**1. Introduction**

It is important to understand the role and function between organisms' interactions in the food web of the aquatic ecosystem. The key biological interaction in the aquatic food web is matter cycling mediated by the food chain, and predation often works as a regulating factor for energy pathways, as well as determining species composition in the ecosystem [1]. In particular, the food sources at the species levels are critical components linking organisms with larger predatory species such as crustaceans and fish within the grazing food chain: rotifers-copepods, micro/macroinvertebrates, and larval/mature fish [2,3]. Consequently, they function as a channel for the flux of organic matter within diverse organism assemblages organized in an intermediate position between the two di fferent food webs, and a way of transferring nutrients and energy from the prey species–predator species loop to higher trophic levels. Thus, the biological prey–predation interactions in the food web are receiving grea<sup>t</sup> attention to understand not only the interrelated biological relationships but also the structure and function of aquatic food webs [4].

In recent years, genomic and next-generation sequencing (NGS) technologies have developed rapidly and been applied to the ecological domain. Meta-barcoding techniques have accreted the reliability of identifying specific taxonomic groups of organisms at both species and genus level [5], and environmental DNA (eDNA) have enabled the detection of invisible species in various situations [6,7]. The eDNA approaches have also been used to clarify and understand systematic ecology, particularly biological trophic interaction in both aquatic habitat environments and food webs by collecting information from food sources found in gu<sup>t</sup> contents of species and the excrement of lived organisms. This helps to overcome unidentified limitations of food source analyses, which were based on microscopic analysis [8–11]. At present, it is necessary to develop a method to separate pure gu<sup>t</sup> content from target organisms for a wide range of applications of DNA technology in food source identification. In addition, the most fundamental methodology is to produce a framed "blocking primer", which removes the DNA of the target species from the target gu<sup>t</sup> contents.

On the other hand, changes in temperature, salinity, and metal contamination could a ffect the uptake, elimination, and biotransformation rates of common organisms [12]. Increasing water temperatures can act as a stressor that impacts the immune and physical responses of aquatic organisms, especially the cascading food chain network linking of plankton–invertebrates–fish communities. Accordingly, a temperature change can significantly a ffect food chains' related development and the health of aquatic prey and predation organisms. Further, temperature is known to have a significant effect on oxidative stress biomarkers for aquatic organisms. Due to the fact that climate change is expected to result in more frequent and intense heat shock events, it is pertinent to investigate the effect of increasing temperatures on the oxidative stress response of common aquatic organisms.

Oxidative stress is induced by a wide range of environmental components including temperature changes, UV stress, chemical action and oxygen shortages, and an over-production of reactive oxygen species (ROS) in relation to defense mechanisms [13]. The overproduction of ROS can generate oxidative stress which leads to permanent cell damage. Thus, the intracellular accumulation of ROS would not only disrupt the functions of specific tissues and organs but also lead to the premature death of the entire organism [14]. Oxidative stress biomarkers have been widely used in the development of ecological indices and in the assessment of the exposure of aquatic organisms to contaminants from agricultural, industrial, and urban pollution [15]. Oxidative stress is also involved in many biological and pathological processes and normal physiological development [13]. Currently, the study of many molecular markers has been developed in order to understand the physiological response of organisms. Superoxide dismutases (SODs) and catalase (CAT) are important antioxidant enzymes to protect the cell from oxidative damage by ROS. Especially, heat shock protein 90 (HSP90), a highly conserved protein, is a dimer that binds to several cellular proteins, including steroid receptors and protein kinases [16,17]. In aquatic animals, the induction of HSP90 genes and HSPs family has been widely reported in response to cellular stress, including temperature elevation, osmotic stress, hormone stimulation, herbicide toxicity, and viral infections [18,19].

This Special Issue ("Food Chains and Food Webs in Aquatic Ecosystems") aims to share recent information on the study for food chains and food webs in aquatic ecosystems focusing on biological monitoring and assessment of aquatic ecosystems.

### **2. Papers in This Special Issue**

The six papers included in this Issue focus on food chains and food webs in aquatic ecosystems as well as on e ffects of environmental factors.

To test a hypothesis that di fferences in invertebrate and fish assemblages in lakes characterized by di fferent trophic conditions determine patterns of variation in the trophic niche width of the fish species depending on their specific feeding habits, Caputi et al. [20] studied the feeding behavior of two omnivorous species (*Anguilla anguilla* and the seabream *Diplodus annularis*), which are ecologically and economically important, using the stable isotope analysis of carbon (δ13C) and nitrogen (δ15N). They found that *A. anguilla* was a generalist in the eutrophic lake, whereas *D. annularis* became more specialist, suggesting that changes in macroinvertebrate and fish community composition a ffect the trophic strategies of high-trophic level consumers.

Identification of gu<sup>t</sup> contents is helpful to analyze the food source of animals. However, it has several limitations such as small size and fragmentation of gu<sup>t</sup> materials. To overcome these limitations, recently, genomic approaches have been applied to understand the biological interaction including food webs [9,10,21]. Oh et al. [21] proposed a pretreatment method for DNA-barcoding to analyze gu<sup>t</sup> contents of rotifers to provide a better understanding of rotifer food sources and showed that the proposed method is useful to identify food sources of small organisms.

Jo et al. [22] and Kim et al. [23] presented the application of eDNA in costal aquatic ecosystems. Jo et al. [22] determined aquatic community taxonomic composition using eDNA based on an NGS and analyzed the community spatial distribution with regard to environmental parameters and the habitat types. Meanwhile, Kim et al. [23] compared water sampling between the eDNA method and

conventional microscopic identification for plankton community composition related to ecological monitoring and assessment of aquatic ecosystems. They found that the eDNA approach provides a wider variety of species composition, while conventional microscopic identification depicts more distinct plankton communities in sites, suggesting that the eDNA approach is a valuable alternative for biological monitoring and diversity assessments in aquatic ecosystems.

Kim et al. [24] assessed the spatial distribution of benthic macroinvertebrate communities responding to their environment such as land use and water quality, and concluded that information such as land use which is easily available characterized e ffectively the distribution of benthic macroinvertebrates.

To evaluate the toxic e ffects of di-2-ethylhexyl phthalate (DEHP) on cellular protection in *Macrophthalmus japonicus* crabs, Park et al. [25] identified two stress-related genes and investigated the genomic structure, phylogenetic relationships with other homologous heat shock proteins (HSPs), and transcriptional responses of HSPs under DEHP stress. Their results suggested that DEHP toxicity could disrupt cellular immune protection through transcriptional changes to HSPs in the test organisms.
