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Friday, November 12, 2010

"Weird" Science #5: What happened with the nematodes?

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

I ended my last Weird Science post with two photos: one of a nematode that had been trapped by a fungal hypha, and another of a nematode as it made its way into the stem of a tomato plant, unhindered by fungal hyphae or any other defensive mechanisms. And my last words in the post were these:
"Why wasn't this [second] nematode attacked, and where were the fungal hyphae that killed off the first nematode?"
I promised to answer those questions. And the answers are clear. It has to do with the soil in which the plants were being grown.

In the first photo--the one in which the nematode is trapped by the hypha--the plant was growing (and the fungus and the nematode were living and growing) in healthy soil--soil filled with a huge variety and quantity of protozoa, earthworms, arthropods, algae, bacteria and fungi.

The second photo was taken of a plant that was being grown in typical modern agri-soil--soil that had been tilled and sprayed and treated with pesticides and herbicides and NPK fertilizer and in which, therefore, there was almost none of the microbial life that healthy soil exhibits.

Funny (or maybe not): The use of herbicides and pesticides and NPK (and no other) fertilizers can actually, over time, reduce plants' ability to protect themselves from predators. It can increase plants' susceptibility to disease.

As Elaine Ingham, president of Soil Food Web, Inc., suggests in her Foreword to Teaming with Microbes,
Urban dwellers and other growers have been pouring toxic chemicals on their soils for years, without recognizing that those chemicals harm the very things that make soil healthy. Use of toxics to any extent creates a habitat for the "mafia" of the soil, an urban war zone, by killing off the normal flora and found that compete with the bad guys and keep them under control. . . . If toxic material was applied only once in your life, the bad situation we have today would not have developed, but typically with that first application, thousands of organisms that were beneficial to your plants were killed. A few bad guys were killed as well, but good guys are gone, and they don't come back as fast as the bad guys.

Think about your neighborhood: who would come back faster if your neighborhood was turned into a chemical war zone? Opportunistic marauders and looters, that's who comes back in after disturbances. In the human world, we send in the National Guard to hold the line against criminals. But in soil, the levels of inorganic fertilizers being used, the constant applications of toxic pesticide sprayed, mean the National Guard of the soil has been killed, too. We have to purposefully restore the beneficial biology that has been lost.

--Teaming with Microbes, p. 9

Thursday, November 4, 2010

"Weird" Science #4: Microbes and Soil

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

(If you've been following my "'Weird' Science" series, I hope you'll forgive me as I slip in at least one intervening post in the series before I get to the one I suggested would be next.)

As I began digging into Lynn Margulis' Kingdoms & Domains, I was struck by the diversity of microbial life she describes. And I was struck by the thought that microbes are not only invisible to the naked eye, but they are, as it were, largely invisible to our minds. We don't think about them.

Not only do we not think about bacteria and protozoa; we tend to ignore fungi, algae, worms and beetles, too.

As E. O. Wilson says in the Foreword to Margulis' book:
About 1.8 million species [of living organisms] . . . have been discovered and described [as of 2009]. that includes perhaps three-fourths of the extant hundred thousand or so vertebrates, and, at a guess, ninety percent of the quarter million species of flowering plants thought to exist. But the sixty thousand known fungi are fewer than five percent of the estimated total, and the fewer than twenty thousand named nematode worms, the most abundant animals on Earth, are probably an even smaller fraction of the whole. Moreover, all this ignorance shrinks in the dismaying presence of the "dark matter" of the eukaryotic universe--or if you prefer, the Subkingdoms (Domains) of Archaea and Eubacteria. The exploration of what could turn out to be tens of millions or even hundreds of millions of well-differentiated strains of these subvisible organisms has scarcely begun.
--Kingdoms & Domains, p. lxi

What Wilson says is one way to look at or think about the diversity of life of which we are unaware.

I would like to suggest a few other ways, too . . . for your thoughtful consideration.

  1. Dr. Bonnie Bassler of Princeton University describes an amazing bacterial "social life." Yes, they actually communicate . . . in rather intricate ways. --That's the primary thrust of the following video. But she says something else, about a minute into the video, that ought to catch your attention, I think. Paraphrased: The human body has about a trillion cells in it. And those trillion cells host--either in you or on you--about 10 trillion bacteria. You have about 30,000 genes in you; the bacteria you host have about 100 times the amount of genetic material or information. "So," says Bassler, "when I look at you, I think of you as 1 or 10 percent human and either 90 or 99 percent bacterial."

