Elevated micro-topography boosts growth rates in <i>Salicornia procumbens</i> by amplifying a tidally driven oxygen pump:Implications for natural recruitment and restoration

• Background and Aims: The growth rate of pioneer species is known to be a critical component determining recruitment success of marsh seedlings on tidal flats. By accelerating growth, recruits can reach a larger size at an earlier date, which reduces the length of the disturbance-free window required for successful establishment. Therefore, the pursuit of natural mechanisms that accelerate growth rates at a local scale may lead to a better understanding of the circumstances under which new establishment occurs, and may suggest new insights with which to perform restoration. This study explores how and why changes in local sediment elevation modify the growth rate of recruiting salt marsh pioneers. • Methods: A mesocosm experiment was designed in which the annual salt marsh pioneer Salicornia procumbens was grown over a series of raised, flat and lowered sediment surfaces, under a variety of tidal inundation regimes and in vertically draining or un-draining sediment. Additional physical tests quantified the effects of these treatments on sediment water-logging and oxygen dynamics, including the use of a planar optode experiment. • Key Results: In this study, the elevation of sediment micro-topography by 2 cm was the overwhelming driver of plant growth rates. Seedlings grew on average 25 % faster on raised surfaces, which represented a significant increase when compared to other groups. Changes in growth aligned well with the amplifying effect of raised sediment beds on a tidally episodic oxygenation process wherein sediment pore spaces were refreshed by oxygen-rich water at the onset of high tide. • Conclusions: Overall, the present study suggests this tidally driven oxygen pump as an explanation for commonly observed natural patterns in salt marsh recruitment near drainage channels and atop raised sediment mounds and reveals a promising way forward to promote the establishment of pioneers in the field

Growth forms and life-history strategies predict the occurrence of aquatic macrophytes in relation to environmental factors in a shallow peat lake complex

Aquatic ecosystems provide vital services, and macrophytes play a critical role in their functioning. Conceptual models indicate that in shallow lakes, plants with different growth strategies are expected to inhabit contrasting habitats. For shallow peat lakes, characterized by incohesive sediments, roles of growth forms, life-history strategies and environmental factors in determining the occurrence of aquatic vegetation remain unknown. In a field survey, we sampled 64 points in a peat lake complex and related macrophyte occurrence to growth forms (floating-leaved rooted and submerged), life-history strategies for overwintering (turions, seeds, rhizomes) and environmental factors (water depth, fetch, and porewater nutrients). Our survey showed that macrophyte occurrence relates to water depth, wind-fetch, and nutrients, and depends on growth form and life-history strategies. Specifically, rooted floating-leaved macrophytes occur at lower wind-fetch/shallower waters. Submerged macrophytes occur from low to greater wind-fetch/water depth, depending on life-history strategies; macrophytes with rhizomes occur at greater wind-fetch/depth relative to species that overwinter with seeds or turions. We conclude that growth form and life-history strategies for overwintering predict macrophytes occurrence regarding environmental factors in peat lakes. Therefore, we propose an adapted model for macrophyte occurrence for such lakes. Altogether, these results may aid in species-selection to revegetate peat lakes depending on its environment

Life cycle informed restoration:Engineering settlement substrate material characteristics and structural complexity for reef formation

