Phytoplankton Ecology - Science topic

You can even isolate the cultures and do a study. Its not that difficult. In case you need my help, you can contact me

Yes, You can use many methods of cluster or ordenation analysis. May be the assay with PRIMER software could help you and select the methods that you want.

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.

Well time series include serial correlations, trend & seasonality features. So any prediction or results are conditional on data treatment and/or model. you will need to qualify your conclusions by "de-trended series shows..." or "seasonally adjusted series shows..." or "De-trended and seasonally adjusted series shows...".

***in your question you rightly tell that you fitted linear model and the size of p-value...try models like Fourier curve (single or double)...good luck

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 go through the following PDF attachment.

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

All best

'Gap in knowledge' can be applicable to any field of study or scientific discipline. Basically it means there are several aspects of any particular subject, in your case being freshwater phytoplankton that have not yet been worked out, discovered and/or not well discussed that need detailed studies or further evaluations. 'Limitations in study' stand completely different as they are the influences which a researcher cannot control and can include any shortcomings that restrict his/her work methodology and to a certain extent the conclusions too.

Dear Mike,

I am working in this field on fresh waters and I would recommend:

Bukata, Robert P., et al. Optical properties and remote sensing of inland and coastal waters. CRC press, 1995;

Lee, Robert Edward. Phycology. Cambridge University Press, 2008;

Bellinger, Edward G., and David C. Sigee. Freshwater algae: identification and use as bioindicators. John Wiley & Sons, 2015;

Reynolds, Colin S. The ecology of phytoplankton. Cambridge University Press, 2006;

If you are working with satellite remote sensing data I would recommend spending some time reading the IOCCG report number 15, 2014 (attached)

regards,

Isabel

Hello,

Be carefull,  if you got nitrogen in your medium this will interact. I advice you to do a dyalisis before your quantification to remove all salt wich could interact during the colorimetric method.

Regards

Hi Aysha. This is definitely Actinocyclus. As well as the very distinct marginal opening (pseudonodulus) and hyaline rays which characterise this genus, it has many rimoportulae (labiate processes) around the edge of the valve, very clear in the internal SEM photo (third one down), and strongly resembles A. octonarius, probably var tenellus. The attached publication may be useful (see figs 1-14). Best wishes, Alex 

Great! Thank you very much.

Do yo know if this species form colonies instead chains?

Hello Malcolm, hello Salah

i have just learned from my colleagues in the laboratory that they have already used the sampling equipment in marine water, and there is no connection between lake and sea. I apologize for the inconvenience.

Best regards

ARAB S

Sanjay:

Better images are needed to offer you helpful insights.

Best

Syed

Phaeocystis?

Dear Natalia:

I think that your specimens are Gloeocapsa sp. Gloeocapsa has several species with wide gelatinous sheaths, concentrically lamellate (lamellation distinct or scarcely visible),intensely or partly coloured by sheath pigments (gloeocapsin, scytonemin), yellow, yellow-brown, orange, red.

You can consult http://www.cyanodb.cz/Gloeocapsa

Kind regards.

Eugenia

Hi,

As a biologist I can suggest you two methods to estimate carbon biomass of phytoplankton (No idea about mathematical model!).

1). To estimate the biovolume of phytoplankton, geometric shape based formulae are available. From the biovolume of each group/species, we should calculate the carbon biomass using published conversion factors.

(Eg. Biovolumes and Size-Classes of Phytoplankton in the Baltic Sea).

So many standard articles are available online about the biomass content of each plankton group.

2). Biomass estimation of the substance/phytoplankton using the equipment CHN analyzer (carbon, hydrogen and nitrogen).

It really depends on the context. If you are interested in grazing rates of cells, then size can be a better predictor. For energy flow through a food web, C is typically the currency of choice. However, there can be other currencies such as N or P, depending on the purpose of the calculation. Typically (but not always) the lower the carbon content per cell, the faster the doubling rate. That is because the smaller the amount of carbon, the less carbon that is required to double. However, that relationship may not hold if the cells are light (e.g. C limited). For example, if the cells are P limited, it is the cells which require the lowest amount of P that will likely double most quickly. The same is true of nitrogen, if N is limiting to growth. There are many classic papers in this area e.g. http://www.whoi.edu/cms/files/Droop_ThoughtsonGrowth_JPhycol1973_52468.pdf

Thank you very much for the references, very helpful.

