San Diego T & E Species

The U.S. Fish and Wildlife Service has a new website to identify species of conservation concern.  This system is easy enough that anyone can search for and learn about the Threatened and Endangered species in their county.

 For example, here is the list for San Diego County, California:

Cultivating a Healthy Skin Microbiome

A company is marketing a probiotic spray designed to help cultivate a healthy skin microbiome.  The spray contains Ammonium Oxidizing Bacteria (AOB; specifically the genus Nitrosomonas) that derive their energy solely from consuming the ammonia and urea found in sweat.  Supposedly, if you have enough AOB, you don't smell bad because they consume all your sweat, releasing beneficial nitric oxide gas!



I wanted to learn more about the skin microbiome, and found this comprehensive article with diagrams to show skin follicles, etc the complex topography and ecology of the skin environment.

These new data are based on DNA assays, and with improvements to these techniques, viruses, mites, and fungi are also being inventoried. This is certainly an improvement from the old days when only culturable bacteria were studied.  Here is a classic paper about the microbial correlates of dandruff.  Apparently there is no cause of dandruff, but simply a feedback between bacteria and fungi and the scalp. A fungus called Malassezia spp can release compounds that stimulate epidermis to proliferate.    Fungicides cure dandruff by killing the Malassezia spp, but many people harbor Malassezia spp without dandruff.   Perhaps an "ecological" cure could involve cultivating probiotic bacteria?

The same article also has the classic diagram showing different microbial communities on different body parts, based on their temperature, moisture and oilyness (sebum versus apocrine ).

Interestingly, soap and shampoo may be destabalizing our skin microbiome, in the same way that antibiotics can impact the gut microbiome.  For example, many ingredients in personal care products have been found in laboratory tests to inhibit "good-guy" AOBs, including sodium lauryl sulfate (SLS is one of the harshest detergents), sodium coco-sulfate, and even castile-type soaps. (Source)

To maximize ammonia utilization, AOBsproduce unique enzymes on elaborately folded cell membranes. These membranes are intricately folded so that they can increase the surface area for ammonia-oxidation. This means that they are able to boost both their ammonia-oxidizing capacity and their energy output.  However, this elaborate membrane architecture also renders AOBs particularly sensitive to membrane-disrupting chemicals, such as anionic surfactants found in modern soaps and detergents.

Detergents replaced simple soap in our hygiene routine soon after WWII and form a major part of most bath products. Anionic detergents such as lauryl sulphates, sarcosines and sulfosuccinates can be harsh to the skin and especially the microbiome.

When reading the ingredients list on your cleaning products, you can identify anionic surfactants as those that have the following in their names:

Sodium
Ammonium
Magnesium
Sulfate
Sulfonate
Gluconate

(For example, sodium laurel sarcosinate, magnesium laurel sulfate, and sodium gluconate.)

Nonionic surfactants are gentler to the skin microbiome, although not entirely harmless. (Source) They include:

Ethoxylates
Alkoxylates
Cocamide

All of my soaps and shampoos contain these ingredients, except for Black African soap "made from shea butter and palm kernel oil mixed with ashes".  The detergent in this soap is laurel glucoside, (AKA dodecyl glucoside) a non-ionic surfactant molecule.  Because it is non-ionic, it is a milder detergent, often used in cosmetics, shampoos, etc. Glycosides are produced from lauryl alcohol and glucose.

It may be possible to specially order detergents from companies like this one.  

The Theory and the Reality of Shelterbelt Afforestation Projects

The Theory of Shelterbelts

The Reality

Introduction:  dust bowl, us efforts

Following the dust bowl years in the U.S. the government planted 220 million trees in a strip 100 miles wide, stretching 18,600 miles from Canada to the Brazos river.  1935-1942  Today, the growth and vigor of many trees has declined due to close spacing, age, and invasion of undesirable short-lived trees.  Wikipedia.

There are currently two major afforestation programs, one in China, and one in the Sahel.

Great Green Wall in China. 

This project aims to afforest 90 million hectares and eventually contain 100 billion trees in a 4500km belt.

