Frayed at the edges: selective pressure and adaptive response to abiotic stressors are mismatched in low diversity edge populations

Theory predicts that population structure and dynamics affect a population's capacity for adaptation to environmental change. For isolated, small and fragmented populations at the trailing edge of species distributions, loss of genetic diversity through random genetic drift may reduce adaptive potential and fitness levels for complex traits. This has important consequences for understanding population responses to, for example changing climate, but has rarely been tested in natural populations. We measured the intertidal thermal environment and tidal exposure (emersion) times for natural populations of the intertidal seaweed Fucus serratus at the centre (southwest UK) and southern edge (northern Portugal) of its range in the Eastern Atlantic, and for a congener, F. vesiculosus, whose range extends further south to Morocco. Fitness-related traits of individuals at each location were measured in common garden experiments: physiological resilience to desiccation and heat shock (PSII quantum yield), and the molecular phenotype of the heat shock response (quantitative PCR of heat shock protein gene transcripts). The realized thermal environment experienced by F. serratus was similar at the centre and southern edge of its distribution because the maximum shore height (and emersion period) was reduced in southern populations. For F. vesiculosus, thermal maxima were higher and occurred more frequently in the south, although maximum vertical height (emersion time) remained similar to central populations. Edge populations of F. serratus were less resilient to desiccation and heat shock than central populations, and expression of heat shock genes was higher at the same temperature, suggesting greater cellular stress. In contrast, there was no evidence for physiological divergence in heat shock response in F. vesiculosus, and little variation in gene expression. Synthesis. We provide evidence that compared with range-centre populations upper intertidal limits of F. serratus at the southern edge are 'pruned back' by abiotic stressors. Rather than being locally adapted, these small populations are less resilient to abiotic stresses and experience greater cellular stress during heat shock. These results suggest that ongoing climate forcing factors may threaten small, fragmented rear edge populations because of inherently reduced fitness and lower adaptive capacity relative to larger central populations.Network of excellence Marine Genomics Europe (EU); FCT-FEDER; FCT-ESFinfo:eu-repo/semantics/publishedVersio

Genomic insights into aquimarina sp. strain EL33, a bacterial symbiont of the gorgonian coral eunicella labiata.

To address the metabolic potential of symbiotic Aquimarina spp., we report here the genome sequence of Aquimarina sp. strain EL33, a bacterium isolated from the gorgonian coral Eunicella labiata This first-described (to our knowledge) animal-associated Aquimarina genome possesses a sophisticated repertoire of genes involved in drug/antibiotic resistance and biosynthesis

Metagenome-assembled genome sequences of three uncultured planktomarina sp. strains from the Northeast Atlantic Ocean

We report three metagenome-assembled genomes (MAGs) of Planktomarina strains from coastal seawater (Portugal) to help illuminate the functions of understudied Rhodobacteraceae bacteria in marine environments. The MAGs encode proteins involved in aerobic anoxygenic photosynthesis and a versatile carbohydrate metabolism, strengthening the role of Planktomarina species in oceanic carbon cycling.Portuguese Foundation for Science and Technology: EXPL/MAR-EST/1664/2013 PTDC/MAR-BIO/1547/2014, UIDB/04565/2020, PD/BD/143029/2018, CEECIND/00788/2017,PTDC/BIA-MIC/31996/2017;Institute of Bioengineering and Biosciences (iBB) by the Programa Operacional Regional de Lisboa 007317; Helmholtz Association VH-NG-1248.info:eu-repo/semantics/publishedVersio

The gorgonian coral Eunicella labiata hosts a distinct prokaryotic consortium amenable to cultivation

Microbial communities inhabiting gorgonian corals are believed to benefit their hosts through nutrient provision and chemical defence; yet much remains to be learned about their phylogenetic uniqueness and cultivability. Here, we determined the prokaryotic community structure and distinctiveness in the gorgonian Eunicella labiata by Illumina sequencing of 16S rRNA genes from gorgonian and seawater metagenomic DNA. Furthermore, we used a 'plate-wash' methodology to compare the phylogenetic diversity of the 'total' gorgonian bacteriome and its 'cultivatable' fraction. With 1016 operational taxonomic units (OTUs), prokaryotic richness was higher in seawater than in E. labiata where 603 OTUs were detected, 68 of which were host-specific. Oceanospirillales and Rhodobacterales predominated in the E. labiata communities. One Oceanospirillales OTU, classified as Endozoicomonas, was particularly dominant, and closest relatives comprised exclusively uncultured clones from other gorgonians. We cultivated a remarkable 62% of the bacterial symbionts inhabiting E. labiata: Ruegeria, Sphingorhabdus, Labrenzia, other unclassified Rhodobacteraceae, Vibrio and Shewanella ranked among the 10 most abundant genera in both the cultivation-independent and dependent samples. In conclusion, the E. labiata microbiome is diverse, distinct from seawater and enriched in (gorgonian)-specific bacterial phylotypes. In contrast to current understanding, many dominant E. labiata symbionts can, indeed, be cultivated.Portuguese Foundation for Science and Technology [EXPL/MAR-EST/1664/2013, SFRH/BPD/34282/2006]German Volkswagen (VW) foundation [Az. 81 040-2]info:eu-repo/semantics/publishedVersio

