We started to collect GPS locations for specific findings using Epicollect5 about a year ago. Now what? In a previous blog we discussed distance measuring using tape and compass measurements and GPS locations. This method exceeds that technology by light years.

A general map plot of all of our findings is available on the Epicollect5 data site. If you want to see something specific you can make a custom map to see where all of our areas of special interest are located using Google Maps! Even though the project is public you must create a login to access the epicollect5 site to download data. Go to Epicollect5 and log-in.

In Epicollect5 the data comes in two forms. The first is the data Table. The second is a Map of all of the sightings. You can see it by clicking on the word map located in the upper right side of the site banner. The third is a data file available through Download. If you want to map a specific set of data you can do this by some manipulation of the data. You will use two types of software. Use Excel for data manipulation and Google Maps for custom mapping. You must have a Google identity. Follow these steps:

MOVING DATA FROM THE EPICOLLECT5 DATA BASE:

• In your web browser search for Epicollect5
• On its home page upper right of the navigation banner click on FIND
• Enter the name Everglades Ark the query box
• When the image of the site appears click on VIEW DATA on the right side
• View data opens the data page the Epicollect5 for the Everglades Ark
• In the left of the view data navigation banner click on Survey and Catalogue
• The table of the collection will appear
• On the right side of the navigation bar there are three choices click on Download
• A new drop down menu will open on the left side with several selections
• Select EC_Auto, Select your Timeframe, Select CSV. CSV (comma delimited) works well for Excel.
• Click on Download. The entire file will appear in your downloaded files folder.
• Once downloaded you will find several data sets in the folder. These folders contain the sets named in the headings of the Epicollect5 folders
• Click on the data set appropriate for your interest
• To use the data, select Open the download with the Microsoft Excel. Your manipulation of the Excel date does not effect the Epicollect master data file.

MANIPULATION OF THE DATA IN EXCEL:

• In Excel open file called “1-survey_and_catalogue.cvs”
• Sort the desired new data sets for the selected criteria. Be sure to lock the appropriate fields. For mapping, always include the GPS columns and any mix of data columns to match your interest criteria.
• Make a new Excel file with an appropriate title (like December flowering plants.cvs) and paste the data into a new sheet.
• Save this to your computer desktop as a .cvs file

MAPPING WITH GOOGLE

The goal is to plot a specific selection of the data for characterization of a set of the collection. For this we can use google maps through their portal at: Visualize your data on a custom map using Google My Maps

• Log in to your Google account
• Go to Google My Maps: https://www.google.com/mymaps
• In the welcome pop-up, select Create a new map:
• In the text Untitled map, edit the map title and description in the Map title dialog box:
• In the Description dialog box enter a description of your map
• In the menu, select Import:
• Select your saved data sheet from your desktop. This will be the first data layer we upload. Drag and drop your GPS data file on your desk top to the Import Your Data into Google Earth. Following the instructions at Visualize your data on a custom map using Google My Maps. After uploading your data, you’ll be asked to select the column(s) with location information, so that your data will be correctly placed on the map (e.g. columns with latitude and longitude information). For this example, select the Lat and _ Long columns_, and hit Continue. You can hover over the question marks to see sample data from that column.
• Pick the column you’d like to use to title your markers. For this example, select the Date column and click Finish:

WORKING WITH GOOGLE MAPS:

The Google map function is very versatile and very powerful. You can enter multiple layers of data on the same map. The maps can be enhanced with colors, icons, add titles, search for types, collaborate with colleagues, all available in the instructions on the GoogleMap instruction site. For example on one map you could overlay flowering undergrowth plants, blooming in the month of February, where observations of Monarch butterflies were recorded. Different symbols and colors could be used to separate the two types of data for easier visualization. You can measure distances, map directions, chart changes in observation patterns, estimate rate of spread of changing conditions… it is almost endless!

It is just that easy ! Try it out using the technique described. You will be amazed !

WE NEED MORE OBSERVERS IN THIS PROJECT. GO TO OUR CONTACT PAGE AND VOLUNTEER.

References:

Visualize your data on a custom map using Google My Maps

https://www.google.com/mymaps

Please send comments and let us know what you discover.

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#Google #map #excel #database #create map #custom map #GPS

Ode to Eko

Eko Eko burning bright
In thy heart beats delight.
So quiet and calm, hold your power
Waiting for the rightful hour.

That immoral hand comes to spy.
I cannot ask the question why.
All I know is that I must bite
And I do with all my might!

Through the cage comes a shot.
The pain is great, searing hot.
Man kills me, He makes his choice
Species die without a voice.

Eko Eko eyes were bright.
Now they're dark as the night.
What loss we have no more to see.
What have we lost for you and me.

By John Knapp with inspiration from: Bill Blake, David Attenborough and the late Eko, Malayan tiger, Nalpes Zoo. 

Please donate to support the excellent work of the Naples Zoo Donation

# Eko #tiger #Naples #zoo #shot

Ref:

Naples Daily News

Naples Zoo

Comments:

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Green Fluoresence Protein

I’ve seen this green color in the past. It seems relatively obvious now that the green color that we are looking at in the reefs is wild Green Fluorescing Protein (GFP)^1. It is one of the most important biologic markers used today. It was initially discovered in a jellyfish, Aequoria Victoria, and reef polyps. Its development as a synthesized reagent was awarded the Nobel prize. It is one of a class of reagents that radiate fluorescent green, red, yellow and blue when exposed to special wavelengths of light. They are used as bioluminescent markers in biochemistry and cell biology in a wide array of research and industry. I used this marker some years ago when using molecular imaging to search for circulating tumor cells (CTC) at the Barbara Ann Karmanos Cancer Institute, Tumor Biology and Microenvironment Program, the School of Medicine and the Bioengineering departments of Wayne State University and the associated NIH National Cancer Institute in Detroit.

