Vol. 85: 101–119, 2020 AQUATIC MICROBIAL ECOLOGY Published online October 8 https://doi.org/10.3354/ame01944 Aquat Microb Ecol OPEN ACCESS Microbial and nutrient dynamics in mangrove, reef, and seagrass waters over tidal and diurnal time scales Cynthia C. Becker1,2, Laura Weber1, Justin J. Suca1,2, Joel K. Llopiz1, T. Aran Mooney1, Amy Apprill1,* 1Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA 2MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge 02139, and Woods Hole 02543, MA, USA ABSTRACT: In coral reefs and adjacent seagrass meadow and mangrove environments, short tem- poral scales (i.e. tidal, diurnal) may have important influences on ecosystem processes and commu- nity structure, but these scales are rarely investigated. This study examines how tidal and diurnal forcings influence pelagic microorganisms and nutrient dynamics in 3 important and adjacent coastal biomes: mangroves, coral reefs, and seagrass meadows. We sampled for microbial (Bacteria and Archaea) community composition, cell abundances and environmental parameters at 9 coastal sites on St. John, US Virgin Islands that spanned 4 km in distance (4 coral reefs, 2 seagrass meadows and 3 mangrove locations within 2 larger bays). Eight samplings occurred over a 48 h period, cap- turing day and night microbial dynamics over 2 tidal cycles. The seagrass and reef biomes ex - hibited relatively consistent environmental conditions and microbial community structure but were dominated by shifts in picocyanobacterial abundances that were most likely attributed to diel dy- namics. In contrast, mangrove ecosystems exhibited substantial daily shifts in environmental pa- rameters, heterotrophic cell abundances and microbial community structure that were consistent with the tidal cycle. Differential abundance analysis of mangrove-associated microorganisms re- vealed enrichment of pelagic oligotrophic taxa during high tide and enrichment of putative sedi- ment-associated microbes during low tide. Our study underpins the importance of tidal and diurnal time scales in structuring coastal microbial and nutrient dynamics, with diel and tidal cycles con- tributing to a highly dynamic microbial environment in mangroves, and time of day likely contribut- ing to microbial dynamics in seagrass and reef biomes. KEY WORDS: Tide · Picoplankton · Mangrove · Coral reef · Seagrass · Time series · 16S rRNA gene 1. INTRODUCTION the zonation of intertidal flora and fauna along coast- lines, influencing local community processes (Alongi Short temporal rhythmicities resulting from daily 1987, Peterson 1991). Coastal ecosystems must cope sunlight cycles and lunar-influenced tidal cycles with the interaction of both diurnal and tidal forcings, have governed the dynamics of living organisms and the effects of these cycles are apparent on micro- throughout evolutionary history. Light is a funda- bial scales. The tidal cycle influences virus-microbe mental source of energy for the photosynthetic cells interactions in estuaries (Chen et al. 2019), bacterial that dominate in the surface ocean worldwide and abundances in salt marshes (Kirchman et al. 1984), produce approximately 46% of global net primary and even the presence of enterococci, fecal bacteria production (Field et al. 1998). Tidal elevation directs used as a metric for water quality, on beaches (Boehm © The authors 2020. Open Access under Creative Commons by *Corresponding author: [email protected] Attribution Licence. Use, distribution and reproduction are un - restricted. Authors and original publication must be credited. Publisher: Inter-Research · www.int-res.com 102 Aquat Microb Ecol 85: 101–119, 2020 & Weisberg 2005). Diurnal cycles, on the other hand, tant for remineralization as they harbor microorgan- govern microbial nitrogen fixation on mangrove root isms in sediments, roots, and seawater that include systems (Toledo et al. 1995), bacterial production denitrifying and nitrogen-fixing bacteria (Reef et al. rates in seagrass meadows (Moriarty & Pollard 1982), 2010, Liu et al. 2012). Mangrove sediment microbial and coral reef microbial community changes (Kelly et community dynamics are well studied and have been al. 2019, Weber & Apprill 2020). Together, tidal and shown to respond to tidal changes, which affect eco- diurnal forces play major roles in shaping microbial system processes such as rates of nitrogen fixation life in coastal environments. and denitrification (Lee & Joye 2006, Chen et al. Seawater bacterial and archaeal communities are 2016, Gong et al. 2019). Given the influence of tide fundamental to ocean ecosystems. These prokaryotic on sediment microbial communities, there may be a microbes form the basis of the marine food web concomitant shift in the overlying