Freshwater Ecosystems—Biodiversity and Protection

1. Introduction to the Special Issue

In recent times, there have been growing concerns about biodiversity and habitat protection in all ecosystems, especially freshwater ecosystems, since some of the strongest negative anthropogenic influences are evident in lakes, rivers, ponds, and floodplains [1,2,3]. Globally, efforts are being made to protect biodiversity, reduce habitat destruction, and ensure vital ecological services through the assessment and monitoring of aquatic habitats and communities, as well as the development of protection, revitalization, and restoration plans for natural freshwater ecosystems [2,3,4]. To achieve these goals, it is essential to understand how ecosystems function, the status of present communities, and the main environmental factors influencing them [5,6]. Furthermore, biotic elements or multi-indicator approaches can be instrumental in the protection and management of freshwater systems [5,6,7].

It is vital to approach these issues from different angles and disciplines because freshwater bioassessment is complex process. Certain taxonomic groups, such as Ephemeroptera, Plecoptera, Trichoptera (EPT), oligochaetes, and chironomids, are particularly important as indicators of water quality, reflecting both good and degraded status [5,6,7]. With increasing anthropogenic pressures and climate change, there is a pressing need for regular monitoring of aquatic ecosystems and for updating and improving applied bioassessment methods. Large-scale international initiatives, such as the Joint Danube Survey, play a critical role in comprehensive data collection and analysis regarding aquatic biodiversity, biotic community structure, chemical status, pollution, microplastics, hydromorphological alterations, and other ecosystem parameters [8,9].

Microplastic pollution has emerged as a major concern in recent years, affecting organisms across trophic levels and potentially impacting human health [8]. Molecular approaches such as eDNA metabarcoding have advanced our ability to accurately assess biodiversity. For instance, Pleše and Buj assessed endangered lamprey species in Croatia, providing insights into their phylogeny, ecology, and conservation needs. Similarly, Šimunović et al. studied the phytoplankton community in a karstic lake, using both morphological and molecular methods to evaluate the applicability of eDNA metabarcoding as a biomonitoring tool.

The aim of this Special Issue is to highlight contemporary challenges in freshwater ecology, including biodiversity loss, environmental stressors—both natural and anthropogenic—biotic community structure and functional complexity, and the application of molecular analyses in hydrobiological research and bioassessment. The contributions gathered here provide valuable insights from diverse studies and demonstrate the importance of integrating classical ecological approaches with modern molecular, chemical, and biotic assessment tools [1,2,3,4,5,6,7,8,9,10,11,12].

2. A Summary of the Special Issue

This Special Issue presents 11 research articles focused on the ecology, biodiversity, and monitoring of freshwater ecosystems under increasing anthropogenic pressures. The studies cover a wide range of topics, including phytoplankton assessment using morphological and molecular approaches, ecological differentiation of oligochaete communities, and conservation of Unio crassus. Other contributions explore the application of the EPT index for water quality assessment, microplastic pollution in benthic organisms, and the genetic diversity and conservation requirements of lampreys in Croatia. Research on meiofaunal assemblages in Baiyangdian Lake (China) further advances understanding of ecosystem health and restoration priorities. Together, these studies provide valuable insights into freshwater biodiversity and highlight the importance of integrating classical and modern approaches for effective ecological assessment and management.

Šimunović et al. presented a study characterizing the phytoplankton community of a natural karstic lake by combining and comparing morphological and molecular approaches to check the applicability of eDNA metabarcoding as a biomonitoring tool. A total of 51 phytoplankton taxa were found using the morphological approach, whilst the molecular approach discovered 97 ASVs that corresponded to the algal community. The comparability of both approaches in describing phytoplankton communities is evident in the designation of centric diatoms, dinoflagellates and cryptophytes as descriptive taxa. The authors also showed that both approaches proved reliable in detecting functional groups (Lo, C, X2, X3) with similar ecological demands. It was confirmed that eDNA metabarcoding is an applicable tool for biodiversity monitoring of a natural karst lake and should be used as a feasible supplement to traditional microscopy in phytoplankton community assessments.

