Lakes are active components of the global carbon cycle and host a range of processes that degrade and modify dissolved organic matter (DOM). Through the degradation of DOM molecules and the synthesis of new compounds, microbes in aquatic environments strongly and continuously influence chemodiversity, which can feedback to influence microbial diversity. Developing a better understanding of the biodiversity patterns that emerge along spatial and environmental gradients is one of the key objectives of community ecology. A changing climate may affect ecological feedback, including those that affect microbial communities. To maintain the function of a lake ecosystem and predict carbon cycling in the environment, it is increasingly important to understand the coupling between microbial and DOM diversity. To unravel the biotic and abiotic mechanisms that control the structure and patterns of DOM and microbial communities in lakes, we combined high-throughput sequencing and ultra-high resolution mass spectrometry together with a null modeling approach. The advantage of null models is their ability to evaluate the relative influences of stochastic and deterministic assembly processes in both DOM and microbial community assemblages. The present study includes spatiotemporal signatures of DOM and the microbial community in six temperate lakes contrasting continental and Mediterranean climates during the productive season. Different environmental conditions and nutrient sources characterized the studied lakes. Our results have shown high covariance between molecular-level DOM diversity and the diversity of individual microbial communities especially with diversity of microeukaryotes and free-living bacteria indicating their dynamic feedback. We found that the differences between lakes and climatic regions were mainly reflected in the diversity of DOM at the molecular formula-level and the microeukaryota community. Furthermore, using null models the DOM assembly was governed by deterministic variable selection operating consistently and strongly within and among lakes. In contrast, microbial community assembly processes were highly variable across lakes with different trophic status and climatic regions. Difference in the processes governing DOM and microbial composition does not indicate weak coupling between these components, rather it suggests that distinct factors may be influencing microbial communities and DOM assemblages separately. Further understanding of the DOM-microbe coupling (or lack thereof) is key to formulating predictive models of future lake ecology and function.

Riverine floodplains are ecologically remarkable systems that have historically faced strong anthropogenic pressures. The aim of this study was to examine whether the phytoplankton functional approach by Reynolds is a useful tool for disentangling anthropogenic pressure from the impact of natural flooding on a riverine floodplain lake. Lake Sakadaš, part of the large conserved river–floodplain system along the Danube River (Kopački Rit, Croatia), was used as a case study. Historical data on phytoplankton dynamics from the 1970s, when the lake was exposed to direct inflows of agricultural wastewater, were compared with current data from a time when the lake was a strongly protected area. Analysis of the phytoplankton community, based on functional groups and their beta diversities, revealed clear variation between the observed periods. The heavy bloom of species from only one functional group with extremely high biomass indicated a highly impacted environment in the past. Recent data suggest that, with the cessation of direct pollution, near-natural hydrological conditions with flooding as a fundamental environmental driving factor, support algal assemblages characteristic of a naturally eutrophic lake. Assessing multiple pressures on floodplain lakes and disentangling their specific impacts on ecological statuses are crucial for defining the protection and sustainable management of these particularly sensitive and endangered freshwater systems.

