Climate Change Causes Salinity To Become Determinant in Shaping the Microeukaryotic Spatial Distribution among the Lakes of the Inner Mongolia-Xinjiang Plateau

Climate change greatly affects lake microorganisms in arid and semiarid zones, which alters ecosystem functions and the ecological security of lakes. However, the responses of lake microorganisms, especially microeukaryotes, to climate change are poorly understood. Here, using 18S ribosomal RNA (rRNA) high-throughput sequencing, we investigated the distribution patterns of microeukaryotic communities and whether and how climate change directly or indirectly affected the microeukaryotic communities on the Inner Mongolia-Xinjiang Plateau. Our results showed that climate change, as the main driving force of lake change, drives salinity to become a determinant of the microeukaryotic community among the lakes of the Inner Mongolia-Xinjiang Plateau. Salinity shapes the diversity and trophic level of the microeukaryotic community and further affects lake carbon cycling. Co-occurrence network analysis further revealed that increasing salinity reduced the complexity but improved the stability of microeukaryotic communities and changed ecological relationships. Meanwhile, increasing salinity enhanced the importance of deterministic processes in microeukaryotic community assembly, and the dominance of stochastic processes in freshwater lakes transformed into deterministic processes in salt lakes. Furthermore, we established lake biomonitoring and climate sentinel models by integrating microeukaryotic information, which would provide substantial improvements to our predictive ability of lake responses to climate change. IMPORTANCE Our findings have important implications for understanding the distribution patterns and the driving mechanisms of microeukaryotic communities among the lakes of the Inner Mongolia-Xinjiang Plateau and whether and how climate change directly or indirectly affects microeukaryotic communities. Our study also establishes the groundwork to use the lake microbiome for the assessment of aquatic ecological health and climate change, which is critical for ecosystem management and for projecting the ecological consequences of future climate warming.

Significant Effects of Associated Microorganisms on the Community of Photosynthetic Picoeukaryotes

Photosynthetic picoeukaryotes (PPEs) form associations with other microorganisms. However, whether and how the associated microbes affect PPE communities remain unknown. We used flow cytometric cell sorting combined with parallel high-throughput sequencing of the 18S and 16S rRNA genes to simultaneously investigate PPEs and their associated microbial communities in the Yangtze-connected Lake Dongting. The lake harbors a great diversity of PPEs. PPE communities exhibited significant temporal rather than spatial variations. Two distinct PPE taxa affiliated with Discostella nipponica and Poterioochromonas malhamensis were dominant during winter/spring and summer, respectively. Parallel high-throughput sequencing revealed a great diversity of associated bacteria and non-pigmented eukaryotes (NPEs) in PPEs sorts. Proteobacteria, Actinobacteria, Bacteroidetes, and Cyanobacteria among the associated bacteria and fungi among the associated NPEs were dominant. PPEs were more apparently associated with bacteria than with NPEs. The co-occurrence network of PPEs and associated microbes formed five major modules, which exhibited distinct temporal patterns, being specific to a certain period. Variations in PPEs communities were significantly correlated with both environmental factors and associated microbial communities. In variation partitioning analysis, the associated bacteria explained the greatest variations in PPE communities, and associated bacteria and NPEs co-explained a large portion of environmental effects on PPE communities. Our results highlight the significance of associated microbes in shaping PPE communities.

Finding needles in a haystack-Extensive diversity in the eustigmatophyceae revealed by community metabarcode analysis targeting the rbcL gene using lineage-directed primers

Sequences from the Stramenopile class Eustigmatophyceae are rarely reported in metabarcoding studies, and when they have been reported, there are very few haplotypes. We hypothesized that the paucity of eustigmatophyte species detected in these studies may be a result of the metabarcoding techniques used, which have primarily employed universal ribosomal RNA gene regions. In this study, we examined environmental DNA samples from 22 sites in southwestern Virginia, some of which had previously been studied using ribosomal RNA analysis. We used metabarcoding techniques targeting the plastid rbcL gene with new primers designed to produce a 370 bp amplicon from all lineages of the Eustigmatophyceae in a reference collection. The amplicons were then analyzed with DADA2 to produce amplicon sequence variants (ASVs). Our results revealed 184 rbcL haplotypes that can be tentatively assigned to the Eustigmatophyceae from these sites, representing much higher diversity than has been detected by ribosomal DNA-based studies. The techniques employed can be used for future studies of population structure, ecology, distribution, and diversity of this class. With these techniques, it should be possible to make realistic estimates of the species-level diversity of the Eustigmatophyceae on local, regional, and perhaps global scales.

