Does Mesquite encroachment alter soil microbiota in the Great Plains of Texas?

17 Sep

Spines and leaflets of the Mesquite.

I grew up in East Texas, where armadillos, cowboy boots, cattle ranching, state pride and Stetsons are just a natural part of daily life. But, I’ll never forget the year my older brother went away to a “summer camp” somewhere in West Texas, where instead of swimming and skiing all summer, the kids were involved in Mesquite removal.  His letters home complained of unendingly deep tap-roots and 6-inch long spines along the branches which would occasionally penetrate the bus tires and leave them stranded in the desert for hours.  This tree, although native to the plains of South and West Texas, is actually considered one of the world’s most problematic invasive species due to its hardy nature and ability to proliferate under adverse conditions.  It is the cattle-rancher’s foe since cattle typically won’t eat it because of the spines, the seeds can be toxic, the taproots deplete the water table, and they often crowd out the grasses and forbs the cattle need to survive.  

So, when I stumbled across this article in the most recent Soil Biology & Biochemistry on bacterial and fungal communities of soils underlying the Mesquite and native grasses of the southern Great Plains in Vernon, TX, I decided to check it out and share it here.

Let’s get my little pet peeve out of the way…

First, I would like to establish the fact that Mesquite (all the various species of Mesquite) are leguminous plants; this means they belong to a family of plants typically referred to as legumes, just like soybeans, peas, alfalfa, and many others.  This is where I want to get an issue of semantics (although I would argue it’s much more than simple semantics) out of the way.  Most people would say that these plants fix nitrogen, or add nitrogen to the soil.  I’m sure you’ve heard this before, and even the Wikipedia article on Mesquite says “Being a legume, it fixes nitrogen in the soil where it grows.”  This is where my head explodes.

PLANTS DO NOT FIX NITROGEN!  In fact there are no known eukaryotic organisms (plants, animals, fungi, etc.) that posses the genes encoding nitrogenase, which is the enzyme required for this process.  That means, no multicellular life-form has the capacity to fix nitrogen at all!  Only bacteria and archaea are capable of fixing atmospheric nitrogen gas into biologically available forms of nitrogen.  These very special bacteria establish symbiotic (a.k.a. mutually beneficial) relationships with leguminous plants by forming nodules on the roots.  The bacteria live in these tiny protected environments, where the plant feeds them carbon (food) and they, in return, feed the plant fixed nitrogen.  There are also free-living nitrogen fixing bacteria in soil and marine environments (we call them diazotrophs), but when you hear someone refer to “nitrogen fixing plants” they are actually referring to the work of bacteria attached within the roots of a specific group of plants.  It kills me every time I hear it.

Moving on… Mesquite encroachment.

Several facts regarding woody plant invasion into grasslands, like the Great Plains, have been established for some time now:

  1. Above-ground productivity is permanently altered – typically reflected as increased biomass production and altered rates of net primary productivity;
  2. Carbon and nitrogen are enriched in the soil directly under the trees; and
  3. Complex and biochemically recalcitrant (resistant to break-down) compounds accumulate in the soil directly under the trees.

So that all seems to make sense if you really think about it… from the macroscopic point of view:  We go from an ecosystem dominated by grasses like Buffalo grass and blue grama, which are very short (typically no more than 6 inches in height), sod-forming grasses with fairly shallow rooting systems, to an ecosystem dominated by large (up to 30 feet or more) trees.  We also know that these trees:   1.)  Form symbiotic associations with not only nitrogen fixing bacteria, but also mycorrhizal fungi which enhance their ability to scavenge phosphorus and other nutrients from a huge volume of soil; and 2.)  Shed their leaves each year to deposit a significant proportion of these accumulated nutrients onto the soil below.  There have been a number of studies establishing these facts, but none to date examine how this all impacts the diversity of soil microbial communities – until now.

What happened in Vernon?

Hollister, et al. (2010) compared soil carbon and nitrogen content, as well as soil fungal and bacterial community genetic diversity amongst the various vegetation types (Mesquite, perennial grasses, midgrass, and shortgrass) of the southern Great Plains near Vernon, TX, by means of cloning and sequencing as well as functional gene microarray technology.

