Pangenome Evolution in theMarine Bacterium Alteromonas

Wehave examined a collection of the free-livingmarine bacterium Alteromonas genomeswith cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., frommicrobes that can be consideredmembers of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, itsmain expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche andmustflowfast throughout thewholegenus as they are found, withnearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.This work was funded by the Spanish MINECO (Grants BFPU2013-48007-P)This work was funded by the Generalitat Valenciana PROMETEO (Grants II/2014/012

Networking in microbes: conjugative elements and plasmids in the genus Alteromonas

Abstract Background To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time. Results We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far ( ca . 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold. Conclusion We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity

Combined floating offshore wind and solar PV

To mitigate the effects of wind variability on power output, hybrid systems that combine offshore wind with other renewables are a promising option. In this work we explore the potential of combining offshore wind and solar power through a case study in Asturias (Spain)-a region where floating solutions are the only option for marine renewables due to the lack of shallow water areas, which renders bottom-fixed wind turbines inviable. Offshore wind and solar power resources and production are assessed based on high-resolution data and the technical specifications of commercial wind turbines and solar photovoltaic (PV) panels. Relative to a typical offshore wind farm, a combined offshore wind-solar farm is found to increase the capacity and the energy production per unit surface area by factors of ten and seven, respectively. In this manner, the utilization of the marine space is optimized. Moreover, the power output is significantly smoother. To quantify this benefit, a novel Power Smoothing (PS) index is introduced in this work. The PS index achieved by combining floating offshore wind and solar PV is found to be of up to 63%. Beyond the interest of hybrid systems in the case study, the advantages of combining floating wind and solar PV are extensible to other regions where marine renewable energies are being considered

Differences in gene expression patterns between cultured and natural Haloquadratum walsbyi ecotypes

Solar crystallizer ponds are characterized by high population density with a relatively simple community structure in terms of species composition. The microbial community in the solar saltern of Santa Pola (Alicante, Spain), is largely dominated by the hyperhalophilic square archaeon Haloquadratum walsbyi. Here we studied metatranscriptomes retrieved from a crystallizer pond during the winter of 2012 and summer of 2014 and compared Hqr. walsbyi’s transcription patterns with that of the cultured strain Hqr. walsbyi HBSQ001. Significant differences were found between natural and the cultured grown strain in the distribution of transcript levels per gene. This likely reflects the adaptation of the cultured strain to the relative homogeneous growth conditions while the natural species, which is represented by multiple ecotypes, is adapted to heterogeneous environmental conditions and challenges of nutrient competition, viral attack, and other stressors. An important consequence of this study is that expression patterns obtained under artificial cultivation conditions cannot be directly extrapolated to gene expression under natural conditions. Moreover, we found 195 significantly differential expressed genes between the seasons, with 140 genes being higher expressed in winter and mainly encode proteins involved in energy and carbon source acquiring processes, and in stress responses.RR received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 818431 (SIMBA). This output reflects only the author’s view, and the European Union cannot be held responsible for any use that may be made of the information contained therein. FRV was supported by grants “VIREVO” CGL2016-76273-P [MCI/AEI/FEDER, EU] (cofounded with FEDER funds) from the Spanish Ministerio de Ciencia e Innovación and “HIDRAS3” PROMETEU/2019/009 from Generalitat Valenciana

