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Abstract Background The backbone of the eukaryotic tree of life contains taxa only found in molecular surveys, of which we still have a limited understanding. Such is the case of Picozoa, an enigmatic lineage of heterotrophic picoeukaryotes within the supergroup Archaeplastida, which has emerged as a significant component of marine microbial planktonic communities. To enhance our understanding of the diversity, distribution, and ecology of Picozoa, we conduct a comprehensive assessment at different levels, from assemblages to taxa, employing phylogenetic analysis, species distribution modeling, and ecological niche characterization. Results Picozoa was among the ten most abundant eukaryotic groups, found almost exclusively in marine environments. The phylum was represented by 179 Picozoa’s OTU (pOTUs) placed in five phylogenetic clades. Picozoa community structure had a clear latitudinal pattern, with polar assemblages tending to cluster separately from non-polar ones. Based on the abundance and occupancy pattern, the pOTUs were classified into four categories: Low-abundant, Widespread, Polar, and Non-polar. We calculated the ecological niche of each of these categories. Notably, pOTUs sharing similar ecological niches were not closely related species, indicating a phylogenetic overdispersion in Picozoa communities. This could be attributed to competitive exclusion and the strong influence of the seasonal amplitude of variations in environmental factors, such as temperature, shaping physiological and ecological traits. Conclusions Overall, this work advances our understanding of uncharted protists’ evolutionary dynamics and ecological strategies. Our results highlight the importance of understanding the species-level ecology of marine heteroflagellates like Picozoa. The observed phylogenetic overdispersion challenges the concept of phylogenetic niche conservatism in protist communities, suggesting that closely related species do not necessarily share similar ecological niches. Video Abstract

Measurement(s) taxonomic diversity assessment by targeted gene survey Technology Type(s) next generation DNA sequencing Sample Characteristic - Organism Bacteria • Archaea Sample Characteristic - Environment aquatic environment Sample Characteristic - Location South America

Abstract Background Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data. Results Overall, freshwater strains had larger genomes (≈2.9 Mb) and %GC content (≈64%) compared to brackish (2.69 Mb and 64%) and marine (2.5 Mb and 58.5%) isolates. Genomic novelties/differences across the salinity divide highlighted acidic proteomes and specific salt adaptation pathways in marine isolates (e.g., osmolytes/compatible solutes - glycine betaine/ggp/gpg/gmg clusters and glycerolipids glpK/glpA), while freshwater strains possessed distinct ion/potassium channels, permeases (aquaporin Z), fatty acid desaturases, and more neutral/basic proteomes. Sulfur, nitrogen, phosphorus, carbon (photosynthesis), or stress tolerance metabolism while showing distinct genomic footprints between habitats, e.g., different types of transporters, did not obviously translate into major functionality differences between environments. Brackish microbes show a mixture of marine (salt adaptation pathways) and freshwater features, highlighting their transitional nature. Conclusions The plethora of freshwater isolates provided here, in terms of trophic status preference and genetic diversity, exemplifies their ability to colonize ecologically diverse waters across the globe. Moreover, a trend towards larger and more flexible/adaptive genomes in freshwater picocyanobacteria may hint at a wider number of ecological niches in this environment compared to the relatively homogeneous marine system.

El bacterioplancton es un componente esencial en el funcionamiento de los ecosistemas acuáticos y tiene un profundo impacto en la calidad del agua de los sistemas. Por lo tanto, es importante ampliar el conocimiento sobre su dinámica y diversidad genética. Los objetivos del presente estudio fueron evaluar la estructura y la dinámica del bacterioplancton en cuatro lagunas pertenecientes a la Región Pampeana, ubicadas en la cuenca superior (Gómez, Carpincho) e inferior (Chascomús, El Triunfo) del río Salado, y también analizar la influencia de los factores ambientales y espaciales sobre estas comunidades. Para ello se realizaron muestreos estacionales durante un año (enero 2015-enero 2016) en los que se analizaron parámetros limnológicos y la estructura del bacterioplancton mediante secuenciación masiva del gen 16s ARN ribosomal con la plataforma Illumina MiSeq. Los índices de diversidad resultaron significativamente mayores en las lagunas de la cuenca superior, en comparación con las lagunas de la cuenca inferior. La riqueza fue significativamente más baja en la laguna de régimen claro y desconectada del río (El Triunfo), en comparación con el resto de las lagunas de régimen turbio y conectadas al río (Gómez, Carpincho y Chascomús). La composición resultó diferente entre todas las lagunas, excepto entre aquellas interconectadas y cercanas (Gómez y Carpincho). Variables ambientales como el fósforo total, la conductividad eléctrica y Secchi influyeron en la composición del bacterioplancton de las lagunas estudiadas. Asimismo, la similitud en la composición del bacterioplancton se incrementó significativamente con el aumento de la similitud ambiental de las lagunas, y disminuyó con la distancia espacial entre ellas. Los resultados evidencian una variación sustancial en la estructura comunitaria entre los sistemas estudiados, explicada tanto por factores ambientales como espaciales. La estructura bacteriana no solo varió entre cuencas, sino también entre sistemas con diferentes regímenes o conexiones al río.

To study (16S rRNA-sequencing) the impact of gestational and corrected ages on the microbiota profile of human milk (HM) of mothers that delivered full-term and pre-term children, HM samples were obtained and classified according to the gestational age as group T (full-term births ≥37 weeks), and group P (pre-term births Staphylococcus and higher levels of Rothia and Streptococcus, as compared to group P. The alpha Simpson diversity value was higher in group T than in P, whereas no differences were found between groups T and PT, suggesting a microbial evolution of the composition of group P towards group T over chronological age. Full-term delivery was associated with a greater diversity of microbes in HM. The microbial composition of pre-term HM, at the corrected age, did not show significant differences, as compared to the samples obtained from the full-term group, suggesting that it would be appropriate to consider the corrected age in terms of the composition and the diversity of the milk in future studies.