Submit Manuscript | http://medcraveonline.com Introduction Phytoplankton play a crucial role in the global ecosystem, contributing to a signifcant portion of primary production.1,2 While they support marine food-webs, certain species can also form deleterious harmful algal blooms (HABs) or, under eutrophic conditions, result in detrimental ecosystem outcomes such as hypoxia or the loss of submerged aquatic vegetation.3–5 Shifts in community composition and the factors that underlie them have been studied extensively in the context of HABs because of their ecological and economic costs. Generally, phytoplankton community composition is determined by the availability of nutrients and light, temperature, salinity, physical losses such as sinking and fushing, biotic interactions such as grazing, competition and viral lysis, and susceptibility to toxins and allelopathic compounds.6 It is a specifc combination of the above factors, at a given point in time that enables one or a few species to dominate over others, and ultimately shape the community.7 Humans directly or indirectly affect all of these factors. Although nutrient cycling has received much attention, the ability of a population to accumulate in an ecosystem depends on the relative rates of growth and losses, including fushing.8 Variation in river discharge alters hydraulic residence time but can also infuence the concentration and chemical species of nutrients, the stability of the water column and water clarity. The majority of studies describing the effect of discharge and transport on marine phytoplankton biomass and composition have focused on large estuaries such as San Francisco and Chesapeake,9–11 river plumes12–14 or coastal systems such as the Baltic Sea15 that have relatively long residence times of several months. Shallow sub-tropical estuaries have received less attention, with the exception of a small number of well-studied systems such as Thau Lagoon, France16 and Indian River Lagoon, USA17,18 which also have relatively long residence times. In contrast, there is very little information on the dynamics of phytoplankton community composition in small estuaries with short residence times, particularly those infuenced by submarine groundwater discharge. The goal of this study was to assess the appropriate descriptors of ecological status in a shallow, tropical estuary, Weeks Bay, Alabama (USA). The bay has been the site of dense HABs of the dinofagellates Karlodinium venefcum, Prorocentrum minimum, Heterocapsa triquetra and Kryptoperidinium foliaceum and the raphidophytes Chattonella subsalsa and Heterosigma spp. (unpublished data). There was a bloom of Heterosigma during the study but dominance by HAB taxa was correlated with neither chlorophyll a (Chla) nor nutrient concentrations. We show that the annual temperature cycle and hydrology are major drivers of both phytoplankton biomass and community composition. Neither detection not prediction of HABs could be achieved by monitoring Chla and nutrients alone. J Aquac Mar Biol. 2019;8(3):69‒80. 69 ©2019 Novoveská et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and build upon your work non-commercially. Study of the seasonality and hydrology as drivers of phytoplankton abundance and composition in a shallow estuary, Weeks Bay, Alabama (USA) Volume 8 Issue 3 - 2019 Lucie Novoveská, 1,2 Hugh L. MacIntyre 1,3 1Department of Marine Sciences, University of South Alabama, USA 2Industrial Phycology, Bristol, UK 3Department of Oceanography, Dalhousie University, Canada Correspondence: Lucie Novoveská, Department of Marine Sciences, University of South Alabama, USA Email Received: April 29, 2019 | Published: May 07, 2019 Abstract Small, shallow estuaries can be highly vulnerable to land use changes, eutrophication and habitat loss but are understudied with respect to their larger counterparts. Where they are monitored, the descriptors of their environmental status are typically chlorophyll a as a proxy for phytoplankton abundance and nutrient concentration as a presumed driver of the phytoplankton community. We present data from a shallow estuary, Weeks Bay, Alabama (USA), that demonstrates that chlorophyll a and nutrient concentrations are inadequate descriptors of ecological state. Weeks Bay had relatively high nutrient concentrations (86– 169µM total nitrogen and 1.0–5.2µM total phosphorus) and highly variable chlorophyll a concentrations (2.2–160.5μgL-1). The variability in chlorophyll a was most highly correlated with nutrient levels and river discharge. There was no relationship between chlorophyll a and community composition. Two of three maxima in chlorophyll a (>100μgL-1) were caused by non-toxic chlorophytes and diatoms; the third was dominated by potentially toxic raphidophyte Heterosigma akashiwo. The phytoplankton were diverse even at the class level and community composition varied on both annual and inter-annual scales. The best overall descriptor of phytoplankton composition was the annual cycle in temperature, but inter-annual variability was correlated with hydrology. In the winter, dominance by dinofagellates, including several taxa that form harmful algal blooms, was correlated with low river discharge, low turbidity and high zooplankton numbers, while dominance by diatoms was correlated with high and variable river discharge and high turbidity. In the summer, dominance by cryptophytes versus diatoms was consistent with changes in groundwater discharge. The dominance of harmful algal bloom taxa vs non-toxic ones could not be inferred from chlorophyll a and/or nutrient concentrations. Keywords: phytoplankton, composition, chlorophyll, estuary, variability Journal of Aquaculture & Marine Biology Research Article Open Access