Here are two examples of green and blue fluorescent proteins seen in two different coral species as they respond differently to the same blue light. Note that the GFP reef corals are stricken with SCTPD while the red fluorescent protein (RFP) reef coral seems to be unaffected.

The colorful green bioluminescence occurs when the GFP is exposed to a particular energy of blue light. The light excites electrons in the molecule which, when they return to their rest state, emit green light. In this case blue light exposure radiates green fluorescence. Cells continually manufacture the florescent protein for replacement as it matures.

Wouldn’t it be ironic to think that the polyps that gave us the GFP may help us to understand the cause of their disease?

I’ll make this very clear. This is just my conjecture. I am not an expert in any of the following issues. This is the realm of highly sophisticated experts in multiple specialized fields.

Thoughts on tracing down an idea for cause and effect

There may be a relation between protein structure and spectroscopic function. Loss of fluorescence may indicate that the GFP molecule is misfolded, split or destroyed. There are some things that can cause these molecules to stop performing including: insufficient molecular oxygen, increase in temperature above 70 degrees Celsius (15.8 F); exposure to an acid with a pH less than 5.4, age degradation, or protein modification. Some of these are not likely because the water temperature, acidity, and the rate of aging of the reef in the ocean are relatively constant. Temperature, acidity and aging is not what is at work in the polyps or in the reef. What is not constant is a biologic process which may alter the GFP. A virus or other pathogen could invade a cell and change the proteins including production of GFP. Lack of fluorescence may be a direct symptom of a disease. GFP labels living cells therefore it can be used to monitor infectious processes in plants and animals.³ GFP behavior part of a larger process causing death of the polyp complex.

Problem statement:

Is there a direct correlation between the lack of the GFP and the cause of SCTLD?

Method:

Establishing a causal relationship. Is the disease infectious:

In an earlier posts Fluorescent Photos to Measure Reef Viability (2) and Hunting the Cause of Stony Coral Tissue Loss. Looking at the Reefs with Scientific Vigor (3) I suggested a test of infection showing a controlled method of applying the diminished green polyps or BFP (blue fluorescing protein) polyps to GFP polyps. If the trial infection works then the cause is either a bacteria or a virus. This may depend upon identification and use of a vector organism which may be critical for the test to work.

If there were a virus in a polyp or associated zooxanthellae, a comparison of DNA before, during and after exposure could be made. Sample both at various stages of the disease using the GFP as an indicator of the staging. Additionally, special techniques of microscopic dissection, staining and a variety of light and electron microscopy should show some evidence. The polyps and the zooxanthellae are higher level organisms and their DNA should to be decoded. If the disease is virus specific, PCR testing may be done to discover it. DNA sequencing and Crisper technology might be used to find a place in the DNA where a lethal virus could attach.

Discussion of findings:

If the pathology is the result of viral infection of the polyp, crisper technology could be used to modify the DNA to engineer a resistant strain of stony coral. The strain could be cloned and reproduced in vast colonies. Multiple coral polyp types could be added to make a more representative colony. The harvested viral resistant polyp strains could be explanted back onto the dead wild coral reefs that were cleaned of dead coral tissue, algae and debris. These are all untried technologies.

Spread of the disease:

Polyps are filter feeders. They harvest their sustenance from the organisms in the float of water of the ocean directly into their gut. they have a mutualistic relationship with some species of dinoflagellates found in the ocean. This sounds like a combination of opportunity: portal of entry, susceptible host, and an obviously virulent pathogen. Viruses are frequently carried by arthropods (insects) that can spread the virus in the viral particle of their bodies. while not arthropods, dinoflagellates (DFs) can freely interact with coral polyps. They could inject a particle or a toxin into host cells. Arthropods could also infect the DFs or the polyps using their sharp, piercing or cutting anatomy as do mosquitos, ticks, flees and others. Viruses can also spread by through the water. An arthropodal nymph acting as a vector could easily be carried by currents, ships and wind for hundreds or even thousands of miles where it could start another colonial infection.

There may be a number of contributing factors such as rising water temperatures, pollution, habitat destruction, water depth, invasive species, symbiotic species relationships which may exacerbate the process. This deserves further investigation.

Search for complicating factors:

• How long does GFP continue to fluoresce without replacement
• Discover the virus pathogen and its structure
• Unravel the complexities of the method of action of the pathogen
• Geographically locate areas of afflicted coral
• Calculate the rate of spread, rate of infection, time from onset to death
• Identify the origin of the disease and the vector
• Identify potential causes of increased susceptibility of the reefs
• Search geological and anthropological history for episodes of similar reef diseases

Discussion on actions:

• Consider possible unintended consequences of well intended actions
• Search for other possible causes such as prions, rickettsiae and other outliers.

Next step:

• Form a team of experts in the necessary fields
• Estimate the cost of the project in stages
• Form a group of interested parties of influence
• Promote the idea seeking funding and permission to act on findings.
• Begin the search for the cause and form an action plan
• Begin at a fixed base location with relative separation from recreational or commercial activity
• Start small with two isolated sites each with differing characteristics in reef health
• Engage in work to slow or stop SDTLD

Limitations:

Not much is known about reef ecosystems, polyps and their physiology, diseases, and pathogens. Additionally, they are part of a larger oceanic system of which we have limited knowledge. The current blog is biased by knowledge of land based diseases. There may be causes of which we are completely unaware. It is a voyage of discovery aboard Everglades Ark.