Ecosystems are degrading world-wide, with severe ecological and economic consequences. Restoration is becoming an important tool to regain ecosystem services and preserve biodiversity. However, in harsh ecosystems dominated by habitat-modifying organisms, restoration is often expensive and failure prone. Establishment of such habitat modifiers often hinges on self-facilitation feedbacks generated by traits that emerge when individuals aggregate, causing density- or patch size-dependent establishment thresholds. To overcome these thresholds, adult or juvenile habitat-forming species are often transplanted in clumped designs, or stress-mitigating structures are deployed. However, current restoration approaches focus on introducing or facilitating a single life stage, while many habitat modifiers experience multiple bottlenecks throughout their life as they transition through sequential life stages. Here, we define and experimentally test ‘life cycle informed restoration’, a restoration concept that focuses on overcoming multiple bottlenecks throughout the target species’ lifetime. To provide proof of concept, and show its general applicability, we carried out complementary experiments in intertidal soft-sediment systems in Florida and the Netherlands where oysters and mussels act as reef-building habitat modifiers. We used biodegradable structures designed to facilitate bivalve reef recovery by both stimulating settlement with hard and fibrous substrates and post-settlement survival by reducing predation. Our trans-Atlantic experiments demonstrate that these structures enabled bivalve reef formation by: (a) facilitating larval recruitment via species-specific settlement substrates, and (b) enhancing post-settlement survival by lowering predation. In the Netherlands, structures with coir rope most strongly facilitated mussels by providing fibrous settlement substrate, and predation-lowering spatially complex hard attachment substrate. In Florida, oysters were greatly facilitated by hard substrates, while coir rope proved unbeneficial. Synthesis and applications. Our findings demonstrate that artificial biodegradable reefs can enhance bivalve reef restoration across the Atlantic by mimicking emergent traits that ameliorate multiple bottlenecks over the reef-forming organism’ life cycle. This highlights the potential of our approach as a cost-effective and practical tool for nature managers to restore systems dominated by habitat modifiers whose natural recovery is hampered by multiple life stage-dependent bottlenecks. Therefore, investment in understanding how to achieve life cycle informed restoration on larger scales and whether the method it is applicable to restore other ecosystems is now required

Early indicators of tidal ecosystem shifts in estuaries

Forecasting transitions between tidal ecosystem states, such as between bare tidal flats and vegetated marshes, is crucial because it may imply the irreversible loss of valuable ecosystem services. In this study, we combine geospatial analyses of three European estuaries with a simple numerical model to demonstrate that the development of micro-topographic patterning on tidal flats is an early indicator of marsh establishment. We first show that the development of micro-topographic patterns precedes vegetation establishment, and that patterns tend to form only on tidal flats with a slope of <0.3 degrees. Numerical modelling then provides an explanation for the formation of micro-topography due to the natural concentration of draining surface water over very gentle slopes. We find this early indicator to be robust across three estuaries where anthropogenic deepening and narrowing has occurred in recent decades, which may suggest its broader applicability to other estuaries with similar morphological management

Best practice guidelines for cetacean tagging

Animal-borne electronic instruments (tags) are valuable tools for collecting information on cetacean physiology, behaviour and ecology, and for enhancing conservation and management policies for cetacean populations. Tags allow researchers to track the movement patterns, habitat use andother aspects of the behaviour of animals that are otherwise difficult to observe. They can even be used to monitor the physiology of a tagged animal within its changing environment. Such tags are ideal for identifying and predicting responses to anthropogenic threats, thus facilitating the development of robust mitigation measures. With the increasing need for data best provided by tagging and the increasing availability of tags, such research is becoming more common. Tagging can, however, pose risks to the health and welfare of cetaceans and to personnel involved in tagging operations. Here we provide ‘best practice’ recommendations for cetacean tag design, deployment and follow-up assessment of tagged individuals, compiled by biologists and veterinarians with significant experience in cetacean tagging. This paper is intended to serve as a resource to assist tag users, veterinarians, ethics committees and regulatory agency staff in the implementation of high standards of practice, and to promote the training of specialists in this area. Standardised terminology for describing tag design and illustrations of tag types and attachment sites are provided, along with protocols for tag testing and deployment (both remote and through capture-release), including training of operators. The recommendations emphasise the importance of ensuring that tagging is ethically and scientifically justified for a particular project and that tagging only be used to address bona fide research or conservation questions that are best addressed with tagging, as supported by an exploration of alternative methods. Recommendations are provided for minimising effects on individual animals (e.g. through careful selection of the individual, tag design and implant sterilisation) and for improving knowledge of tagging effects on cetaceans through increased post-tagging monitoring.Publisher PDFPeer reviewe

Initiating and upscaling mussel reef establishment with life cycle informed restoration:Successes and future challenges

