Single colony genetic analysis of epilithic stream algae of the genus Chamaesiphon spp

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

BACKGROUND

Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world's best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria.

RESULTS

Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota.

CONCLUSIONS

We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction. Video Abstract.

Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition

In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.

An updated classification of cyanobacterial orders and families based on phylogenomic and polyphasic analysis

Cyanobacterial taxonomy is facing a period of rapid changes thanks to the ease of 16S rRNA gene sequencing and established workflows for description of new taxa. Since the last comprehensive review of the cyanobacterial system in 2014 until 2021, at least 273 species in 140 genera were newly described. These taxa were mainly placed into previously defined orders and families although several new families were proposed. However, the classification of most taxa still relied on hierarchical relationships inherited from the classical morphological taxonomy. Similarly, the obviously polyphyletic orders such as Synechococcales and Oscillatoriales were left unchanged. In this study, the rising number of genomic sequences of cyanobacteria and well-described reference strains allowed us to reconstruct a robust phylogenomic tree for taxonomic purposes. A less robust but better sampled 16S rRNA gene phylogeny was mapped to the phylogenomic backbone. Based on both these phylogenies, a polyphasic classification throughout the whole phylum of Cyanobacteria was created, with ten new orders and fifteen new families. The proposed system of cyanobacterial orders and families relied on a phylogenomic tree but still employed phenotypic apomorphies where possible to make it useful for professionals in the field. It was, however, confirmed that morphological convergence of phylogenetically distant taxa was a frequent phenomenon in cyanobacteria. Moreover, the limited phylogenetic informativeness of the 16S rRNA gene, resulting in ambiguous phylogenies above the genus level, emphasized the integration of genomic data as a prerequisite for the conclusive taxonomic placement of a vast number of cyanobacterial genera in the future.

DNA sequence and taxonomic gap analyses to quantify the coverage of aquatic cyanobacteria and eukaryotic microalgae in reference databases: Results of a survey in the Alpine region

The taxonomic identification of organisms based on the amplification of specific genetic markers (metabarcoding) implicitly requires adequate discriminatory information and taxonomic coverage of environmental DNA sequences in taxonomic databases. These requirements were quantitatively examined by comparing the determination of cyanobacteria and microalgae obtained by metabarcoding and light microscopy. We used planktic and biofilm samples collected in 37 lakes and 22 rivers across the Alpine region. We focused on two of the most used and best represented genetic markers in the reference databases, namely the 16S rRNA and 18S rRNA genes. A sequence gap analysis using blastn showed that, in the identity range of 99-100%, approximately 30% (plankton) and 60% (biofilm) of the sequences did not find any close counterpart in the reference databases (NCBI GenBank). Similarly, a taxonomic gap analysis showed that approximately 50% of the cyanobacterial and eukaryotic microalgal species identified by light microscopy were not represented in the reference databases. In both cases, the magnitude of the gaps differed between the major taxonomic groups. Even considering the species determined under the microscope and represented in the reference databases, 22% and 26% were still not included in the results obtained by the blastn at percentage levels of identity ≥95% and ≥97%, respectively. The main causes were the absence of matching sequences due to amplification and/or sequencing failure and potential misidentification in the microscopy step. Our results quantitatively demonstrated that in metabarcoding the main obstacles in the classification of 16S rRNA and 18S rRNA sequences and interpretation of high-throughput sequencing biomonitoring data were due to the existence of important gaps in the taxonomic completeness of the reference databases and the short length of reads. The study focused on the Alpine region, but the extent of the gaps could be much greater in other less investigated geographic areas.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Emendation of the Coccoid Cyanobacterial Genus Gloeocapsopsis and Description of the New Species Gloeocapsopsis diffluens sp. nov. and Gloeocapsopsis dulcis sp. nov. Isolated From the Coastal Range of the Atacama Desert (Chile)

