Science topic

# Biological Oceanography - Science topic

Biological Oceanography is the study of life in the oceans - the quantity, productivity, and geographic distribution of marine life.
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I have a netCDF4 (.nc) file having ocean SST data, with coordinates (lat, lon, time). I want to predict and plot maps for the future. How can I do this using python?
Please recommend a python code for time series forecasting based on this approach.
This is not a programming question. It's a time-series question. Imagine measuring temperature in your back yard every hour for a day. You could use that to make predictions, but they might not be very useful, because weather changes from day to day. So, you need more than a day. Maybe you measure for 3 days. That would be better. But maybe those were 3 warm days, which are followed by 3 cool days. Etc.
Depending on your background, you might start by reading books on time-series analysis. Then move on to books about ocean physics. And then climate physics. You will soon see that statistical prediction is a weak approach, and that dynamical models are required. That takes you from the domain of reading and plotting with python to the domain of building PhD-level scientific and computing skills. The latter go way beyond plotting with python; you'll need to deploy supercomputers to run models that were took many person-decades to develop and take person-years to learn to run. Oh, and the end result will be a model prediction that will not agree with other model predictions to within the error bars we want for climate prediction.
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How can I convert plankton concentration (micro, nano, pico) from mg/m3 into mol/m3
@Kunal Madkaiker I see, that information was missing from your question. To do that, you could start with this one: Behrenfeld, M.J.; Boss, E.; Siegel, D.A.; Shea, D.M. Carbon-based ocean productivity and phytoplankton physiology from space. Glob. Biogeochem. Cycles 2005, 19.
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Artificial intelligence (AI) is a rapidly advancing tool. It is heavily reliant on programming languages, data manipulation and analysis. As colleagues in the field of oceanography, I would like to know your opinions on the use of AI in this field. Furthermore, I would appreciate any recommendations for publications that could support your viewpoints.
It is important to be transparent about the limitations in terms of programming for the diferent subfields of oceanography, such as physical, chemical, biological, ecosystemic, and geological; how the incorporation of AI may lead to new disparities in scientific research; and how careful you would be with the use of these tools.
Sebastian Enrique Cornejo Guzmán AI is becoming an increasingly significant tool in oceanography because of its ability to handle and analyze vast volumes of data rapidly and efficiently. It is crucial to highlight, however, that the application of AI in oceanography may result in research inequities, since certain subfields may have more resources and skills to deploy AI-based methodologies than others. Furthermore, it is critical to be open about the limitations of AI in each sector and to utilize the technology with caution, ensuring that the findings are accurate and dependable.
There are several papers that explore the application of AI in oceanography, some of which are as follows:
• "Deep Learning in Oceanography: A Review" by B. Kostas et al. (2019)
• "Artificial Intelligence in Oceanography: Challenges and Opportunities" by J. Chen et al. (2019)
• "The Role of Artificial Intelligence in Oceanography and Marine Affairs" by S. J. Kim et al. (2018)
These papers can give more thorough information on the application of AI in oceanography, including possible advantages and problems.
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I am masters student and I will be studying micro plastics on a river system in the UK.  I have only found one location that sells Manta nets in USA but I was wondering if anyone knew of one to buy or borrow in the UK.
KC Denmark A/S is a global supplier of equipment. They have a range of Manta nets complete with accessories such as digital flow meters. I have just received a quotation from then.
You may consider visiting their website.
Regards
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I am working on fish ecology in an Indian estuary. However, proper identification of species belonging to Mugilidae is very difficult particularly of the genus Mugil and Liza. Most of the references available (FAO identification sheets and some Indian keys) differentiate the species based on the premaxillae shape which is difficult to ascertain in juveniles of the family. Also the family is highly dynamic with many new or updated genus and species. So, are there any recent comprehensive taxonomic keys available for the family from the Eastern or Western Indian Ocean regions?
Hope for u always success
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Currently, microplastics (MPs) occurence researches in coastal and marine animals are performed in huge amounts, but their results concerning MPs abundances are not always given with the same unity.
• From what I can tell from studies I read, most provide data using MPs/individual. There are some studies that sample in pools, and then, after ending samplings, calculate the MPs/individual data. It would be an issue if we compare MPs/individual data of two different studies: one that sampled in each individual and another that sampled in pools?
• Should a specific study provide just the MPs/individual data? I think this study it would be sort of incomplete, considering that this data would not totally reflect the abundance of animals with different sizes, weights, and possibly ages, etc.
• What is the best approach between other unities, such as MPs/g of the whole sample, MPs/g of their dry or wet weight? That are some formulas to convert samples weight for dry and/or wet. This is applicable for MPs?
I know much of that depends on the study's biological samples, and objectives, but I would enjoy reading researchers opinion about it.
Dear Victor
Mostly expressed as items/m3, but you use another unites according to your specified work too!
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Related Research and studies, books, and any other references, please?