I am very interested in your thoughts on the subject of reefs, polyps, fluorescence, viral biology, or any of the topics which are presented. Additionally, if you are interested in helping or would like to report on your findings please contact me.

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References:

1. The GFP page
2. Fluorescent Proteins
3. Split green fluorescent protein as a tool to study infection with a plant pathogen, Cauliflower mosaic virusFluorescent protein microscopy
4. Algorithms and Datasets for Colour Science
5. Spectrum or excitation and emission of protein fluorescence microscopy

#RFP #GFP #fluorescing protein #vector #SDTLD #stony coral tissue loss disease #virus #crisper #spectroscopy #polyp #crisper #DNA

Stony Coral Tissue Loss Disease in Florida Is Associated With Disruption of Host–Zooxanthellae Physiology is a must read for those who seek more in-depth information ¹

This blog is a continuance of previous blogs Death in Paradise and Fluorescent Photos to Measure Reef Viability. In this post I’m looking at two things: 1. Possible SCTL by infection and 2. Genetic engineering a replacement polyp to grow new SC surface tissue. Here is what can be done with fluorescent lighting.

Method:

Expose a fixed area to white light and with UB light. Photograph the area with the appropriate light filter. Similarily, expose variations of coral varieties, stages of disease, seasons, depth and other variables. Compare data among and between them.

In Figs. 1 and 2 look at the condition of the coral. They are suffering Stony Coral Tissue Loss Disease (SCTLD) with accumulation of dirt and covered with algae. This was typical of many areas of the reefs.

In the previous blog , a fixed area was photographed with illumination to near ultraviolet (UB) light. Data of light, hue, chroma, luminance (CieLab. color space) was recorded. This can be seen in Fig. 3.

Identification of stages of SCTLD:

Fluorescence may facilitate a systematic description of SCTLD at the gross and microscopic levels. Photoshop CieLab, combined with white light examination may provide a better description of the disease stages.

Further research to be done to test infection-by-transference hypothesis:

A section of the coral with healthy and distressed polyps could be easily identified and biopsied as described by Woodly et.al. This identified area would look like the amber outlined section in Fig. 5.

Method to rule out the infection-by-transference hypothesis:

1. Isolation of healthy SC GFP polyps
   • Propagation of healthy polyps in sheet form
2. Isolation of distressed polyps
3. Application of distressed polyps to surface of healthy polyps
4. Examination of time-lapsed photographs to determine if application causes distress and/or death of healthy polyps.
5. Repeat
6. Evaluate results
7. Refine method and repeat

Method to detect the source of the infection hypothesis:

• Select the healthy GFP polyps and their associated Zooxanthella 
• Extract the DNA²
• Select the FP polyps
  • Extract the DNA²
  • Sample for toxins produced by the dinoflagellates
• Contrast and compare the two samples
• Identify the point of difference.

Further research to be done:

• Reengineering from knowledge of this area as shown above is a path not yet reported. Replacements for a variety of SC polyps might be engineered with the purpose of replacing the currently susceptible species.
• Consider a new infective agent or toxin that is otherwise undescribed. (prion?)

Reef Quality Assurance:

In order to determine the changes in large areas of a reef wall, fluorophotography may be applied for a quick scan. Large scale examination of a reef wall could be done using the photographic method described below. Fig 6. shows an area low in expectation for SC polyps. Fig. 7 shows the same area using UB lighting confirming that expectation.

A wide angle view can show an area which fluoresces. This photograph shows an area of coral reef with heads illuminated with UB light that brightly reflect GFP. Estimates of the viability of an entire reef can be determined based on a percentage of an area which is bright.

Significance:

From the previous blog it was shown that coral fluoresence shows viable stony coral polyps. Reefs do vary in terms of variables mentioned above. Reef color value does indicate viability across all species. CIE Lab values do indicate the progress of SCTLD.

At least one method of reef biome intervention may be possible. Reef interventions can be measured at a large scale.

What measures should be initiated:

• Pursue testing and rule out an infection or toxin hypothesis
• Test genomic differentiations searching for genetic causative agent
• Systematize wide angle, macro and micro fluorophotography methods for reef quality assurance purposes
  • Use high resolution macro photographic camera
  • Use microscopic dissection and photography with UB lighting
  • Use variable blue to ultraviolet wavelength light sources in photography

Help is needed in this effort. If you have comments, questions or greater interests in the investigation and fight against SCTL disease please leave remarks and comments.

References:

1. SCTLD in Florida
2. A genomic view of the reef-building coral Porites lutea and its microbial symbionts

#Fluorescent photography #SCTLD #stony coral #green fluorescing protein #GFP #BFP #DNA #Zooxanthella #polyps #coral #Caribbean #Lab #dinoflagellate

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The condition of the Caribbean reefs has been observed for decades thanks to dedicated marine biologists and experienced scuba divers. I wanted to observe, document, and inform others about the disease which is unseen and under-appreciated by most during this time of our human Covid epidemic. The disease is called Stony Coral Tissue Loss Disease (SCTLD). See previous post Death in Paradise. Also see Marine Life Could Be Like This In SWFL.