The taxonomy of coccoid cyanobacteria, such as Chroococcidiopsis, Pleurocapsa, Chroococcus, Gloeothece, Gloeocapsa, Gloeocapsopsis, and the related recent genera Sinocapsa and Aliterella, can easily be intermixed when solely compared on a morphological basis. There is still little support on the taxonomic position of some of the addressed genera, as genetic information is available only for a fraction of species that have been described solely on morphology. Modern polyphasic approaches that combine classic morphological investigations with DNA-based molecular analyses and the evaluation of ecological properties can disentangle these easily confusable unicellular genera. By using such an approach, we present here the formal description of two novel unicellular cyanobacterial species that inhabit the Coastal Range of the Atacama Desert, Gloeocapsopsis dulcis (first reported as Gloeocapsopsis AAB1) and Gloeocapsopsis diffluens. Both species could be clearly separated from previously reported species by 16S rRNA and 16S–23S ITS gene sequencing, the resulting secondary structures, p-distance analyses of the 16S–23S ITS, and morphology. For avoiding further confusions emendation of the genus Gloeocapsopsis as well as epitypification of the type species Gloeocapsopsis crepidinum based on the strain LEGE06123 were conducted.

Contrasting endolithic habitats for cyanobacteria in spring calcites of the European Alps

It is often difficult to decide which cyanobacteria found in endolithic habitats of calcite spring-tufa deposits are present as ephemeral components of the biota or are persistent, structural elements. To answer this question, we repeatedly studied two microhabitats of contrasting calcareous tufa springs in the European Alps. Pigment extracts, fluorescence probe measurements of in situ samples and traditional microscopy confirmed the dominance of cyanobacteria over eukaryotic algae and their viability in both microhabitats. Spring Site 1 (Laas, Northern Italy) is characterized by a highly variable, moist to dry and sun-exposed waterfall tufa consisting of fibrous calcite. A segment of these deposits in the lateral flank of a grotto contained dark endolithic layers in dim light, 1-2 mm below the surface, where aggregated cyanobacterial cells were dominant but not directly attached to calcites, a potential sign of gentle endolithic dissolution rather than calcite precipitation induced by cyanobacteria. Site 2 (Mühlau, Austria), in contrast, is a moss-tufa microhabitat associated with a seepage spring situated in a shady gorge, where the targeted stromatolites consisted of bark-like sheets of friable, orange to light-brown when wet (drying violet) 'styrofoam'- like aggregates of minute crystallites on the day-light exposed surfaces. These calcites were observed to nucleate directly on external sheaths of viable cyanobacteria trichomes. A polyphasic approach including LM, SEM, TEM exhibited a number of identical but also some divergent cyanobacteria of which two key taxa were specific for each of the two microhabitats (Nostoc and Pseudoscytonema at Sites 1 and 2 respectively). Both cyanobacterial communities characterised, by the cloning of 16S rDNA showed a dominance of mostly unknown and partly divergent filamentous cyanobacteria assigned to the order of Synechococcales. Our microhabitat study of alpine crenal calcites highlights the rather divergent biotic responses of cyanobacteria within spring tufa deposits.

Interaction of cyanobacteria with calcium facilitates the sedimentation of microplastics in a eutrophic reservoir

Low-density microplastics are frequently found in sediments of many lakes and reservoirs. The processes leading to sedimentation of initially buoyant polymers are poorly understood for inland waters. This study investigated the impact of biofilm formation and aggregation on the density of buoyant polyethylene microplastics. Biofilm formation on polyethylene films (4 × 4 × 0.15 mm) was studied in a eutrophic reservoir (Bautzen, Saxony, Germany). Additionally, aggregation dynamics of small PE microplastics (~85 µm) with cyanobacteria were investigated in laboratory experiments. During summer phototrophic sessile cyanobacteria (Chamaesiphon spp. and Leptolyngbya spp.) precipitated calcite while forming biofilms on microplastics incubated in Bautzen reservoir. Subsequently the density of the biofilms led to sinking of roughly 10% of the polyethylene particles within 29 days of incubation. In the laboratory experiments planktonic cyanobacteria (Microcystis spp.) formed large and dense cell aggregates under the influence of elevated Ca²⁺ concentrations. These aggregates enclosed microplastic particles and led to sinking of a small portion (~0.4 %) of polyethylene microplastics. This study showed that both sessile and planktonic phototrophic microorganisms mediate processes influenced by calcium which facilitates densification and sinking of microplastics in freshwater reservoirs. Loss of buoyancy leads to particle sedimentation and could be a prerequisite for the permanent burial of microplastics within reservoir sediments.

