Add mercury time series [minor]

Hg/DMA_Protocol.md

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+# DMA Operating Protocol
+
+For a typical daily sample run
+
+### Cleaning Procedure
+To clean used quartz boats:
+
+1. Gently scrape ash out of quartz boats with spatula and/or kimwipes.
+
+2. Rinse quartz boats in acetone. Perform this step in the fume hood to prevent inhalation
+of harmful acetone vapors.
+
+3. Rinse quartz boats in deionized water and place on rack to air dry.
+
+4. Place quartz boats in DMA turntable.
+
+5. Open new “sample” file under the “measurements” tab.
+
+6. Enter 1.0 gram weight for each empty quartz boat to clean.
+
+7. Under the “Methods” tab, select “cleaning procedure”.
+
+8. Under the “Calibration” tab select current calibration file.
+
+9. Return to sample and save sample file as “trash.”
+
+10. Start DMA and the cleaning procedure begins.
+
+11. Once the procedure is complete, determine if any sample boats had high levels of Hg
+residue (>0.005 mg/kg.) These boats may need to be burned again.
+
+### Starting Up the DMA
+
+To prepare the DMA for sample runs each morning, it is necessary to remove residual Hg within
+the machine and check the accuracy of the calibration curve.
+
+1. Turn DMA-80 machine on using power button
+
+2. Open oxygen tank and adjust pressure to just below 60 PSI
+
+3. Login on the terminal by selecting “administrator” and entering the password “123456”
+
+4. Wait for the machine to warm up (about 15 minutes) and when it is ready the start
+button will become functional
+
+5. Under the “Measurements” tab, select the “sample” tab and select the blank sheet to
+start a new file. Save file as “trash”
+
+6. Run two “ghost samples” i.e. no boats in positions 1 and 2 on the turntable to vaporize
+any mercury that may remain in the system. Select “clean procedure” in the “Methods”
+tab.
+
+7. Under the “Measurements” tab, select the “sample” tab and select the blank sheet to
+start a new file. Select the add line button for each sample. Save file as trash.
+
+8. Run two samples of powdered standards dorm and dolt to determine machine is still
+accurately calibrated. Select “organic fish” in the methods tab and current calibration
+curve in the calibration tab. Dorm and dolt mg/kg of Hg should fall within the given
+ranges.
+
+### Running Samples
+
+When running bird samples in the machine, each run must be accompanied by blanks and
+standard reference materials to make sure the machine is performing the analysis accurately.
+
+1. Under the “Measurements” tab, select “Sample,” and select the new file button to
+create a new sample file. Select the add line button for each sample.
+
+2. Under the “Methods” tab, select organic fish method
+
+3. Under the “Calibration” tab, select desired calibration curve file
+
+4. Return to “Measurements” tab and save sample file with desired file name (e.g.
+mm_dd_yyyy_feathers_LG)
+
+5. Place a clean and empty sample boat in turntable position 1 as a blank. Enter 1.0
+gram for the weight.
+
+6. Weigh around 0.025 grams of dorm, dolt, and tort standards and place boats in
+turntable positions 2, 3, and 4. Enter actual weight and sample names in sample
+sheet.
+
+7. Weigh albumen, blood, or feather samples one at a time using analytical scale and
+place boats in the correct turntable positions. Record data from samples on data
+sheet.
+
+8. Enter sample ID and weight in grams in the sample table.
+
+9. Save sample file again. After all samples have been measured and placed in the
+turntable, hit the green start button to begin the analysis.
+
+10. Once the run begins, make sure the method and calibration selected are still
+selected (*sometimes the machine switches the calibration file on its own, we don’t
+want that to happen)
+
+11. Once sample run is complete, save the measurement file, and record the mercury
+concentration mg/kg on the datasheet.
+
+12. Place datasheet in binder

