Diatoms, a unique group of algae colonising a wide range of aquatic habitats and contributing to human well-being in many ways. We list and summarise these services using the classification of the Millennium Ecosystem Assessment (MEA), i.e. supporting, regulating, provisioning and cultural services. The most relevant supporting services are photosynthesis and primary production, as well as sediment formation. They also play a key role in nutrient cycling and habitat provisioning and serve as food for many organisms. Regulating services as oxygen production, climate control or sediment stabilisation are difficult to discuss without diatoms. Many provisioning services, directly used by humans, can be obtained from diatoms. These are tangible products such as medicines and immunostimulants but direct technologies such as wastewater treatment, micro- and nanotechnologies were also developed using diatoms. Studying of the past, present, and future linked to diatoms as a tool for palaeolimnology, ecological status assessment of waters and climate modelling is essential. Finally, the impressive morphology and ornaments of diatom frustules make them one of the most spectacular microorganisms, inspiring artists or providing a number of educational opportunities. Therefore, protecting aquatic habitats they inhabit is not simply a nature conservation issue but the key for human well-being in the future.

Both natural and anthropogenic processes can lead to the increasing salinity of surface waters. The knowledge about the ecological consequences of salinization on the biota is limited especially in case of microbiota, like diatoms. We collected the existing knowledge about the relationship between salinity and diatoms in fresh and saline waters. Based on the available papers, conductivity and ion composition are the most important variables shaping diatom communities. Secondary salinization can mask regional differences in diatom assemblages. Trait-based analyses highlight the competitive advantages of motile guild and the extreme trait categories in these environments. The increasing conductivity along a wide conductivity scale decreases the alpha-diversity. Salinization induces the spread and invasion of marine and brackish species into inland freshwaters as well as that of freshwater species tolerating elevated conductivity and/or need specific ions. Concerning food webs, salinity can directly change diatom communities and the subsequent upper trophic levels but most likely this effect manifests as a top-down regulation. Applicable diatom indices are available to assess the level of salinization. Furthermore, diatom-inferred salinity reconstructions are widely applied to assess the past changes of salinity. However, future models predicting ecological consequences of salinization are scarce and sometimes contradictory.

Climate warming and legacy phosphorus (P) in sediments are two main factors counteracting current efforts to prevent eutrophication of temperate freshwater lakes and reservoirs. Climate warming impacts lacustrine thermal regimes, accelerates harmful cyanobacterial growth, and increases the probability of periodic anoxic bottom conditions. Legacy P in sediments becomes influential over eutrophication because of its reactivation under anoxic conditions. Lake Stechlin is a deep glacial lake of the Baltic Lake area, Germany in which artificial external P loading has been effectively blocked for more than 3 decades. The lakes trophic status was oligotrophic, until roughly 2 decades ago when it accelerated toward higher trophic levels. Here we analyse the temporal dynamics of Lake Stechlin phytoplankton biomass and composition in relation to chemical and hydrological covariates, based on monitoring data from 1994 to 2019 at sampling frequency of c. 27 samples per year. Our results show an assemblage change toward cyanobacterial dominance that took place at several temporal scales. Intra‐annual compositional change became more pronounced over the study period, mainly because of changes during the autumn and winter seasons. Results from a structural break point analysis of the phytoplankton time series with covariates, and from a hierarchical cluster analysis show that major changes occurred in 2007–2011. An analysis of early warning indicators did not unambiguously support this period as a critical transition. The change rather occurred as a rapid succession of major events during these years. Results from convergent cross‐mapping causality tests are consistent with the hypothesis that increasing relative water column stability may drive eutrophication, and additionally, that the intra‐annual timing of the biomass change plays an important role in the lakes P loading. Although quantitative data on internal P loading are unavailable, internal P mobilisation from sediments appears to be the most plausible mechanism behind the increased phytoplankton biomass. Lake Stechlin, therefore, is an example of the challenges that legacy P poses to the management of freshwater ecosystems in the context of climate warming, even when external P sources are effectively blocked, and local protective measures are in place.

Amplicon sequencing tools such as metabarcoding are commonly used for thorough characterisation of microbial diversity in natural samples. They mostly rely on the amplification of conserved universal markers, mainly ribosomal genes, allowing the taxonomic assignment of barcodes. However, linking taxonomic classification with functional traits is not straightforward and requires knowledge of each taxonomic group to confidently assign taxa to a given functional trait. Zoosporic parasites are highly diverse and yet understudied, with many undescribed species and host associations. However, they can have important impacts on host populations in natural ecosystems (e.g., controlling harmful algal blooms), as well as on industrial‐scale algae production, e.g. aquaculture, causing their collapse or economic losses. Here, we present ParAquaSeq, a curated database of available molecular ribosomal sequences belonging to zoosporic parasites infecting aquatic vascular plants, macroalgae and photosynthetic microorganisms, i.e. microalgae and cyanobacteria. These sequences are aligned with ancillary data and other information currently available, including details on their hosts, occurrence, culture availability and associated bibliography. The database includes 1131 curated sequences from marine, freshwater and industrial or artificial environments, and belonging to 13 different taxonomic groups, including Chytridiomycota, Oomycota, Phytomyxea, and Syndiniophyceae. The curated database will allow a comprehensive analysis of zoosporic parasites in molecular datasets to answer questions related to their occurrence and distribution in natural communities. Especially through meta‐analysis, the database serves as a valuable tool for developing effective mitigation and sustainable management strategies in the algae biomass industry, but it will also help to identify knowledge gaps for future research.

A number of studies evidenced the impact of human activities on aquatic environments worldwide. The availability of nutrients in lakes is strongly influenced by watershed land use patterns depending on the share of forestry, agriculture and urbanization level. Nearly all the previous studies, which examined the relationships between the phytoplankton community and the land use pattern on the watershed of lakes or reservoirs were performed on a taxonomic basis. In this study, 78 lakes were sampled to analyse how the different land use types affect their phytoplankton functional group compositions. Our results concluded that land use is a complex driver, and it cannot provide an unequivocally straightforward forecast, which could result in the selection of a specific functional group or taxa. Thus, land use alone is a weak predictor, but the shared effects may structure the phytoplankton assemblage composition.