New record of the rare genus Crinalium Crow (Oscillatoriales, Cyanobacteria) from sand dunes of the Baltic Sea, Germany: epitypification and emendation of Crinalium magnum Fritsch et John based on an integrative approach

Representatives of the Gomontiellaceae (Oscillatoriales) are rare and hence unstudied cyanobacteria with unusual morphology, distributed in terrestrial and aquatic habitats all over the world. Investigation of the group based on an integrative approach is only beginning, and to understand the actual biodiversity and ecology, a greater number of cultivated strains is necessary. However, some ecological traits of these cyanobacteria (e.g. low population densities, the absence of conspicuous growth in nature) led to methodological difficulties during isolation in culture. One species in the family Gomontiellaceae, Crinalium magnum Fritsch et John, is characterized by prominent wide and flattened trichomes, and represented by the non-authentic strain SAG 34.87. Detailed previous investigation of this strain clearly showed its morphological discrepancy with the original description of C. magnum and the genus Crinalium in general. The new isolate from maritime sand dunes of the Baltic Sea coast (Germany), however, revealed morphological characters completely corresponding with the diagnosis of C. magnum. Phylogenetic analysis based on 16S rRNA sequences indicated a position of the new strain inside Gomontiellaceae. Both morphology and ultrastructure of the strain are congruous with characters of the family. Epitypification and emendation of C. magnum are proposed since the ecology and habitat of the original strain are congruent with the type locality of this rare species (sand, Irish Sea coast, North Wales, UK). We expanded the description of C. magnum by details of the filament development and specified dimensional ranges for trichomes and cells, as well as by new data about the transversely striated structure of mucilaginous sheath.

Epilithic Chamaesiphon (Synechococcales, Cyanobacteria) species in mountain streams of the Alps-interspecific differences in photo-physiological traits

Many alpine streams inhabit conspicuous epilithic biofilms on pebbles and rocks that are formed by members of the cyanobacterial genus Chamaesiphon (Synechococcales). In the Austrian Alps, some Chamaesiphon species can even overgrow up to 70% of the surface of river rocks, and hence they must play an important but still unstudied ecological role in the organic matter flux. Since photo-biological traits have not been investigated so far, photosynthetic features, pigments, and UV-sunscreen compounds were studied in three Chamaesiphon morphospecies (C. geitleri, C. polonicus, C. starmachii). These species form conspicuously differently colored spots on cobbles and boulders in the alpine streams. While C. polonicus typically forms red crusts on flat pebble conglomerate, C. geitleri and C. starmachii are characterized by dark brown and black biofilms in the field, respectively. Photosynthesis-irradiance (PE) curves indicate that all three Chamaesiphon species have different light requirements for photosynthesis, with C. starmachii and C. polonicus preferring high and low photon fluence rates, respectively, while C. geitleri takes a position in between. This low-light requirement of C. polonicus is also reflected in ca. ten-times lower chlorophyll a, zeaxanthin, and ß-carotene concentrations, as well as in a lack of the UV-sunscreen scytonemin. All Chamaesiphon morphospecies exhibit the mycosporine-like amino acid porphyra-334. The physiological and biochemical data indicate strong intraspecific differences in photosynthetic activity and pigment patterns, which explain well the distinct preferences of the three studied Chamaesiphon morphospecies for sun-exposed or shaded habitats.