Hg/Feather_Mercury_Collection.md

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+# Feather Sampling for Mercury
+
+### Background and Rationale:
+Mercury is a heavy metal that has no known biological function in any organism.
+It is therefore not a trace element, and a contaminant at any level. Its detrimental
+effects on wildlife at high doses have been known for some time (severe neuronal
+degeneration, powerful developmental effects) but the effects at low levels are only just
+being discovered, particularly in wild populations of fish and birds (reproductive failure,
+endocrine disruption, loss of appetite, increased susceptibility to disease, and others).
+Under anaerobic conditions prevalent in many wetlands, elemental mercury (the
+stuff in thermometers) may be converted to methylmercury as a byproduct of the
+metabolism of sulfur-reducing bacteria. Methylmercury is at least ten times more toxic
+than elemental mercury, in part because it can cross the blood-brain barrier, and in part
+because it is excreted very slowly. Because of the latter property, it also bioaccumulates
+very efficiently in wetland food webs.
+
+In most terrestrial and lake systems, mercury eventually accumulates in
+sediments where it is largely unavailable to biota. But in shallow wetlands that wet and
+dry regularly, mercury in sediments is regularly re-exposed and recycled. So wetlands
+like the Everglades are extremely good at keeping mercury available, and keeping it in
+its most toxic form.
+
+During the late 1980’s and 1990’s, Everglades biota were extremely
+contaminated with mercury, with some of the highest values measured in vertebrates
+recorded – this was true for predatory fishes, mammals and wading birds. The
+contamination from mercury resulted in direct mortality of some Florida Panthers,
+endocrine disruption in birds, and probably reduced fecundity and survival in birds and
+fishes. Human consumption advisories were issued for Largemouth Bass and other
+predatory freshwater fishes.
+
+The mercury was coming largely from municipal waste incinerators in the urban
+areas of Miami and Ft. Lauderdale. Beginning in the early 1990’s, federal legislation
+mandated that mercury be taken out of household batteries, a major source of mercury
+in municipal waste. Florida (and later federal) legislation also mandated the installation
+of scrubbers on municipal waste stacks, further reducing emissions of mercury aerosols
+and particulates.
+
+After about a 7-year lag time, mercury concentrations in Everglades biota began
+dropping precipitously – a 75% reduction in two years, for example. The existence of the
+mercury problem in wildlife, and the massive reduction in contamination, were both the
+result of a long-term mercury sampling program in the Everglades for sport fishes and
+for wading birds.
+
+Although mercury may have declined for good, there remain good reasons for
+continuing to monitor for mercury contamination. First, it’s not clear that mercury will
+remain low – in years following droughts, for example, we may expect to see spikes of
+mercury that result from re-liberating mercury tied up in sediments. These spikes could
+turn out to be a natural experiment that allows further understanding of the effect of
+mercury on nest success. Second, other mercury sources could emerge over time –
+some of these might be through atmospheric deposition, or other currently unknown
+local sources. Keep in mind that none of the mercury contamination or its decline in the
+1980’s and 1990’s would have been discovered without fish and bird monitoring.
+
+### Sampling – tissue, age group and species
+
+Nearly all of the mercury in fish is in the methylated form, and consequently the
+same is true in birds. Birds are able to excrete methylated mercury primarily through
+feathers as they grow, largely because methylmercury has a very strong affinity for
+keratinized tissue. So feathers serve as an accurate record of the amount of mercury
+circulating in the birds body at the time that the feathers were grown. The
+concentrations of methylmercury in feathers are quite large relative to the amounts in
+other tissues, and so feathers give a strong and definite signal if mercury is present.
+Feathers from adult birds have two problems – we don’t usually know when they
+were grown, and we don’t know where they were grown. Thus they could represent
+mercury contamination acquired from outside the Everglades. Young birds are an
+excellent indicator, however, if feathers are collected while they are growing. We know
+from research that not much mercury gets into young from the egg resources, and we
+also know that all of the food the chick gets comes from an easily defined area
+surrounding the colony. Chicks are also growing feathers at a rapid rate, and are getting
+lots more food per body weight than are adults – so they are excellent bioaccumulators,
+and excellent bioindicators of mercury in prey items in the surrounding marsh.
+As an aside, the chicks are growing so many feathers during the fast growth
+period, they are in effect protected from the effects of methylmercury – nearly all gets
+excreted into the feathers. It’s when they stop growing feathers and fledge that the
+nasty effects of mercury probably come into play.
+
+We sample feathers from Great Egret chicks – these animals feed almost
+exclusively on fish, they are relatively high in the trophic web, they nest reliably from
+year to year, and typically nest throughout the study area. So we can get good