A recent paper by Tan (2014) found decreased dust transport due to the plantings so far.  But independent Chinese media reported in 2013 that dust storms were increasing:  For centuries in northern China, annual sandstorms, called the Yellow Dragon, have been ripping through the city.  Wind erosion is obvious and most pronounced in spring, when sandstorms are common and the vegetation is still absent or dormant after severe winter temperatures. Sandstorms have increased in the last few years, calling into question whether the Great Green Wall is working.

Liu Tuo, head of the desertification control office in the state forestry administration, is of the opinion that there are huge gaps in the country's efforts to reclaim the land that has become desert. At present there are around 1.73 million sq kilometers that have become desert in China, of which 530,000 km2 are treatable. But at the present rate of treating 1,717 km2 per year, it would take 300 years to reclaim the land that has become desert.  

Background
In early times, Korqin was not a semi-desert, but savannah-type woodland, in transition between dense forest and the steppe zone. The rolling sand-sheet was deposited during the last glacial period (12000 years BP). During 10,000 years of vegetation growth, thick dark topsoil developed. Since historical times, the region has gone through several cycles of man-induced desertification and subsequent recovery, when human pressure lessened. Fertile dark topsoil vanished and extensive dune fields gradually build up.  Overgrazing (by cattle, goats, sheep, camels, horses), clearing of land for agriculture and over-cutting of trees and shrubs in this vulnerable ecosystem have resulted in an increasingly severe land degradation and desertification.

Other Approaches?

There are many who do not believe the Green Wall is an appropriate solution to China’s desertification problems. Gao Yuchuan, the Forest Bureau head of Jingbian County, Shanxi, stated that “planting for 10 years is not as good as enclosure for one year,” referring to the alternative non-invasive restoration technique that fences off (encloses) a degraded area for two years to allow the land to restore itself.  Soil fertility, already critically low, has shown a sharp decline as all organic residues from crops are removed for fuel and fodder during wintertime. Willow and poplar stands are pollarded in autumn, before leaf fall, for the same purpose. The continuous removal of potential nutrients to the soil is not balanced by the relatively small amounts of manure and inorganic fertiliser applied to crops.

Problems

 Jiang Gaoming, an ecologist from the Chinese Academy of Sciences and proponent of enclosure, says that “planting trees in arid and semi-arid land violates [ecological] principles”.The worry is that the fragile land cannot support such massive, forced growth. Tree growth in Korqin is largely dependent on the presence of a high groundwater table, fed by percolation and inflow from the western and southern mountainous areas. The long-term trend of a decreasing depth of the groundwater table is due to an increasing demand for water to irrigate crops and for human and industrial needs. If the trees succeed in taking root, they could soak up large amounts of groundwater, which would be extremely problematic for arid regions like northern China.  For example, in Minqin, an area in north-western China, studies showed that groundwater levels have dropped by 12–19 metres since the advent of the project.

Progress So Far

As of 2009 China’s planted forest covered more than 500,000 square kilometers (increasing tree cover from 12% to 18%) – the largest artificial forest in the world.However, of the 53,000 hectares planted that year, a quarter died. In 2008 winter storms destroyed 10% of the new forest stock, causing the World Bank to advise China to focus more on quality rather than quantity in its stock species.  FAO report

But the program’s widespread tree planting campaigns typically allot only one or two species of tree to an area. Professor Jiang wrote in a 2009 Epoch Times article, “In Ningxia, for example, 70 percent of the trees planted were poplar and willow. In 2000, one billion poplar trees were lost to a disease (Anoplophora), wiping out 20 years of planting efforts.”  FAO report followup

More criticisms:  Wikipedia.

Great Green Wall in Africa - the Sahel

The Great Green Wall initiative is much more nuanced than simply planting a belt of trees across the continent: “Behind the name or the brand ‘Great Green Wall,’ different people see different things. Some people saw just a stripe of trees from east to west, but that has never been our vision,” he says. “In Niger, Mali, and Burkina Faso . . . natural regeneration managed by farmers has yielded great results. We want to replicate and scale up these achievements across the region. It’s very possible to restore trees to a landscape and to restore agroforestry practices without planting any trees. This is also a sustainable way of regenerating agroforestry and parkland.”

