RESEARCH ARTICLE Real Time PCR detection of Macrobrachium rosenbergii (de Man, 1879) larvae with emphasis to their ecology Mahadevan Harikrishnan 1 , Deepak Jose 1,2,* , B. Nidhin 1 and K.P. Anilkumar 1 1 School of Industrial Fisheries, Cochin University of Science and Technology, Kochi 682016, Kerala, India 2 CSIR-NIO, Dona Paula, Goa 403004, India Received 15 February 2021 / Received in final form 24 April 2021 / Accepted 3 May 2021 Handling Editor: Antonio Figueras Abstract – Species specific identification of early larval stages of many decapod crustaceans sampled from plankton collections remains cumbersome owing to lack of distinguishable characteristics, where DNA based molecular methods provide accurate results without taxonomic ambiguities. In the present study, an attempt was made to detect temporal occurrence of early zoea of freshwater prawn Macrobrachium rosenbergii (de Man) using real-time PCR assays in polyhaline, mesohaline and oligohaline areas of a tropical positive estuary, the Vembanad lake (S. India). High caridean larval abundance could be recorded in polyhaline areas in all seasons while it could be recorded in monsoon season in mesohaline and oligohaline areas. 113 DNA isolations were successfully made from morphologically identified taxonomic units (MOTU) and SYBR Green based RT-PCR amplifications using designed primer for M. rosenbergii yielded positive detections in 38 samples (34%) representing all seasons in all three zones. Positive detections could be recorded in all months except May in mesohaline areas and differed significantly (F = 17.2 p < 0.01) with the same in polyhaline and oligohaline areas. The present results of molecular detection of M. rosenbergii larvae extend confirmation of its breeding ground in Vembanad lake where appropriate management strategies could be enforced for stock conservation of this species. Keywords: Plankton samples / M. rosenbergii larvae / COI / absolute quantification / SYBR green 1 Introduction Members of family Palaemonidae (Infraorder Caridea; Order Decapoda) are known to be amphidromous with females releasing their ripe eggs in freshwater stream flow and embryos hatching out to meroplanktonic larvae that get passively dispersed to low saline regions where they complete metamorphosis before returning to freshwater conditions at advanced life stages (Bauer, 2011). The plankton trophic larval phase in their early development facilitates them in achieving wider spatial dispersion and thereby, in confronting with ecological challenges including food availability, favourable environmental conditions and predation (Rumrill, 1990; Morgan, 1995; Pechenik, 1999; Anger, 2006; Pineda et al., 2007). Some palaemonid larvae get dispersed to limited spatial distances which support stable genetic exchange and popula- tion connectivity through regular recruitment. In many species of Macrobrachium, females undertake downstream breeding migrations to low saline areas in estuaries during seasonal stream flows for facilitating larval release and metamorphosis (Hartmann, 1958; Ling, 1969; Ibrahim, 1962; Bauer and Delahoussaye, 2008). Extensive breeding migration has also been reported in Macrobrachium rosenbergii (de Man) inhabiting Indian waters (Rao, 1967; Raman, 1967; Kurup et al., 1992; Harikrishnan and Kurup, 1996). Females of this species undertake extensive differential breeding migration to downstream regions of Vembanad lake, South India and release their larvae in areas of congenial environmental conditions which return to upstream rivers after metamor- phosing to post larval stages (Raman, 1967; Kurup et al., 1992; Harikrishnan, 1997). However, closure of a barrage for arresting salinity intrusion into oligohaline regions of the lake has been reported to have seriously affected its larval ecology and stock conditions (Kurup et al., 1992; Kurup and Harikrishnan, 2000: Harikrishnan and Kurup, 2001). Information on larval ecology of estuarine fauna is important as they yield precise insights into ecological processes that influence their populations (Schwamborn et al., 1999; Queiroga and Blanton, 2015; Dos Santos et al., 2008). Information on life history, population abundance, distribution, role to play in ecosystem etc. are *Corresponding author: deepak140887@gmail.com Aquat. Living Resour. 2021, 34, 12 © EDP Sciences 2021 https://doi.org/10.1051/alr/2021012 Aquatic Living Resources Available online at: www.alr-journal.org