Monday, February 23, 2015

Biological Soil Crust Restoration?

The biotic soil crust in Red Rock Canyon, Lake Mead National Recreation Area, NV is showing clumps of the dominant moss species, Syntrichia caninervis. Each black dot represents a separate plant. This extreme arid-dwelling moss inhabits the loose sandy soils of the Mojave Desert. [Credit: Alexis Wartelle]
1.  What Biological Soil Crusts (BSC) occur in the desert? Gallery of BSC: from Canyonlands Research Station

Major types (easily observable):
(NB: A misting of water can make crustal organisms more visible...)

Three soil lichens dominate crusts of both the Sonoran and Grea Basin deserts:

Collema: a genus of gelatinous lichen (blackish, jelly-like when moist). First to colonize.

Placidium: a genus of squamulose lichen (discrete rounded flakes, convex or concave). Usually a secondary successional species.

Psora: a genus of squamulose lichen (discrete rounded flakes, convex or concave), a late-successional stage lichen.

Short moss:  Mosses <10mm and="" b="" bryum="" nbsp="" spp.="">Certodon purpureus 
Heterocystic cyanobacteria: (Notoc, Schizothrix)
Large thalloid liverworts:

Source:  Biological Soil Crusts: Ecology and Management.   Technical Reference 1730-2 2001.
2.  Where do BSC occur?
Soils having high electrical conductivity, high phosphorous, and high salt contents facilitate the
formation of cryptogam crusts. Shrink-swell clays (smectites, montmorillonites dervied from volcanic ash) are the worst.

Sonoran and Chihuahan deserts have more heterocystic cyanobacteria lower lichen, but lichen like Collema, Placidium, and Peltula do occur.  Ecoregions that receive summer monsoons (e.g., the Sonoran Desert) tend to have a greater diversity of heterocystic cyanobacteria (such as Lyngbya, Calothrix, Schizothrix, and Nostoc) and lower lichen abundance. Lichens in these areas generally include the gelatinous genus Collema and squamulose genera Placidium and Peltula.  Large thalloid liverworts are more common in warm deserts than cool deserts.

Sonoran:  heterocystic cyanobacteria (Notoc, Schizothrix), gelatinous (nitrogen-fixing) lichens (e.g. Collema), squamulose lichens, short mosses
Chihuahan:  heterocystic cyanobacteria (Notoc, Schizothrix), short moss

3. Resources for mapping BSC distribution?

Map shrink/swell clays!
Some mosses are on Seinet
Lichen image gallery (from Europe) organized by structure.
Lichens on LichenPortal
Lichens on iNaturalist
USFS Database

Tuesday, February 17, 2015

Clay minerals determine shrink/swell soils

Geology and Climate Control the Formation of Clay Minerals

Granite is made up of quartz, mica and feldspar. As quartz is resistant to chemical weathering, it may be eroded only as mineral grains of quartz. Feldspars and micas are susceptible to chemical weathering and break down to form clay minerals.

The main group of clay minerals are kaolinite, illite and montmorillonite. The layers in kaolinite are held together by fairly weak bonds, whereas there is strong bonding in illite and montmorillonite because of the presence of positively charged metal ions; potassium in the case of illite, and calcium and sodium in the case of montmorillonite.

Generally, potassium feldspar breaks down to form kaolinite; micas weather to give illite, and ferromagnesian minerals break down to form montmorillonite.  This chart shows that precipitation is also an important factor:
Source (PDF): Clay mineral formation and transformation in rocks and soils.  Eberl.  Phil. Trans. R. Soc. London 1984 

Alternating dry and wet climates can be inferred by the types of clays formed:

The major types of clay
Kaolinite, smectite (montmorillonite) and Illite:

1:1 Kaolinite
The sum of the many hydrogen bonds between micelles results in the micelles being very strongly bonded together and nearly impossible to separate. This bonding of the layers together results in kaolinite being a nonexpanding clay mineral. Since each micelle is constructed of a layer of silicon tetrahedral units and a layer of octahedral units, kaolinite is called a 1:1 clay mineral.

Kaolinite is formed by weathering or hydrothermal alteration of aluminosilicate minerals. Thus, rocks rich in feldspar commonly weather to kaolinite.  In order to form, ions like Na, K, Ca, Mg, and Fe must first be leached away by the weathering or alteration process.  This leaching is favored by acidic conditions (low pH).  Granitic rocks, because they are rich in feldspar, are a common source for kaolinite.

2:1 Smectite (AKA Bentonite) and Vermiculite
Smectites have more Mg2+, Fe2+, or Mn2+ substituted for Al, giving their sheets a permanent negative layer charge, which in turn leads to high CEC values.  Montmorillonite is a type of smectite.  Montmorillinite is the main constituent of Bentonite, derived by weathering of volcanic ash.   Smectites have a high shrink/swell capacity because water molecules can intercalate between the clay sheets, greatly expanding their total volume.

2:1 Illites
Illite clays are non-expanding.  Illites are formed from weathering of K and Al-rich rocks under high pH conditions. Thus, they form by alteration of minerals like muscovite and feldspar. Illite clays are the main constituent of ancient mudrocks and shales.

2:1 Vermiculite
Vermiculite weathers from mica, which often forms at the contact between felsic and mafic rocks.  It swells intermediate amounts.