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula

Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for <10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO3 uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4 degrees C range, possibly reflecting constraints on translational efficiency and protein production in cold environments.Portuguese Science Foundation (FCT) [PTDC/MAR/72630]; Spanish Ministry of Economy and Competitiveness (under the scope of the International Polar Year (IPY)) [POL2006-00550/CTM]info:eu-repo/semantics/publishedVersio

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. Results Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. Conclusion This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large.info:eu-repo/semantics/publishedVersio

Transcriptomic Analysis Reveals Insights on Male Infertility in Octopus maya Under Chronic Thermal Stress

Octopus maya endemic to the Yucatan Peninsula, Mexico, is an ectotherm organism particularly temperature-sensitive. Studies in O. maya females show that temperatures above 27°C reduce the number of eggs per spawn, fertilization rate and the viability of embryos. High temperatures also reduce the male reproductive performance and success. However, the molecular mechanisms are still unknown. The transcriptomic profiles of testes from thermally stressed (30°C) and not stressed (24°C) adult male octopuses were compared, before and after mating to understand the molecular bases involved in the low reproductive performance at high temperature. The testis paired-end cDNA libraries were sequenced using the Illumina MiSeq platform. Then, the transcriptome was assembled de novo using Trinity software. A total of 53,214,611 high-quality paired reads were used to reconstruct 85,249 transcripts and 77,661 unigenes with an N50 of 889 bp length. Later, 13,154 transcripts were annotated implementing Blastx searches in the UniProt database. Differential expression analysis revealed 1,881 transcripts with significant difference among treatments. Functional annotation and pathway mapping of differential expressed transcripts revealed significant enrichment for biological processes involved in spermatogenesis, gamete generation, germ cell development, spermatid development and differentiation, response to stress, inflammatory response and apoptosis. Remarkably, the transcripts encoding genes such as ZMYND15, KLHL10, TDRD1, TSSK2 and DNAJB13, which are linked to male infertility in other species, were differentially expressed among the treatments. The expression levels of these key genes, involved in sperm motility and spermatogenesis were validated by quantitative real-time PCR. The results suggest that the reduction in male fertility at high temperature can be related to alterations in spermatozoa development and motility

Functional divergence in heat shock response following rapid speciation of Fucus spp. in the Baltic Sea

In the Baltic Sea, the broadly distributed brown alga Fucus vesiculosus coexists in sympatry over part of its range (south west Gulf of Bothnia) with the Baltic endemic F. radicans sp. nov, while further north in colder and lower-salinity areas of the Baltic F. radicans occurs alone (north west Gulf of Bothnia). F. radicans appears to have arisen via rapid speciation from F. vesiculosus within the recent history of the Baltic (ca. 7500 BP). Possible functional divergence between the two species was investigated by comparing stress-responsive gene expression in a common-garden experiment. The experiment used two allopatric populations of Fucus vesiculosus from the Skagerrak (North Sea) and Central Baltic, as well as F. radicans from the same Central Baltic site. The two species in sympatry displayed divergent heat shock responses, while F. vesiculosus populations from allopatric sites did not. F. radicans was more sensitive to heat shock at 25°C, either alone or together with high irradiance and desiccation, than Baltic or Skagerrak F. vesiculosus. The results indicate that rapid functional divergence in the inducible heat shock response has occurred between sympatric species on a timescale of thousands of years

Rapid identification of differentially expressed genes by in situ screening of bacteria

The identification of differentially expressed genes is a key step in the understanding of specific molecular mechanisms. Various methods have been developed to search for differences in expression but most of them are time or money consuming. We present here an alternative technique that connects standard suppression subtractive hybridization with in situ screening of bacteria to isolate and identify differentially expressed transcripts. The in situ differential screening is based on the transfer of bacteria directly from cultures onto nylon membranes with no need of phenol/chloroform extraction, colony lifting, or polymerase chain reaction amplification. This improved method was successfully applied and must be seen as a simple, low-cost, time-saving, and reproducible approach to identify differentially expressed genes