  2. Based on a study of the bacteria on 51 different people's hands, researchers found that the average person had more than 150 different species of bacteria living on his or her hands. But get this. The researchers summarize their findings in this way: "[W]e identified a total of 4,742 unique phylotypes [species of bacteria] across all of the hands examined. Although there was a core set of bacterial taxa commonly found on the palm surface, we observed pronounced intra- and interpersonal variation in bacterial community composition: hands from the same individual [i.e., the left and right hands--JAH] shared only 17% of their phylotypes, with different individuals sharing only 13%." [Emphasis added.]
  3. "Good soil is absolutely teeming with life. . . . A mere teaspoon of good garden soil, as measured by microbial geneticists, contains a billion invisible bacteria, several yards of equally invisible fungal hyphae, several thousand protozoa, and a few dozen nematodes." 
  4. "Remember that teaspoon of good garden soil? Perhaps 20,000 to 30,000 different species make up its billion bacteria--a healthy population in numbers and diversity."
    --Ibid., p. 24.
  5. "[A]n acre of good garden soil teems with life, containing several pounds (about 1 kilogram) of small mammals; 133 pounds of protozoa; 900 pounds each of earthworms, arthropods, and algae; 2000 pounds of bacteria; and 2400 pounds of fungi."
    --Ibid., p. 28.
  6. Allan Savory presents a fairly standard food-web energy pyramid in his Holistic Management book (mentioned in my Monday post, "Weird" Science #2: Soil, Part 1):

    I think this is pretty common knowledge: Animals are unable to convert solar energy into forms useful for metabolism. Therefore, in order to survive, they (we!) depend upon plants and algae to convert the energy from sunlight into organic matter--carbohydrates, fats, proteins and innumerable vitamins and phytonutrients--that we are then able to ingest and metabolize for our life needs.

    However, Savory pushes this energy pyramid idea forward several more steps . . . in ways I had never imagined . . . primarily due to my blindness to the world of microbes and soil:

    The energy pyramid also extends below ground where the energy flow greatly affects . . . a biologically active soil community that [also] requires solar energy to be conveyed underground mainly by plant roots or surface-feeding worms, termites, dung beetles, and others.

    --Holistic Management, pp. 151-152.

From here, things get really strange.

I first heard about what I am about to share in a series of lectures from Acres USA. But now I am reading all about these things, in detail, in Lowenfels and Lewis's truly wonderful Teaming with Microbes.

In the same way we humans have domesticated and now farm plants and animals for our benefit, so (say leading soils researchers) plants have established interdependent, symbiotic relationships with most of the protozoa, earthworms, arthropods, algae, bacteria, and fungi that surround their roots. The plants send food (about half of all the carbohydrates and other nutrients they produce) down to their roots . . . and then, through their roots, they exude these nutrients (in a liquid called exudate), into the soil. This exudate, in turn, feeds the bacteria and other organisms that live in the rhizosphere (the area of the roots).

Meanwhile--hang onto your hat!--the microbes in the soil protect the plants' roots. Literally. And, in many ways, they also feed the plant.

As Lowenfels and Lewis explain things: "In return for exudates, [mycorrhizal] fungi provide water, phosphorus, and other necessary plant nutrients" (p. 25). Similarly, some plants prefer nitrogen in the form of ammonium (NH4) while others prefer it in the form of nitrate (NO3). Well guess what? The types of nitrogenous compounds available to plants are largely controlled by the microbes in the soil: "In fungally dominated soils, much of the nitrogen remains in ammonium form." In bacterially dominated soils, certain bacteria will convert the ammonium into nitrate. . . .

I'm going to quit here.

. . . Oh!

No I'm not.

I wanted to show you two photographs. So let me do that and then I'll quit.

These two photos are from Teaming with Microbes, pp. 12 and 13.

I said above, "[T]he microbes in the soil protect the plants' roots. Literally."

Lowenfels and Lewis discuss many ways they do this besides what I am about to show you. But these two photos did for me what the authors say they did for them. They woke them up--and they snapped me to attention--and they caused me to think: What is going on that I am unaware of down there under the soil?

The authors explain: "[O]ne autumn, . . . a gardening friend e-mailed two stunning electron microscope pictures. The first showed in exquisite detail a nematode trapped by a single looped fungal strand, or hypha. . . ."

Continuing with the story as the authors tell it:
Wow! This was quite a picture--a fungus taking out a nematode! We had never heard of, much less seen such a thing, and it started us wondering: how did the fungus kill its prey? What attracted the blind nematode to the rings of the fungus in the first place? How did the rings work?