But it should be noted that the Great Green Wall is not designed to prevent the Sahara Desert from expanding. “We are not fighting the desert,” he says. “In the majority of the areas we are working in these 11 countries, the desert is not advancing. The [Sahara] Desert is a very stable ecosystem. Of course, there are some areas on the margins—for instance in Senegal, Mauritania, and Nigeria—where there are some sand movements. But from a geographic perspective, over time the desert has been relatively stable in this area.” (Source)

But some authors advocate  "a shift from planting trees in the GGW to utilizing shrubs (e.g., Leptospermum scoparium, Boscia senegalensis, Grewia flava, Euclea undulata or Diospyros lycioides), which would have multiple benefits, including having a faster growth rate and proving the basis for silvo-pastoral livelihoods based on bee-keeping and honey production.” (Connors and Ford, 2014 Sustainability)

Problems with Roundup?

Roundup  was recently labelled by the WHO as a "probable human carcinogen".

But farmers still love it: LibertyLink soybeans testimonial

Because it works:  Time-lapse video of herbicide treatment


I previously wrote about chemical use versus abuse in American agriculture, as well as some of the new stacked-trait GMO crops that are resistant to multiple herbicides.

Geoengineering: Salmon Runs and Sequestering CO2??

A project to fertilize the oceans with iron to sequester CO2 and feed wild salmon runs has generated controversy.

Four Forests Restoration Project

The draft EIS for the first 500,000 acres has been released.

Thinning work is already ongoing, but is behind schedule:

"The company said it is now thinning about 30 acres a day, which works out to about 625 acres a month. That’s a significant increase in the pace of operations since January, but still far behind the schedule established for the project nearly four years ago.  Ultimately, the company’s 10-year contract with the Forest Service requires it to clear 40,000 acres annually. In the nearly two years the company has had the contract, it has cleared about 3,700 acres. That puts the company about 70,000 acres behind the original schedule."

In my experience, in the Jemez, the major time lags are for completing NEPA and EIS and waiting for good prescribed fire weather.  Cutting the trees is fast and easy, and if they skip the fire (unnecessary and possibly environmentally detrimental) nothing should slow them down.  One of my other main criticisms from the Jemez is that they're not thinning enough trees to reduce the basal area to the most beneficial levels.  I know the ideal density and pattern of trees has been argued about ad infinitum... it seems they are trying to avoid conflict by cutting less trees, which totally defeats the purpose of preventing catastrophic crown fire.

Fence Line Contrasts

Sitting on the fence has become a metaphor for ambivalence, but actual fence lines are some of the clearest lessons in land management.  Fencelines can be the best place to study ecology, because most fences divide two different land management histories.  The easiest places to learn from fence line contrasts is where the land management history is known.  For example, along highway right-of-ways (ROWs), the strip of land between the road and the fence is almost never grazed, whereas the private or public alotment on the other side of the fence has almost certainly been grazed and/or farmed.

However, just because the ROW hasn't been grazed doesn't mean that it has escaped disturbance. While comparing two disturbed areas can yield some insights, the multiple factors at work will make cause and effect deductions extremely difficult. To find a good comparison, look for areas that are relatively far from the road; immediately adjacent to the road is a zone of disturbance, which can include vehicle traffic, trash, mowing, and runoff from the road (i.e. increased moisture).

The best comparison areas occur where the ROW is relatively higher than road (so there is no possibility of runoff and little chance of other human disturbance).  However, areas with cutbanks below them are not good for comparisons, because of excess erosion, different microclimates around bare rock or exposed subsoil, and lowered water table.   A zone of depression in soil moisture can also occur around ditches, trenches, gullies, roadcuts, etc.

The actual fence-line itself may have different species due to fence-line drip of dew and the ability of fences to catch seeds, especially tumbleweeds. (photo).

On the ground immediately beyond the fence there may be an area of extra disturbance due to cattle trails, etc, and any areas near stock tanks or gates are also likely more heavily used (and hence a more extreme contrast).  In cases with less grazing on the private land, such as on steep hill slopes, vegetation and soils may look quite similar across fence-lines.  Of course, there will always be variable disturbance on both sides of the fence, but that is part of the challenge and opportunity of observing fence-line contrasts.