Janaki Sandamali, there are several remote sensing satellites that have been used for Sea Surface Temperature (SST) measurements. MODIS onboard Terra/Aqua, VIIRS onboard Suomi NPP, AVHRR, Metop-A,B,C are commonly used in this regard. There are also Geostationary satellites such as GOES that are used for deriving SST products. You might be interested in some of the webinars that are conducted by NASA ARSET for Coastal and Ocean Applications.
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I am working on MODIS-SST, I need SST in situ data and water column data, Please guide me in this.
Imran AHMED Khan, Apart from the Coriolis ARGO products, I would recommend using US-GODAE ARGO data. Please, go to the following links:
To answer your questions, the Argo data are very useful with a careful choice based on the quality flags.
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I do not have the PAR data. Fluorescence can be detected from dead particles too, but can it be utilized to get an idea about the euphotic depth.
Have a look at our paper, "Resolving the Euphotic Zone," Deep-Sea Research I, vol. 83, pp. 45-50. We propose that the biological compensation depth is roughly equivalent to the depth of the base of the fluorescence maximum.
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I have downloaded one EO-1 Hyperion image, removed the bad bands, de-stripped the image using THOR De-striping in ENVI and applied the atmospheric correction using FLAASH in ENVI. Now I have the surface reflectance data in my hand. I need to apply some bio-optical algorithm for ocean colour application (IOP and Bathymetry Retrieval). For that I need the Remote Sensing Reflectance as an input. How can I get Remote Sensing Reflectance (Rrs) from Surface Reflectance? What are the procedures?
Poddar, S.; Chacko, N.; Swain, D. Estimation of chlorophyll-a in northern coastal bay of bengal using landsat-8 OLI and sentinel-2 MSI sensors. Front. Mar. Sci. 2019, 6, 598.
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I have CTD and Chlorophyll data for an upwelling location from two different years (Aug 2017 and Aug 2018). What should I be looking at to get an idea about the age of upwelled waters?
Hi Saumya,
Here are some clues with regard to your question.
Radiocarbon (14C) in dissolved inorganic carbon in the ocean can trace the age of ocean water relative to the atmosphere and provide insight into climate‐driven changes in ocean circulation since the last glaciation.
The surface waters of the modern ocean are not in 14C isotopic equilibrium with the atmosphere. A steady state balance exists between the slow invasion of atmospheric 14C into surface waters following production in the atmosphere and the aging of isolated interior water (marked by the decay of 14C over time) with the subsequent cycling of those waters back to the mixed layer. These dynamics result in an age difference between surface waters and the atmosphere termed the reservoir age.
I think you can follow the approach outlined above to determine a possible age difference between your 2017 and 2018 water samples. Evidently you will have to apply a good statistical test to determine whether a difference in reservoir age is statistically significantly different. This requires a very accurate estimate of the variability (or standard deviation) on your reservoir age measurements. Furthermore, two samples in time are not enough to elicit a trend in reservoir age I am afraid. For this type of analysis you need more sampling in function of time (years).
Lots of success.
Frank
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Which grab type would you suggest for sampling marine benthic macroinvertebrates in sandy substrate or maerl? We would like to use it in coastal samplings, often in recreational boats carrying a small winch, by one or two people. So, it shouldn’t be very heavy, and the ideal surface would be around 0.05m2.
In our lab we have a 30-years old Ponar grab (9”x9”) that needs to be replaced. Every time we tried using this specific grab, it had serious issues sampling sufficiently any substrate than mud. In muddy sediments it was capable to collect almost full volumes of samples. However, both in the description from Wildco and references (e.g. Elliot & Drake, 1981), Ponar grab is suggested as the ideal type for sampling coarse material. So, I wonder if the issues in our Ponar are due to old age or maybe poor maintenance.
Has any of you had trouble sampling coarse material with a Ponar grab? Would you suggest another type for this substrate?
Thank you in advance for any suggestions.
Van-Veen grab 1/40 m2
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This is in relation to the sampling done at various stations along a cruise track at different times of the day. The surface temperature would be affected by the time of the day it was sampled. How can I eliminate that difference to look at the trend?
Working with time-of-day as a factor will be a challenge because I assume your sampling times are random randomly spaced. That means you might be better off fitting for a trend plus some model of diurnal variation. The problem is that latter can take many functional forms, depending on solar forcing, whether there is nighttime convection, and so on.
I would advise starting by regressing to a formula that has a trend, plus both a sine() and a cosine() with period one day. (Using both sin and cos lets you find the phase, but still in a linear regression, which is easier to deal with than a nonlinear one, unless you are experienced.) Then add a twice-daily harmonic. Then add a thrice-daily harmonic. By comparing the results you may start to learn how the diurnal variation is affecting your estimate of the trend.
I would start with artificial data, so you can test the accuracy. AIC or other methods should be used to avoid overfitting. (If you don't know what AIC means, you ought to give yourself some time to learn elementary stats, before trying anything complicated with your data.)
Whether you will see a linear trend is questionable. I've never seen such a simple pattern in ocean data. So you might want to start by fitting this sort of sequence of diurnal models, then removing the diurnal signal, and then simply plotting the results, rather than expecting a trend.
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I am wondering if storing biological samples in ethanol is acceptable, if these organisms are to later be tested for their mercury concentration.