The second image showed what appeared to be a similar nematode, only this one was unimpeded by fungal hyphae and had entered the tomato root. . . .

The authors ask about this photo: "Why wasn't this nematode attacked, and where were the fungal hyphae that killed off the first nematode?"

--Stay tuned for the answer in "'Weird' Science #5"!

Tuesday, November 2, 2010

"Weird" Science #3: Symbiosis, Part 1

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

I'm writing this as if it is its own separate subject, even though, in my mind, it's not. (It's closely related to what I began to touch on in my preceding post about Soil.)

My friend Perry Marshall encouraged me to read some books by Lynn Margulis, former wife of Carl Sagan. He mentioned her books in his article The New Atheism, Genesis 2 & Symbiogenesis. What he said there intrigued me. But then I wrote to him and he made some stronger recommendations. So I picked up a number of Margulis' books and was promptly impressed.


If you have any training in modern biology, you will, I'm sure, find me hopelessly behind the times. But I might as well reveal my inadequate training--or, perhaps, my failure as a student in high school.

Until I had begun looking at Margulis' Kingdoms & Domains, I was still working largely under a two-kingdom model of biology: there are plants and there are animals. Of course I knew there were bacteria and other microbes. But I don't think I ever placed them into a hierarchy of biological kingdoms. I think I considered them as a kind of cross between or not fully within either the plant or animal kingdom.

So it came as quite a shock when I discovered there are at least five biological kingdoms now recognized in the profession: prokaryotic (non-nucleated) Bacteria, eukaryotic (nucleated--i.e., having a nucleus) Protoctista (unicellular microorganisms), and the three eukaryotic multicellular kingdoms of Plants, Animals, and Fungi.

And then, upon a little further study, I found that even Margulis' taxonomy is . . . well . . . a little parochial. I found that many biologists actually prefer to speak of six kingdoms: the prokaryotic Bacteria (now identified as Eubacteria), and the eukaryotic Protoctista (or Protists), Plantae, Animalia and Fungi--as Margulis acknowledges, plus another kingdom of prokaryotes (non-nucleated organisms), the Archae or Archaebacteria, which are distinguished from the Eubacteria primarily by genetic differences.

As Wikipedia says,
Based on such RNA studies, Carl Woese divided the prokaryotes (Kingdom Monera) into two groups, called Eubacteria and Archaebacteria, stressing that there was as much genetic difference between these two groups as between either of them and all eukaryotes. Eukaryote groups, such as plants, fungi and animals may look different, but are more similar to each other in their genetic makeup at the molecular level than they are to either the Eubacteria or Archaebacteria.
Well, it turns out there are other ways of dividing the kingdoms. The Wikipedia article actually concludes with a kind of throw-up-your-hands-in-despair gesture when it says, "[R]esearch in the 21st century does not support the classification of the eukaryotes into any of these systems."

But back to my notes about Margulis.
Margulis' prime thesis in Microcosmos, Symbiotic Planet, and Acquiring Genomes, is that random mutation is a minor contributor at best to genomic drift (and, therefore, evolutionary change-through-time). Far more significant, she urges, is the acquisition and integration of genomic information through symbiotic merger of organisms, . . . most especially at the level of bacteria.

Indeed, she suggests that the nuclear contents of all eukaryotes come from bacteria: the chloroplasts from cyanobacteria and the mitochondria from oxygen-respiring proteobacteria. The basic cell itself, she suggests, comes from a merger of motile eubacteria and protein-synthesizing archaebacteria.

Perry Marshall provides a simple, graphically-engaging presentation of the basic ideas on his Cosmic Fingerprints website.

But he does more than that. A lot more. He proposes that
over the last 3.5 billion years . . . [DNA] has efficiently adapted and evolved from a single cell to occupy every ecological niche imaginable.

From the frozen ice sheets of the Antarctic to the punishing heat of the Sahara. From the ants under your kitchen sink to glorious singing birds in the Amazon rain forest.
This did not happen through accidental random mutation, . . . [but] through an ingenious algorithm that engineers its own beneficial mutations.
In essence, he says, God engineered into DNA (and all the carriers of genetic information--i.e., viruses, bacteria, and all the eukaryotic organelles that bear genetic information) . . . --God engineered these things to work together (through symbiosis) and intermingle (symbiogenesis) and self-adapt and "upgrade" to survive and thrive in virtually all future circumstances.

