Soil: an under-appreciated dynamic consortium of communities. Part 1?


Quick fact: the amount of data generated by analyzing the genetic make-up of 1 gram of soil would surpass the total for the entire Human Genome Project. That is because a gram of soil may contain between 2,000 and 18,000 different genomes comprised within roughly 40,000,000 to 2,000,000,000 bacteria cells (1) and (2). Soil; we all walk on it, but do we ever think about what might be lurking in it? My daughter does, for instance, because she looks for tiny black snails to bring into our house and put in potted plants. However, I’m referring to things much smaller and much more influential to the overall ecosystem. Bacteria and fungi have mostly beneficial impacts on the lives of plants, but we know only a fraction of a fraction of the total species present. Many of us think of soil as dirt; dry and inorganic, but soil is a dynamic matrix of clay, sand, and silt particles with a mix of decomposing matter and living organisms. The surfaces of these particles make good niches for bacteria to live if they can survive the extreme variation in water and nutrient availability due to the wet/dry cycle.

Soil is a vast reserve of organic carbon, but only a fraction is usable due to decomposition of most carbon into hummus. So, bacteria and other microorganisms are in eternal competition with each other for precious nutrients in their microenvironments. This makes life arduous for soil organisms that are loners or isolated from good sources of nutrients. This is one reason the root zones of plants are like retirement communities to bacteria and fungi; and the plants know it.

animated bacteria, rhizosphere bacteria
Depiction of bacteria colonizing a plant root

Plants are like shipwrecked sailors stranded on a desert island. They have no where to go if conditions change. To help themselves out, they recruit bacteria and fungi to live on, or within, their roots by excreting valuable nutrients into the soil. Surrounding microorganisms take to this like sharks to blood which is what the plants want and need. These bacteria and fungi offer several advantages to plants. First, they can simply take up space; space that plant pathogens would like to inhabit. On top of this, the good bacteria can readily produce antibiotics to kill off any pathogens that might kill their food source. Second, many of these bacteria have the genetic machinery to produce a class of plant hormones called auxins, derivatives of the amino acid tryptophan. Auxin is like human growth hormone. When the bacteria excrete auxin, the plants take it in because it is a cue to increase water and nutrient uptake. So, plants increase nutrient uptake, become healthier and bigger, and by default excrete larger amounts of nutrients for the bacteria. Genius.

The third reason plants attract bacteria is because plants have a big problem; they can’t make useful sources of nitrogen out of thin air. Luckily, many soil bacteria can, and it’s called nitrogen fixation. These bacteria are able to take nitrogen gas from the air and convert it into a form useful to both plant and bacterium: ammonium. This is an energetically expensive process for the bacterial cell. So, in order to make it as easy as possible on the bacteria, plants will protect the cells from nitrogen fixation inhibitors like oxygen and provide essential carbon in the form of amino acids. For this to happen, the bacterial cell literally crawls inside the root cell and becomes a bacteroid encapsulated within a special structure, a nodule, and ultimately becoming an endosymbiont.

And you thought only mammals had beneficial internal bacterial ecosystems. Just like humans, plants would be in a sorry state if it were not for the bacteria that they associate with. I haven’t even touched upon the benefits of fungi, but I’m definitely not a fungal expert. Any takers?

(1) How Deep Is Soil? Daniel D. Richter and Daniel Markewitz BioScience , Vol. 45, No. 9 (Oct., 1995), pp. 600-609

(2) Paul, E. A. & Clark, F. E. Soil microbiology and biochemistry (Academic Press, San Diego,1989).

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Image: Cells of the Rhizosphere


I have a blog post that I have been trying to write for weeks about the soil and rhizosphere. Until I can get a handle on it, here is a little image I did today to illustrate how cells initiate colonization of plant root surface. An example bacterial species would be Azospirillum brasilense, a personal favorite.

animated bacteria

 

 

Infographic: I’m glad we don’t have as much impact on the atmosphere as bacteria


As humans, we are contributing to global warming every time we breathe. Luckily, this contribution doesn’t amount to a hill of beans. The amount of carbon dioxide we excrete while breathing is easily converted to other molecules by other organisms on Earth. We, as humans, number roughly 7 billion. That is a lot of carbon dioxide. However, we are outnumbered by plants and trees by several orders of magnitude that consume this carbon dioxide and convert it back to the oxygen we so desperately need and make carbohydrates in the process.

Now, think about this: 7 billion humans converted to microbes living in the soil would amount to a pinch of soil. As you should know, there is much more than a pinch of soil on the planet, and that does not take into account the waters of Earth. So, doesn’t it make sense that what these microbes take in and “breathe” out has a much much greater impact on the composition of our atmosphere? Luckily, microbes, in the general sense, don’t breathe carbon dioxide under most conditions and some microbes like algae consume carbon dioxide like plants and give us oxygen in return.

bacteria, climate change
Affect of each domain of life on the composition of the atmosphere.

The figure above shows how simplistic plants and animals are compared to prokaryotes in regards to what we all “breathe”. This is not an exhaustive list of molecules microbes use; it’s just one small group of bacteria from the genus Geobacter. This complexity helps put things in perspective.

MyTH: Week 7 focus: Pseudomonas fluorescens


Swimming bacteria
Swimming bacteria

My Tiny Highlight (MyTH) has been on hiedas for a while. However, I’m glad to introduce this week’s organism, Pseudomonas fluorescens. This will be the second highlight featuring a Pseudomonad (Week 5). For short hand, I will write the name Pfu. This is an interesting organism due to its effects on plants and other soil organisms. Pfu is a major constituent of the rhizosphere of plants. The rhizosphere is an active zone surrounding plant roots where soil microbes interact with the roots and each other usually in a symbiotic relationship. This is certainly the case for Pfu due to the benefits this microbe bestows upon host plants. First, Pfu produces many secondary metabolites that are probiotic for plants and can control bacterial and fungal plant pathogens. A major class of secondary metabolites produced are derivatives of phenol that display antifungal properties including 2,4-Diacetylphloroglucinolphloroglucinol, and phloroglucinol carboxylic acid. Secondly, Pfu also produces a type of antibiotics from phenazine that can be beneficial to both plant and microbe. Third, Pfu produces siderophores than can scavenge essential iron from the environment with very high affinity giving Pfu an advantage against other soil inhabitants that are less efficient at acquiring elemental iron. Siderophores are produced within the cell and excreted into the surrounding environment. Pfu contains outer membrane receptors that can transport iron-containing siderophores back into the cell. One specific siderophore, pyoverdin, has green fluorescent properties which give P. fluorescens its name.

Image of pyoverdin, also known as fluorescein.
Image of pyoverdin, also known as fluorescein.

In a later post, I will detail more about the rhizosphere and soil in general.

A New Way to Study Permafrost Soil, Above and Below Ground | Lab Manager Magazine® « Taking Science to the People


Permafrost - polygon
Permafrost – polygon (Photo credit: Wikipedia)

A New Way to Study Permafrost Soil, Above and Below Ground | Lab Manager Magazine® « Taking Science to the People

Once again, DOE is innovative and making climate research better.