Thank you both so much for the feedback. It is very appreciated.
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I will be increasing T by 2C every few days and need a heater that can do this accurately for a few gallons of seawater
Tubular Immersion heaters are best option. It can be designed to based on Tank dimensions n with a suitable control System ( Panel). We make such heaters.
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Seto Inland Sea, the largest semi-enclosed sea in Japan,
Some researchers provide the M2, S2, K1, Ovalues of the main strait of the Seto Inland Sea, Some provide the mean surface current of the whole Seto Inland Sea, which one or someone else is the best descriptor of the current speed? I want to investigate the influence of current (speed) on water stability and red tide occurrence.
Thank you!
For the residual current speed, you need to take out the tides and analyze the sub-tidal velocities. sub-tidal velocities can be obtained by low-pass filtering your original raw time series. You can also use Tidal harmonic analysis packages like t_tide  to find the tidal velocities and remove it.
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This far the species are identified as:
2. Sarcophyton sp
3. Heteractis magnifica
4. Red Mushoom / Stone ? - what is the latin name?
5. some kind of sponge?
6. seastar
7. Zebrasoma scopas
6 is definitely an asterina star. Hard to elucidate a species in a photograph. That is a common "pest" in the aquarium hobby. Some are known to feed on crustose coralline algae, while others will feed on zoanthids.
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Is there a consensus on the optimal concentration of glutaraldehyde for the preservation of marine phytoplankton?  I typically use 1%, but notice that other researchers use from 0.1% to 3%.
I am interested in maintaining as many taxonomic features as possible for LM and SEM with the lowest concentration of glutaraldehyde that is acceptable, since I don't like working with this chemical at sea. I typically work in low chlorophyll high nutrient areas of the Southern Ocean, but may find sea-ice blooms from time to time.
I appreciate you thoughts and recommendations :).
HI.
usually working stock of 10% then between 1% and 2% is where I have usually gone. I have a paper which I used as a good reference for marine samples, ya no lugols, as the colour issue and also the degradation with diatom frustules getting broken down. My lowest would be 1% pretty smelly still, but I make it on board ship in fume hood then you can pre-spike vials keep it in the fridge and then out samples back into the fridge after sample is added, I hope that helps? Ya more is better than less. Also remember that lugols does colour the organelles so harder to identify, much better to use glut.
I hope this helps, let me know if you need the paper?
Di
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i have been collected my samples from Persian gulf, hard bottom, that they were attached to a soft coral.
i think it is a Ophiothrix sp, but i cant identify it in species level
if you know its name, please send me a reference
thanks a lot
Definitely not Ophiolepis. Ophiotrichidae is correct and I think it is Ophiopsammium not Ophiothela but needs to be verified with literature and close examination.
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I need to control pH and oxygen levels for acidification and hypoxia purpose. It will be carried out in seawater. Anyone has experience on this kind of stuff?
Hi, you can use CO2 gas or carbonate for pH and N2 for hypoxia. Check out the new guideline on conducting and reporting ocean acidification experiments. http://www.epoca-project.eu/index.php/guide-to-best-practices-for-ocean-acidification-research-and-data-reporting.html
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Found in a marine plankton sample
scale of butterfly
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Many gastropods are predators that drill or bore through their prey's body covering (shell, exoskeleton, etc.) using a combination of radular scraping and chemical dissolution. Examples I know well include moon snails (Euspira (= Lunatia) spp. (Naticidae)), "whelks" (e.g., Nucella spp. (Muricidae), Buccinum spp. (Buccinidae)), but I suspect there are many others.
I am gathering information on gastropods that feed in this way, and would like to assemble a list of as many (or all) species that do so as possible. There is a lot of literature on fossil borehole/drilling predation, but I am interested in EXTANT species. Are there any good resources (reviews, book chapters, etc.) that might present such a list? Are there other taxa within the Gastropods beside the Muricidae, Naticidae, and Buccinidae that contain boring/drilling predatory species?  Just how many gastropods do this?
Hi Brady, find a comprehensive list of boring gastropods in the Table 2 of this paper by Michal Kowalewski
You may obtain a decent estimate of the total recent species diversity of each family (and global georeferenced occurrences) at the Ocean Biogeographic Information System
Best regards
Marcelo
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working on sparids diet i'm looking for a site or link for identification of preys mainly:
-crustacean, annelids, fish, echinoderms, algae...etc
All very good advice!  I dissected flounder juveniles and knew what species the single eyeballs in the gut were from.  I was able to infer how many of that species had been ingested! Good Luck!
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I am checking the biological production rate in a particular season and hence studying seasonal variability.
Dear Samiran,
2. For chlorophyll check http://oceancolor.gsfc.nasa.gov/cms/
Rgds.
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These are formations found in the pump house of a salt work near Port Elizabeth, South Africa. The amber-like yellowish-brown substance inside the formation is hard at the edges but still soft in the middle. What is it and what is likely to produce it?
I've also been trying to figure out what the formations are. Adding onto the possible cyanobacteria answer, Nostoc pruniforme heterocysts (Mare's eggs) are formed in fresh water environments but there may be similar nitrogen fixing cyanobacteria formations in saline or hypersaline environments; purely a guess but would be interested to find out.
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Hi! Everyone,
Could someone help me in identifying the brittle star in attached photo. It was collected  from massive coral colonies mostly Porites spp and Cyphastrea spp in Kuwait, Arabian  Gulf.
Best Regards,
M. Nithyanandan
Thanks! Dave,
I will do the needful and try to get hold of Clark, 1938.
Best Regards,
Anand.
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I found them from low saline condition of Cochin back water system. Initially I thought both could be species of Staurastrum/ Actinastrum (green algae). But I cant find out the specimen (b). Kindly help me to identify.
Thank you.
1) Staurastrum
2) Eunotia
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How to rear Macrobrachium rosenbergii larvae? Whether 1 or 2 litre plastic containers are enough? What will be the preferred feed at diff. stages?
Hello,
This depends upon the number of larvae you are intended to rear together. If you rear them individually 50 or even 20 ml per larva could be enough. Anyway, be sure that oxygen concentration remains at a hight level according to temperature.
As for food, you may use Artemia  nauplii for the first stages, may be larger Artemia larvae later.
Cordially
Auguste
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the images was attached
salinity of the collected water  is 4 ppt, almost freshwater resource.
Rajan:
You have not provided magnification. Still upper two forms show affinity with Spirogyra and lower one with Pediastrum.
Best
Syed
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Plotting real tidal data from different regions and different tidal reference stations, it is clear that some tidal datums often have the same relative position.
Trivial examples are the relative positions of the Lowest High Water (LHW) and the Highest High Water (HHW); or of the Mean Lower High Water (MLHW) and the Mean Higher High Water (MHHW) in a semidiurnal cycle.
However, the relative position of some other datums does not appear as trivial, especially when considering the neap-spring synodic cycle.
For example, the Lowest High Water Neap (LHWN) can be lower or higher than the Highest Low Water Neap (HLWN), i.e. the range of the neap high tide can overlap or not with the range of the neap low tide. Another example is the relative position of MLHW and the Mean High Water Neap (MHWN).
I wonder if there is any classification of tidal regimes that describes these types of patterns, that is or might be related to geographic areas, or ecological patterns.
Dear Polgar,
Have you checked the NOAA websites on Tides and Currents?
There are regional tidal datums as well....
I am not sure if this will help.
Ciao
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I've read that SST fronts stimulate biological productivity (e.g. Woodson and Litvin 2015, PNAS). But my question is how strong of a SST front is needed to significantly enhance productivity? Of course this will be dependent on a number of factors, but what is a rough estimate? Will a front with 1 ℃ SST change be relevant? Or is this only found with much bigger gradients (e.g. 10 ℃ change)?
I'm particularly interested in the application of this question in the Gulf of California, Mexico.
Particularmente en el Golfo de California ocurren demasiados procesos de diferente índole que resultan en frentes superficiales de temperatura. En el norte la mezcla de marea genera frentes térmicos de hasta 3 grados en el archipielago central, y frentes más difusos en el alto golfo. En el sur del golfo los procesos predominantes que generan frentes son la surgencia en invierno/primavera y los remolinos en verano, En la boca por otro lado la interacción con la corriente de California y el agua tropical generan frentes de masas de agua.
Entonces, todo el golfo es susceptible a los procesos de mesoescala, pero hablar de un frente superficial, sin tomar en cuenta su origen, dificulta evaluar en que medida promueve el aumento de la productividad.
Particularly in the Gulf of California too many different kinds processes resulting in surface temperature fronts. In the north, tidal mixing generates thermal fronts up to 3 degrees in the central archipelago, and more diffuse fronts in the upper gulf. In the southern Gulf, predominant processes that generate fronts are upwelling in winter / spring and eddys in summer. In the mouth, interaction with the California current and tropical water, and gulf water generate fronts throughout the year.
Then, the entire Gulf is susceptible to mesoscale processes, but talk of a surface front, regardless of its origin, difficult to assess to what extent promotes increased productivity.
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Can anyone help me to identify this DINO?
Dear Jackson, thanks for your attention. I suspect it's C. helix or C. convolutum, but I am not sure, I will try to establish pure culture and do 28s LSU DNA to confirm it.
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I found this species under the rock by attaching firmly. Its almost around 7-8 cm long. Collected along the coast of southern Tamilnadu. The body was so soft feels like worm. Help me to identify this.
Dear Nandha,
I think it is white sea cucumber probably Eupentacta quinquesemita.
Best regards
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I need help to calculate NBSS for zooplankton biomass.
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I use sea surface temperature (SST) from satellites to assess marine mammal and sea turtle bycatch, habitat, and distribution. Recently the primary SST data source that we had been using (Pathfinder SST) has not been updated. So, we are looking for a new satellite SST source. Websites such as JPL's PO.DAAC (http://podaac.jpl.nasa.gov/) have added lot of choices in the last few years for different SST products, many of which blend data from multiple satellites and often interpolate to fill in areas that would other wise be missing data due to cloud cover. Can anyone suggest which data product would be best? We would prefer products with <= 4km resolution that go back a few years, if not many years. One source that seems promising is the G1 SST (http://podaac.jpl.nasa.gov/dataset/JPL_OUROCEAN-L4UHfnd-GLOB-G1SST), though it would be great if it went back further in time. If anyone could offer advice as to which data products are likely to be the most accurate, I would greatly appreciate it.
I suggest you MODIS SST. You can refer to the following publication for investigation and validation of MODIS SST:
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Hi, I would like to know if any has some insights about colonial stage conservation of P. pouchetii at long term. I stored seawater samples with lugol at 4C for above a year. I was wondering if the colonies could have been disrupted over time. Thank you!
I would be pretty certain that the integrity of the colonies are not preserved, certainly not over that time. Even if "Psedulogols" are used as this mixture of glutaraldehyde and lugs are often called. Instead the best you can do is live samples in a FlowCam, or put them on a filter and freeze (Estep et al)
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I'm trying to determine some preliminary distribution info for a few soft coral species that may cross over from temperate to tropical waters.  I'm particularly interested in Telesto sanguinea, Leptagorgia virgulata, L. hebes. Have you seen them further south than mid-Florida and if so where did you locate them? Also, have you seen them in the Gulf of Mexico?
Thanks!
You may wish to check out NOAA's Deep-Sea Coral & Sponge Data Portal.
The map portal (click on the map) has a data query tab, where you can enter a scientific name.  While most of the records are currently from US waters, there are quite a few records from elsewhere in the Caribbean (mostly from the Smithsonian's National Museum of Natural History).  Our database focuses on species that occur deeper than 50 m, so it may not capture some of the species you are interested in.
There are records of Telesto sanguinea from the Florida Keys and the Gulf of Mexico.
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For modelling of species distribution in North Sea waters, I am looking for the best source for high resolution gridded oceanographic data for the North Sea. Since the North Sea is a small sea, I think the smallest resolution available is best.
Currently I am downloading the MARSPEC dataset (http://www.marspec.org), which seems one of the highest resolutions available (ESRI raster grids at a 30 arc-second spatial resolution). But they only offer derivations of Bathymetry, Sea Surface Salinity and SS Temperature. I also want to use current velocity and organic matter content (e.g. detritus or POM) in my model.
Can anybody advise me on what source to use?
Other sources I looked at are:
http://www.oracle.ugent.be/ - This is on a much lower resolution than my intended modelling resolution of 1,000x1,000 m.
http://www.aquamaps.org - This has an even lower resolution.
Edit (16-08-2015): http://marine.copernicus.eu - This does offer high resolution data sets for ocean colour (e.g. Chlorophyll content or DOM) but sets on other variables are all >7km.
Hi Joop,
A new publication just appeared
Monthly maps of optimally interpolated in situ hydrography in the North
Sea from 1948 to 2013 by Núñez-Riboni and Akimova in Journal of Marine Systems 151, 15-34
Possibly this is useful to you.
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I am on a study regarding the impact of unregulated fishing practices on stock and biology of yellowfin tuna. I understand biological assessments are used to tell whether or not a body of water can support survival and reproduction of fish.
Although this is not strictly my area of expertise, I am currently involved in a aquatic study that consists of a biological characterization in the vicinity of a water intake structure.  To begin with, such factors as bathymetry, prevailing weather, currents, air/water temperature, and insolation obviously play a significant role. Remotely sensed and bathymetric data may help give a general picture of physical conditions over a large area, which could then be used to identify possible sample locations and design a sampling plan.  The approach in general is to assess the habitat - water quality parameters (temperature, dissolved oxygen, pH, salinity/conductivity, and turbidity/Secchi depth), as well as the presence of structure or vegetation - along with sampling of the biological communities present, both plankton and nekton, and in near-shore cases, perhaps even benthic communities, to evaluate the number and diversity of species present. One goal of this sampling is to obtain, if possible, eggs, larvae and/or juvenile organisms to evaluate reproductive activity.  For this reason sampling might need to be undertaken at various times and locations throughout the year to obtain a complete picture of the fishery and spawning patterns.  The species data collected are then statistically evaluated to determine richness, evenness, calculate net productivity, etc.   A good place to start is by reviewing the literature for your fishery or comparable fisheries or species to see the specific approaches and techniques used, as what I have described is a very high-level overview.  Studying a pelagic species like tuna poses challenges, but a skilled fisheries or marine biologist/ecologist could also give you a more detailed (i.e. site-specific) approach tailored to your particular needs.
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How can I get a complete identification key of Zooplanktons ?
It depends on the zoogeographical region, freshwater or brackish or salt. General keys are based on the most typical (in author's opinion) species. In first approximation such general keys can be used, but you should support tham by specialised keys, e.g. with regional or world fauna books. In post soviets countries f. ins.  when identifying Rotifers we use normally perfect Kutikova book, when have to do with Chidoridae – Smirnov Fauna of the world (1971) (in Russian). As well, Cyclopoidea by Monchenko, Harpacticoidea by Borutzky etc. So, you should define more accurately you interest.
Andrey
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This jellyfish was caught in the eastern central Atlantic in depths between 100 and 600 meters. There was just individual of it. Can anybody identify it?
I agree with the other comments as it does look like Pelagia noctiluca and it does not have a sedentary life history stage.  So finding it well offshore is very likely. Its nematocysts can penetrate human skin and can leave a weal.  This is a further test! hope this helps. Dan
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These are copepod grazing experiments, where the particle size spectra and abundance were measured with a coulter counter particle counter in initial samples, and final control (no grazer) and treatment (with grazers) bottles.
This is a new area for me, any help is greatly appreciated.
Aha, I misunderstood. Some do test that, you could e.g. make a t test between grazed and control treatments. But i usually do not. Maybe I would if there is no clear grazing effect to be able to state "no significant grazing" Regarding the shrinking I would not worry for short (over night?) incubations. But several common colony forming species do split up in response to copepod grazing. E.g Skeletonema (Bergkvist et al 2012 L&O) Phaeocystis (Long et al 2007 PNAS), and Alexandrium Selander et al 2011 PNAS). At least for Skeletonema and Alexandrium the response typically takes longer than an over night grazing experiment to develop fully. If you do total bio volume it should not matter anyway, the cells are still there. So this probably added more confusion than solution, but I think normally stats is not necessary to prove grazing in a grazing experiment, rather to prove differences in grazing between treatments, prey etc. Best wishes /Erik
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If trapezoidal integration method is used, it provides value with units of mg/m2 (which is per area) but I need to know is there any way to get chlorophyll value for entire water column in terms of mg/m3 (which is per volume)?
using  the published methods of chlorophyll determination , such as the method of Holden(1965), the results are given in mg per liter. It is very simple to convert these values as follows:mg per cubic meter =0.001mg per liter.
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This "jelly ball" has been saw twice floating in shallow marine waters in Sicily (Mediterranean Sea). Someone suggested that it might be a damaged jelly umbrella but the evident bilateral symmetry suggests that it should not be a jellyfish. Hence the "damaged jellyfish umbrella" seems improbable. It might possibly be part of an organism or even an ooteca (mollusk ooteca?). What's your idea about?
No doubt, this is what remains of a scyphozoan jellyfish Chrysaora hysoscella. Probably it has experienced a turtle bite! Keep it in ethanol, we are working on this species, please!! Grazie, Luigi
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VGPM- Vertically Generalized Production Model
SeaBAM model
I might suggest some absorption-based approaches, especially for coastal area, here are two examples:
Smyth, T. J., G. H. Tilstone and S. B. Groom (2005). "Integration of radiative transfer into satellite models of ocean primary production." J. Geophys. Res. 110: C0014.
Barnes, M. K., G. H. Tilstone, T. Smyth, D. J. Suggett, R. Astoreca, C. Lancelot and J. C. Kromkamp (2014). "Absorption-based algorithm of primary production for coastal waters for total and size-fractionated phytoplankton." Mar. Ecol. Prog. Ser. 504: 73-89.
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I am mostly interested in species identification. Maybe there is some general book about the biological diversity with photos and drawings?
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I have sea surface temperature data from model (numeric model) and in situ measurement (logger). I would like to know quality of my model compare to in situ data. What kind of methods I must used?
Dear Eko,
I forgot to mention in my last response, a good tool to present the results of your comparison (if you do not already know the method), is to use the Taylor diagram (Taylor, 2001: JGR 106D7, 7183-7192).
(Here also you can contact me for further details at guy.caniaux@meteo.fr)
Best
G.C.
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What are Spatial and seasonal differences in the diet of sedentary annelida polychaeta of Mediterranean sea?
In addition with the previous comment from Florian, the feeding guilds defined by Fauchald and Jumars were recently updated.
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The distribution of annelid species is based on what? Are there documents on this research?
Have a look there:
QUIROZ-MARTINEZ, B., FRANÇOIS G. SCHMITT, F.G., DAUVIN, J.C., DEWARUMEZ, J.M., FOVEAU, A. & GARCIA, C.. Distribution patterns of annelid polychaetes species from the continental shelf (0-200 m) in the North Sea, English Channel, Irish Sea and Outer Bristol Channel. Italian Journal of Zoology 78(S1), 324- 332.
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If we have remarkable decrease in fish production, what are the priority suggestions to take?
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Indeed, those are extended tentacles. The pink indicates damage and that regeneration (growth) is going on. Species: Fungia fungites.
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Can I have information or links on ecology and biological study of the polychaete species of the Algerian coast, and I would like to have some literature on invasive species and endemic to the Mediterranean Sea. Grazie
Buongiorno F. Kies.
Bakalem A. Diversité de la macrofaune des sables fins de la côte algérienne.
Rebzani-Zahaf C. & al. Cycle annuel du peuplement macrobenthique du port d'Alger.http://archimer.ifremer.fr/doc/00093/20458/18130.pdf
Rouabah A. & Rouabah L. Biodiversité et complexe Perinereis cultrifera Grube (Pelure) : un exemple de spéciation.
