  Citation: Fondo, E.N.; Omukoto, J.O.; Wambiji, N.; Okemwa, G.M.; Thoya, P.; Maina, G.W.; Kimani, E.N. Diversity of Shallow-Water Species in Prawn Trawling: A Case Study of Malindi–Ungwana Bay, Kenya. Diversity 2022, 14, 199. https:// doi.org/10.3390/d14030199 Academic Editors: Thomas J. Trott and Bert W. Hoeksema Received: 4 February 2022 Accepted: 6 March 2022 Published: 9 March 2022 Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affil- iations. Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). diversity Article Diversity of Shallow-Water Species in Prawn Trawling: A Case Study of Malindi–Ungwana Bay, Kenya Esther N. Fondo 1, * , Johnstone O. Omukoto 1,2 , Nina Wambiji 1 , Gladys M. Okemwa 1 , Pascal Thoya 1 , George W. Maina 3 and Edward N. Kimani 1, * 1 Kenya Marine and Fisheries Research Institute, Mombasa P.O. Box 81651-80100, Kenya; jomukoto@gmail.com (J.O.O.); nwambiji@gmail.com (N.W.); gladysokemwa@gmail.com (G.M.O.); pascalthoya@gmail.com (P.T.) 2 Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK 3 The Nature Conservancy, Africa Regional Office, Nairobi P.O. Box 19738-00100, Kenya; gwmaina@tnc.org * Correspondence: efondo@yahoo.com (E.N.F.); edwardndirui@yahoo.com (E.N.K.) Abstract: Bottom trawling is a common fishing method that targets bottom-dwelling fisheries re- sources. It is non-selective and large amounts of by-catch are discarded, raising serious sustainability and ecosystem conservation concerns. In this study, a shallow-water bottom-trawl fishery was evalu- ated using logbook catch data between 2011 and 2019 and the species composition data collected by fisheries observers between 2016 and 2019. The logbook data showed a twenty-fold increase in the annual catches with a ten-fold increase in fishing effort and an increase in the proportion of retained catch from 2011 to 2019. The observer data showed that for prawn, the by-catch ratio ranged from 1:3 to 1:9 during the four years. Multivariate analysis revealed significant differences between the compositions of retained and discarded catches mainly attributed to Pellona ditchela, Nematopalaemon tenuipes, and Secutor insidiator. There was no significant decline in species diversity and the trophic level of the catches over the 4-year observer period indicating no marked impact of trawling on the stock at the current level of fishing effort. This study provides baseline information on the prawn trawl fishery against which the performance of the management regulations may be evaluated towards the Ecosystem Approach to Fisheries management. Keywords: shell-fish; fish; by-catch; discards; species composition 1. Introduction Bottom trawling and dredging contribute a significant part to capturing finfish and shellfish worldwide. Global evaluation of the contribution of bottom trawling and dredging to capture fisheries indicate approximately 28% [1], while long-term FAO data show that trawling has contributed about 25% of capture fisheries between 1950 and 2018 [2]. However, evaluation shows that bottom trawling generates the most waste in fisheries, accounting for nearly 60% of the fish dumped back into the ocean [1]. The sustainability and conservation concerns of bottom trawl fisheries have attracted attention in the past [1,3–5]. Trawling is considered a wasteful and destructive fishing method associated with large amounts of discarded by-catch leading to changes in trophic structure and loss of fishery resources [6,7]. Changes in the trophic structure and function of benthic communities have im- portant implications on primary production and the wider functioning of the marine ecosystem [8,9]. Ecological studies on bottom trawling have focused on ecosystem impacts through widespread physical disturbance of the bottom substrate, excessive removal of juveniles, and the potential of modifying ecosystems’ trophic structure [10,11]. There are claims that any trawl fishery is unsustainable due to its environmental and ecosystem im- pacts [12,13], and there have been suggestions for bans on some types of trawling [3,14,15]. However, bottom trawling continues to be one of the most common fishing methods and Diversity 2022, 14, 199. https://doi.org/10.3390/d14030199 https://www.mdpi.com/journal/diversity