Seeing the ‘unseen’: a spotlight on lesser known inhabitants of freshwater ecosystems

Freshwater biologists Sameer Padhye and Avinash Vanjare talk about smaller and lesser known animals that live in freshwater ecosystems and the importance of studying them. 
20 May 2023
0 mins read
Freshwater ecosystems, under threat (Image Source: Biologia Life Science LLP)
Freshwater ecosystems, under threat (Image Source: Biologia Life Science LLP)

A number of large and small - and very interesting animals inhabit freshwater ecosystems, depend on them for their survival and play an important role in maintaining the health of freshwater ecosystems. A number of them are vanishing and being threatened as urbanisation, and human induced activities are taking a toll on the natural environment. Making efforts to save them and restoring the health of ecosystems is the need of the hour to save the environment - and people depending on it. 

Freshwater biologists Dr Sameer Padhye and Dr Avinash Vanjare speak to the India Water Portal about the interesting animals that inhabit freshwater ecosystems and what needs to be done to save them.

Freshwater ecosystems such as rivers, lakes, streams, ponds etc are known to support incredible biodiversity. Could you please describe the various kinds of animals - small and large that live/reside in and near freshwater ecosystems? Why are they important? 

Surface freshwater ecosystems not only include rivers, lakes, streams, but also  ponds, pools as well as certain unique types like phytotelma (water filled spaces enclosed by plants) that exist throughout the world. These systems harbour a vast number of organisms ranging from sponges to mammals like dolphins and seals adapted to living in one or more of these ecosystems.

Freshwater ecosystems are classified based on a number of factors including size (large like lakes or small like pools), water flow (static/lentic like ponds or flowing/lotic like streams), permanence (temporary like pools or permanent like water reservoirs) amongst others. 

Each water body in itself is divided into specific zones based on factors like temperature, light penetration, presence of aquatic vegetation, geochemical properties (pH, Dissolved oxygen) etc. For example, the littoral zone (vegetated zone) adjacent the shore of many water bodies receives a lot of sunlight, is warm, nutritionally rich and supports a range of animals including phytoplankton, zooplankton and fish. In contrast, the deep water zone (benthic zone) is cooler, receives little or no sunlight and has no aquatic vegetation yet certain crustaceans, molluscans and fishes are found inhabiting it.

Image 1
A rock pool from Ahmednagar, Maharashtra (Image Source: Avinash Vanjare)


Animals have managed to inhabit every ‘nook and cranny’ of all these freshwater ecosystems. Still, the presence (or absence) of many organisms can be determined by the classifications mentioned above. For example, many rotifer and crustacean species are adapted to survive and thrive only in temporary water systems and not seen in permanent water bodies like lakes and water reservoirs.

Members of certain invertebrate groups like ostracod crustaceans and tardigrades (water bears) are known to specifically live in phytotelma and not seen in any other water body. Some snail species are only associated with flowing water and not observed in lentic water bodies. Freshwater dolphins and manatees are only found in rivers while seals are known only from certain lakes.

Image 2
A temporary water body formed in the monsoon (Image Source: Avinash Vanjare)


Your work has mostly focused on smaller animals residing in freshwater habitats? Could you describe a few of them for us? Why are they important? Why is it important to study them? How do they maintain the health of the freshwater ecosystems?

Biodiversity studies have mostly concentrated on larger animals like mammals, birds, amphibians and reptiles. Smaller organisms are generally ignored as they are not easily visible with many having no direct benefit to humans. There are many groups which come under this ‘smaller organisms’ category such as  ‘protozoans’, multicellular animals like flat-worms, nematodes, tardigrades, hydrozoans (hydra), rotifers, gastrotrichs and micro-crustaceans (cladocerans, copepods, ostracods) to name a few.

These animals are important ecologically with most being part of food chains acting as prey for predators like fish. For example, primary producers like algae trap the sun’s energy; this algae is eaten by smaller primary consumers like rotifers and micro-crustaceans like cladocerans and copepods; these are preyed upon by planktivorous fish and insects which themselves are subsequently preyed upon by piscivorus fish and birds. A major shift in the biodiversity of these animals can disrupt such chains which themselves are part of more complex ‘food webs’ and result in an eventual ecological degradation.

Image 3
A rotifer from Pune and Ahmednagar (Image Source: Avinash Vanjare)


These animals being a regular prey base for fishes also makes them important commercially as a feed in aquaculture setups. Some representatives of rotifers, cladocerans and copepods are characteristically present/absent due to certain environmental changes in the water (in context of anthropogenic disturbance) making them potential bioindicators of water quality. Rotifers and micro-crustaceans like the water fleas are also used as models in eco-toxicological experiments.

