The evolution of realized niches within freshwater Synechococcus

Understanding how ecological traits have changed over evolutionary time is a fundamental question in biology. Specifically, the extent to which more closely related organisms share similar ecological preferences due to phylogenetic conservation – or if they are forced apart by competition – is still debated. Here, we explored the co-occurrence patterns of freshwater cyanobacteria at the sub-genus level to investigate whether more closely related taxa share more similar niches and to what extent these niches were defined by abiotic or biotic variables. We used deep 16S rRNA gene amplicon sequencing and measured several abiotic environmental parameters (nutrients, temperature, etc.) in water samples collected over time and space in Furnas Reservoir, Brazil. We found that relatively more closely related Synechococcus (in the continuous range of 93%–100% nucleotide identity in 16S) had an increased tendency to co-occur with one another (i.e. had similar realized niches). This tendency could not be easily explained by shared preferences for measured abiotic niche dimensions. Thus, commonly measured abiotic parameters might not be sufficient to characterize, nor to predict community assembly or dynamics. Rather, co-occurrence between Synechococcus and the surrounding community (whether or not they represent true biological interactions) may be a more sensitive measure of realized niches. Overall, our results suggest that realized niches are phylogenetically conserved, at least at the sub-genus level and at the resolution of the 16S marker. Determining how these results generalize to other genera and at finer genetic resolution merits further investigation.     

Optimizing canopy‐forming algae conservation and restoration with a new herbivorous fish deterrent device

The role of herbivorous fish in threatening marine forests of temperate seas has been generally overlooked. Only recently, the scientific community has highlighted that high fish herbivory can lead to regime shifts from canopy‐forming algae to less complex turf communities. Here, we present an innovative herbivorous fish deterrent device (DeFish), which can be used for conservation and restoration of marine forests. Compared to most traditional fish exclusion systems, such as cages, the DeFish system does not need regular cleaning and maintenance, making it more cost‐efficient. Resistance of DeFish was tested by installing prototypes at different depths in the French Riviera and in Montenegro: more than 60% of the devices endured several years without maintenance, even if most of them were slightly damaged in the exposed site in Montenegro. The efficacy of DeFish in limiting fish herbivory was tested by an exclusion experiment on Cystoseira amentacea in the French Riviera. In a few months, the number of fish bite marks on the seaweed was decreased, causing a consequent increase in algal length. The device here presented has been conceived for Mediterranean canopy‐forming algae, but the same concept can be applied to other species vulnerable to fish herbivory, such as kelps or seagrasses. In particular, the DeFish design could be improved using more robust and biodegradable materials. Innovative engineering systems, such as DeFish, are expected to become useful tools in the conservation and restoration of marine forests, to complement other practices including active reforestation, herbivore regulation, and regular monitoring of their status.     

Warming counteracts defoliation‐induced mismatch by increasing herbivore‐plant phenological synchrony

Climate change is altering phenology; however, the magnitude of this change varies among taxa. Compared with phenological mismatch between plants and herbivores, synchronization due to climate has been less explored, despite its potential implications for trophic interactions. The earlier budburst induced by defoliation is a phenological strategy for plants against herbivores. Here, we tested whether warming can counteract defoliation‐induced mismatch by increasing herbivore‐plant phenological synchrony. We compared the larval phenology of spruce budworm and budburst in balsam fir, black spruce, and white spruce saplings subjected to defoliation in a controlled environment at temperatures of 12, 17, and 22°C. Budburst in defoliated saplings occurred 6–24 days earlier than in the controls, thus mismatching needle development from larval feeding. This mismatch decreased to only 3–7 days, however, when temperatures warmed by 5 and 10°C, leading to a resynchronization of the host with spruce budworm larvae. The increasing synchrony under warming counteracts the defoliation‐induced mismatch, disrupting trophic interactions and energy flow between forest ecosystem and insect populations. Our results suggest that the predicted warming may improve food quality and provide better growth conditions for larval development, thus promoting longer or more intense insect outbreaks in the future.     