 Minerology maps of the U.S (PDF)
example:  calcium carbonate map:

 New Mexico shrink/swell clays:

Source:  Swelling clays map of the conterminous United States.  From a good website.
Unit contains abundant clay having high swelling potential
Part of unit (generally less than 50%) consists of clay having high swelling potential
Unit contains abundant clay having slight to moderate swelling potential
Part of unit (generally less than 50%) consists of clay having slight to moderate swelling potential
Unit contains little or no swelling clay
Data insufficient to indicate clay content of unit and/or swelling potential of clay (Shown in westermost states only)

Saturday, February 14, 2015

Permian / Delaware Basin Maps

BLM Land Ownership:

GAP Landcover data for SE NM from the Webviewer. Version 2.0 is available here. Lime green is Sandhill Shrubland mixed in with light green Chihuahan Semi-Desert Grassland.  Lavender is Mesquite Shrubland (AKA degraded grassland).  Orange is Great Plains Shortgrass Prairie.  Teal is Chihuahan Desert Scrub.  Detailed descriptions of the landcover classes are available (PDF):  Landcover descriptions for the southwest regional GAP analysis project. Compiled by NatureServe 10 September, 2004.  

Geology of the basin:  (Click here for more info on the geology of the Guadalupe Mountains)

Friday, February 13, 2015

Mushrooms of Arizona

I just came across this great website with information on the common mushrooms in different biomes of AZ:

Wednesday, February 11, 2015

Riparian Restoration in a Time of Changing Hydrographs: La Jencia 2008-2014

A talk presented at the 2015 Tamarisk Coalition Conference in Albuquerque, New Mexico.

Sunflowers in NM

Common sunflowers in NM:
Helianthus ciliaris Blue-green, short, forming extensive colonies from perennial roots.  Leaves sessile.

Annual (no rhizomes):
Helianthus annuus  -Phyllaries ovate, abruptly narrowed to acuminate tip, ciliate
Helianthus paradoxus  phyllaries lanceolate, gradually tapering to the tip, not ciliate.  Usually no branches, no white “eye” in flower center. In wetlands.
Helianthus neglectus  phyllaries lanceolate, gradually tapering to the tip, not ciliate.  Usually branched, with a white “eye” in flower center.  Lower leaves w/ cordate bases.  Larger heads than H. petiolaris. 
Helianthus petiolaris  phyllaries lanceolate, gradually tapering to the tip, not ciliate.  Usually branched, with a white “eye” in flower center. Lower leaves w/o cordate bases.

Key based on Allred's Flora Neomexicana

Thistles in NM

I've compiled a list of common Cirsium species in the lowlands (not mountains) of Southern New Mexico, and mapped their collectioned vouchers from across NM.

Map created using 

Cirsium ochrocentrum – common.  Flower heads are bigger, and petals are longer than C. neomexicanum, often more brilliantly-colored, but plant is smaller.  Flowers usually taller than wide. 

Cirsium neomexicanum  -- Flower head looks more “bushy” because spines are more strongly spreading than on C. ochrocentrum, allowing flower to open more (wider than tall)

Cirsium texanum  - like C. ochrocentrum, but flower heads less than 25mm long, smaller overall.

-Based on Allred's Flora Neomexicana

Wednesday, February 04, 2015

H2S: A Toxic Gas, and an Important Metabolic Neurotransmitter!

Hydrogen sulfide, in addition to being a poisonous gas associated with oil and gas wells, plays a huge number of critical metabolic and neurotransmitting roles in the human body.

Source.  Hydrogen sulfide-based therapeutics and gastrointestinal diseases: translating physiology to treatments
Melissa V. Chan , John L. WallaceAmerican Journal of Physiology - Gastrointestinal and Liver PhysiologyPublished 1 October 2013Vol. 305no. 7, G467-G473DOI: 10.1152/ajpgi.00169.2013


Source.  Physiological Implications of Hydrogen Sulfide: A Whiff Exploration That BlossomedRui WangPhysiological ReviewsPublished 1 April 2012Vol. 92no. 2, 791-896DOI: 10.1152/physrev.00017.2011

Different signaling pathways in cardiovascular system modulated by H2S. AC, adenylyl cyclase; sGC, soluble guanylyl cyclase; PDEs, phosphodiesterases. The inhibitory effect is denoted with (−), and the stimulatory effect is denoted with (+).  Source: 

To research about a specific enzyme, the Human Metabolome Database HMDB works well.  To view maps of enzyme reactions, I recommend this interface:

Sunday, February 01, 2015

What is the Microbiome Good for?

How Inhibit Ammonia Production in Large Intestines?
"In general, the treatment of [excess ammonia] has as common elements the reduction of protein in the diet, removal of excess ammonia and replacement of intermediates missing from the urea cycle."

Eating large amounts of protein feeds harmful bacteria: "Protein fermentation by human faecal bacteria in the absence of sugars not only leads to the formation of hazardous metabolic products, but also to the possible proliferation of harmful bacteria [such as Clostridium, Enterococcus, Shigella and Escherichia coli]."

text below from:

Increasing the amounts of alimentary proteins results in a spectacular increase of the luminal and faecal ammonia [92]. In humans, the ammonia luminal concentration progressively increases from the ascending to the descending colon [93] in accordance with a higher rate of protein fermentation in
the distal than in the proximal colon. The two environmental characteristics of the proximal colon (low pH and high carbohydrate) explain the reduced net production of ammonia. [13]

Large amounts of ammonia can be absorbed through the large intestine mucosa [96]. Ammonia has been considered as a metabolic troublemaker since this compound is able to inhibit in a dose-dependent manner the mitochondrial oxygen consumption [104]. In addition, high millimolar concentrations of ammonia inhibit short-chain fatty acid oxidation [105,106] in colonic epithelial

Also of concern is H2S:  H2S is a bacterial metabolite produced through fermentation of sulfur containing amino acids (methionine and cysteine). Interestingly, there is a correlation between the level of meat intake and the level of faecal excretion of sulfide. [110]  H2S at excessive concentrations inhibits colonic epithelial cell respiration [120] and provokes genomic DNA damage [121], [122].

What to do?
inhibit large intestine production of ammonia!
Lactulose (comalose) would help acidify colon, feed good bacteria: