Biological Oceanography - Science topic

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.

@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.

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:

These papers can give more thorough information on the application of AI in oceanography, including possible advantages and problems.

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

Hope for u always success

Dear Victor

Mostly expressed as items/m3, but you use another unites according to your specified work too!

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.

Imran AHMED Khan, Apart from the Coriolis ARGO products, I would recommend using US-GODAE ARGO data. Please, go to the following links:

ftp://usgodae.org/pub/outgoing/argo and

To answer your questions, the Argo data are very useful with a careful choice based on the quality flags.

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.

Hello. This paper can help you with the answer to your question.

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.

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

Van-Veen grab 1/40 m2

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.

Thank you both so much for the feedback. It is very appreciated. 

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.

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.

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. 

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

Definitely not Ophiolepis. Ophiotrichidae is correct and I think it is Ophiopsammium not Ophiothela but needs to be verified with literature and close examination.

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 

scale of butterfly

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

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!

Dear Samiran,

1. For SSS check the websites: http://www.salinityremotesensing.ifremer.fr/  and https://podaac.jpl.nasa.gov/SeaSurfaceSalinity

2. For chlorophyll check http://oceancolor.gsfc.nasa.gov/cms/

Rgds.

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.

Thanks! Dave,

I will do the needful and try to get hold of Clark, 1938.

Best Regards,

Anand.

1) Staurastrum

2) Eunotia

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

Rajan:

You have not provided magnification. Still upper two forms show affinity with Spirogyra and lower one with Pediastrum.

Best

Syed

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

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.

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.

Dear Nandha,

I think it is white sea cucumber probably Eupentacta quinquesemita.

Best regards

Dear Reliana, read these articles 

I suggest you MODIS SST. You can refer to the following publication for investigation and validation of MODIS SST:

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)

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.

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.

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.

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

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

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

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.

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

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.

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.

In addition with the previous comment from Florian, the feeding guilds defined by Fauchald and Jumars were recently updated.

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.

Thanks for your collaborations

Indeed, those are extended tentacles. The pink indicates damage and that regeneration (growth) is going on. Species: Fungia fungites.

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.

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

 christian.grenz@mio.osupytheas.fr 

best regards

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.

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

e-mail: marc.bouvy@ird.fr

+33 (0) 4 67 14 41 28 (tel)

+33 (0) 4 67 14 37 19 (fax)

+33 (0) 6 13 53 24 02 (port)

Web site: http://www.ecolag.univ-montp2.fr

Evaluation of stress index, where both opportunistic and sensitive species are present in the matrix

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.

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!

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

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.

you images are not clear for identification

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.

Dear Ramadan,

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.

Hi both,  that's great thanks I'll get in touch with them.

Cheers

Kate

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

Jesús, Triakis megalopterus is confined to the South African coast (of the Atlantic and Indian oceans).

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.

Hi Nicolas,

you can use the model of morel (1988) and take a look to Morel and Maritorrena (2001) for updated parameterizations.

Besides, you can use standard models for IOPs in case 1 waters, see for instance this publication by André morel which give a good summary of all these relationships (MOrel, 2009), and then calculate Kd as a function of IOPs using MOrel and Loisel (1998) pour each wavelenghts to get Ed at each wavelenght, and integrate over the visible domain.

hope it helps

hubert

Morel, A., and S. Maritorena (2001). Bio-optical properties of oceanic waters: A reappraisal. Journal of Geophysical research, 106, 7763-7780

Morel, A. and J.F. Berthon (1989). Surface pigments, algal biomass profiles, and potential production of the euphotic layer: Relationships reinvestigated in view of remote-sensing applications, Limnology and Oceanography, 34, 1545-1562.

Morel, A. (1988). Optical modeling of the upper ocean in relation to its biogenous matter content (case 1 water), Journal of Geophysical Research, 93, 10,749-10,768.

Morel, A. and H. Loisel (1998). Apparent optical properties of oceanic water: Dependence on the molecular scattering contribution. Applied Optics, 37, 4765-4774.

Morel, A. (2009). Are the empirical relationships describing the bio-optical properties of case 1 waters consistent and internally compatible? Journal of Geophysical Research, 114, C01016, doi:10.1029/2008JC004803.