Stream hydrological fragmentation drives bacterioplankton community composition

In Mediterranean intermittent streams, the hydrological fragmentation in summer and the successive water flow reconvergence in autumn allow exploring how local processes shape the microbial community within the same habitat. The objectives of this study were to determine how bacterial community composition responded to hydrological fragmentation in summer, and to evaluate whether the seasonal shifts in community composition predominate over the effects of episodic habitat fragmentation. The bacterial community was assessed along the intermittent stream Fuirosos (Spain), at different levels of phylogenetic resolution by in situ hybridization, fingerprinting, and 16S rRNA gene sequencing. The hydrological fragmentation of the stream network strongly altered the biogeochemical conditions with the depletion of oxidized solutes and caused changes in dissolved organic carbon characteristics. In the isolated ponds, beta-Proteobacteria and Actinobacteria increased their abundance with a gradual reduction of the alpha-diversity as pond isolation time increased. Moreover, fingerprinting analysis clearly showed a shift in community composition between summer and autumn. In the context of a seasonal shift, the temporary stream fragmentation simultaneously reduced the microbial dispersion and affected local environmental conditions (shift in redox regime and quality of the dissolved organic matter) tightly shaping the bacterioplankton community composition

Effect of Saharan dust inputs on bacterial activity and community composition in Mediterranean lakes and reservoirs

11 páginas, 5 tablas, 6 figuras.We assessed the effects of Saharan dust inputs of particulate matter (PM), total phosphorus (TP), total nitrogen, and water soluble organic carbon (WSOC) on bacterial abundance (BA) in two alpine lakes and two reservoirs in the Mediterranean region. We also experimentally assessed the effects of dust inputs on bacterial activity and community composition and explored the presence of airborne bacteria. We found synchronous BA dynamics at least in one of the study years for each corresponding pair of ecosystems, suggesting an external control. The link between BA dynamics and inputs of PM, WSOC, or TP occurred only in those ecosystems with severe P-limitation and low dissolved organic carbon. The response was most intense in the most P-limited ecosystem. Dust addition had a significant positive effect on bacterial growth and abundance, but not on richness, diversity, or composition of the indigenous bacterial assemblages. We also obtained experimental evidence that some airborne bacteria could develop in oligotrophic waters by observing the growth of gamma-proteobacteria, a group poorly represented in natural aquatic environments.This research was supported by the projects ECOSENSOR (Fundación BBVA, BIOCON04/009) and MICROBIOGEOGRAPHY (080-2007) to IR, REN03-03038 (Ministerio de Ciencia y Tecnologı´a) to RMB, and AERBAC (079-2007) to EOC, FPU (Formacio´n del Profesorado Universitario), and FPI (Formacio´n del Personal Investigador) grants from Spanish Government to E. Ortega-Retuerta, E. Pulido-Villena, and O. Romera.Peer reviewe

Morfospecies and zOTUs interacting with each host plant from the PERDIVER project

[Description of methods used for collection/generation of data] For Morphospecies_abundance.csv: Aerial sampling, Berlese sampling, cafeteria experiments, vacuuming sampling, shake sampling. For zOTU_Abundance.csv: DNA extraction was carried out with 0.05-0.1 grams of root material using a Mobio PowerSoil DNA Isolation Kit (Mobio Laboratories). PCR and sequencing of the 16 rRNA gene was done with Illumina MiSeq (NGS) following the methods from the central genomic services of RTSF-MSU (Michigan State University, USA) (https://rtsf.natsci.msu.edu/). We analyzed the V4 variable region of the 16S rRNA gene (250 nucleotides) using primers F515 (5'-GTGCCAGCMGCCGCGGTAA-3') and R806 (5'-GGACTACHVGGGTWTCTAAT-3'). Raw rRNA gene sequences were processed using the UPARSE pipeline (Edgar, 2013) to identify zOTUS (zero-radius operational taxonomic units). Taxonomic assignment used the naive Bayes scikit-learn classifier implemented in QIIME2 (Caporaso et al., 2010) and the SILVA 132 database (Quast et al., 2012). Chloroplast, mitochondrial, and unclassified sequences were excluded from further analyses. For PERDIVER_Alpha_diversity.csv: Multiple diversity metrics using R. For each community associated with each plant species: Species richnes, Shannon and Simpson diversity indices and standard effect size of the phylogenetic mean pairwise distance between species in the community (mpd.obs.z). Above ground phylogenetic distances come from Chesters, D. (2020), The phylogeny of insects in the data-driven era. Syst Entomol, 45: 540-551. Belowground distances from QIIME2 (Caporaso, J., Kuczynski, J., Stombaugh, J. et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336 (2010).) and the SILVA 128 reference database (Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012). The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590–D596.)Data from the PERDIVER and INTERACTOMA projects. The goal of the projects was to characterize the communities of species that interact with seven rare or endangered plants in Aragón and if those communities changed between isolated and non-isolated plant populations. The aboveground was surveyed in 2016, 2017, and 2018 during the flowering season of the host plant. All individual animals, visiting any part of flowering and non-flowering plants over an area covered visually by the observer were either visually identified or sampled, if needed to confirm identification. All animals trapped by the sticky leaves of pinlon were also identified. Sampling area and length of surveys varied among plant species, depending on size of plants and frequency of interactions, but ≥ 20 surveys were performed at each site, resulting in a total of > 9,000 minutes and 638 surveys. Sampling investment varied among plant species, because they differed in interaction detectability. However, sampling effort was always similar among patches of the same plant species. Other methods like Berlese funnnel traps, fruit sampling or cafeteria experiments were used to unveil interactions that are not easily visible, like those by small or camouflaged animals. Below ground microbial communities were characterized for each plant population with three samples composed of root material from different individuals.PERDIVER Project (Fundación BBVA). INTERACTOMA Project RTI2018-101205-B-I00.Morphospecies_abundance.csv zOTU_Abundance.csv PERDIVER_Alpha_diversity.csvPeer reviewe