6.1 Introduction

Recirculating water in the aquaculture portion of an aquaponics system contains both particulate and dissolved organic matter (POM, DOM) which enter the system primarily via fish feed; the portion of feed that is not eaten or metabolized by fish remains as waste in the recirculating aquaculture system (RAS) water, either in dissolved form (e.g. ammonia) or as suspended or settled solids (e.g. sludge). Once the majority of sludge is removed by mechanical separation, the remaining dissolved organic matter must still be removed from a RAS system. Such processes rely on microbiota in various biofilters in order to maintain water quality for the fish and to convert inorganic/organic wastes into forms of bioavailable nutrients for the plants. Microbial communities in aquaponics system include bacteria, archaea, fungi, viruses and protists in assemblages that fluctuate in composition based on an ebb and flow of nutrients and changes in environmental conditions such as pH, light and oxygen. Microbial communities play a significant role in denitrification and mineralization processes (see Chap. 10) and thus have key roles in the overall productivity of the system, including fish welfare and plant health.

The challenges within any aquaponics system are to control inputs — water, fingerlings, feed, plantlets — and their associated microbiota to maximize the benefits of organic matter and its breakdown into bioavailable forms for target organisms. Given that optimal environmental growth parameters and nutrients differ for fish and plants (see Chap. 8), various separation and aeration systems, and biofilters containing relevant microbial assemblages, must be situated at strategic points in the water supply in order to help maintain nutrient levels, pH and dissolved oxygen (DO) levels within desired ranges for both target fish and plant species. Indeed, water quality parameters, including temperature, DO, electrical conductivity, redox potential, nutrient levels, carbon dioxide, lighting, feed and flow rates, all affect the behaviour and composition of microbial communities within an aquaponics system (Junge et al. 2017). In this regard, it is important to refine setup and operation so that each unit contributes adequate quantities of bioavailable forms of nutrients to its successor, rather than enabling proliferation of pathogens or opportunistic microbes that can consume the bulk of macronutrients needed downstream.

Various techniques for the analysis of microbial communities can yield important information about changes in community structure and function over time in different aquaponic configurations. By correlating these changes with nutrient bioavailability and operational parameters, it is possible to reduce over- or under-production of essential nutrients or the production of noxious by-products. For instance, maximizing recovery of beneficial plant nutrients from waste organic matter in the fish component depends primarily on the ability of microbiota to facilitate breakdown of nutrients within a series of biofilters and sludge digesters, whose performance is based on a range of operational parameters such as flow rates, residence time and pH (Van Rijn 2013). Since not all aquaponics system include sludge digesters, we will address this aspect in more detail in the latter half of this review whilst referring the reader to Chap. 3 for more details on solid separation techniques and Chaps. 7 and 8 for discussions on coupled vs decoupled aquaponics system. If we consider here only dissolved and suspended particulates in the water (and not sludge), all aquaponics system employ a range of different biofilters that expose the attached microorganisms to organic matter passing through the filter and provide an appropriate substrate and sufficient surface area for microbial attachment and formation of biofilms. Degradation of this organic matter provides energy to the microbial communities, which in turn release macronutrients (e.g. nitrate, orthophosphate) and micronutrients (e.g. iron, zinc, copper) back to the system in usable forms (Blancheton et al. 2013; Schreier et al. 2010; Vilbergsson et al. 2016a).

There is considerable agricultural research on the role of microbiota in plant rooting, growth and health. The preponderance of this research focuses on soil-based systems; however, research on hydroponics has also increased in recent years (Bartelme et al. 2018). The microbiota in aquaculture have also been similarly well-characterized, where the role of microbes in fish health and digestion has received considerable attention as researchers attempt to better characterize the role of gut health on nutrient assimilation. Given the importance of biofiltration in RAS systems, bacteria involved in the nitrification process for RAS have also been comparatively well-studied and thus are not be addressed here (see Chaps. 10 and 12). However, there has been comparatively limited research on microbes in aquaponics system, especially the crucial interactions of microbiota amongst various compartments of the system. This lack of research currently limits the scope and productivity of such systems, where there is considerable potential for enhancement with pre- and probiotics, as well as other opportunities to improve the health of aquaponics system through a better understanding, and thus better ability to control, the vast set of uncharacterized microbiota that affect system health and performance.

As such, this chapter focuses primarily on recent studies that reveal how and where microbial communities determine productivity within compartments, whilst also highlighting the relatively small number of studies linking those microbial communities to interactions amongst components and overall system productivity. We attempt to identify gaps where further knowledge about microbial communities could address operational challenges and provide important insights for enhancing efficiency and reliability.