I believed that for the observation of reef polyp viability an adjunct to visible light one should consider a non-invasive test using reef fluorescence observation to determine SCTLD extent and its progress. The green fluorescent proteins (GFP) of many living reef polyps can fluoresce in response to exposure to specific light wavelengths.¹ They exhibit variations in fluorescence in terms of wavelength (color) and intensity (brightness).² We will call this reef temperature. Non-viable reef polyps and plant forms appear to differ significantly in fluorescent wavelength and dimmer luminance or appear black.⁷

Examples of observations and photographs that I made made between December 12 and December 14, 2012 in the Caribbean Site #16. The light sources were: White light from Nikonos S1B flash and Blue light (Ultra Blue UB) source from SeaLife FluroDive gear which generates Ultra Blue (UB) light.^3,4 No GPS or location descriptions are provided. Imbedded in the images are CieLab* notations.

Fig. 1a shows an area of coral with damage probably a result of SCTLD. Fig. 1b shows a similar area with UB lighting where the damage has lost the polyp layer and the accompanying protein of those polyps is missing. Since the polyps are the source of the fluorescence when dead they do not reflect.

This small area shown in Figs. 2a and b may show the advancement of the process where mottled dark areas without fluorescence are present. Green areas circled in amber are not yet afflicted. The circled blue areas show disease in progress and black areas are dead. The different spectrum shows compromised surface. The amber circled areas were color sampled via Photoshop. The blue area sampled is smaller than the green area. The blue area L.a.b. is 54,-48,-33. The green area L.A.B. is 15,20,26. This is a remarkable difference in light values.

These color extracted areas in Figs. 2ac and 2d permit visualization of the percentage of healthy and compromised polyps.

The Fig. 3 series of photos show another reef area.

Figs. 3a through 3d show a different variety of stony coral which is not suffering any apparent SCTLD but is surrounded by areas that are dead coral overgrown with algae.

CieLab:

CieLab⁵ is a photometric method of describing a three dimensional color space. It is more comprehensive than RGB, Panatone, CMYK or HSB.

This appears to be a useful method for assessing reef viability. Here is what I propose:

The Important question (null-hypothesis):

Why aren’t reefs all the same color temperature?

Method:

Expose a fixed area to white light and the same area with the UB light and photograph each using an appropriate filter. Similarily, photograph variations in coral species and other variables and photograph them. Compare the photos using Photoshop to interpret the light of the ultra blue photograph. Record the data of light hue, chroma, luminance (CieLab. color space )

Materials:

• UW camera with filter (SeaLife)
• UW fluorescent blue light lamps aimed for even distribution of light
• Plastic pipe square frame 1 meter X 1.5 M with fixed 1.5 M legs to support camera
• Software (Photoshop and Excel)

Exposure technique:

Establish a standard normal site. Select an ideal healthy reef area and use this as a basis. Photograph it using the method listed above with the camera at the center of a standard square. Mark GPS location (Drop a weighted line from dive boat). Include other very pertinent information like temperature, current flow and other variables as noted below.

Select a typical affected reef test site and use this as a basis. Photograph it using the method listed above with the camera at the center of the square. Mark GPS location (Drop a weighted line from dive boat). Repeat additional test sites.

Data collection technique using Photoshop for each photo:

Data is collected in a selected photo area as numeric readings in CieL.a.b.. Include a standard sample (B&W and Color). Collect CieL.a.b. data in photo as a fraction or total picture.

Number of sites

The number of sites depends on the area of interest and existing information. Examples include proximity or remoteness to areas of traffic or resort, city, sewage effluent, runoff’s, windward, and leeward sides of island . Ten to one hundred sites are conceivable.

Variables:

Seasons, lunar cycles, temperature, months, storms, rise in water level, toxic products, population growth, recreational usage, associated life forms and structures.

Findings:

Findings could be collected in an Epicollect5 data base in a standard fashion⁶. This would be available to the public for observation or assessment and downloadable in a cd file. The file could be manipulated in Excel at the discretion of interested parties. At this time I have included a simple table for data presentation.

Num.

Subject

GPS

Time

Date

Tempe C

Source

Photo #

Pic Area

L

a.

b.

Observer

2b

sc

18:45

27.2

UB

DSCI12795

G

54

-48

-33

Knapp

2b

sc

18:45

27.2

UB

DSCI12795

B

15

20

24

Knapp

2a

sc

18:50

27.2

W

DSCI127

Knapp

3d

ag

19:15

27.2

UB

DSCI12797

A

9

27

0

Knapp

3d

sc

19:15

27.2

UB

DSCI12797

B

20

40

-68

Knapp

3d

sc

19:15

27.2

UB

DSCI12797

R

21

34

-1

Knapp

3d

sc

19:15

27.2

UB

DSCI12797

G

81

-60

-40

Knapp

3c

sc

19:15

27.2

W

DSCI12798

Knapp

Data manipulation in Excel:

Statistical analysis of findings by comparing normal to test site data will be done when an adequate number of observations are gathered. This could imply what is happening to the reef by comparing measures between and among species and locations. Measurement may make possible knowledge based judgements.

Results:

Given this limited data base all conclusions are still speculative. In image Fig. 2b area G exhibits a Luminance value 54%, 48% green value, and a 33% blue value. In image 2d area B L is 15%, 20% green value, 24% red value. This suggests that viable polyps in this image are 34% more luminescent, 28% more green and 57% more blue than their counter parts in the blue areas. In image Fig 3d area G is very polyp viable and area R appears to have little or no polyp viability. Areas G in both Fig 2b and 3d are remarkable similar. They may have similar GFP. Better controls and more numerous observations may provide improved accuracy.⁸

Conclusion:

UW Fluorophotography seems to have the ability to distinguish viable from absent, unhealthy or dead coral polyps.