The spatial distribution of the photosynthetic picoeukaryotes community structure in Lake Hongze

The spatial dynamics of picophytoplankton were investigated by flow cytometry and high-throughput sequencing in Lake Hongze, a large river-connecting lake. Picophytoplankton were mainly composed of phycocyanin-rich picocyanobacteria (PCY) and photosynthetic picoeukaryotes (PPEs). Picocyanobacteria was the dominant picophytoplankton group since the contribution of PPEs to total picophytoplankton was only 11.78%. However, PPEs were highly diverse and were composed of Chlorophyta, Bacillariophyta and Chrysophyceae. Environmental factors showed spatial differences, particularly in total phosphorus (TP), suspended solids (SS) and chemical oxygen demand (CODMn), which showed relatively high concentrations around the river channel. The abundances of PPEs and PCY showed similar spatial patterns, which were relatively low in the river course since they were negatively related to SS and CODMn. The top 10 OTUs contributed 79.18% of the total PPEs reads and affiliated with main species in PPEs. CCA results showed that, PPEs community composition was significantly impacted by temperature and DO at sites away from river channel, while was only influenced by nitrite at sites around the river channel.

Temporal patterns in the interaction between photosynthetic picoeukaryotes and their attached fungi in Lake Chaohu

The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota and Ascomycota. Temperature, Si and PPE community structure are the most important driving factors for the temporal succession of PPE-attached fungal communities. In particular, PPE-attached fungi can be divided into three groups from high to low temperatures. Phylogenetic molecular ecological network results indicated that the connectivity and the total number of links in the network of the high-temperature group (> 21.82°C) are higher than those in the other two temperature groups (between  9.67 and  21.82°C, and < 9.67°C, respectively). Moreover, the interaction between PPE-attached fungi and the PPEs changed from antagonistic to cooperative, with the decline in temperature. The most abundant operational taxonomic units of PPE-attached fungi were affiliated with the Cladosporium, the most common saprophytic fungus, whereas most fungal hub taxa were Chytridiomycota, the main parasite fungi of phytoplankton.

Temperature mainly determines the temporal succession of the photosynthetic picoeukaryote community in Lake Chaohu, a highly eutrophic shallow lake

Photosynthetic picoeukaryotes (PPEs) are key players in aquatic systems, while their diversity and community composition dynamics remain poorly understood. The monthly composition of PPEs in Lake Chaohu was investigated using a combination of flow cytometry sorting and high throughput sequencing. Results indicated that temperature is the most important factor shaping PPEs community structure. The PPEs community can be categorized into three groups that are dominant at different temperature ranges: high temperature (>21.8 °C), intermediate temperature (between 9.8 °C and 21.8 °C) and low temperature (<9.8 °C). At the supergroup level, Cryptophyta were dominant at the intermediate temperature level, and Bacillariophyta were prevalent at low temperatures. In comparison, Chlorophyta PPEs were sensitive to temperature at the order level. Molecular network analysis using 18S rDNA sequencing results from sorted samples revealed that the Operational Taxonomic Units (OTUs) of PPE from the same taxonomic groups were predominantly positive, implying that they were occupying similar niches. The cooccurrence patterns between PPEs and fungi were mostly negative. In particular, OTU101, which was associated with Chytridiomycota, was negatively related to many OTUs belonging to Chlorophyta and Diatom, indicating that their potential parasitic associations may be not species-specific.

The Community Structure of Picophytoplankton in Lake Fuxian, a Deep and Oligotrophic Mountain Lake

Spatial and seasonal dynamics of picophytoplankton were investigated by flow cytometry over a year in Lake Fuxian, a deep and oligotrophic mountain lake in southwest China. The contribution of picophytoplankton to the total Chl-a biomass and primary production were 50.1 and 66.1%, respectively. Picophytoplankton were mainly composed of phycoerythrin-rich picocyanobacteria (PE-cells) and photosynthetic picoeukaryotes (PPEs). PPEs were dominant in spring, reaching a maximum cell density of 3.0 × 10⁴ cell mL^–1, while PE-cells were prevalent in other seasons. PE-cell abundance was relatively similar throughout the year, except for a decrease in summer during the stratification period, when nutrient concentration was low. High-throughput sequencing results from the sorted samples revealed that Synechococcus was the major PE-cell type, while Chrysophyceae, Dinophyceae, Chlorophyceae, Eustigmatophyceae, and Prymnesiophyceae were equally important PPEs. In spring, PPEs were mainly composed of Chlorophyceae and Trebouxiophyceae, while in summer, their dominance was replaced by that of Chrysophyceae and Prymnesiophyceae. Eustigmatophyceae and Chlorophyceae became the major PPEs in autumn, and Dinophyceae became the most abundant in winter. Single cells of Microcystis were usually detected in summer in the south, suggesting the deterioration of the water quality in Lake Fuxian.