Best regards, Ioannis

As Harold C. Bold of the University of Texas and his students discovered, more than four decades ago, time and patience is required using microbiological techniques to classify soil algae.  I would recommend the 12 publications by the University of Texas as your starting point -  published under the heading “Phycological Studies” from 1960 to 1974.   The Botanical Review paper by Metting cites most of them.  

Metting, B. 1981. The systematics and ecology of soil algae. The Botanical Review 47(2):195-312. 

Phycological Studies--VIII. The Taxonomy and Comparative Physiology of the Chlorosarcinales and Certain Other Edaphic Algae 

 https://utexas-ir.tdl.org/handle/2152/27521

Phycological Studies--XI. The Genus Chlorococcum Meneghini 

I believe several of the Chlorococcum-like taxa that were isolated from soil continue as unialgal, axenic culture and available for purchase at the University of Texas Algal Culture Collection with some also shown as photomicrographs.    

Pollen is very important.It may constitute approx. 50% yearly external P input to the lakes and it increases the plankton productivity:

Kind regards,

Michał Filipiak

It´s difficult to be sure that the material is Oedogonium: the  typical ringlike caps are not visible and neither the pyrenoids . It´s necessary to look for these so common and evident morphological features  in Oedogonium. Good luck, Célia sant´Anna

Dear Raghdah:

In my opinion your material labeled as B is a Chlorophyta, Prasinophyceae, as Elaya comments, it could be Tetraselmis. I include a transcription of the description of Tetraselmis given by Lee (2008), as you can see the differential features are basically ultrastructural. “Tetraselmis is commonly found in marine waters. The cells are oval-shaped and surrounded by a theca that is formed by the coalescence of many small stellate scales that are produced in the Golgi apparatus. Four flagella are inserted in an apical pit in the cell. The flagella are covered with hairs and scales, and the flagella emerge from an opening in the theca. There is a cup-shaped chloroplast with a basal pyrenoid. A nucleus occurs in the center of the cell, and Golgi bodies are found anterior to the nucleus”.

I suggest consulting Thronsen in Tomas (1996) Identifying Marine Phytoplankton, Academic Press, New York.

Your material labeled as B5 is probably a small naviculoid or nitzschioid diatom.

Is your material labeled as Di fixed? It shows similitude with the material labelled B5.

Kind regards.

Eugenia

Dear Anila,

the question with primary production isn't so simple.  You have to do with alive system and photosynthetic activity of algae depends on a lot of factors of surroundings. E.g, in the Carpathians streams, brooks and  small rivers smthms appear that the highets primary productivity (in benthos and periphyton) appears in the Winter time! (Look, please, my page). In plankton also would be blocking of the development by intensive sun rays... So, should take into consideration the deeper layers, as we have to do with the effect of redistribution of production in the column.

The very interesting question is water transparency influence. We have some theoretical elaborations in this question.

As well you should know that net productivity is approximation closely related with science fiction! DIFFERENCE BETWEEN PRODUCTION AND WHAT DECOMPOSITION? What method of determination of decomposition - on oxygen, on balance of carbon??? Anaerobic metabolism can be very high in shallow waters esp with the higher aquatic vegetation! It can differ several times

Plankton is only subsystem and important is productivity in total or General productivity of the ecosystem, and this is connected with redistribution of primary productivity of plankton (depends on depth of the system - what "net" productivity of the deap sea area? So, we can speak about balance of subsystems, budget etc.

So, the answer can be: you have to do with the more eggective functioning of the sytem of pl comm in mooson perion. As well can be better situation with biogens...

Andrey

Dear Sir, Thank you so much for your answer. Yes, I knew about all pioneers from Kakatiya University. I met Vidyavati mam and she also helped me for my studies. Anyway I will ask them further. Thank you sir. 

I used to use unglazed floor tiles. (in the US these are sometimes called "unglazed quarry tiles" although I think that the more generic name is terra cotta tiles). They provide a standardized area which makes quantitative analysis much easier and they are relatively inexpensive and easily obtained. If you use the extruded ones then you have a choice of either the smooth, flat top surface or the ridged bottom.