+geographic representation that is reliable from year to year.
+
+Typically, there are large differences in contamination between colonies in
+different parts of the Everglades as a result of “hotspots” of mercury contamination.
+These differences are probably due to a complicated mix of water and soil chemistry
+factors that favor or disfavor the bacteria that methylate (or demethylate) mercury.
+
+### Sampling protocol
+
+#### Safety: 
+
+Make absolutely sure everyone has eye protection and wears it during
+the capture attempt. Those with dime store sunglasses should not consider them
+adequate protection. They also tend to be taken off in cloudy or closed canopy
+environments, so make everyone who doesn’t were prescription glasses to carry and
+use safety goggles or something comparable. Take care too if prescription glasses are
+small. The bird’s bill can slip under or around them and still reach the eye.
+
+#### Where to sample: 
+
+Aim to sample chicks from 5 – 10 colonies. In the past, we
+have usually sampled from Alley North, JW1 (not recently active), L-67 (a.k.a. Horus),
+Vacation, Hidden, Tamiami West, Mud Canal, and 3B Mud Canal. Typically, one or more
+of these colonies will not be active or accessible in any year, so we may substitute
+others. We are now collecting in cooperation with the SFWMD. Check with Ms. Shane
+Atkins ( [email protected] ) before the nesting season begins in earnest.
+
+#### When to sample: 
+
+When chicks are large enough to walk and young enough they
+do not walk or fly fast enough to escape you. The older, the better. To gauge this, you
+need to know the approximate date of laying eggs or hatching chicks – this should be
+done either from aerial surveys or (preferably) from visits on the ground.
+
+#### What to collect: 
+
+Feathers from the scapular region – middle of the back in
+between the shoulders. Feathers should be fairly well developed to obtain enough
+material – newly erupting ones are not appropriate. If the birds you are sampling are
+mostly down, you are way too early. The birds need to be able to stand up on their own,
+and probably run from the nest. Feathers should be pulled individually (not in bunches)
+with a quick, firm yank in a direction parallel to the angle of insertion in the skin. These
+feathers may be well connected to the blood supply, being growing feathers. If a feather
+shaft is broken off, it could allow heavy bleeding – make sure the entire feather base
+comes out. If it bleeds heavily, try to remove all of the shaft, and damp bleeding with
+cotton until it clots. Collect at least five feathers 2 – 3 inches long, and ten if you can get
+them.
+
+Be sure to measure the bill length (culmen, tip of bill to beginning of skin on
+dorsal surface of bill) for each bird – this gives us a way to correct each sample for age.
+We have also been taking weight information, but this may be optional. Check with
+SFWMD.
+
+Very often, the birds will regurgitate their most recent meal. This is unavoidable,
+and since you cannot stuff it back in, you may as well collect it. Take extra ziplocs, and
+label the sample by date, colony, and culmen of the bird that threw it up. Keep boluses
+from individuals separate. Place in a cooler on the boat, and in the freezer AS SOON as
+you get back home.
+
+What to do with the bird after you’re done: Release it back into the nest or as
+close to the nest as is possible. Be sure to get the rest of the crew out of the nest area in
+the future direction of travel. Sometimes the juv seems frozen after its release and may
+
+be experiencing some level of stress or injury. In that case, walk slowly up to it and
+encourage it to move a foot or two. It’s wise to carry a small first aid kit to treat any
+injuries, bird or biologist.
+
+#### Marking and storage: 
+
+Each feather sample should be placed in a marked paper
+envelope or ziplock bag. Paper envelopes are preferable because pulpy tissue attached
+to the base of the feather will rot and not dry in plastic. However, plastic bags may be
+used in the field in wet conditions. If plastic is used, samples MUST be transferred to
+paper as soon as you return for the day. Mark each envelope sample individually – never
+mix birds. Note the colony, date, culmen, number of chicks in the nest (if available) and
+the hatch order of the chick in the nest if known.
+
+#### Sample size in each colony: 
+
+We try to get between 10 and 20 individual birds in each colony. We only sample one chick from each nest, and only the eldest (largest).
+
+How to catch chicks – Chicks may very well be large enough to leave the nest by
+walking or climbing at the age you are supposed to be sampling. Often the trick is to
+approach the nest from two or more sides simultaneously. Mirror poles help – try to
+hook the bird’s leg, or apply pressure on the head or neck (without hurting the bird)
+enough to slow the bird down to the point that it can be caught. Speed and agility are
+important here, so do those leg stretches and hyperventilating before you get into the
+colony. Note that at this stage if the bird leaves its nest it can generally get back in on its
+own. So if you chase but cannot catch a bird, don’t fret about its fate too much.

Hg/README.md

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+# Feather Mercury Monitoring
+
+Measurements for Hg levels in individual feathers. 
+
+### Field Collection Methods
+
+Field collection methods are described in Feather_Mercury_Collection.
+
+### Hg Analyzer Methods
+
+A quick guide to protocol is listed in DMA_Protocol.