Are you only interested in species richness and relative abundance?

-> counting of different species in a sample of e.g. 100 individuals

Are you as well interested in the absolute abundance, i.e., the number of species in a specific volume of water?

-> quantitative sampling with special samplers closable under water at different levels of depth.

Especially in monococcal green algae there are some species very similar to each others and thus often sequencing is the only way to identify them reliably if you do not have a monoalgal strain of them.

So maybe an approach with cloning of the whole sample may be possible to reflect genetic diversity in the sample. However, the whole species community is difficult to identify.

Maybe you can specify your aims?

At how many different systems you are looking?

How many sites or plots do you have?

How many samples do you need?

What is your hypothesis to be prooved?

What methods are availabe at your lab?

Best wishes

For species diversity,you need quality, i.e.the different species & not their number.If you need the number in any other case,you will have to take samples from different depths & find out the quantity,for algal species.

”it is hard to count it for each species in aquatic systems (specially for algal species), what is the solution for this problem? ”

one of the solutions: use statistics!

As i mentioned in the question, I'm looking to find a method for measuring species diversity (heterogeneity) in aquatic systems, not species richness or anything else.

dear Bastian, thanks for your comprehensive answer. it is only a theoretical question, thank you very much.

dear Chandravadan, what is the meaning of "quality" ?, if you look in the most of Species Diversity indices, you see for computation of these indices, we need two parameters: number of species and number of individuals.

if you look for the practical solution, I would hazard a guess there is no satisfying one, - Bastian gave all the answers I guess. Cell counters can be used of course to derive the TOTAL number of (algal) cells, but they cannot discriminate between species - I think thats what Chandravadan was getting at when he mentioned quality. For species-specific counting, you will have to take SMALL samples, you will never be able to process the whole water body in question. And that's why Zsolt suggested statistics to derive a representative picture from the small sample. There are methods where you can somehow mark particles and/or you can look at the size range of particles, used for bacterial analyses under certain circumstances, e.g. fluorescence-activated cell sorting (FACS). No idea whether that's applicable at all for algae. AND of course it would not resolve to species level. If you need the species level, then some sort of microscopy is needed (if you cannot afford sequencing) where you count every single cell within a given minute volume, and you do that MANY times in order to arrive at representative numbers.

If you are working on macroalgae, sponges or crustose organisms, you can use biomass or percentage of cover. For instance, "Iberian intertidal turf assemblages dominated by Erythroglossum lusitanicum (Ceramiales, Rhodophyta): structure, temporal dynamics, and phenology" Díaz-Tapia et al., 2011

The number of species detected depends on sample size. Especially when working with microalgae, counting all species in large sample is very time consuming and impractical. When analysing smaller samples or sub-samples you will find (and get a reliable count) for dominant, common and abundant species. You will most likely find species that occur occasionally but miss some of the rare ones. A lot of authors use diversity indices to give an accurate measure of diversity. The Shannon and Weaver index (H') for example is quite robust. Rare species affect the index only on the 3rd or 4th decimal place. Washington (1984) gives an overview:

Washington, H. G. (1984). Diversity, biotic and similarity indices. Water Research 18, 653-694.