If you do a google search on "periphyton  quarry  tiles" you should be able to see a whole bunch of research pubs that have used these.

looks in first instance like a scale from a butterfly or a moth.

Best wishes, René

Definitely the question needs narrowing down. Cyanobacteria are another common bloom-forming group of phytoplanktonic organisms.

I would vote for Tetraedon as it looks like more irregular and polygonal than Staurastrum. Furthermore, on this picture, there is no visible isthmus/constriction in between the two semi-cells (=taxonomic feature of Desmids).

What we did is transfer our culture to filtered sea water with a bit of nutrients (F10, F20 final nutrient concentration) in a 10 L cylinder with an helicoidal paddle that rotated at 10 rpm. What you actually need is to keep the algae in suspension, but in a gentle way. Not by shaking.

I hope this helps

Albert

Dear Mr. Tahon,

I like to use the IPCC reports as strong reference numbers such as here:

and then search the papers citing the IPCC report and its references to dig more recent information on specific components.

Hope that helps, much luck.

Neera:

You may like to have a look at this link for the viewpoint of Global Biodiversity Information facility:

Best

Syed

I think maybe you can contact the author of this paper, Discrimination of marine algal taxonomic groups based on fluorescence excitation emission matrix, parallel factor analysis and CHEMTAX (http://www.hyxb.org.cn/aosen/ch/reader/view_abstract.aspx?file_no=20141221). They have collected a lot EEM spectra from 60 kinds of phytoplankton.

In the literature this somewhat depends on the method you use to measure phytoplankton cell size. If you use conventional particle counter e.g. Coulter Counter or Elzone, the instrument expresses the cell size as "equivalent spherical volume". If you measure the linear dimensions of the cells (e.g., length and width) by microscopy or other means (e.g. imaging device), you can calculate the volume using simple geometry. This works well for cells of simple shapes (e.g. cylindrical and spherical), but more challenging for others (e.g. cells with complex morphology). Cell volume is usually expressed in cubic micrometers.

Dear Eyasu. Species identification using an key is complicated. Tipically, more powerful tools for ultrastructure determination are necesary. A good strategy: Identify to genera level and later use phycological specie level description from research articles.

Regards. 

besides Chl a, Phaeodactylum  is kown to contain chlorophyll c, fucoxanthin, diadinoxanthin and β-carotene .  Hence the wavelength  625-630 is preferred  over other nm 

maybe the toxin-producing dinoflagellate Cochlodinium

See :

Zhao et al. (2015) Characterization of harmful algal blooms (HABs) in the Arabian Gulf and the Sea of Oman using MERIS fluorescence data. ISPRS Jurnal pf Photogrammetry and Remote Sensing, Vol 101: 125-136.

Dear Mohamed, as others have stated this is indeed A.sanguinea (also known as Gymnodinium sanguineum ). It is thought to be a non-toxic dinoflagellate but it has been implicated in seabird deaths (see Jessop et al. 2009). 

Jessup DA, Miller, MA, Ryan, JP, Nevins, HM, Kerkering, HA et al. 2009. Mass stranding of marine birds caused by a surfactant-producing red tide. PLoS ONE 4: e4550. doi:10.1371/journal.pone.0004550.

Dear Mohammed, if that is the species then it is a red-tide blooming species - is there a history of eutrophication in the area? Have there been any associated symptoms such as fish kills, bird deaths, anoxia in the water column, benthos dying? It may become a public health issue as well. best wishes, Mike

This is Heliocotheca (= Streptotheca) tamensis (SHRUBSOLE) RICARD (centric diatoms).

Best regards

Lothar Täuscher

Dr. rer. nat. Lothar Täuscher

- Diplombiologe -

Petersburger Str. 44

D-10249 Berlin

Dear Reliana, read these articles 

Dear Anton:

Besides the diatoms, other organisms produce siliceous pieces as: statospores i. e. Chrysophyceae, Synurophyceae; silicified cell wall composed of five to eight plates occur in the Parmales (Chrysophyceae); siliceous scales on the outside of the cells also occur in the Synurophyceae and siliceous skeletons occur in some Dictyochophyceae.

For examples see

Graham et al. (2015) Algae

Lee (2008) Phycology

Van den Hoek et al. (1995) An introduction to Phycology

Bold & Wynne (1985) Introduction to the algae. 