Significance:

This pilot study suggests that the null-hypothesis may be refuted. The answers to some important questions can be implied from the data. All of the reefs are not the same color temperature. This may point to answers for these questions. Reefs do vary in terms of variables mentioned above. Reef color values indicate viability across all species. Color does indicate the progress of SCTLD. At a larger level; there is a general trend in reef viability, measures taken can show an improvement, stabilization, or degradation the reef in size, viability, or level of SCTLD. This answers can be substantiated in a more controlled test with measures mentioned in the statement of method noted below.

This trial test suggests that there may be additional documentable methods for judging the reef system. These important questions need to be addressed. Should intervention of reef life be done? How do you know if interventions are effective?

These measures should be initiated:

• Expanded use of communal data base
• Expanded data collection to multiple data collectors.
• Improved method;
  • Photo fluoro-microscopy of sectons of coral polyp growth
  • Differentiation of CieLab images of coral species
  • Inclusion of a photo standard B&W and Color into photos
  • Stabilization of position of UW camera
• Further infrastructure development;
  • Capacity of shores and islands to continue development
  • Sustainability measures
    • Water supply, sewage treatment, electricity supply, 
• What is the expectation for the future?
• Can information of effectiveness of measures be transferred to other locations?

The motivations are critical to the stakeholders of the entire Caribbean:

• Should further research be done? 
• Will reef conditions effect resort business?
• Should reef recreation and fishing business models be modified?

My hope is to continue to help in the management of this problem and that you, too, are willing to help. Please let me know of your interest and comments. Please look for the next post in this series to see plans for further work in marine biology.

References:

1. Applying new methods to diagnose coral disease.
2. Fluorescence-Based Classification of Caribbean Coral Reef Organisms and Substrates David G.
3. Fluorphotorgaphy Zawada , Charles H. Mazel
4. SeaLife
5. Three dimensional representation of CieLab space
6. Epicollect5
7. Fluorphotorgaphy
8. Fluorescence-Based Classification of Caribbean Coral Reef Organisms and Substrates David G. Zawada , Charles H. Mazel

Important supporting references:

• Glowing coral | University of Southamptonhttps://www.southampton.ac.uk › news › 2017/07 › glo…
• Spectral Diversity and Regulation of Coral Fluorescence in a …https://www.ncbi.nlm.nih.gov › articles › PMC4479885
• https://doi.org/10.1371/journal.pone.0084570
• Fluolight
• Florida Keys coral disease

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#fluorophotography #green fluorescent protein #CieLab #color temperature #research #marine biology #Caribbean

This is not a British mystery drama. In fact, it is a serious very real mystery story with life and death consequences that will affect all of us. Earlier I posted three blogs titled Florida Reefs Could Be Like This. This blog is about a more likely scenario for our reefs and coastline. The scenario is affecting all of the Caribbean as we watch.

I had an eye opening under water SCUBA trip a week ago. I visited a place where I had been before and enjoyed very much. I dove in 20 widely separated reef locations. I was intentionally looking to see the condition of the reef system. I had an excellent trip but an extraordinarily disturbing finding. I took photographs of the reefs during the day and at night with white light. I also took photographs of the same sections of the reef at night with high energy blue light. The images might make you more aware of an advancing, worrisome problem. Previously I saw gorgeous, colorful panoramas of reefs teaming with all imaginable genus and species of marine life. Now many are completely or partially dead; covered with algae, decayed plants and a dirty mixture of sand plant detritus and broken coral. The larger fish were gone; tunicates not seen; smaller life forms missing, fewer small fish were present.

The pillar coral in the center of this image shows the relative indiscriminate action of the problem. It affects most of the stony (hard) coral of the reef. The soft coral and sponges are not directly effected, however, without the hard coral anchorage they don’t survive long.

Here is the mystery.

What is causing the problem? How big is the problem? Where did it come from? What if anything can or should we do about it? These topics will be discussed in the following blogs. Your thoughts are not only welcome but encouraged.

References:

Race to stop stony coral disease

Rapid spread of stony coral disease in the Mexican Caribbean

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#coral #stony coral #soft coral #sponges #tunicates #brain coral #pillar coral #dead coral

Did I tell you that I love Christmas trees? 

These are the flowering trees of Christmas that I found while bicycling in the surrounding area here in SW Florida. They are so remarkable. It is difficult to imaging the range of chroma and combinations of hues. Some of these are so spectacular that the photographs simply cannot capture the full essence of the visual impact. When I stopped to admire them, I was surprised to find the pleasant aroma that added to the sensory experience.

When we decorate our Christmas trees, they may be very beautiful and have a significant personal context, but these trees are naturally decorated for all to enjoy during this holiday season.

I’m tempted to have a monthly blog showing the flowers of the month. I’m sure that you will want to see the Jacaranda and the Flamboyant Royal Poinciana Please comment and let me know what you think.

Many of these trees are originally derived from other continents. They are not classified as invasive or ecologically advantaged here in Florida. In some areas the streets are lined with them resulting in a magnificent display of brilliant colors. Some are rarely found and may be in private landscaped gardens. When I see them, it is like discovering a hidden treasure. 

On occasion we may visit some of these plants and discuss them in greater detail, but today this is just fun for the eyes.

