Phytoplankton - Science topic

After segregating through separate mesh sized nets, staining methods can distinguish between both types of phytoplankton

If you want to know what phytoplankton is in your system don’t use a net all. Phytoplankton can be as small as 1 μm.

Roksana, thank you.

I agree that Synedra is a likely ID but you may also want to consider Pinnularia. They are both pennate diatoms with a raphe and similar morphology. There are some slight differences in the shape particularly in the terminal morphology. When you encounter this taxa again carefully read the descriptions to tease out which genus you in fact have. A very good guide book to use is

Identifying Marine Phytoplankton Editor: Carmelo Tomas https://doi.org/10.1016/B978-0-12-693018-4.X5000-9

Solved the problem! Acetone was the problem.

When I changed acetone to another company's product, chlorophyll was extracted again.

Perhaps there was a problem with the acetone produced at this time.

Mar Fernández-Méndez

Hi Mar,

The core part of CHEMTAX is basically to solve an overdetermined linear inverse problem. If you are an R player, the package `limSolve` by Karline Soetaert et al. provides an example of how you can do it. Try `help(limSolve::Chemtax)` in your console once you install it. Or find it in this link: https://search.r-project.org/CRAN/refmans/limSolve/html/Chemtax.html

Hope this helps. Good luck and regards,

Shun

When doing as Michel suggested, there may be weather abnormalities that correspond to differences observed and predicted.

Interesting & valuable question! we are waiting for the experts.

Shannon Weiner indicates the degree of better/stressful environment.

Thanks you, Zahidul Islam :

As you said, If i had two spp., i.e., Oscillatoria 4, Chlorella 3 etc.

Thus, My Index values 4 + 3 = 7

Does is indicate Lack of pollution as per above index table

( Index values between 0-10 = Lack of organic pollution)

review genus Zygnema

Hi !

If you get satisfactory results after checking the blank filters, you can use the scraping method for d15N. Just scrape off the layer of filter paper from behind without disturbing the top layer (avoid any contamination while doing so). For d13C, use a part of filter paper if the content is too high after acid fumigation.

Hope this helps !

Prachi

Thank you Mohamed Ben-Haddad . :)

It might look easy to just sieve your samples as many suggested, but in the end, it is advantageous to identify the species. E.g. so many of the protists are mixotrophs, i.e. fall in both categories (phyto- and zooplankton). Why do you need this distinction anyway? Maybe for writing it up, it might be easier to stick to the size fractions, instead of using the terms phyto- and zooplankton.

Gonzalo Martín Thank u so much sir.

Shyam Kishore and Maria Van Herk Thank you so much .

Let's start with a general linear model. This is a class of models that include simple linear regression, multiple linear regression, one-way anova, two-way anova, ancova, an so on. These models assume that the data are conditionally normal in distribution. Generalized linear models extend this to different types of observed data. For example, if you have a dichotomous outcome you might use logistic regression. If you have a count outcome variable, you might use Poisson regression. The Wikipedia article may be helpful: https://en.wikipedia.org/wiki/Generalized_linear_model#General_linear_models

It is well described in the book by Brian Fry 'Stable Iostope Ecology'. Also very useful when it comes to calculation of mixing-models.

Hi Willow;

Phytoplankton are fixed with a Lugol-glycerol solution (2-3 % glycerol). Glycerol is required for flagellates. Please look at European Committee for Standardization, 2015. According to the standard method (European Committee for Standardization 2006), phytoplankton enumerations were carried out under an inverted microscope (Olympus CKX41) at magnifications of 400 and 600X. For each sample, at least 350 settling units of the dominant species were counted. Phytoplankton biovolume was calculated by multiplying the cell density and mean biovolume of the taxon, which was taken approximating geometric shapes of the least 25 individuals (Sun and Liu 2003).

Also check https://link.springer.com/article/10.1007/s40899-015-0014-7

2. You can consider a one-isotope mixing model and take into account trophic enrichment factors to estimate trophic contribution from producers to consumers.

Hi Demtew Etisa,

To relate hydrographical parameters and biological parameters, the RDA or CCA results can represent in Triplot. In the ordination diagram, relationship between environmental and biological variables were determined by considering length and directions of orientations and its angle between the variables. The arrows representing species which are pointing in the same direction of environmental variables or towards stations shows high positive correlation whereas, the opposite oriented arrows indicates high negative correlations. Similarly, the shorter the angle between the variables, greater the correlation and larger the angle, lesser the correlation. For better understanding , you can check the attached pdf.