Worldwide, coastal ecosystems are rapidly degrading in quality and extent. While novel restoration designs include facilitation to enhance restoration success in stressful environments, they typically focus on a single life-stage, even though many organisms go through multiple life-stages accompanied by different bottlenecks. A new approach – life cycle informed restoration – was designed to ameliorate multiple bottlenecks throughout an organism's life cycle. It has successfully been tested on a small scale to facilitate intertidal bivalve reef formation in the Netherlands and Florida. Yet, it remains unknown whether this approach can be scaled to ecosystem-relevant scales. To test whether life cycle informed restoration is upscalable, we conducted a large-scale restoration experiment using blue mussel reefs as a model system. In our experiment, we used biodegradable structures to temporarily facilitate mussel reef formation by providing early-life settlement substrates, and subsequently, reduce post-settlement predation on an intertidal flat in the Wadden Sea, the Netherlands. The structures were placed in 10 × 20 m plots, mimicking bands found in natural mussel beds, spread out across 650 m, and were followed for two years. Our results show that the structures enhance mussel biomass (0.7 ± 0.2 kg DW m−2), as mussels were absent in bare plots. However, biomass varied within plots; in intact structures it was 60 times higher (1.2 ± 0.2 kg DW m−2) than in those that became buried (0.02 ± 0.009 kg DW m−2). Next to burial, 18–46% of the structures were lost due to technical failure, especially during winters at this exposed site. We show that the life cycle informed restoration principle works, but we encountered technical challenges due to larger scale processes (e.g. sedimentation). Furthermore, environmental information is essential for site selection, and for restoration, the functioning of such structures should be tested under extreme conditions before upscaling

Mimicry of emergent traits amplifies coastal restoration success

Contains fulltext : 221224.pdf (publisher's version ) (Open Access

Identification of constrained sequence elements across 239 primate genomes

Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in the human genome3–9. Identifying the genomic elements that have become constrained specifically in primates has been hampered by the faster evolution of noncoding DNA compared to protein-coding DNA10, the relatively short timescales separating primate species11, and the previously limited availability of whole-genome sequences12. Here we construct a whole-genome alignment of 239 species, representing nearly half of all extant species in the primate order. Using this resource, we identified human regulatory elements that are under selective constraint across primates and other mammals at a 5% false discovery rate. We detected 111,318 DNase I hypersensitivity sites and 267,410 transcription factor binding sites that are constrained specifically in primates but not across other placental mammals and validate their cis-regulatory effects on gene expression. These regulatory elements are enriched for human genetic variants that affect gene expression and complex traits and diseases. Our results highlight the important role of recent evolution in regulatory sequence elements differentiating primates, including humans, from other placental mammals

Epithelial-Mesenchymal Transition in Cancer: Parallels Between Normal Development and Tumor Progression

From the earliest stages of embryonic development, cells of epithelial and mesenchymal origin contribute to the structure and function of developing organs. However, these phenotypes are not always permanent, and instead, under the appropriate conditions, epithelial and mesenchymal cells convert between these two phenotypes. These processes, termed Epithelial-Mesenchymal Transition (EMT), or the reverse Mesenchymal-Epithelial Transition (MET), are required for complex body patterning and morphogenesis. In addition, epithelial plasticity and the acquisition of invasive properties without the full commitment to a mesenchymal phenotype are critical in development, particularly during branching morphogenesis in the mammary gland. Recent work in cancer has identified an analogous plasticity of cellular phenotypes whereby epithelial cancer cells acquire mesenchymal features that permit escape from the primary tumor. Because local invasion is thought to be a necessary first step in metastatic dissemination, EMT and epithelial plasticity are hypothesized to contribute to tumor progression. Similarities between developmental and oncogenic EMT have led to the identification of common contributing pathways, suggesting that the reactivation of developmental pathways in breast and other cancers contributes to tumor progression. For example, developmental EMT regulators including Snail/Slug, Twist, Six1, and Cripto, along with developmental signaling pathways including TGF-β and Wnt/β-catenin, are misexpressed in breast cancer and correlate with poor clinical outcomes. This review focuses on the parallels between epithelial plasticity/EMT in the mammary gland and other organs during development, and on a selection of developmental EMT regulators that are misexpressed specifically during breast cancer