Ocean microorganisms constitute ~70% of the marine biomass, contribute to ~50% of the Earth’s primary production, and play a vital role in global biogeochemical cycles. The marine heterotrophic and mixotrophic protistan and fungal communities have often been overlooked mainly due to limitations in morphological species identification. Despite the accumulation of studies on biogeographic patterns observed in microbial communities, our understanding of the abundance and distribution patterns within the microbial community of the largest subtropical gyre, the South Pacific Gyre (SPG), remains incomplete. Here, we investigated the diversity and vertical composition of protistan and fungal communities in the water column of the ultra-oligotrophic SPG. Our results showed apparent differences in protistan community diversity in the photic and aphotic regions. The entire protistan community diversity was significantly affected by temperature, salinity, oxygen, and nutrient concentrations, while the parasitic community diversity was also affected by chlorophyll a concentration. The parasitic protists were assigned to the class Syndiniales accounting for over 98% of the total parasitic protists, exhibiting higher relative sequence abundance along the water depth and displaying consistent patterns among different sampling stations. In contrast to the protistan community, the fungal community along the SPG primarily clustered based on the sampling station and pelagic zones. In particular, our study reveals a significant presence of parasitic protists and functionally diverse fungi in SPG and their potential impact on carbon cycling in the gyre. IMPORTANCE: Our findings carry important implications for understanding the distribution patterns of the previously unrecognized occurrence of parasitic protists and functionally diverse fungi in the nutrient-limited South Pacific Gyre. In particular, our study reveals a significant presence of parasitic Syndiniales, predominantly abundant in the upper 300 m of the aphotic zone in the gyre, and a distinct presence of fungal communities in the aphotic zone at the central part of the gyre. These findings strongly suggest that these communities play a substantial role in yet insufficiently described microbial food web. Moreover, our research enhances our understanding of their contribution to the dynamics of the food webs in oligotrophic gyres and is valuable for projecting the ecological consequences of future climate warming.

Ciliates (protozoa) are a very large and diverse group of microeukaryotes that occupy a central position in the trophic web of freshwater ecosystems. Ciliates exhibit high ecological sensitivity and have tremendous bioindicator potential, but they are largely ignored in routine biomonitoring, mainly due to limitations in morphological diagnosis, which is both time-consuming and costly. In this study, we combined molecular (Illumina sequencing of the hypervariable V9 region of the SSU rRNA gene) and morphological approaches to get a detailed insight into the periphytic ciliate community structure and function within a karst, tufa-precipitating hydrosystem (National Park Krka, Croatia). Periphyton (biofilm) was sampled from light- and dark-exposed lithified tufa/stones at four representative locations within the Krka River, including upstream, midstream, and downstream river sections. We identified hydrological parameters and saprobiological classification of the sampling locations as the main structuring factors for ciliate communities. The molecular approach showed a clear separation of sampling locations in beta diversity analyses, as confirmed by PERMANOVA test. In contrast, alpha diversity was mostly affected by light exposition of the lithified tufa/stones, as confirmed by morphological approach. Environmental conditions consistently affected ciliate community composition at all locations, resulting in clear separation of periphyton samples. Our results indicate that ciliates should be considered as important bioindicators in monitoring tufa-forming rivers and streams, and the molecular approach (V9 region) proved to be applicable because as it efficiently captured the diversity of ciliates in periphyton. Validation of such an approach would lead to significant progress in extending monitoring to a broader range of indicator organisms than those now included in standard monitoring.

The process of travertine formation and carbonate deposition in the rivers is unique, delicate, and depends on the activity of algae and mosses. Although diatoms have been used extensively in hydrobiological studies, the comparative analysis data on diatom communities of the travertine barriers in karstic rivers are still scarce. The study aimed to detect the diatom composition on travertine barriers in the Una River, the large karstic river in Bosnia and Herzegovina. An integrated classical morphological identification approach with metabarcoding was applied on eight samples across the river length profile. Morphological analyses were performed using both light and scanning electron microscopes. Subsequent DNA metabarcoding of the chloroplastic gene 312bp rbcL was done. The DADA2 pipeline was used for the bioinformatic treatment of the demultiplexed MiSeq reads to infer Amplicon Sequence Variants (ASVs). ASVs were taxonomically assigned using the Diat.barcode v7 reference database. A total of 126 species were identified using the morphological approach, while 133 ASVs were taxonomically assigned to 58 unique taxa with the molecular approach. Diatom community structures in terms of molecular and morphological approaches were congruent with 49 shared species. Species from genera Gomphonema, Navicula and Encyonema were less assigned in molecular analysis. The most abundant taxa in the Una River are alkaliphilous, belonging to the genera Gomphonema, Nitzshia and Navicula. Although specific for their extremely good chemical status, the travertine barriers of the Una River are largely inhabited with meso-eutraphentic taxa.