When I say they examined “genetic diversity” in this case, they looked specifically at two different types of genes.  The first set of genes were those we typically used to identify organisms, conserved regions of the microbe’s DNA that allow us to differentiate genus and species, but tell us little to nothing about what the organism actually does.  For these identification genes, they employed standard cloning-and-sequencing protocols and ended up with a clone library for each of the vegetation-types.  In this way they could compare the species diversity of bacteria and fungi between soils.

They found differences in overall community structure, as well as a greater level of diversity (number of species) and richness (evenness of the distribution of these species) in the bacterial and fungal communities under the Mesquite trees than under the short grasses.  This is not terribly surprising if we consider that under the Mesquite trees we already understand that there is greater nutrient availability and substrate diversity.

However, the second type of genes the authors were interested in were those conferring functional ability to the soil organisms, such as genes that encode various enzymes like nitrogenase for N2 fixation, or efflux pumps for contaminant elimination from the cell, etc.  These types of genes may be shared across several genera and tell us very little about the identity of the organism, but give us some insight into what function the organism may be capable of performing in a given ecosystem.  To approach this question, the authors utilized the oh-so-sexy GeoChip Microarray: a commercially available array designed to probe for around 10,000 genes involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation.

Using this approach, they found no significant differences between the communities of the different vegetation types.  The authors concluded (albeit “with caution”) a great deal of functional redundancy exists across all of the communities they characterized.

This is where I have some questions…  ok, a lot of questions.

I tend to have a strong opposition reflex against the idea of high levels of functional redundancy because it’s been used so often as an argument against the need for biodiversity.  Perhaps functional redundancy is the answer, but before I can possibly yield to that idea, I need to know more.

In order to draw my own conclusions from the data presented, for one, I’d like to know more about the site history.  How long had each of the veg types been established where sampling took place? What was the grazing and management history at the site? And what was the understory below the Mesquite trees?  Perhaps these particular trees hadn’t been established for a significant period of time to afford appreciable changes in the soil functional diversity, or some of the understory was particularly similar to the plants interspersed with the grasses at the grass sampling locations.  The site was described as “ungrazed” but was wildlife also excluded from the site?

Also, why sample in August?  Most likely for simple logistical reasons, but it means that soil moisture (or rather the lack thereof) and heat were very likely limiting soil microbial activity, both directly and indirectly by limiting plant respiratory activity and therfore root exudation rates.  This brings me to the obvious issue, also cited by the authors as a potential problem for interpreting their results, of the fact that they used DNA rather than RNA for this analysis.  Sure, the organisms under each type of vegetation may contain the genetic information for the same functions (DNA) but the functions they are actually performing at any given time could be drastically different, and only revealed through RNA analyses (or by using more classical techniques).

The authors also make reference to potential design flaws in the GeoChip probes specifically for this study (i.e. 98% of the probes were bacterial in origin, excluding fungal functional genes).  So, then, why not couple the molecular techniques with old-fashioned laboratory functional assays on carbon and nitrogen mineralization or enzyme assays?

What does it all mean?

The authors made a pretty clear case for altered soil microbial community structure and phylogenetic (species) diversity under Mesquite encroachment, but not for soil microbial community function.  This is most likely due to the method applied to the question, but either way, it doesn’t align with virtually everything else we know about the macroecology of these systems.  It does, however, give us valuable insight into the limitations of the GeoChip in assessing soil microbial community function (at least, this is my assertion, which of course can’t be validated without further research).

Overall, a nice application of advanced molecular techniques to the issue of microbial response to Mesquite in a native grassland.  But I have to wonder if there will be more to come on this subject, particularly to double-check the cool and scientifically-sexy technology of functional gene microarrays against the more classical techniques for measuring soil microbial community function.

________________________________________________________________________________________________________ Hollister, E.B., Schadt, C.W., Palumbo, A.V., Ansley, R.J., & Boutton, T.W. (2010). Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains. Soil Biology & Biochemistry, 42, 1816-1824 : 10.1016/j.soilbio.2010.06.022


One Response to “Does Mesquite encroachment alter soil microbiota in the Great Plains of Texas?”


  1. Shall we dance?… « Microbial Modus - September 29, 2010

    […] when, in my previous post, I mentioned the fact that it perturbs me when people dismiss the role bacteria play in symbiotic […]

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