Thanks @John machell

Renan Ribeiro , Hello ,

how to add a porous plate in the flow (tidal current flow), to simulate the effect of the turbine (energy extraction) in the tidal current flow, in delft3d?

Thanks

Long wish I could afford a fluoroprobe. I use the haemocytometer and differential interference contrast on the microscope. Thinking about whether I can use my vis-spectrometer (not UV, sadly) To do quick throughput of samples. Any thoughts?

Desmidiales - Euastrum sp

I am not specifically familiar with MODIS or this type study. My experience with fluorescence determination and analytical work using fluorescent dye tracing, which is dated. There was an apparent abrupt change, that suggests to me an equipment shift, method or calculation shift. I don’t know specifically what is meant by line height, but am familiar enough to know that sometimes the graphical responses can change with equipment, so the running of fluorescent concentration standards before and after each sample, should take care of many or most differences as equipment or detectors age. And perhaps there has been a shift in phytoplankton function, that is causing the normalized values to be depressed, and at times below zero, so one would need to look into why there were no values below zero until the erratic response. If you are running standards, you might check if the line heights of the standards have been drifting or shifting. Sensors, light sources in fluorometer or other equipment shifts might also be considered.

Yes, people frequently use measured dimensions along one or two axes and simplified geometric shapes to estimate biovolume, see e.g. this one:

Hillebrand H, Dürselen C-D, Kirschtel D, Pollingher U, Zohary T (1999) Biovolume Calculation for Pelagic and Benthic Microalgae 1. J Phycol 35:403–424

...and then to convert from biovolume to biomass use for example:

Menden-Deuer S, Lessard EJ (2000) Carbon to volume relationships for dinoflagellates, diatoms, and other protist plankton. Limnol Oceanogr 45:569–579

hope this helps

-Leni

Many species in Amphora sensu lato are marine but an increasing number of species are being described from inland habitats. However, in spite of recent revisions of Amphora s.l. that included the elevation to the generic status of the subgenus Halamphora (Levkov 2009), the genera Amphora and Halamphora still appear to be insufficiently known in freshwater habitats.

The salinity barrier dividing the freshwater from the marine realm was supposed to be virtually impassable but Alverson et al. (2007)

showed that this did not apply to the thalassiosiroid diatoms.

More recently, Ruck et al. (2016),

working on the Surirellales and Rhopalodiales, proposed an interesting ‘stepping-stone’ hypothesis, based on comparative molecular-phylogeny evidence supporting the idea that the ancestrally-marine diatoms belonging to these groups would have used brackish waters as an intermediate habitat to which to adapt before invading freshwater environments. In the light of these papers, the most recent study by Stepanek & Kociolek (2019)

suggests that inland saline habitats are of particular interest for such studies: for diatom groups, such as Amphora and Halamphora, that have representatives

colonizing smaller inland waterbodies with elevated conductivity, these waterbodies might represent potential intermediate habitats from which the colonization of surrounding freshwaters could have taken place.

It thus makes sense from an evolutionary point of view that an Amphora s.l. species can become dominant in a slightly saline lake. However, as suggested by my Colleagues in previous replays, much more information on the taxon involved and on the environmental conditions would be needed to provide more ecological interpretation of your observation.

i highly recommend CytoExploreR

Dear Prof. Carlos Pereira

Well received, thank you so much.

Kind Regards

Fatima

Follow

Hi Rahul,

I tried with Qiagen DNeasy Plant mini Kit with modification, u can use filter paper method or plankton from net for extraction, but freeze throwing at Liquid nitrogen, and homogenization using bead beating is essential and after that incubation at 3-6hr at 55C

please refer: Nowinski et al.,2019(Nature -Scientific data)

Please, refer to the following links:

https://dash.harvard.edu/bitstream/handle/1/13031960/19743427.pdf?sequence=1&isAllowed=y

https://www.nature.com/scitable/knowledge/library/eutrophication-causes-consequences-and-controls-in-aquatic-102364466/

for M. wesenbergii the cels are too small, if it is not a Coelosphaerium, perhaps it is an Aphanocapsa.