Kind regards.

Eugenia

My dear, this seems to be a fungus.

My greetings.

Hello Liu Jiangsi,

Yes indeed, its looks different ... You may check:

Toomey, D.F. & Nitecki, M.H. (1985): "Paleoalgology: Contemporary Research and Applications." x + 376 pp.; Berlin & Heidelberg (Springer). (incl. a chapter on Permian algae) ...

Best wishes,

Mike

Dear Anila,

I agree with Dr.Kevin regarding the number of striae and its significance in the  identification of diatoms. My suggestion on your photomicrograph is  that  it could be a species of Pinnularia.

Best regards

CDOM might be causing the sensor to give a false-positive.  Try diluting an organic-rich water sample with expected chl-a content with filtered clear water.  The y-intercept (chl-a on ordinate, dilution factor (<1) on the x-axis) should be the chl-a concentration in the organic rich sample.  Any curvature of  the curve would indicate CDOM providing a false signal of "chl-a".

Dear EI Mahdi Bendif,

Thanks for your good suggestion. It also helped me.

Is there also a simple way for distinguish live and dead diatoms?

Lihua

Your culture is probably way into stationary phase so you have a mix of cells that are either dead, dying, or slowly growing. Try growing to a lower OD where the organism is in log phase. E coli at an OD of 0.5 equates to about 4E8 cells/ml. Make sure you mix the culture well before pipetting. Also, it may be that P. gingivalis has started to form biofilms or cell clumps and your bacteria are not as "planktonic" and evenly distributed as you think. This will skew cfu counts.

Check this paper:

Biomass and lutein productivity of Scenedesmus almeriensis: influence of irradiance, dilution rate and temperature J. F. Sanchez & J. M. Fernandez-Sevilla & F. G. Acien & M. C. Ceron & J. Perez-Parra & E. Molina-Grima

Appl Microbiol Biotechnol (2008) 79:719–729 DOI 10.1007/s00253-008-1494-2

Multivariate analysis is the place to end, not the place to start. If you want to understand your data, then you first have to do some exploratory data analysis... and given the number of variables you have measured and the amount of data that you have, this will take a considerable amount of time, effort and creativity.

Often diatoms especially planktonic taxa undergo size reduction due to increase in phosphorus and drop in silica

The attached paper may help.

Genomic DNA can be isolated from the cyanobacterial cultures using MiniPrep Bacterial Genomic DNA method (Ausubel, 1999) . The forward primer CY106F (5’-CGG ACG GGT GAG TAA CGC GTG A-3’) and reverse primer CY781R {equimolar mixture of CY781R(A) 5’-GAC TAC TGG GGT ATC TAA TCC CAT T-3’ and CY781R(B) 5’-GAC TAC AGG GGT ATC TAA TCC CTT T-3’} can be used for amplification of a fragment of the 16S rRNA gene from the isolated DNA (Nubel, 1997).

Hi

What sort of sample are your looking at? how are they preserved?  What level of ID do you require?  Are you working with wet samples, or permanent mounts? All these factors will influence the choice of microscope.

If you have access to SEM, this is really the best for coccolithophorids, but you can resolve some of the larger species with good LM.  If you are using LM for diatoms, DIC or phase contrast is essential.  Fluorescence will be very important for resolving the plate tabulation of dinoflagellates, but you may not need this level of discrimination?

If you are working with cleared diatom material, an oil immersion x63 or x100 objective, will help enormously.  

Please send some more details on what information you need from your samples, and what type of sample you have (sediment/water/sea-ice etc etc)

Good luck with your research, Regards Ruth

Not sure quite what you are asking.I have harvested attached diatoms diatoms with a sterile rubber policeman. If you are careful you can do this without damaging the cells. Stopping adhesion in the first place can be achieved by reducing the Ca++ content in the medium to about 10% of the initial recipe. This works well with marine species and we have used it for cyanos too.

Hello Alessandra,

I strongly advise you look into William Peterson's work with the NOAA Northwest Fisheries Science Center. His research has been integral on the effect of the Pacific Decadal Oscillation (PDO) on zooplankton community composition with emphasis on fisheries management. 