Buona fortuna e successo.
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Could you suggest any information or links on the ecology and biology of rivers of the Mediterranean sea, especially North Africa (Algeria)
The University of Aix Marseille in France are working on the modelling and monitoring of the Po River in the mediterranean sea in the French coast. But I know they have data from the Italian and the rivers from Spain. A good contact point could be: the Dr. Christian Grenz
best regards
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I am working on using  normal Digital camera (gopro, CanonSX230) to capture aerial images and analyze it to be able to identify various benthic organism in tropical marine water. Am a little new to the process, can anyone walk me through a simple approach.
Sample image attached
Hola Emmanuel, I have done extensive work in this area (we made an atlas for the entire coastline of Mauritius; mapped seagrass in Florida; intertidal vegetation in both Canadian coasts, and other projects), BUT we used our compact airborne spectrographic imager (CASI); yet, some of the methods might be useful to you.
Asier's points are good, but we found that using unsupervised classification provided better results. Normally, unless you know with some degree of certainty the composition of your study area, or you cannot account for its diversity (and have all the required end members). Having said that, if what you want is to identify certain "classes", the rule image generated from the supervised (we use mostly S.A.M.) gives you nice spatial probabilities.
I advocate for unsupervised, creating a lot of output classes, and then use clear criteria for manual groupings.
I can send you some papers if you want; let me know! and best of luck.
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I am working with phylogeny of venus clams, and there are some weeks I am trying to keep contact with any researcher from Senagal or Nigeria. I need go there to examine some Pitar species to put in my morphological matrix. Unfortunatelly, all my efforts failed.
I know this person in Senegal, hope this helps :
Dr Marc BOUVY
Directeur de recherche IRD
Directeur adjoint UMR 5119, Ecologie des Systèmes marins côtiers (ECOSYM)
Université Montpellier II, Place Eugène Bataillon
Case 093, F - 34095 Montpellier cedex 5, FRANCE
+33 (0) 4 67 14 41 28 (tel)
+33 (0) 4 67 14 37 19 (fax)
+33 (0) 6 13 53 24 02 (port)
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From your knowledge and opinion, what are the most efficient protocols (in term of cost and information quality) to monitor the good environment status of marine benthos (hard substrate) in your marine region and why?
Evaluation of stress index, where both opportunistic and sensitive species are present in the matrix
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I am correlating pCO2 with fluorescence in the Western basin of the Mediterranean Sea. This basin is oligotrophic, but in the spring blooms can occur. I was expecting during this season the pCO2 to decrease due to the biological activity, but the correlation coefficient is positive. What could be the cause behind that?
I do not agree with what Alastair has said, pCO2 depends on pH of the water, it is other way around, pH of the sea water is dependent on pCO2. moreover, blooms can be also limited by CO2 in the oceans if not having constitute CCM. an increase in pH has been observed many times with enhancement in phytoplankton biomass. However, I agree with the last part of your answer. and also what Koji has mentioned. This is possible that for warming or upwelling, significant amount of CO2 is added up to the surface water and there could be simultaneous uptake also by phytoplankton and enhancement of fluorescence. However, the net increase in CO2 could be more and hence positively correlating with the fluorescence. In the Oligotrophic condition under high solar light there can be photo-inhibition leading to net heterotrophy and can may not uptake considerable amount of pCO2. As Koji said, phytoplankton stock is also important.
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Maybe you have already seen this paper of Morabito et al. 2013, they found that ocean acidification affected the osmotic swelling etc of nematocysts. That would hamper their capacity for food capture. This is a really interesting, and devastating, effect that has received very little attention.
Morabito et al. 2013. Sea Water Acidification Affects Osmotic Swelling, Regulatory Volume Decrease and Discharge in Nematocytes of the Jellyfish. Cellular Physiology and Biochemistry 32(suppl 1): 77-85.
It’s an incredibly interesting question, Susanna. We’ve known for many decades and across a fairly wide body of literature that pH affects the discharge of nematocysts: in some cases, this is inhibitory, while in other cases this is stimulatory. Most of this work has been done in the context of first aid for things that sting us, rather than on the subtler shifts that could alter an organism’s ability to survive. But given everything we know about nematocysts, it seems completely plausible to me that yes, OA could conceivably alter the discharge of nematocysts. In fact, I would go so far as to say it would be surprising if it didn’t. It’s just an educated guess – certainly the research needs to be performed! Man, this is exciting!
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I currently identify zooplankton to broad categories such as Echinoderm.  I would like to start identifying the echinoderms further to class, but am concerned about being able to tell the difference between the bipinnaria and auricularia larvae.  I understand that the main difference is that the bipinnaria larvae have two ciliary bands whereas the auricualria have only one. Can you see this readily with a stereoscope?  Is there another way to differentiate the two?
Thanks!
Hello Nicole,
in bipinnaria larvae (=Asteroidea) there is no trace of calcitic skeletal elements or ossicles ... in auricularia larvae (=Holothuroidea) there are calcitic skeletal elements (1: undiferentiated mesh work = Holothuriidae or Stichopodidae; 2: small wheels = Synaptidae) ...