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Water flea (Daphnia sp.) (Image Source: Biologia Life Science LLP)



Tadpole shrimp
Tadpole shrimps (Image Source: Biologia Life Science LLP)



What are the threats that freshwater ecosystems and the rich biodiversity they support experiencing in recent years? How are they affecting the survival of freshwater species?

Major threats faced by any freshwater organisms (including the ones we studied) are habitat degradation and destruction. Water bodies like pools are relatively inconspicuous to a layman in terms of its biodiversity since typical and commonly observed fauna like birds are not usually associated with them. So, people tend to ignore these habitats and its organisms in all aspects of biodiversity management and conservation making it an easy target for destruction.

We have personally observed many such habitats getting destroyed which had a good number of aquatic biodiversity. Some of the animals also lay their eggs in these habitats in order to survive the dry season and hatch in the next monsoon season. This often leads to the formation of ‘egg banks’ (like seed banks), holding a hidden diversity. Destruction of habitats therefore destroys this unseen diversity. 

Modification/degradation of any water body influences the diversity patterns of these animals. Many rare species are lost with increasing habitat deterioration. Since these animals are part of many aquatic food chains, a continual species loss can result in an eventual collapse of such food chains. This is evident in cases like the Pashan lake, an urban water reservoir which has been ‘beautified’ haphazardly, leading to its near complete ecological breakdown. Similarly, increasing disturbance along the rivers flowing through the urban centers like Pune has negatively impacted the riverine biodiversity.

Many species of fish, snails, birds which were reported 50 years ago have now completely disappeared. In many instances, they have been replaced by invasive species like the guppy fish and tilapia. There is no reliable historical data available on many faunal groups including the ones we study, hence, we have no idea about the species loss that has occurred in these animals.

Could you please give us some examples from your studies conducted in different regions of Maharashtra? What did these studies show? What were the threats experienced by freshwater ecosystems and the habitats they supported? How did they impact water quality and the health of animals living in the waters?

We have been surveying and sampling for freshwater invertebrate groups like rotifers and certain crustaceans across Maharashtra and Goa covering a wide range of aquatic habitats (including phytotelma and hot water springs). In some instances, we have specifically focused our efforts in studying the biodiversity found in characteristic habitats like the rock pools which occur on many hills located in the Western Ghats, temporary pools which form during the monsoon season in the semi arid parts of the state as well some urban polluted water bodies. 

The results of this endeavor have been rewarding with discovery of over 200 species with 7 new species of crustaceans to Science, a few new records to India and several new discoveries still awaiting a formal description. Our findings also highlight the possibility of many new discoveries still.

Many of these species also showed associations with particular water bodies. For example, the micro crustacean Daphnia carinata (water flea) was only seen in rock pools on lateritic outcrops, the tadpole shrimp Triops granarius was only seen in temporary water bodies, the rotifers were less diverse in rock pools, but abundant (Brachionus spp.) in eutrophic water bodies (both  lakes and slow flowing rivers).

We found these animals thriving in phytotelma as well as hot water springs where the temperatures were as high as 36°C! Investigations using their genetic material (DNA, RNA) are underway to answer questions like, ‘where do our species come from’ and ‘who are their closest ancestors’. Observations from our studies on urban water bodies showed that  many species do tolerate a certain degree of pollution with very few species able to tolerate high levels as well. Lotic disturbed habitats show a seasonality in the type of species observed depending on the monsoon, water flow and pollution levels.

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New water flea Moina hemanti found in Pune (Image Source: Biologia Life Science LLP)


They also seem to form epizoic associations (Moina macrocopa - Brachionus rubens) between them i.e. one species benefits while the other is not harmed, and change their colors (some crustaceans develop red coloration due to hemoglobin production as a result of low oxygen concentration in the water) during summer season underscoring their potential as indicators of increasing pollution. 

What in your opinion needs to be done to protect biodiversity and save freshwater ecosystems in the country? What steps do you recommend from your experiences while working in freshwater ecosystems in different parts of Maharashtra?

Development is inevitable and needs to carry on, but has to be done in a sustainable and scientific manner. There are many success stories of such sustainable development in urban areas around the world where both the needs of humans and other organisms have been considered. A general awareness has to be created on a large scale involving scientists, citizen scientists and the general public about the importance of the freshwater biodiversity (diversity being all diversity and not just focused on large animals like birds), the habitats which harbor them and their significance in our well being. 

Design and implementation of policies pertaining to freshwater habitat and biodiversity conservation will not be possible without involving the general public. An informed community will in turn always question the relevant authorities on any such wanton destruction. We have to consider the importance of these organisms and the associated ecology before making more mistakes which are already affecting the way we live.

Dr Sameer Padhye is a Principal Scientist at Biologia Life Science LLP, Ahmednagar, Maharashtra, India. He can be contacted at

Dr Avinash Vanjare is an Assistant Professor in Zoology at Ahmednagar College, Ahmednagar, Maharashtra, India. He can be contacted at

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