References:

Urban Tropicals

University of Florida Gardening Solutions

#December flowering trees #flowering trees #Bauhinia #Powder puff #Tulip tree #frangipani tree #silk floss tree #wild olive tree #pliumeria #

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The apex alligator in photo #6436 described in the Alligator post is the Keystone animal for the Bird Island lake. Its behavior allows all of this balanced ecosystem to survive. Alligators are very territorial. There are only one or two and rarely three alligators that patrol the Bird Island lake. They feast on the other animals which attempt crossing the lake. The size of Apex Allie reflects the size, diversity and health of the system. The mass of the alligator pales in comparison to the mass of all of the birds, secondary predator animals and vegetation.

The birds seek out the areas that are protected by the alligators. Bird droppings are rich in nitrogen and other plant nutrients, therefore these areas have lush growth of native plants. The plants provide shelter for the birds. The secondary predators are attracted to the birds like a magnet, the alligators are attracted to the secondary predators. The alligators which eat the second level predators grow to substantial size.

If one of the layers such as the bird population collapses then the system is unsustainable. The isolation of the islands provided by the alligator shows their Keystone role in this collaborative circular economy.

In this schematic are four environments which are interconnected by bridges. These include air, water mainland and island. The two bridges shown here are soil and trees which support the bird populations. The water environment is dominated by the alligator. The alligator cannot climb the trees to threaten the wetland bird population. So they are safe if an alligator enters the island because the reptiles can’t climb trees. The aquatic birds are threatened by the alligator if they stay in close proximity to the island shore. If they move inland or from the shore to the undergrowth then they are at less risk. If a land bridge (shown in dotted amber line in the schematic) becomes available to the raccoon or other land based predators then the ecosystem will collapse. If the rats, snakes and especially the raccoons gain land access to the islands the birds and eggs will be eaten or the birds will abandon the islands. Raccoons are especially dangerous because they are prehensile and clever.

Characterizing the population of the Bird Islands. The island is populated by water birds many of which are moderate to large, big winged, long legged, migratory birds that roost and nest in the trees. There are many others. They typically feed on fish, insects, seeds, frogs, and anole. The overgrowth of trees provides perches and nesting areas for the birds. The interior has nests for the lower dwelling birds and some of the larger birds. There is nothing on the islands to feed on except for smaller birds. The population may be self limiting as determined by space.

Organism	Takes	Gives	Relationship
Alligator	Food	Controls aqua population	Predator
Bird	Shelter and food	Nitrogen and nutrients	Predator
Raccoon	Food	Controls terra population	Predator
Tree	Nitrogen and nutrients	Shelter, Food	Mutualist

The combination of these predators results in a stable system controlled by limitations imposed mostly by the animal niche behavior. This mutualist system is characterized by the cross predatory behavior.

If you look at the Bird Island apex alligator and compare it to this alligator you can see that it is at best one third of the size of the Bird Island lake alligator. True to the concept, the pond in which it resides is approximately one third of the size of the other lake. The pond also has no island. The iguana is a herbivore and the alligator is a carnivore. Mr. Iguana is very fast, climbs trees and is a very capable swimmer. He walked to the screen right. Thanks to Mr. Alligator my hibiscus survives for another day.

Naturally we can appreciate the beauty of the birds of the islands. Here are some busy birds on the island.

People provide the ultimate ecologic advantage to the species which satisfy their interests at the time. Human intervention provides an ecologic advantage to the birds by controlling the bridges to the islands, thus favoring the birds. Sometimes intervention can have unintended consequences.

References:

* Alligator Biology

Wetland Bird environments

Florida water bird Colony locator

#Alligator #balance #ecosystem #interdependence #interactions #predator #mutualist #barrier #bridge #niche #keystone #balance #ecologic advantage

Bird Islands

There are three artificially created islands in an artificial lake. It is interesting because especially during the warmer months they are full with nesting birds. They appear to be favoring these areas because the islands that are separated from the mainland. Separation allows access to only those who can reach them. The birds have no problem flying in to roost, build nests, procreate, lay eggs, hatch, develop, fledge and fly away. The islands are strategically positioned along an untamed slough which acts as a natural fly-way for the migratory birds. The highly protected Bird Islands are a sanctuary located on private property and cannot be accessed without expressed permission from the management and property owners. Stepping onto the islands is done only by the grounds maintenance crew of the property.

During the wet season there may be a thousand birds flying in and out on a daily basis. Here is a general list of more than 30 varieties of birds which I have sighted on and around these islands. Others may have identified many more. These are all wetlands birds but other species fly near and around the islands.

• Heron
• Egret
• Ibis
• Duck
• Thrush
• Cormorant
• Predatory birds

The islands provide local birders and wild life enthusiasts an opportunity to watch and enjoy the busy birds flying, competing, feeding, migrating and all of the activities for which the birds are known*.

The birds use all of the microenvironments on the islands from the tree tops to the swampy edges.

The birds congregate on the Bird Islands. The birds can carry out most of their activities in daily living except eating. Eating is no problem because they can easily fly to fertile areas along the slough and to the glades, shores and bodies of water well within easy distance. The additional important aspect to these places as islands is the absence of ground based predators. The birds, eggs, and chicks are vulnerable to predation by raccoons, black rats (Palm Rats), snakes, and the plethora of other ground based animals. These are missing on the islands because they are unapproachable without swimming. across the lake.

Here are some examples of the everyday bird activities on these islands.

The secondary predators are attracted to all these birds like a magnet. The alligators are attracted to these predators. The alligators eat the predating animals which in turn supports their grow to substantial size. The birds seek out the areas that are protected by the alligators. Bird droppings are rich in nitrogen and other plant nutrients therefore these areas have lush growth of native plants. This becomes a mutually supportive cycle.