You can check this easily in using a light microscope with a polarizer (in switching between plane- and cross-polarized light) ... calcite is normally colourless/transparent, but has a strong (so-called) double refraction and will appear (with crossed nicols=cross-polarized light) pinkish to greenish white under the microscope (if present).
For other detailed characteristics you may read: "Atlas of Marine Invertebrate Larvae" (2002) ... p. 499ff. (Asteroidea), p. 513ff. (Holothuroidea) ...
Best wishes,
Mike
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These specimens are collected from North Norway. As I know there is more than one Mytilus species and it is hard to identify those from photos. Here are some of the photos of the specimens collected.
Hi Lennart
I agree with Andrey; Arctica islandica.
I think the mussels are Mytilus edulis, one is extremely distorted.
One of the best bivalve guides for NW Europe is http://naturalhistory.museumwales.ac.uk/britishbivalves/Browse_taxa.php
Click the “here” button to get all species displayed.
If you want a particular species just type its name into Google (or other search engine) followed by the Welsh word for museum “amgueddfa” and you will be directed to the page.
Give it a try with “Arctica islandica amgueddfa”;  it should come top of the list.
Plate 1 shows an adult, more circular than yours which are not full size, and young ones of various sizes. They darken with age (they can live to over 500 years old). The Norwegian name for it is still used in Orkney, same pronunciation, different spelling: Ku shell.
A useful facebook group for help with identifying marine molluscs is https://www.facebook.com/groups/british.marine.mollusca/ It has members from Norway to Portugal.
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Dear Fellows,
I have identified some of plankton but because I am new in this field, I need your correction as an expert in phycology.
Thank you so much in advanced !
you images are not clear for identification
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Hi Friends,
I found this sample(which is attached) along with the phytoplankton samples collected. Suggest me weather its a kind of plankton or some other thing. If its a plankton help me to identify its name.
I am fairly sure that it is a cycloid fish scale, as others have suggested. We frequently encounter them in plankton-net samples. They (1) get knocked off of fish that are caught by the plankton net and (2) exist in sediment largely as the result of predation events; sedimented scales may be easily re-suspended into the water column, where they may be collected by plankton nets.
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Two species of recent foraminifera , i have some difficulties how can i differentiate between both of them .
from the original description Challengerella brady differs from  Ammonia  with similar shape by the imperforate cover of the spiral fissures transformed into a spiral canal in the internal whorl.
Challengerella is very similar to A. gaimardi and some authors consider them as synonyms.
Some nice images are reporetd in the Hottinger,  Halicz and Reiss, Atlas published in 1993. Recent Foramnifera from the Gulf of Aqaba. Slovenska Academjia Znanosti in Utmenosty, Ljubljania.
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We found from a recent study on a number of small groups that they appeared to orientate North (hinges South) and wondered if anyone else had come across this?
Hi both,  that's great thanks I'll get in touch with them.
Cheers
Kate
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I'm trying to reconstruct the productivity changes in the southeastern Arabian Sea, during the last glacial period. The foraminiferal proxies suggest an increased glacial productivity in this region. I want to understand the physical forcing, responsible for high surface primary productivity in this region during the last glacial period.
My co-authors and I provide a partial review of the impact of changing glacial winds on the Agulhas Retroflexion during the LGM in this paper. We discuss the impact of variation in regional winds on marine production and coastal currents off West Africa. The results should help you to hypothesize changes you may see in the Indian coastal currents for comparison with your study.
You can also review the chapter from my dissertation work on the California Current during the LGM for comparison. Primary production can be enhanced by several processes in addition to the Fe hypothesis noted in the prior answer. For example, increased offshore Ekman transport, or increased Ekman pumping via enhanced wind stress curl will increase the nutrient flux to the surface ocean, thereby potentially increasing primary and by inference secondary production.
D Nof, V Zharkov, J Ortiz, N Paldor, W Arruda, E Chassignet, The arrested Agulhas    retroflection, Journal of Marine Research 69 (4-6), 4-6, 2011
J Ortiz, A Mix, S Hostetler, M Kashgarian, The California Current of the last glacial maximum: Reconstruction at 42 N based on multiple proxies, Paleoceanography, 12, 191-206, 1997
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Found it on Pachacamac island, near to the central coast of Perú. It was caught last Friday. A female had 6 spotted-young sharks to a litter. My doubt is that females were plain-coloured and the others had tenuous black spots.
Jesús, Triakis megalopterus is confined to the South African coast (of the Atlantic and Indian oceans).
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Turbid water generally affect the biodiversity badly.
Well I guess, a phytoplankton bloom increases turbidity, especially in eutrophic waters. And the other way of the causal chain is also possible, in waters with high sediment induced turbidity, phytoplankton may be affected. However, I think submerged macrophytes are generally more affected by turbidity than phytoplankton.
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I would like to get an idea of the depth of light penetration using calibrated chl fluorescence (and transmittance if necessary) depth profiles. Casts were performed before dawn yielding poor PAR profiles.
Is there an up to date version of the Morel 1988 equation: Ctot = 4910*Ze-1.34?