The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective

The SAR11 clade of Alphaproteobacteria is the most abundant group of planktonic cells in the near-surface epipelagic waters of the ocean, but the mechanisms underlying its exceptional success have not been fully elucidated. Here, we applied a metagenomic approach to explore microdiversity patterns by measuring the accumulation of synonymous and nonsynonymous mutations as well as homologous recombination in populations of SAR11 from different aquatic habitats (marine epipelagic, bathypelagic, and surface freshwater). The patterns of mutation accumulation and recombination were compared to those of other groups of representative marine microbes with multiple ecological strategies that share the same marine habitat, namely, Cyanobacteria (Prochlorococcus and Synechococcus), Archaea (“Candidatus Nitrosopelagicus” and Marine Group II Thalassoarchaea), and some heterotrophic marine bacteria (Alteromonas and Erythrobacter). SAR11 populations showed widespread recombination among distantly related members, preventing divergence leading to a genetically stable population. Moreover, their high intrapopulation sequence diversity with an enrichment in synonymous replacements supports the idea of a very ancient divergence and the coexistence of multiple different clones. However, other microbes analyzed seem to follow different evolutionary dynamics where processes of diversification driven by geographic and ecological instability produce a higher number of nonsynonymous replacements and lower intrapopulation sequence diversity. Together, these data shed light on some of the evolutionary and ecological processes that lead to the large genomic diversity in SAR11. Furthermore, this approach can be applied to other similar microbes that are difficult to culture in the laboratory, but abundant in nature, to investigate the underlying dynamics of their genomic evolution.This work was supported by grants VIREVO CGL2016-76273-P (AEI/FEDER, EU) (cofunded with FEDER funds) from the Spanish Ministerio de Economía, Industria, y Competitividad and HIDRAS3 PROMETEU/2019/009 from the Generalitat Valenciana to F.R.-V. and by grants CGL2013-40564-R and SAF2013-49267-EXP from the Spanish Ministerio de Economía, Industria, y Competitividad; grant ACIF/2015/332 from the Generalitat Valenciana; and grant 5334 from the Betty Moore Foundation to M.M.-G. F.R.-V. was also a beneficiary of the 5top100-program of the Ministry for Science and Education of Russia. J.M.H.-M. was supported by a Ph.D. fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). F.H.C. was supported by a postdoctoral fellowship from the Generalitat Valenciana (APOSTD/2018/186). M.L.-P. was supported by a postdoctoral fellowship from the Spanish Ministerio de Economía, Industria, y Competitividad (IJCI-2017-34002)

Genome diversity of marine phages recovered from Mediterranean metagenomes: Size matters

Marine viruses play a critical role not only in the global geochemical cycles but also in the biology and evolution of their hosts. Despite their importance, viral diversity remains underexplored mostly due to sampling and cultivation challenges. Direct sequencing approaches such as viromics has provided new insights into the marine viral world. As a complementary approach, we analysed 24 microbial metagenomes ( > 0.2 μm size range) obtained from six sites in the Mediterranean Sea that vary by depth, season and filter used to retrieve the fraction. Filter-size comparison showed a significant number of viral sequences that were retained on the larger-pore filters and were different from those found in the viral fraction from the same sample, indicating that some important viral information is missing using only assembly from viromes. Besides, we were able to describe 1,323 viral genomic fragments that were more than 10Kb in length, of which 36 represented complete viral genomes including some of them retrieved from a cross-assembly from different metagenomes. Host prediction based on sequence methods revealed new phage groups belonging to marine prokaryotes like SAR11, Cyanobacteria or SAR116. We also identified the first complete virophage from deep seawater and a new endemic clade of the recently discovered Marine group II Euryarchaeota virus. Furthermore, analysis of viral distribution using metagenomes and viromes indicated that most of the new phages were found exclusively in the Mediterranean Sea and some of them, mostly the ones recovered from deep metagenomes, do not recruit in any database probably indicating higher variability and endemicity in Mediterranean bathypelagic waters. Together these data provide the first detailed picture of genomic diversity, spatial and depth variations of viral communities within the Mediterranean Sea using metagenome assemblyThis work was supported by projects MEDIMAX BFPU2013-48007-P, VIREVO CGL2016- 76273-P [AEI/FEDER, EU], (cofunded with FEDER funds) and Acciones de dinaminación REDES DE EXCELENCIA CONSOLIDER CGL2015-71523- REDC, from the Spanish Ministerio de Economía y Competitividad; and project AQUAMET PROMETEOII/2014/012 from Generalitat Valenciana. JMHM was supported with a PhD fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). MLP was supported with a Postdoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (APOSTD/2016/051). RGS was supported with a Predoctoral fellowship from the Valencian Consellería de Educació Investigació, Cultura i Esport (ACIF/2016/050

