion we are not to the stage of this investigation where any evidence can be ignored unless it is demonstrably wrong.

Below are three pictures of the Oakville Field Station 10-24-09. The first, a native image, shows a gross infection, possibly with several viruses, and a progressive infection in neighboring vineyards.

Ok 10 09 base annotated

The second image is saturated in Picassa and more detail of the surrounding vineyards and hints of infection within the Station can be found.

Ok 10 09 saturated

The third image is boosted with high dynamic range which becomes granular but polarizes green and red. This clearly shows edge effects. It is difficult to separate “edge” effects from “road” effects as edges are nearly always roads.

Ok 10 09 hdr

Moving to a remote mountain vineyard using a base image similarly enhanced from the same day, October 24, 2009, we show the block suspected of being ground zero. We find no apparent edge effect in play. This block is CS337 on 44-53 rootstock. The rootstock was thermally sterilized and propagated on site from cuttings procured in Oregon about the turn of the millennium. The 337 from numerous sources was field grafted. The partial block above and to the right also showing symptoms is CS4 on 44-53. The asymptomatic partial block to the right is CS4 on 1103P and remains one of the least symptomatic blocks today.

Blocks 14,15, 16.png

This year we marked the vines we judged to be grossly symptomatic defined as over 50% red. Here they are superimposed over the same image as 5′ diameter circles in accordance with vineyard spacing. There is a slide in the middle where vines were removed. Once again we find no edge effect.

Gross 141516 2014

When the less symptomatic vines are removed (it should be noted that it is very difficult to find completely asymptomatic vines in this block), we find a poor correspondence between the grossly symptomatic vines this year and those from 2009. Although symptoms are progressive and great caution must be exercised comparing different seasons and mapping dates, we feel that this at least leaves open the possibility that vines develop resistance over time.

14 15 16 2014.png

There are no surviving tissue samples so there is no way to be certain the symptoms from 2009 were GRBaV, but all qPCR assays from this block and the entire vineyard to date indicate the presence of only GRBaV and RSPaV.

We take this analysis one step further with a look at dead and missing vines.

Missing 141516 2014.png

The slide and the sorry row where machinery was moved in are apparent, but again we find poor correspondence with vines symptomatic in 2009. We find therefore no evidence of increased mortality.

We must constantly remember that our minds are wired to find patterns and conclusions from insufficient information. Yet it strikes us that edge and/or road effects are key to understanding the recent explosion of symptoms in Northern California. Other blocks in this vineyard show striking edge/road effects and even indication of infection from adjacent woodland.

We had been watching the wild grapes for a couple years and in  August 2014 noticed red leaf symptoms in wild grapes on the St. Helena Road in a location miles from any vineyard. Careful (but not rigorous) examination of this and many subsequent wild grape symptoms, which have also exploded in the last year, suggest that the source of infection is the road. Vines remote from the road are initially asymptomatic and infections always seem to begin at the road.

Some time ago Dr. Golino demonstrated that wild grapes harbor leafroll virus and we took a poorly collected sample of these new red leaf symptoms to Mike Anderson at the Oakville Field Station. Subsequent work showed that GRBaV is indeed present in wild grapes.

What remains haunting to us about the location of our first observation in wild grape is its remoteness, yet trucks from the vineyard discussed above and others have passed beneath this spot overhanging the road for years. If our intuition serves us, at least one vector must be capable of riding considerable distances on harvested grapes or machinery.

When nearly every vineyard seems suddenly symptomatic, and when nearly every vine seems to show some level of symptoms, it is easy to consider a null hypothesis that the disease has always been latent and that drought stress or some other environmental variable is causing the current expression of symptoms. This hypothesis cannot be completely ruled out, but considerable evidence argues against it.

 

Posted in Biology, GRBaV, Red Blotch Disease, Wine | Tagged , , | 1 Comment