On the use of adenovirus dodecahedron as a carrier for glycoconjugate vaccines

Glycoconjugate Journal - Virus-Like Particles (VLPs) have been used as immunogenic molecules in numerous recombinant vaccines. VLPs can also serve as vaccine platform to exogenous antigens, usually...     

Growth-enhanced salmon modify stream ecosystem functioning

Use of fast-growing domesticated and/or genetically modified strains of fish is becoming increasingly common in aquaculture, increasing the likelihood of deliberate or accidental introductions into the wild. To date, their ecological impacts on ecosystems remain to be quantified. Here, using a controlled phenotype manipulation by implanting growth hormone in juvenile Atlantic salmon (Salmo salar), we found that growth-enhanced fish display changes in several phenotypic traits known to be important for ecosystem functioning, such as habitat use, morphology and excretion rate. Furthermore, these phenotypic changes were associated with significant impacts on the invertebrate community and key stream ecosystem functions such as primary production and leaf-litter decomposition. These findings provide novel evidence that introductions of growth-enhanced fish into the wild can affect the functioning of natural ecosystems and represent a form of intraspecific invasion. Consequently, environmental impact assessments of growth-enhanced organisms need to explicitly consider ecosystem-level effects.     

The SSV-Seq 2.0 PCR-Free Method Improves the Sequencing of Adeno-Associated Viral Vector Genomes Containing GC-Rich Regions and Homopolymers

Adeno-associated viral vectors (AAV) are efficient engineered tools for delivering genetic material into host cells. The commercialization of AAV-based drugs must be accompanied by the development of appropriate quality control (QC) assays. Given the potential risk of co-transfer of oncogenic or immunogenic sequences with therapeutic vectors, accurate methods to assess the level of residual DNA in AAV vector stocks are particularly important. An assay based on high-throughput sequencing (HTS) to identify and quantify DNA species in recombinant AAV batches is developed. Here, it is shown that PCR amplification of regions that have a local GC content >90% and include successive mononucleotide stretches, such as the CAG promoter, can introduce bias during DNA library preparation, leading to drops in sequencing coverage. To circumvent this problem, SSV-Seq 2.0, a PCR-free protocol for sequencing AAV vector genomes containing such sequences, is developed. The PCR-free protocol improves the evenness of the rAAV genome coverage and consequently leads to a more accurate relative quantification of residual DNA. HTS-based assays provide a more comprehensive assessment of DNA impurities and AAV vector genome integrity than conventional QC tests based on real-time PCR and are useful methods to improve the safety and efficacy of these viral vectors.     

Post-Glacial Climate–Fire Interactions Control Tree Composition of Mesic Temperate Forests in Eastern North America

Stand-scale gap-phase dynamics is generally viewed as the main driver of development in mesic deciduous forests of the temperate biome. Soil charcoal of temperate forests in eastern North America are unnoticed in most surveys, thus explaining why fire is undervalued as a driver of forest succession. The extent to which gap-phase, fire, or other processes are responsible for the regeneration and maintenance of mesic deciduous forests is unknown because paleoecological evidence is lacking. We tested the fire-driven succession hypothesis on the development of this major forest type. Based on charcoal ¹⁴C dates of two sites, 44 and 55 fires occurred since early Holocene, with a mean interval of 170 to 215 years. The vegetation of both sites followed comparable post-glacial trajectories consisting of three distinct periods. Conifers dominated the two first periods during 5200–6000 years and were replaced by hardwoods–conifers over the last 3500 years. The first period was represented by boreal conifers, whereas the second period, dominated by white pine (Pinus strobus) forests, persisted during 3000–4300 years. The third period marked the development of hardwood (sugar maple, Acer saccharum) forests. Fires occurred continuously on the sites since early Holocene likely under dry conditions during the conifer periods and cooler and moister conditions during the hardwood–conifer period. Recurrent fires appear with climate as key drivers of the long-term dynamics of several temperate forests in eastern North America. Similar studies on other temperate forests should be pursued to test the hypothesis of climate–fire interactions influencing tree composition change.