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Phytoplankton Ecology - Science topic

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For community studies like species succession, variation in composition, especially for plankton and benthos, what are the appropriate statistical methods? One such method is MDS with cluster overlay. Similarly what else can be applied for such studies?
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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.
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I have been exploring data in the Agean sea from MODIS product normalized fluorescence line-height (nFLH).
In many control areas, I have noticed a strange pattern on the fluorescence line-height values. Does anyone know if this is due to a problem in the sensor?
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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.
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I have a time series of monthly chlorophyll-a observations that spans from 1997 to present day. I have computed the p-value of the time series without removing the seasonality, and it doesn't quite show much of a trend. So, my question is, is the seasonality of the data affecting my computation, and if so, should I remove it? And, any recommendation on which methods that I should use to deseasonalise the time series.
I apologise if my question makes no sense. Thank you in advance.
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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
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CTAB or Phenol chloroform, which is better? Please guide me in detail
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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)
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Fatty acids composition of microalgae differed from species to species.
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Please go through the following PDF attachment.
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These Imaging FlowCytobot (IFCB) images were taken during a December cruise in the Santa Barbara Channel during the Thomas Fire. They were imaged after tripping a fluorescence trigger. These species appear at the surface and at the deep chlorophyll max. The cells look like they are in various stages of dividing and were maybe pulled apart by the IFCB during intake. Any help with identification would be much appreciated!
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Those looks like coccolithophores, probably shed their calcite discs..
All best
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Dear Researchers,
please share your valuable understanding on the 'gap in knowledge' especially in freshwater phytoplankton study. How do it dis/similar with 'limitations in study'? Is there any relation with each other?
Thanks in Advance.
sincerely
Anila P Ajayan
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'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.
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i am more interest to know what kind of hypothesis, question, or objective that each index usually answer. surprisingly that both indices has quite the same definition in a term of scribing the reason of using them to define diversity.  i calculate both indices and i would like to discuss the results. simply my objective is to see if there are special and temporal differences in phytoplankton diversity among 8 sampling stations.
  also i am interested to know what are the main objectives or questions of your researches that you answered using such indices. thanks
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Parallel use of species diversity indices in ecological studies is a general practice, and a typical case is the parallel application of the
Shannon–Wiener and Simpson index. However, while the Shannon–Wiener index is strongly influenced by species richness and by
rare species, the Simpson index gives more weight to evenness and common species. The effect of the sample size is generally
negligible for both of them.
The use of both diversity indices improves the output information of the dataset, which is unique for each community or sample
analyzed. Looking at the wider content—both emphasizing the richness, and the specimen distribution into the individual
species—adds to the more complex information of the diversity in ecosystems.
In this sense, H has an advantage over D because it depends more on species richness and less abundant species, so it is very
sensitive to even small diversity changes, and thus is widely used to assess the actual state of environment. On the other hand, D has
the advantage over H in counting more on dominant species and is not affected by less abundant elements; therefore, it is used to
show the trend of ecosystem diversity heading.
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I am interested in citations that explore the relationship of phytoplankton with the reflective, absorptive, and refractive properties of water in estuarine systems or alternatively to direct measures of water clarity or light attenuation. I am interested in knowing whether or not changes in community composition could result in changes in water clarity or light attenuation. For example, changes in species composition might result in changes in the overall average size, shape, or concentration of accessory pigments in the water column which could alter the properties I mention above.
I would appreciate any citations, particularly review papers, that you folks might think would be useful. Although the focus of my interest is estuarine and marine, I would also appreciate freshwater citations. Thanks.
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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
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Am trying to extract exopolysaccharides from fresh water microalgae. So far I was unable to obtain polysaccharide precipitate in considerable quantity. Still I want to check if there is an enhancement in the production of polysaccharides against stress factors. For this, can I perform Phenol sulphuric acid assay with the supernatant obtained after centrifugation of the biomass? Will this method give result or must I do it only with an eps precipitate?
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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
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I'm not really sure whether this diatoms are from genus Actinocyclus. Can anyone help me identify this diatom? Thank you.
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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 
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Sample was taken at the Guadalquivir estuary and fixed with formaldehyde.
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Great! Thank you very much.
Do yo know if this species form colonies instead chains?