Take a look at the article:

http://www.paper.edu.cn/scholar/showpdf/OUT2EN4IOTD0kxeQh

Please go through the following PDF attachment.

https://www.amamanualofstyle.com/page/si-conversion-calculator check this website

Plot logarithmic values of concentrations at the X-axis and mortality at the Y-axis.

Unfortunately not! This photo was taken from a sample that has already been dismissed.

thank you my dear, I believe it is this genre.

Ranielton

" Q-index for phytoplankton "

Which paper/report did you see? Can you send? I've never heard of it before.

by saying correlation do you mean what are the other organisms present in the two samples apart from your target organism?

For analyzing amplicon sequencing there are quite a number of programs and pipelines (QIIME2, MOTHUR) but this requires special environment, knowledge of Linux based languages and are a bit complexed.

The easiest method you can use is the GAIA platform (https://metagenomics.sequentiabiotech.com/). It is user friendly, more accurate and fast. you can use it for free upto 2GB of data. if you have more than 2GB of data then you nedd to avail the paid services.

What is the possibility of separating the plastic particles from the plankton at the point of collection and then using two different preservation media? It might be worth investigating by looking to see how plastic particles are concentrated now from water samples. Low velocity flow through centrification?

Thanks Silvia Haydee Otaño for your answerd. It s true that my filaments looks diferent as those from your publication. But in the publication : First report of Aphanizomenon favaloroi ocurrence in Europe associated with saxitoxins and a massive fish kill in Lake Vistonis, Greece from Maria Moustaka-Gouni et all Marine and Freshwater research, 2016,67,1-8 there are some filaments with spherical akinetes and at both sides.

But it is true it must be another Aph/Chrysosporum or and hibridus

Thanks

Maria

No amount of testing of different kits/methods is going to improve the quality of your input ("shit in shit out"). Is the DNA fresh, or has it been preserved from fresh and the number of cell input is high, then to be honest most methods will give you what you need, obviously with a slight variation (this is also dependent on what your doing downstream). Personally CTAB with phenol chloroform is the best, but for a kit Qiagen DNeasy plant works well. If you're getting a smear then do an RNase treatment. Lots of papers explain these methods clearly for protist. Once you have DNA (in H2O or tris, EDTA is an inhibitor) run a Qubit to quantify and a gel to qualify. Is the DNA fragmented then you can forget PCR, especially if it is long range. If you have high weight DNA and you'r PCR isn't working then the problem isn't the DNA but an element in the PCR. The first guess being the primers, but that's a whole new question ;)

I have no idea about the fresh water organisms as my research area is different.

The alga is a taxa of Dinophyta: Ceratium hirundinella.

Best regards

Lothar Täuscher

Thank you Dr. Mukherjee

It's common to report more than one index. Diversity indices aren't like statistics where you have parametric and non-parametric methods, and only one is appropriate based on the data. They are attempts to describe different aspect of diversity, such as richness, evenness, rareness, etc. Ultimately, it's up to the researcher to interpret what the index is saying because it's just a number from a formula that is meaningless without context and a description. The tool needs to fit the question and what you're seeking to find.

Yes

It don't have an open access

I agree to Nicolas,

It seems to be trichomes, maybe from bromeliads, which are pretty common in Bahia mountains. I have found these also in phytotelmata samples.

Numerical estimation of planktonic species are performed by many, but it is indeed a sorry state of affair that many of such reports are the results of extrapolated data obtained from very least volume of water sample and that too without establishing a mean data. Normally manual or instrumental enumeration of species assemblages, if performed on only 0.5 to 1 ml of water sample, results in amplification of the data when extrapolated to a litre of water and often the data exceeds what would have been actually present there.

With this being written, it is also possible for many workers to simply misidentify the more mature copepodite stages of mesozooplankton as adults and that too often yields exorbitant densities.

Keeping the above statements in mind, we need to consider the fact that aquatic system in highly dynamic and data procured from one such environment can only be contested upon by being at the same sight at the same time, which practically is impossible since the planktonic assemblages varies significantly based on the circadian rhythm as well as the biogeochemistry of the ambient ecosystem. Also the presence of warm discharge water at the vicinity of nuclear power plants might have triggered such a phytoplanktonic bloom as befitting the number of zooplankton reported.