Atanacković et al. examined the distribution of oligochaete species and their ecological differentiation with respect to environmental factors: altitude, temperature, oxygen concentration, conductivity, total organic carbon, and waterbody type. Although they are widespread, differentiation of oligochaete communities in four waterbody types and altitudinal groups was observed through alpha and beta diversity. The study showed that the total beta diversity decreased with a decrease in waterbody size and with an increase in the size of substrate particles, river flow velocity, and altitude. Communities from small mountain rivers and streams and large and medium rivers with coarser substrates differed from other oligochaete communities. The described research represents an important step for using oligochaetes more reliably and effectively, as they are a necessary BQE (biological quality element) in the biological validation of waterbody typology in routine monitoring practice.

Tomović et al. contributed to the knowledge on Unio crassus Philipson, 1788, a species with high priority for conservation. The research covered a variety of waterbody types throughout Serbia, and distribution data were considered over three time periods from 1953 to 2019. The paper summarizes all the available literature data, field research and information obtained during the review of the malacological material collection of the Natural History Museum in Belgrade. The results show a positive population trend, which is reflected in an extension of the distribution area and an increase in population density. The study also revealed better insights into the habitat requirements and limiting factors of the species (e.g., substrate characteristics, waterbody types, altitude, and some nutrients seem to be of great importance for the occurrence of the species).

Tubić et al. evaluated the significance of the EPT index in the water quality assessment of three types of waterbodies in hilly and mountainous regions of Serbia. The authors compared the obtained values of biological indices used for the water quality assessment according to the national legislation with the overall status assessment represented by the ecological quality classes (EQC). The results indicate that the EPT index is an excellent indicator of changes in water quality and an important tool for the ecological categorization of waterbodies in mountainous regions.

Stanković et al. studied microplastics in chosen benthic organisms (Corbicula spp., Limnodrilus hoffmeisteri (Claparede, 1862), and Polypedilum nubeculosum (Meigen, 1804)), obtained during the Joint Danube Survey 4 (JDS4) expedition. Alkaline and enzymatic protocols were performed for tissue degradation, followed by filtering through glass microfiber filters (mesh size 0.5 µm), and MP particles were photographed, measured, and counted. After µ-ATR-FTIR spectroscopy analysis, the particles were characterized as polycarbonate (PC), polyethylene terephthalate (PET), polypropylene–polyethylene copolymer (PP-PE), nylon (polyamide-PA) and cellophane, with PET being dominant. New knowledge on microplastics in aquatic environments and organisms is crucial for the protection of nature.

Pleše and Buj addressed the pressing issue of protecting endangered lamprey species in Croatia, a crucial element in preserving biodiversity, particularly in the face of increasing human-induced impacts on natural ecosystems due to global warming. The study aimed to bridge the knowledge gap by assessing the genetic diversity and structure of identified lamprey species and lineages in Croatia using the gene for cytochrome b. The research revealed four distinct lineages within the species Eudontomyzon vladykovi Oliva and Zanandrea, 1959, confirmed the presence of the species Eudontomyzon danfordi Regan, 1911, in Croatia, and provided important insights into the intricate relationships and conservation needs of lampreys, providing a basis for future discussions involving additional genetic markers. By gaining a comprehensive understanding of the taxonomy, ecology, and genetic diversity of lampreys, we can ensure their conservation and that of associated ecosystems.

Cao et al. conducted their research on the Baiyangdian Lake, North China Plain, which plays a pivotal role in maintaining the regional ecological balance and biodiversity. The aim was to evaluate the density, spatiotemporal patterns, and habitat response dynamics of meiofauna, primarily comprising freshwater nematodes (91.78%), ostracods, and copepods. The study indicated that the distribution and abundance of meiofauna were significantly affected by environmental factors, with water depth and ammonia nitrogen levels being potential key determinants. The authors evaluated the “health status” of the Baiyangdian ecosystem, which can later aid the protection of biodiversity of this area, and can also provide scientific support for its ecological restoration and governance as well as the assessment of ecological service functions.

Together, these studies demonstrate the value of integrating traditional ecological approaches with molecular, chemical, and biotic assessment tools. They contribute to a better understanding of ecosystem responses and inform effective conservation and management strategies, advancing global efforts to preserve freshwater biodiversity and maintain sustainable aquatic environments.