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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
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Can anyone please identify pricesely the attached algae  ( no. 5 and 6 ) ?
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Sanjay:
Better images are needed to offer you helpful insights.
Best
Syed
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Dear all,
We found these organisms in gelatinous material, collected from small scale fishing nets in Cyprus coast. Nets were quite loaded with this mass. It was observed using a microscope (400x). Does anyone know what this might be?
Thank you in advance.
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Phaeocystis?
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Cells are 3-5 μm and the mucilage is red. 
Collected in western Canada
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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.
Kind regards.
Eugenia
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Hello,
does somebody know to suggest me a reference study estimating/measuring the general relationship between PON (particulate organic nitrogen) and chlorophyll-a in marine phytoplankton? Even better, specifically for the groups of marine diatoms and cyanobacteria?
Thank you in advance,
Ioannis
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Thank you very much for the references, very helpful.
Best regards, Ioannis
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Does anyone know these soil algae? They are isolated from biological soil crust in Bremen, Germany.
In the figure, there are 4 species (Non-Gel A1, 2; Gel A1, 2). The left one in each row shows their morphology on agar plate. In the microscopic image, I notice that they have different cell size. Algae (Gel-A1, and A2) both produce 4 daughter cells, and they have gelatinous colony on agar plate, while Non-Gel algae have flat colony. Scale bar stands for 10 um in the figure.
Can phycologists provide me any information from these algae? Like the genus they belong to?
This is a part of the research within my Master program. Thanks in advance~
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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 
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.    
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Chlorophyceae, Algae, Periphyton,  Cochin estuary
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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
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Hello, 
Is there anyone know these marine microalgae?
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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
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But a low phytoplankton density during Monsoon. What all may be the other factors leading to variations in primary productivity of an aquatic ecosystem?
Thanks in Advance !
Anila Ajayan
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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
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Desmids are very diverse in their morphology. To identify this group, kindly suggest me how to deal with it? Cosmarium, Euastrum, Staurastrum all these genera were closely identical. And also, how much light period should be provided to grow a Cosmarium strain in lab culture?
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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. 
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In order to do an experimental approach, we would like to use a substrate that is as equivalent to a natural substrate usually colonized by diatoms (calcareous and silicate-calcareous mix) as possible. In specialized bibliography we have found that artificial sandstone and glass-slides on bricks were used to this end, but wondered if there was any other method I am not aware of. We would also be thankful for any further publications on this subject you could recommend.
Thank you very much in advance.
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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.
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It is look like a leaf under microscope, but it could be a plankton. Earlier I heard that it was a ciliate, but I didn't get this picture again in my samples. This too found in Bay of Bengal waters. Please help me to identify this specimen.
Thank you.
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looks in first instance like a scale from a butterfly or a moth.
Best wishes, René
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I apparently have ever heard that an tendency for dominant algal bloom-forming species was from diatoms to dinoflagellates in most parts of the world. Is that ture? Which paper have mentioned this view ? Thank you!
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Definitely the question needs narrowing down. Cyanobacteria are another common bloom-forming group of phytoplanktonic organisms.
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It is a freshwater desmid generally found in lakes and reservoirs
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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).
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I have strains CCMP1524 and CCMP1528 growing in L1-Si and K-Si media. Cultures are in ambient light and temperature, 22C and 1500Lux, and 18C and 12000Lux, with and without shaking. The cultures are in good condition and reach exponential growth quickly, but will not form colonies! 
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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
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Would anyone know a good article where I can find the gross primary production (total amount) of carbon per year?
On the internet, I find that may different numbers and most are from quite old research papers. It would be helpful to have a recent research paper in which they give the total GPP.
Many thanks!
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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.
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Algaebase mentions it as Syringidium Ehrenberg, 1845, nom. rejic. but also mentions that is currently recognized as a distinct genus and the holotype species Syringidium bicorne Ehrenberg is currently accepted taxonomically.
I have read 
Hasle GR & Sims PA (1985) The morphology of the diatom resting spores Syringidium bicorne and Syringidium simplex , British Phycological Journal, 20:3, 219-225
but cannot find 
Hasle, G.R. 1983. Proposal to conserve the generic name Cerataulina H. Perag. ex. Schütt over Syringidium Ehrenb. Taxon 32: 474-475.