The best comparisons are between areas relatively far from disturbance, close to but not immediately adjacent to the fence-line.  With a good undisturbed ROW as a control, the vegetation on the other side of the fence can be compared to the potential climax community of the site.  

Case Example:

I was recently watching fence-lines along NM highway 285 from Vaughn to Clines Corners, and noticed that typical overgrazed areas are Grama Grass (Bouteloua gracilis) monocultures or low-stature annuals with large amounts of bare dirt.  The ungrazed roadsides still have bare ground, but the vegetation has a starkly different structure and composition:  multiple grass species occur with different growth forms.  But even more noticeable than the grass growth is the shrub encroachment in an area that is pure grassland.  Without fire or grazing, woody growth, especially saltbush (Atriplex canescens) and  Chimisa (Ericameria nauseosa) increases markedly.

While some trees and shrubs (e.g. E. nauseosa) are resistant to grazing when mature, their seedlings are highly palatable.  Cows can completely eliminate woody overstories from riparian areas in a single generation simply be eliminating recruitment (through both grazing and trampling) of Cottonwood and Willow seedlings.  Grazing pressure on seedlings is important, but easily overlooked: as long as there are trees, we describe an ecosystem as a forest. And it may seem strange to say that cows are eating a forest. But without seedling regeneration, no ecosystem is sustainable.

That grazing impacts woody growth as much or more than herbaceous growth is well-known along rivers and wetlands, but I think has been less remarked on in uplands.  From this brief study of fence-line contrasts, it appears that even more of our grasslands would support shrublands were it not for either grazing or fire limiting woody plant establishment.

Two Soils from the Manzano Mountains

Overview SOIL 1

Apparently frost -heaving has raised very weak physical (WP) crust-mounds.

Closeup of a crust mound:  The surface has been softened and the top centimeter has filled in with fine sediments.  This top layer actually has more structure than the frost-heaved material below it, which readily crumbles into its constituent soil particles.  Note the plant root, at top center of the photo, growing in the fine sediment layer.

Where litter is present, but too discontinuous to form duff, the action of frost heaving rapidly incorporates pine and juniper litter into the mineral horizon.

Overview SOIL 2

Some areas have much more biological crust than others.  In these photos, the blue grama grass Bouteloua gracilis (BOGR) is more abundant with denser cryptobiotic crust.  The darkened biological soil crust (BSC) consists of free-living blue-green algae such as Nostoc. 

Compact SP (strong physical) crust with roots and moisture evident underneath.  These cracked peds come up in 5-8 inch radius plates.  Note how different this crust is from the previous “frost-heaved” crust.  This crust has significant structure to it and doesn’t immediately crumble into constituent particles.  

To Burn or Decay? What is the best management practice to deal with excess biomass?

 Conventional forest restoration in Western pine ecosystems involves reduction of biomass through thinning, which is sometimes followed by prescribed burning to further reduce fuels.  Burning slash piles sterilizes soil patches and doesn't decrease overall site litter, so broad-scale prescribed burns have traditionally been the best management practice to reduce fuel loads.

Passing over the discussion of what was historically "natural," is fire the best tool for increasing site productivity?

Apparently not.  Duff burning kills fungi, small roots, and (obviously) removes duff. “EMF mortality and complete duff reduction after fire have been implicated with poor tree survival and slow stand recovery in forest ecosystems world-wide.”  (Smith, McKay, Brenner, mcIver, Spatafora.  2005: Early impacts of forest restoration treatments on the ectomycorrhizal fungal community and fine root biomass in a mixed conifer forest.  (PDF)

As Stametz and others have pointed out, burning is not the best use of available resources: fire volatilizes stored nutrients such as nitrogen and organic carbon (N and SOC).  Fire can also form hydrophobic soil crusts, kill flora and fauna, decrease soil microbiota (important for decomposition), destroy tree roots, mycelial networks, and sometimes mature trees.  In contrast, decomposing organic material could increase site productivity.


