Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.

Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31T, respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fara Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31T, respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.

A georeferenced rRNA amplicon database of aquatic microbiomes from South America.

The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.

Storm impacts on phytoplankton community dynamics in lakes.

In many regions across the globe, extreme weather events such as storms have increased in frequency, intensity, and duration due to climate change. Ecological theory predicts that such extreme events should have large impacts on ecosystem structure and function. High winds and precipitation associated with storms can affect lakes via short-term runoff events from watersheds and physical mixing of the water column. In addition, lakes connected to rivers and streams will also experience flushing due to high flow rates. Although we have a well-developed understanding of how wind and precipitation events can alter lake physical processes and some aspects of biogeochemical cycling, our mechanistic understanding of the emergent responses of phytoplankton communities is poor. Here we provide a comprehensive synthesis that identifies how storms interact with lake and watershed attributes and their antecedent conditions to generate changes in lake physical and chemical environments. Such changes can restructure phytoplankton communities and their dynamics, as well as result in altered ecological function (e.g., carbon, nutrient and energy cycling) in the short- and long-term. We summarize the current understanding of storm-induced phytoplankton dynamics, identify knowledge gaps with a systematic review of the literature, and suggest future research directions across a gradient of lake types and environmental conditions.

Field evidence supports former experimental claims on the stimulatory effect of glyphosate on picocyanobacteria communities.

Glyphosate-based herbicides are the most commonly used herbicide worldwide. Although glyphosate is known to be toxic to aquatic organisms, it can also have stimulatory effects on small-size (ø <2 µm) cyanobacteria (Pcy) able to metabolize and degrade glyphosate and AMPA. Several previous experimental studies in micro- and mesocosms reported increases of Pcy abundance in response to glyphosate additions, but comparable field evidence is presently unavailable. We surveyed a large geographical area in order to collect information on Pcy abundance from lakes within the Pampa region (with over three decades of glyphosate usage) and lakes from Patagonia (with virtually no history of glyphosate usage). Fifty-two Pampean lakes and 24 Patagonian lakes were surveyed. We used three indicators of glyphosate impact: herbicide concentration, the presence of phosphonate metabolism genes (responsible for glyphosate and AMPA degradation) in environmental DNA samples, and descriptors of land use in the surrounding area of each lake. We addressed three questions: (1) is there field evidence of stimulatory effects of glyphosate on picocyanobacteria abundance? (2) is the magnitude of the effects of glyphosate in natural systems comparable to that reported under controlled experimental conditions? and (3), how do the effects of glyphosate compare to the effects of other potential environmental drivers of Pcy biomass? The collected evidence is consistent with the hypothesis that long-term agricultural practices relying on glyphosate-based technologies had important effects on freshwater microbial communities, particularly by promoting increases in picocyanobacteria abundance.

Interplay between stochastic and deterministic processes in the maintenance of alternative community states in Verrucomicrobia-dominated shallow lakes.

We analyzed the interplay between neutral and deterministic processes in maintaining contrasting alternative bacterioplankton communities through time in highly productive shallow lakes and evaluated the relevance of these processes when a regime shift from a clear to a turbid state occurred. We observed that local assembly is ruled primary deterministically, via local habitat filtering, with a secondary role of stochastic processes. We also found a hierarchy in the environmental sorting: while an unusual Verrucomicrobia dominance characterizes the three systems, local conditions limit within-bacterial community membership to closely phylogenetically related and ecologically similar taxa. These results indicate that bacterial abilities to establish in these lakes are strongly determined by their traits, and point toward special physiological adaptations to persist when these systems undergo a regime shift. Altogether, these results hint to a divergence in function among these alternative communities, mediated by major shifts in bacterial community trait structure, particularly regarding carbon use.

Alternative states drive the patterns in the bacterioplankton composition in shallow Pampean lakes (Argentina).

We assessed the influence of environmental factors in shaping the free-living bacterial community structure in a set of shallow lakes characterized by contrasting stable state patterns (clear-vegetated, inorganic-turbid and phytoplankton-turbid). Six temperate shallow lakes from the Pampa Plain (Argentina) were sampled over an annual cycle, and two fingerprinting techniques were applied: a 16S rDNA analysis was performed using denaturing gradient gel electrophoresis (DGGE) profiles, and a 16S-23S internally transcribed spacer region analysis was conducted by means of automated ribosomal intergenic spacer analysis (ARISA) profiles. Our results show that the steady state that characterized the different shallow lakes played a major role in structuring the community: the composition of free-living bacteria differed significantly between clear-vegetated, inorganic-turbid and phytoplankton-turbid shallow lakes. The state of the system was more important in determining these patterns than seasonality, geographical location or degree of hydrological connectivity. Moreover, this strong environmental control was particularly evident in the pattern observed in one of the lakes, which shifted from a clear to a turbid state over the course of the study. This lake showed a directional selection of species from a typical clear-like to a turbid-like community. The combined DGGE/ARISA approach revealed not only broad patterns among different alternative steady states, but also more subtle differences within different regimes.