I encourage you to read Perry's paper. It's quite easy to read and rather inspiring, actually! Even if you're a committed anti-evolutionist. I hope you'll engage in the thought-experiment Perry suggests.

But what I have just written about: That, too, was not really where I wanted to go with this post.

But I think it's as far as I'm going to get.

So next time I'll try to bring Weird Science #2 (Soil, Part 1) together with Weird Science #3 (Symbiosis, Part 1) to generate . . . well . . . you'll see.

Maybe I'll call it Soil Symbiosis. Or something like that.

Monday, November 1, 2010

"Weird" Science #2: Soil, Part 1

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

I've been reading Allan Savory's Holistic Management: A New Framework for Decision Making.

I'm bummed that Savory and/or his publisher try to palm it off as a general management textbook. I'm afraid those who are looking for general management principles and insights will tend to ignore it, because it has a very strong (95% plus) focus on land or soil management. And, I'm afraid, those who should be most interested in it--the students of soil science and/or land management--will ignore it because it won't come up on their radar: "I'm not interested in a generic book about decision-making! I want something about land use, soil conservation, food production, and so forth!"

Well, it is a most worthwhile and interesting book for anyone concerned about these latter subjects. Most worthwhile and interesting, indeed.

Savory teaches--and demonstrates--so many principles that seem counter-intuitive, and go completely opposite standard land management practices.I won't get into too many details, here, but let me point out this one "lesson" I gathered from him. It has to do with letting land "rest." It is a truism amongst most conservationists that a major cause of land degradation and erosion has to do with overgrazing: too much animal and/or human impact. "We need to cordon this area off, so the vegetation can recover. Let's keep animals and people off this land for a few years. Maybe it will recover."

Savory says such a policy is exactly not what is called for. It is a very bad idea.

Oh, yes, land and vegetation need periods of rest, but not for years on end. He provides multiple illustrations of what he is talking about. Two photos, on pages 21 and 22 in his book, are almost all one needs to demonstrate the point:

Why is this?

There are several interlinked phenomena at work, here. I will just mention a couple.
  1. "[E]nvironments may be classified on a continuum from non-Bristol's a very brittle according to how well humidity is distributed throughout the year and how quickly dead vegetation breaks down" (p. 28).
  2. In areas where moisture is less than abundant (i.e., in "brittle" environments), when grasses are permitted to grow without being cut--either by animals who would feed upon them or by humans who may use them for fuel, for thatch, or, for any number of other reasons--the tall, mature growth tends to keep new plants from taking root or flourishing. After a year, the old growth will block new growth. Tall grasses will oxidize standing up. When they eventually fall over, they then create a kind of thatch cover for the soil beneath, providing an effective barrier for any light to hit the soil surface, preventing seeds from germinating, and shedding rainwater before it can soak into the soil. . . .
  3. By the time the old growth has finally oxidized or decayed away, the soil beneath has become hardened, the crumb structure destroyed. (Savory says soil in this condition is "capped.")
    Crumb structure refers to presence of aggregated soil particles held together with "glue" provided by decomposing organic matter. The space around each crumb provides room for water and air, and this in turn promotes plant growth.
    --Footnote, p. 108.
    When raindrop impact breaks down the surface crumb structure, it frees the organic and lightweight material to wash away while heavier fine particles settle and seal, or cap, the soil. The importance of surface crumb structure to water penetration is easily demonstrated by comparing a bowl of wheat grains and one of flour. Neither has a hard cap at the outset, but one has large particles, and the other has lost that structure. Pour a jug of water on each bowl and watch. Most of the water soaks into the grains, but it seals the surface of the flower immediately and runs off.
    --p. 108.
And the solutions to these problems?

In more brittle environments, the only tool that can provide adequate soil cover over large areas is animal impact. On both range lands and croplands animals can be used to trample down old standing vegetation or crop residues to provide letter. Their hooves can be used to break up there, Soil surfaces, preparing a seed bed in which new plants can germinate. On the very hard-capped soils in the tropics, . . . large hoofed animals are only able to break up soil surface capping progressively or when concentrated in large numbers at very high densities.
--p. 110.
The key, says Savory, is "[r]elatively high numbers of heavy, herding animals, concentrated and moving as they once did naturally in the presence of predators" (p. 37). The disturbance of the soil surface and the removal of excess plant cover actually increases the fertility of the soil.

--I'll call that unexpected and pretty "weird" science. And that's enough of a post for one day!