Need help regarding this.
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Neera:
You may like to have a look at this link for the viewpoint of Global Biodiversity Information facility:
Best
Syed
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Need actual spectra from culture work, not figures (have found some already).
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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.
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How to calculate the phytoplankton cell volume and what is the unit to represent the cell volume.
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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.
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Can somebody let me know where I can find a Freshwater Phytoplankton identification Key/Manual?
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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. 
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Today different wavelengths has been chosen to measure diatom optical density. Right now more and more articles select 625nm wavelength to estimate Phaeodactylum tricornutum dry weight. Does anyone know the reason to choose 625nm instead of 750nm or 600, 680nm? Or if you have any good recommendations?
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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 
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Please explain their spectral attributes and show their spectral signature at visible and near infrared spectra. 
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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.
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This species was found to cause blooming in the Mediterranean sea. This species was blooming in the Mediterranean, turning the water brown.
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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.
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Can anyone help identify this phytoplank?
This species was blooming in the Mediterranean turning the water into brown
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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
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The species was collected (in high density) from subsurface plankton tows (100 micron mesh size) in the Persian Gulf in autumn. Both colonial (max 3 specimens) and unicellular forms were present in the samples. 
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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
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The diatoms have siliceous theca (frustule). Are there other microscopic organisms that are also covered by silica?
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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
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Where do we get diatom culture in india???
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Which species of diatom ?
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Water samples were taken from an estuary (Salinity: 15 ppt) and brown colony formed in the agar plates after 4 weeks of plating. Photographs taken at 40 X magnification. Size of the cells: 8-15 micron 
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My dear, this seems to be a fungus.
My greetings.
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Can anyone help me to identify this strange thing in thin section?
From mid-Permian in South China
Is that Algae?   
Someone tell me fig.3 is Archaeolithoporella, but I think it looks diffrent.
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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
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Collected from a freshwater body. This was found common during the Monsoon period. 
Thanks in Advance!
Regards
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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
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Let's assume no malfunction of our YSI sonde, as we are very sure of that. Recently we had spiking chlorophyll a measurements in water from Duluth-Superior Harbor (western Lake Superior), ranging from 16.4-17.9 µg/L, clearly in the "eutrophic" spectrum for this system. A microscopic analysis on slides indicated very few algae specimens (expected for this time of year), including a lack of tiny cyanobacteria (which we first thought it might be). Looking for ambient red signals using fluorescence microscopy also didn't show anything notable. One thought is that something (perhaps leaf litter) is breaking down and filling the water with active chlorophyll or its byproducts (like phaeophytin). I welcome any thoughts or ideas on what could be causing this.
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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".
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Owing to the tiny size of the Coccolithophores their turnover rate is pretty high. Dead cells are continually shed in the water column mixing with live ones and remain there for a long time. Is there a simple method to count dead and live cells?
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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
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I have grown P. gingivalis to an OD of 1.0 in BHI. I then carried out serial dilution to 107 and plated on agar. I repeated this severally but the results for each trial exhibit a range that can not be attributed to pipetting technique. I am pretty confident with my pipetting skills. What are factors can explain this inconsistency? Please advise.
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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.
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When I search papers about phytoplankton grown on a series of  irradiances, nutrients and temperature, I found Michaelis-Menten equation is usually chosen for Irradiance or Nutrients vs Growth rate fitting, but Eppley equation for Temperature vs Growth rate fitting, why? Michaelis-Menten equation could not used for temperature vs growth rate?
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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
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16S rRNA gene or ITS region or other
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CYA 106F/781R primers are good to identify to the genus level. For spesies/strains level you need universal primers for longer sequences (if you have axenic culture) or primers wich produce sequnces including ITS region.
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CANONICAL CORRESPONDANCE ANALYSIS
Dear friends, I would hereby like to inform you that i have a two year data set (monthly observations as data points) consisting of abundance (log transformed) 40 species of phytoplankton and 15 environmental variables.
My objective is to identify the seasonal patterns in environmental parms and species abundance. 
I have tried the canonical correspondence analysis for analyzing this data to identify the linear combination of species scores with environmental variables. But, the results are bit complex and i need your suggestions for analysis (better ordination techniques if any) and the modifications in the same analysis (data as well as analytical steps). 