Unless consistent data of similar magnitude get reported, it will not be prudent to discard (no matter how outrageous it appears) nor incorporate such data in the more practical data pool used by the concerned personnel. Doing either without absolute evidence to disregard the other will simply lead to impractical vilification and unwanted situations. In cases such as this, ignorance is a bliss.

Regards,

Dr. Abhishek Mukherjee

Dear Lin,

For details on best practices for measuring particle absorption (size fractionated or otherwise) on a filter pad, please see: http://ioccg.org/wp-content/uploads/2015/10/absorption_protocol_forcommunitydistribution-sept2017-2.pdf. To use the method you described above, a consistent volume is required for the whole sample and filtered sample, which should be compared to a blank or baseline sample of the same volume.

You may also find these resources helpful: http://www.oceanopticsbook.info/view/absorption/__level_2/benchtop_spectrophotometry_of_solutions_tmode and http://misclab.umeoce.maine.edu/OceanOpticsClass2019/schedule/ (see Lab 3).

Best of luck!

Sasha

Unyime Umoh

Yes, I am totally agree your comments. As the sampling area is a big shallow urbanized lake, many sources was generally mixed and biodegraded. I have already tried to apply the proxy as your recommend, and I got a higher contribution of terrestrial and sometimes petroleum contribution. But what I am confusing is that the particles have lower C/N ratios and relative low POC/chla (<100 microgram per Litter) as I said in my questions. And actually I am not expecting the higher contribution of terrestrial, because the lake is highly eutrophication, and cyanobacteria bloom (I thought they are main contributors to C17 in my case) is serious issues in this lake. So I am wondering if the alkanes indicators are still robust in my case, since I saw some articles showed the diagenesis effect could cause higher contribution of long chain n-alkanes in sediments, even though the allochthonous inputs is few.

And I am very grateful for your suggestion, I will try to test them. Could you tell me the approximate retention time of these compounds basing my TIC graphs, it will be helpful for quickly locating them.

You can go through this book

agree with Marcos Sarmet Moreira Barros Salomão ... the lake water has high content of nutrients... first of all you have to find out the source of nutrient and if possible stop it. It may take time.

to get quick result you can manually collect them and use them as bio-fertilized. yo can also culture herbivore fish species. it will solve your problem and will not harm bids. again, the permanent solution is stopping nutrient flow from outside the lake

If the query is to find the surface to volume ratio of a phytoplankton colony then the answer is pretty simple. One needs to simply measure the dimension of a uniform number (say 50) of cells ranging from the smallest to largest to draw up the mean value. Once done, the mean surface area/volume of random individual cell could be extrapolated based on the arrangement of those cells within the colony and the surface area as well as volume data can be obtained.

BUT,

if the question is intended to procure the biovolume data then, the cells as well as the mucilage or exopolymers as well as intercellular connectivity etc all need to be considered in a colony.More accurately the carbon content or biomass data can be used to generate bioviolume data or vice versa.

3 and 14 - Cilliate (maybe Colpoda)

4 - Dinoflagellate (maybe Gonyaulax)

If the centrally smaller and rather hyaline structures are semi-cells then, judging from their large chloroplasts I think IT IS an image of Staurastrum undergoing asexual reproduction. If you can ascertain the centrally located pyrenoid within the chloroplast in your sample then without a doubt it is an instance of asexual division of desmid cell.

Regards,

You may go for Plant extract or nutrient supplement like single super phosphate to crash it naturally by over crowding that.

Dear Dania,

To calculation the pigments concentration without calibration curve is impossible. Because of at first you should calculate the equation (Y = aX + b) based on standards, then by using it you can gain the final data. 

In one way you can report your results in percentage and comparison between your samples. In another hand, you can use an alternative procedure such as a spectrophotometric method. I attached the original paper for the spectrophotometric method, Lichtenthlaer's protocol, for your reference.

Sincerely yours, Homayoon.

Be sure when you surfing in the net, most of the web site are misleading...

All best

If you fix it with %30 formalin it is not possible...

All best

Many thanks Fatih!

All the best

Paint with Calcofluor and look at the plate under epifluorescent

All best...

It is helpfull for you...

All best

Those looks like coccolithophores, probably shed their calcite discs..

All best

%2-3 Formaldehyde buffored with borax...

All best