• There are other places in Florida that exhibit similar nesting activities. One of the best of them is publicly accessible. Please go to the Ding Darling National Wildlife Refuge on Sanible Island, Florida.

See a following blog “The Beauty and the Beast”

My best reference for bird identification is Cornel Labs at All About Birds.

#predator #birds #islands # sanctuary #Apex animal #Key Stone animal #isolation #limited access #migration #route #slough #bird activities

Earlier we looked at land based turtles and tortoise. The two most commonly found sea turtles that I have watched in the waters around Florida are the Green and the Hawksbill. They are very similar in their habitat, behavior, size, shape and coloration. For me, the distinguishing characteristic most easily spotted is the shape of their jaws. The Hawksbill turtle has the shape reminiscent of a bird with a prominent point to the upper jaw while the Green is quite rounded. There are other characteristics but they are not so obvious. I’ve seen both types swimming about in the off shore reefs of Florida and other parts of the Caribbean. These animals seem mysterious. Unless you are truly intent on watching them as they come ashore for egg laying you would not have any contact with them. The only other way to learn about them is to go underwater to look at them in their environment. They are very benign, are relatively solitary and photographing them can be very rewarding.

The turtles are critically important for the health of the reef. The Greens eat the algae and sea grass, and Hawksbills eat sponges which would otherwise over grow the reefs. The Hawksbilled is endangered and the Green is threatened. There are many authorities who have written scholarly articles in juried publications.

Good resource for general information include Sea Turtle facts and the environmental importance in Oceania.

#turtles #Hawksbill #Green #sea turtles #Caribbean

Alligators are wild and dangerous animals and should be regarded with extreme caution. This hazardous characteristic may be part of their attraction. The species has been in existence almost unchanged for tens of millions of years. They are survivors even in the face of human encroachment in their space. Because of human activity the survival of the alligators is threatened. Despite the apparent stillness they can react very quickly. They eat meat and can take down an adult deer, otter, turtle, raccoon, iguana another alligator or anything else which comes its way in a short distance reach. The bulk of their diet is probably rats or mice. This is our fresh water apex predator. This posting is a prelude to a posting that will later describe a relationship of the alligators and a specific bird nesting location.

Every morning I look out to the pond at the house and see the local “gator” cruising the surface of the water with just the eyes and nose above the surface. On occasion, they will haul themselves out to lie on the grass usually within 20 feet of the bank. If it sees a person it quickly slips back into the water. Obviously the alligator in the pond is not the same throughout the season because it is variable in size however there they are very territorial. Usually only one at any time be seen. On rare occasions a larger one will walk out of the water and cross the street, perhaps to find a more solitary place to or to find a mate during mating season.

Alligators are aquatic reptiles which live on and near the ponds, creeks, streams, swamps or just about any other piece of water. They tolerate brackish water but not oceanic salt water. They are ectothermic (cold blooded) and regulate their body heat by sunning or shading, breathing, resting in the water.

They are relatively solitary, meeting to mate in late spring. Occasionally one can hear the slapping and bellowing of a male in the swamp at night as it tries to attract a female. After weeks of gestation the female may lay as many as 60 eggs in a ground based nest approximating the water. The nest is covered with a blanket of leaves which hold the heat of the day. The hatchlings break through the shell and emerge after three months. The new born are vulnerable and protected by the mother from predation for as much as a year. The survival rate to maturity is about 15%.

They have complex social lives in the wild about which very little is known. Much of their behavior studies are based on observations of captive animals. The maturation stages are egg, hatchling, juvenile, sub-adults, mature.

American alligator Identification marks:

• Blunt nose
• Black in color
• Upper teeth show when mouth is closed
• Yellow marks on young

Later we will compare alligators and crocodiles both of which can be easily seen at the Naples Zoo.

Alligators appear to be so primitive and powerful; and they are. Awesome!

See these references from the Florida Fish and Wildlife Conservation Commission for a more comprehensive description:

• American crocodile
• American alligator
• Alligator facts
• Alligator biology

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#Alligator #primitive #teeth #yellow marks #ectotherm #predator #apex predator

Turtle vs Tortoise:

There are three names for similar animals which live in our region of Florida. The general name for these reptiles is Terrapin (The mascot of the University of Maryland). The specific names are turtle and tortoise. 

I invariably see two varieties of these reptiles: Smooth Soft Shell and Gopher

Every day I spot a Gulf Coast Smooth Soft Shell turtle. (Apalone mutica calvata) I see them swimming and sunning themselves in and about my yard. Their behavior is interesting to watch. They swim just below the surface of the water and extend their heads to breath for a few minutes. The head and neck extension may be up to 8 inches. The body diameter may be up to a meter. The pointed nose is easily identified. They beach themselves on sunny days alone or in groups of three to eight and may spend minutes to hours on land. They usually stay close to the shore and quickly run or slide back into the safety of the water with little provocation. Their eyesight seems to be very good and can spot a threat from at least 30 feet. Note that I used the term turtle to describe them because they are aquatic, have flat shells and wide feet with long claws that are good for swimming. The color of their carapace (upper shell) ranges from brown to green. They may be prey to the alligators and they may predate on the smaller aquatic animals.