Permaculture forest restoration?
Restoration projects proceed with multiple goals, either explicit or implicit.  One such goal has been the return of historical fire to degraded forests.  According to a large body of research, at least some pine forests historically experienced short return-interval, low-intensity fire.  However, using this to justify current prescribed fire approaches assumes that we can --and should-- attempt to replicate historical ecosystems.  I believe it is a fallacy to assume that ecosystems, like species, must be maintained in the face of changing environmental conditions; paleoecology clearly shows that species migrated independently throughout prehistory, indicating that the ecosystems we see today are only contingent associations of species; there may be better arrangements of species and better ways of managing ecosystems than relying on historical norms.

That being said, there are even better reasons to question prescribed fire in forest restoration.  If we abandon the idea of mimicking natural disturbances we are free to innovate more productive restoration methods.  For example, Permaculture-inspired ideas of maximizing species diversity and ecosystem services could inspire a new type of forest restoration.  I envisage a restoration program designed to optimize current site conditions rather than recreate history...

What Controls Decomposition Rate in Conifer Forests?

Source: Litter decomposition, climate, and litter quality. Link.

Nutrients:  Mn and N

Manganese and Nitrogen control forest decomposition, but in an unexpected way. Mn is an essential component of ligninolytic enzymes important for degrading litter in the later stages of decomposition.  But high available N can limit decomposition. The most efficient degraders of lignin and humic acids are wood-rotting or litter-decomposing white-rot fungi (Hintikka 1970; Hatakka 2001).  For several of the lignin-degrading white-rot fungi, high concentrations of low-molecular weight N compounds suppress the synthesis of the lignin-degrading enzymes (Keyser et al. 1978; Eriksson et al. 1990; Carreiro et al. 2000). 

Further, N has repeatedly been reported to react with remains of degrading lignin to form recalcitrant condensation products. Such products form chemically (Vahtras 1982; Stevenson 1982) rather than biologically.  Spaccini (1999) suggested that such bonds create a hydrophobic surface thereby resisting decomposition. The higher the concentrations of lignin and N in a litter material the more likely it seems that such covalent bonds will be formed. Using 106 sets of foliar litter comprising 21 tree species (both coniferous and deciduous) representing a wide range in chemical composition, Berg (2000) found a highly significant negative relationship between limit values and initial N concentrations in litter.

Many examples exist in which addition of N to a N-deficient system slows down decomposition, especially where organic matter with high lignin content is present (Verhoef and Brussaard, 1990; Carreiro et al., 2000). Nitrogen and other fertilizers may negatively influence specific groups of organisms, particularly microbes.  Any shift in microbial composition can have a negative effect on other soil fauna.  As a result, decomposition and mineralization may decrease. Additionally, plants can compete successfully with decomposers for nutrients.  (Neher 2003.)

What about pH?

In a review of 58 studies, Wardle (1998) found that temporal variability in soil carbon (C) was related most closely to soil N content in forests and soil pH in arable and grassland ecosystems. (Neher 2003.)

But a study by Parn et al adding ash to a pine forest to increase soil pH did not observe increased decomposition.  A large meta-review noted that 22-85% of treatment trials have failed to affect decomposition: “This analysis shows that Ca additions are not universally beneficial and provides insight into when Ca additions to forest soils are likely to be most effective." (Evaluating the effects of liming and wood-ash treatment on forest ecosystems through systematic meta-analysis. Carolyn Reid, Shaun A. Watmough)

Decomposition Rate and Ecosystem Integrity

Neher 2003 "Effects of disturbance and ecosystem on decomposition." is a great review of this topic.  (PDF)  They conclude that "decomposition of organic matter is a useful indicator of soil condition because it is measured easily and serves as integrator of the collective activities of organisms within the soil food web."  For example, slowing rates of decomposition serve as an early warning sign of pathology in forest ecosystems (Bormann and Likens 1979),  A difference in decomposition rate between similar sites implies either a change in the decomposer community or quality of the biotic and abiotic resources at a site. 

This WSU website has a great review of pine forest decomposition.