Just like temperature, zooplankton community composition can be used as a metric for stock success, individual growth, and overall fecundity. PDO phase shifts correlate with variation in seasonal upwelling and temperature regimes, resulting in zooplankton community changes that dramatically impact energetic constraints on foraging fishes with carryover effects for piscivorous species. Zooplankton community composition has also been used as a proxy for ecosystem health and assessment of susceptibility to climate change in more recent years. 

Bill Peterson would definitely be the person I would try and contact for specifics on the how's and why's of how these metrics are applied to fisheries analysis and policy.

Cheers,

-Thomas

Karnan,

It is a diplopsaloid type dino.  To get to the genus/species (Diplopsalis, Diplopsolapsis, etc) you need to examine the thecal plates on the bottom half of the cell.

you should get a different answer with a longer incubation. This will differ depending on what media type (mixo vs autotrophic), what is the history of the sample, what time of day it is etc.

I would suggest a 10-15 minute dark incubation followed by 5 minutes of far red light illumination (720nm) to oxidize the quinone pool and preventing state 2 transition in the dark.

 Thank you, Anila. This is a good review on the principles and methods for alga recognize. Although it is not easy to get an ideal solution, the paper gives us a direction to go.

Yes, it does. You will only have to determine experimentally the strategy which willgive what you consider the most desirable result. Personally, I would start looking into N limitation first

Once you have fnished a rtPCR with those resutls, I would run an agarose gel of your products in order to see if you get more than one band. Under my opinion it looks that the primers are not specific enough

Good luck!

Dear Karnan:

The genus Biddulphia is still accepted, and it is not a synonym of Odontella. Many species of the genus Biddulphia were transferred to the genus Odontella because of the ocelli, but not all them. For example, the accepted name for Biddulphia mobiliensis is Odontella mobiliensis and for Biddulphia regia is Odontella regia, but Biddulphia biddulphiana is still accepted in the genus Biddulphia .

Regards,

Margarita

Hi Puganeswary

I want to share my experience in culturing dinoflagellate from the genus Scripsiella.  I isolated them from the bay (Narragansett Bay, Rhode Island) and these isolated cells were placed in an incubator with a photoperiod of 12:12 hour (light:dark cycle), at light intensities of 62-89 µmol photons.m-2.s and at a temperature of 20°C in f/2-Si medium.  They grew well in 150 mL flasks.  Good luck

It is most likely a zoospore.  When Haematococcus is nutrient deplete or limited it can enter a sexual stage, where the zoospore will appear like small Chlamydomonas cells.

Dear all:

In my opinion it is not possible to determine the genus of the material presented by Karnan based on the photographs presented by Karnan.

Karnan I recommend get Sundström’s doctoral thesis, Sundström (1986). The marine diatom genus Rhizosolenia. Lund University code LUNDBS / (NBBS-1008) / 1-196.

This author split Rhizosolenia  s. l. in several marine genera: Rhizosolenia s. str., Proboscia Sundström, Pseudosolenia Sundström as was pointed out in previous comments. The differential features between genera would not be visible in these pictures.

I also recommend you the paper about Rhizosolenia s. st., Neocalyptrella, Pseudosolenia, Proboscia by Sunesen & Sar (2007) in which you can see the necessary features for determining an Rhizosolenia s. str. as R. setigera.

Kind regards.

Eugenia

Independently of the sampling strategy you choose for water collection (surface vs composite samples), you can reach the 'plateau' of the species-area curve by either increasing the number of phytoplankton slides that you will identify/enumerate with your microscope or by concentrating your algal sample using a filtration technique + resuspension of the residue in order to catch the rarest species.

However, the volume of water to be filtered has to be determined and you may have to try several times or keep adding water while filtering until the filter turns green...not too much green because you may collect too much algal biomass and it will be very difficult to count cells.

In addition to some of the earlier advice, there is an extensive literature dealing with sources of alkanes and other lipids for use as sedimentary and geological biomarkers. It might be worth querying your data using the "terrestrial aquatic ratio (TAR)" biomarker index and the "carbon preference index (CPI)" and compare with previously published values to determine source, diagenetic state, as well as possible anthropogenic contamination.

Good Morning

Thank you for your attention to my work. I recommend you to use a principal component analysis (PCA) housed in free software XLSTAT. This is free software for a test a month once installed on your computer. It’s a form of excel very advanced.

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