Less often, I observe another Terrapin in the lightly wooded areas and fields while walking about especially at Barefoot Beach Park. The Gopher Tortoise (Gopherus polyphemus) is a land-based reptile. This tortoise digs holes in exposed sandy soil with a single opening from 10 to 20 cm in diameter and in the created burrow they lay their eggs. This is the only tortoise native to Florida and it is environmentally critically important. Although they have a 40-to-60-year life span, their reproductive rate is low. The female may not reach reproductive capacity until it is 10 to 20 years old.  They may lay approximately 6 eggs at the entrance of their extensive six foot deep, 12-foot-long burrows. The annual success of a clutch is only 10%. The Gopher Tortoise is relatively small, with a compact ball-like shape. The hard shell has lightly textured plates. The feet are small and have short broad claws and those in front are especially suited for digging.The Gopher tortoise is a keystone mutualist.

The Gopher Tortoise are important to the environment for several reasons. Their digging aerates the soil. More importantly, the burrows provide essential shelter for the survival of hundreds of other animal species like snakes, mice, voles and frogs. These other species, called commensals, use them for shelter and nesting. This is even more vital during and after forest fires where the shelters protect the otherwise exposed animals and without which they would not survive. The entire ecosystem and related species would collapse without the Gopher tortoise. A term applied to this importance is “Keystone Species”. When you see these tortoises, please help to protect them and their environment. Don’t backfill their dens, don’t step on the apron of sand around the entrances to their dens, don’t mow the grass near the den, don’t run them over, if possible, don’t build on their territory. If you want to support the survival of hundreds of other species, thousands of animals and an entire ecosystem, leave them alone.

For more information on these subjectrplease link to University of Florida, box turtles, Turtle owner

I hope that you can distinguish between the turtle and the tortoise. Here is a chart of compared characteristics.

Characteristic	Turtle	Tortoise
Environment	Acquatic	Dry
Foot	Long webbed toes	Short
Carapace	Flatter	Rounder
Longer lived	Shorter	Longer

Keystone Species:

It is extraordinarily important to understand and discover Keystone Species. To leave no doubt about understanding what this means I have added the following links which I encourage you to investigate. 

“A keystone species is understood to be a strongly interacting species whose top-down effect on species diversity and competition is large relative to its biomass dominance within a functional group. This definition links the community importance of keystone species to a specific ecosystem process.” ^LINK

For vivid examples of the role of keystone species in an ecosystem go to these linked sites from National Geographic and the Ecologic Society, and Wildlife habitats.

https://www.nationalgeographic.org/encyclopedia/keystone-species/

https://www.nationalgeographic.org/article/role-keystone-species-ecosystem/

https://www.sciencedirect.com/topics/earth-and-planetary-sciences/keystone-species

Link: https://www.ecologyandsociety.org/vol7/iss1/resp11/

Report gopher tortoise locations using this app, http://myfwc.com/wildlifehabitats/managed/gopher-tortoise/app/.

We will discuss other turtles in subsequent postings including those living in fresh, brackish and swamp water as well as sea fairing species.

#Tortoise #Turtle #Soft Shell turtle #Gopher tortoise #Keystone species #Mutualist #Terrapin #Ecosystem #commensal #mutualist #Epicollect5 Observation 8

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While in Florida you rarely see Dahlias. These flowering plants are just not tolerant of the heat, rain and insects of our summer months. None the less I find them amazingly beautiful. The plants grow from tubers that originate from the species found in the cool, moist highlands of Mexico and Central America. However, they are now widely cultivated. I became familiar with them when I resided in Michigan. We grew them in our garden and even then they required special care for winter protection. The following images are my photographs made while in Fulda, Germany. I had forgotten how surprisingly beautiful these flowers are. I wanted to share them with you in case you have not seen them in a while. I hope that you appreciate them as well.

If you are familiar with these blooming plants from your experience in the Northern States or elsewhere then, with special care, there is an opportunity to grow and enjoy Dalias in Florida.*

There are many Dahlia varieties. for a large list with pictures go to the link Gardenia. Also see Dalias compared at this Gardenia comparison link. I intended to look up the names of the flowers shown, however, there are more than 20,000 different varieties and it was impossible for me to check out the exact characteristics to name each specimen.

Here are a few recent examples of the blooms I saw. View the slide show by letting it play or by clicking on the arrows.

*Yes! You can grow Dahlias in Florida. Please visit the blog site of Growing Kindness by Ellen Tongson. I believe that she has all of the information, supplies and plants necessary to start and maintain your own beautiful flowers in Florida.

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#Dalia #Tolerance # #color #Fulda

If we explore birds of color in our view of brilliant chromatic displays then Rainbow Lorikeets are a must.

These friendly feathered friends are members of the same family as parrots and therefore have some of the same features. These include colorful, clever and communal. When we look at the feathers the same physiology and mechanics apply as we have seen in previous postings. Rainbow Macaw and Rainbow Lorikeets same color scheme but only peripherally related.I guess that birds of the rainbow don’t eat from the same bowel.

The rainbow Lorikeets are native to Australia. The males cannot be detected by humans without genetic testing or other more in evasive inspection. They have great human speech mimicing capabilities. They are usually kept as pets and as non-native species must beconfined to prevent predators and from escaping into the wild.

Now think about the feathered dinosaurs. Can you imagine that all of the bipedal Dinos had primitive feathers that were just as colorful as these birds of today.

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#Lorikeet #Feather #Color # #Behavior #Song #Speech #Pets

Here is a phenomenal presentation of bird feathers that are not from parrots but are none-the-less spectacular. The behavior accompanying the feathers includes raising the fan tail, strutting around the area, facing the female and then shaking the tail rhythmically to make the dots dance.

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#peacock #dancing fantail #eye spots #mating behavior #albino #