I found CANCORSP, REDUNDANT, PCA, CORRESP analysis as the best methods for ordination. Please help me in this regard
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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.
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can you help me with classified the following genes:
cymbella: Long= 5, Width=1.25
                long= 4.25, width=1
Amphora: Long= 5.25, Width=2.25
Achnanthus: Long= 5, Width=1.75
Nitzschia: Long= 5, Width=0.5
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Often diatoms especially planktonic taxa undergo size reduction due to increase in phosphorus and drop in silica
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I am trying to quantify live vs. dead cells in my samples. Any thoughts or methods are appreciated! 
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The attached paper may help.
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For identification of marine phytoplanktonic organisms
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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
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Hi I’m culturing diatoms in conical flasks and they tend to stick at the bottom and the wall of the flasks. What is the possible method to get rid of the sticking cells from the flasks wall besides sonication and manual scraping? Any suggestion? Many thanks!
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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.
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Zooplankton are, by definition, drifters in the ocean. Therefore, they are often associated with different water masses and can be ideal indicators for assessing ecosystem status. More specifically, what can they really indicate, how do we incorporate zooplankton indicators into ecosystem assessment framework, and how these indicators can be used in marine policy?
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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
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It was green in colour, Is it autotrophic?
Thanks.
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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.
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I have acquired the use of a Water PAM to measure Fv/Fm in concentrated samples of phytoplankton. In the instrument guide and throughout the published literature it is recommended to measure Fv/Fm on dark-adapted samples. Unfortunately, I can't seem to figure out how long I need to be keeping a sample in the dark before measurement. Some say 30 seconds, while others say that the sample should be "in the dark overnight". For sure there are species variations in what passes for photosystem II saturation after dark adaptation, but I am just looking for a decent overall estimate for freshwater phytoplankton. A 30-second incubation in the cuvette, in the dark, would be ideal. Would I get a substantially different answer if I incubated longer?
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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.
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We are going to develop a software for drinking water plant technicians to identify phytoplankton.
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 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.
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Dear all,
Enhancing/ Altering what factors would influence production of EPS in freshwater microalgae.
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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
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I’m using specific primers to quantify Scrippsiella donghaienis (a phytoplankton species) in DNA extracts from sediments by real time PCR. When total DNA concentration is high, the melting curve shows a specific peak of Scrippsiella donghaienis at 82,5 °C. However, in sediments of low DNA concentration, I get a double peak (a very small peak of Scrippsiella and another higher peak at 88 °C). Do you have an explanation to this ? I attached 2 images of specific amplification and non specific amplification from the same test.
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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!
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I read that the diatom genus Bidduphia renamed as Odontella. But still researchers are using both names. Are they different genus or synonym of each other?
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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
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What are crucial parameters that should be considered in Dinoflagellates  cultivation?
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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
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I frequently encounter tiny fast moving round microalge (?) species as a contaminant in Haematococcus culture when the culture is grown below 0.6 mg/L phophate conditions.
I suspect it to be some haptophyte but not sure.
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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.
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I found these plankton in Arabian sea. Kindly text the species or genus name of the plankton. Also I need e-book to identify fresh water and marine diatoms.
Thanks.
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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
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It is a non-cuantitative study about diversity at genera taxonomic level of planktonic green algae and cyanobacteria in two continental water bodies of 6084 and 4540 m2. I interested in know about of sampling design: techniques for site selection in the water bodies, number of sites and sample volumen.
Thanks.
Best regards,
Gustavo.
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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.
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Zigetang Co is a meromictic endorheic saline lake without any glaciers in the catchment on Tibetan Plateau, which is directly located at the boundary of the Indian monsoon. The short chain n-alkanes C15, C16 and C17, likely derived from aquatic algae, plankton and photosynthetic bacteria, dominated most of the lake sediments. Howerver, we are not sure how to explain the source of these short chain alkanes. Do you have some ideas or some similiar papers discussing the short chain alkanes? Thanks a lot.
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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.
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I am interested in studying the mutualistic relationship between phytoplankton and seabirds, and how it plays a key factor in sensing climate change in a marine ecosystem (the specific mechanism/s). I also want to determine how ecological imbalances can affect climate change regulation.
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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.
ISSOUFOU
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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 !
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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.   
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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.