seawater microbial because they cycle organic matter, remineralize communities with respect to the tidal forcing of sea- nutrients, and take part in all major elemental cycles water. However, the extent of tidal influence on the in the ocean (reviewed by Moran 2015). Extensive microbial dynamics within the overlying seawater study of microbial communities in the ocean has pri- remains to be elucidated in mangrove environments. marily focused on seasonal changes and shown that Seagrass meadows are often found deeper than communities vary predictably with environmental mangroves, where they are constantly submerged, factors, such as temperature (Fuhrman et al. 2006, yet within the photic zone. These environments serve Gilbert et al. 2009, Kim & Ducklow 2016, Bunse & as nursery grounds and habitat for diverse fishes and Pinhassi 2017). The dynamics of microbial communi- invertebrates, and they contribute significantly to ties over short temporal scales (hours to days) are less primary production in tropical ecosystems (reviewed studied. Studies from estuarine and coastal environ- in Ugarelli et al. 2017). Sediment-associated micro- ments showed that tidal mixing and salinity are bial communities in seagrasses are important for major drivers of microbial community structure (Lu et nitrogen cycling and carbon sequestration (Moriarty al. 2015, Chen et al. 2019, Neubauer et al. 2019). In et al. 1985, Sun et al. 2015, Ugarelli et al. 2018). The the case of open ocean environments with more stable seawater microbial community is far less studied but physical and chemical features, observed changes in has been shown to be important for carbon cycling microbial communities may be due to biological and the ultimate transfer of primary production to the interactions. For example, a study centered off the marine food web (Blum & Mills 1991, Peduzzi & coast of California over 3 wk and following a spring Herndl 1991). Ugarelli et al. (2018) recently exam- bloom showed that the microbial community compo- ined the spatial variability in seawater microorgan- sition correlated more closely to biological variables isms across 3 seagrass locations and found quite con- than physical and chemical variables (Needham & sistent patterns in the taxa recovered across sites, but Fuhrman 2016). Short-term microbial dynamics likely small changes in relative abundances of those taxa. play a role in structuring seawater microbial commu- Short temporal scales do appear to exert an effect on nities within coastal tropical marine environments the microbial communities in seagrass environments. (mangrove, seagrass and coral reef), but these dynam- The bacterial production rates within sediment and ics are largely unstudied. seawater in seagrass meadows have been shown to Mangrove, seagrass, and coral reef biomes domi- change on a diurnal cycle in response to the photo- nate the coast of many tropical and subtropical islands synthetic output of the underlying plants, but this did and coastlines. Together, these ecosystems protect not relate to the tidal cycle, according to Moriarty & coastlines from devastating tropical storms and hur- Pollard (1982). The extent that the composition of ricanes, and they sustain local economies that rely on overlying seawater bacterial and archaeal communi- tourism and seafood. Mangroves are halophytic ties changes over similar short temporal cycles plants that thrive in the transition zone between estu- remains to be described. arine and marine environments, tolerating a wide High biodiversity from macro- to micro-organisms range of physicochemical conditions. Collectively, and low nutrient concentrations of overlying sea - these trees make up mangrove forests, which are water are hallmarks of coral reef environments. The critically important coastal biomes. They sequester diverse assemblage of microorganisms is particularly carbon (Donato et al. 2011), provide nursery grounds important in reef seawater for recycling organic for fish (Aburto-Oropeza et al. 2008), and insulate metabolites and nutrients in these apparent nutrient coastlines from storms and erosion (Duke et al. 2007). ‘deserts’ (Gast et al. 1998, Bourne & Webster 2013, At the micro-scale, mangrove ecosystems are impor- Haas et al. 2013). The fundamental role that microbes Becker et al.: Tidal microbial dynamics 103 play in coral reef biogeochemical cycling has made and Fish Bay, during summer of 2017 (prior to hurri- them bioindicators of changing reef environments in canes Irma and Maria). In total, 3 tropical biomes the face of climate change (Glasl et al. 2018). While it were sampled: coral reef (4 sites), seagrass meadow is established that seawater microbial communities (2 sites) and mangrove (3 sites; 2 within the same on