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise

Interactions between co-existing microorganisms deeply affect the physiology of the involved organisms and, ultimately, the function of the ecosystem as a whole. Copiotrophic Alteromonas are marine gammaproteobacteria that thrive during the late stages of phytoplankton blooms in the marine environment and in laboratory co-cultures with cyanobacteria such as Trichodesmium. The response of this heterotroph to the sometimes rapid and transient changes in nutrient supply when the phototroph crashes is not well understood. Here, we isolated and sequenced the strain Alteromonas macleodii str. Te101 from a laboratory culture of Trichodesmium erythraeum IMS101, yielding a chromosome of 4.63 Mb and a single plasmid of 237 kb. Increasing salinities to ≥43 ppt inhibited the growth of Trichodesmium but stimulated growth of the associated Alteromonas. We characterized the transcriptomic responses of both microorganisms and identified the complement of active transcriptional start sites in Alteromonas at single-nucleotide resolution. In replicate cultures, a similar set of genes became activated in Alteromonas when growth rates of Trichodesmium declined and mortality was high. The parallel activation of fliA, rpoS and of flagellar assembly and growth-related genes indicated that Alteromonas might have increased cell motility, growth, and multiple biosynthetic activities. Genes with the highest expression in the data set were three small RNAs (Aln1a-c) that were identified as analogs of the small RNAs CsrB-C in E. coli or RsmX-Z in pathogenic bacteria. Together with the carbon storage protein A (CsrA) homolog Te101_05290, these RNAs likely control the expression of numerous genes in responding to changes in the environmentThis work was supported by the EU project MaCuMBA (grant agreement no. 311975) to WRH and FRVby the German Israeli Foundation grant no. 1133 to IB-F and WRHSupport of ML-P by a postdoctoral fellowship from the Valencian Consellería de Educació, Investigació, Cultura i Esport (APOSTD/2016/051)of SH by the China Scholarship Council is gratefully acknowledged

Salt lakes of La Mancha (Central Spain): A hot spot for tiger beetle (Carabidae, Cicindelinae) species diversity

The tiger beetle assemblage of the wetlands of La Mancha (central Spain) comprises nine species: Calomera littoralis littoralis, Cephalota maura maura, Cephalota circumdata imperialis, Cephalota dulcinea, Cicindela campestris campestris, Cicindela maroccana, Cylindera paludosa, Lophyra flexuosa flexuosa, and Myriochila melancholica melancholica. This assemblage represents the largest concentration of tiger beetles in a single 1º latitude / longitude square in Europe. General patterns of spatial and temporal segregation among species are discussed based on observations of 1462 specimens registered during an observation period of one year, from April to August. The different species of Cicindelini appear to be distributed over space and time, with little overlapping among them. Three sets of species replace each other phenologically as the season goes on. Most of the species occupy drying or dried salt lakes and salt marshes, with sparse vegetation cover. Spatial segregation is marked in terms of substrate and vegetation use. Calomera littoralis and M. melancholica have been observed mainly on wet soils; C. circumdata on dry open saline flats; C. dulcinea and C. paludosa in granulated substrates with typical halophytic vegetation; C. maura is often present in man-modified areas. Cephalota circumdata and C. dulcinea are included as species of special interest in the list of protected species in Castilla–La Mancha. Conservation problems for the Cicindelini assemblage arise from agricultural activities and inadequate use of sport vehicles. Attempts at restoring the original habitat, supressing old semi-industrial structures, may affect the spatial heterogeneity of the lakes, and have an effect on Cicindelinae diversity.This study was possible thanks to the support from the Fundación Global Nature through the European Life European Community Project Humedales de La Mancha (LIFE10 NAT/ES/000563), Spanish Ministry of Agriculture, Food and Environment and to the facilities provided by the Museo Nacional de Ciencias Naturales (MNCN-CSIC).Peer reviewe

Phenotyping Ex-Combatants From EEG Scalp Connectivity

Being involved in war experiences may have severe consequences in mental health. This exposure has been associated in Colombian ex-combatants with risk of proactive aggression modulating emotional processing. However, the extent of the cognitive processes underlying aggressive behavior is still an open issue. In this work, we propose a SVM-based processing pipeline to identify different cognitive phenotypes associated with atypical emotional processing, based on canonical correlation analysis of EEG network features, and cognitive and behavioral evaluations. Results show the existence of cognitive phenotypes associated with differences in the mean value of leaf fraction and diameter of EEG networks across groups. The ability of identifying phenotypes in these otherwise healthy subjects opens up the possibility to aid in the development of specific interventions aimed to reduce expression of proactive aggression in ex-combatants and assessing the efficacy of such interventions