Towards an acoustic‐based coupled observation and modelling system for monitoring and predicting ecosystem dynamics of the open ocean

Assessment of open‐ocean ecosystems relies on understanding ecosystem dynamics, and development of end‐to‐end ecosystem models represents an approach that addresses these challenges. These models incorporate the population structure and dynamics of marine organisms at all trophic levels. Satellite remote sensing of ocean colour and direct at‐sea measurements provide information on the lower trophic levels of the models, and fisheries studies provide information on top predator species. However, these models suffer from a lack of observations for the so‐called mid‐trophic levels, which are poorly sampled by conventional methods. This restricts further development, and we argue that acoustic observations from a range of platforms (e.g. buoys, moorings) can be linked to the ecosystem models to provide much‐needed information on these trophic levels. To achieve this, the models need to be tailored to incorporate the available acoustic data, and the link from acoustic backscatter to biologically relevant variables (biomass, carbon, etc.) needs attention. Methods to progress this issue are proposed, including the development of observation models and focal areas for ground truthing. To ensure full use of the potential of acoustic techniques, we argue that a systematic and long‐term strategy incorporating the following elements is required: development of metadata standards and automated data analysis, inclusion of acoustic sensors in large‐scale observatory programmes, improvement of observation‐model links, and efficient sampling strategies. Finally, these elements should be tied together in an observation‐modelling framework, coordinated by international organizations, to improve our understanding and quantification of open‐ocean ecosystem dynamics.     

1H NMR quantitative determination of photosynthetic pigments from green beans (Phaseolus vulgaris L.)

Using 1H nuclear magnetic resonance spectroscopy (1D and 2D), the two types of photosynthetic pigments (chlorophylls, their derivatives, and carotenoids) of "green beans" (immature pods of Phaseolus vulgaris L.) were analyzed. Compared to other analytical methods (light spectroscopy or chromatography), 1H NMR spectroscopy is a fast analytical way that provides more information on chlorophyll derivatives (allomers and epimers) than ultraviolet-visible spectroscopy. Moreover, it gives a large amount of data without prior chromatographic separation.     

Temperate and boreal forest tree phenology: from organ-scale processes to terrestrial ecosystem models

Key message

We demonstrate that, beyond leaf phenology, the phenological cycles of wood and fine roots present clear responses to environmental drivers in temperate and boreal trees. These drivers should be included in terrestrial ecosystem models.

Context

In temperate and boreal trees, a dormancy period prevents organ development during adverse climatic conditions. Whereas the phenology of leaves and flowers has received considerable attention, to date, little is known regarding the phenology of other tree organs such as wood, fine roots, fruits, and reserve compounds.

Aims

Here, we review both the role of environmental drivers in determining the phenology of tree organs and the models used to predict the phenology of tree organs in temperate and boreal forest trees.

Results

Temperature is a key driver of the resumption of tree activity in spring, although its specific effects vary among organs. There is no such clear dominant environmental cue involved in the cessation of tree activity in autumn and in the onset of dormancy, but temperature, photoperiod, and water stress appear as prominent factors. The phenology of a given organ is, to a certain extent, influenced by processes in distant organs.

Conclusion

Inferring past trends and predicting future trends of tree phenology in a changing climate requires specific phenological models developed for each organ to consider the phenological cycle as an ensemble in which the environmental cues that trigger each phase are also indirectly involved in the subsequent phases. Incorporating such models into terrestrial ecosystem models (TEMs) would likely improve the accuracy of their predictions. The extent to which the coordination of the phenologies of tree organs will be affected in a changing climate deserves further research.

     

Managerial practices and factors influencing reproductive performance of dairy cows in urban/peri-urban areas of Kampala and Gulu,Uganda

Background

Urban/peri-urban dairy production and sales has evolved as an adjustment to cope with food security and economic needs for urban dwellers in low-income countries and created an opportunity to transform from subsistence rural lifestyles of dairy farming to commercial engagement in towns. However, urban/peri-urban dairy farms differ in challenges from rural dairy farms and reproduction is important and critical for assuring sustainable economic output in both environments. Here we recorded for the first time differences between two geographically and economically different cities corresponding to different settings within the same country in managerial factors influencing reproductive performance in urban/peri-urban dairy cowherds.

Results

The urban/peri-urban dairy farmers in the capital Kampala were more often male (P = 0.002) and commercialized (P = 0.0025), more experienced (P = 0.0001) and practiced zero-grazing more often (P = 0.05) than in the regional municipality Gulu. Also, the milk production per herd and cow (P = 0.0005) and calving rate were (P = 0.0001) higher in Kampala and artificial insemination was more commonly (P = 0.002) used than in Gulu. There was no difference in abortion nor neonatal mortality rate between the two locations. Overall, calving rates were higher (P = 0.0003) in smaller (≤3 dairy cows) and open grazing (P = 0.003) herds. Abortion rates were higher among dairy herds practicing late (≥5 months) (P = 0.003) calf weaning and in herds with commercial purposes (P = 0.0001). Neonatal calf mortality was lower (P = 0.01) in small herds.

Conclusion

The study showed significant differences between Kampala and Gulu in reproductive performance and related husbandry factors for cows in the urban/peri-urban dairy farming systems. For several reproductive performance traits we found associations with husbandry and production traits, which should be taken into account when providing advice to the urban and peri-urban dairy farmers in the tropics.     

Alterins Produced by Oyster-Associated Pseudoalteromonas Are Antibacterial Cyclolipopeptides with LPS-Binding Activity

Discovery after discovery, host-associated microbiota reveal a growing list of positive effects on host homeostasis by contributing to host nutrition, improving hosts’ immune systems and protecting hosts against pathogens. In that context, a collection of oyster associated bacteria producing antibacterial compounds have been established to evaluate their role in non-host-derived immunity. Here, we described alterins; potent anti-Gram negative compounds produced by Pseudoalteromonas hCg-6 and hCg-42 isolated from different healthy oyster hemolymph. The strains hCg-6 and hCg-42 produce a set of at least seven antibacterial compounds, ranging from 926 to 982 Da structurally characterized as cyclolipopeptides (CLPs). Alterins share the same cationic heptapeptidic cycle connected via an amido bond to different hydrophobic hydrocarbon tails. Their MICs disclosed a potent antibacterial activity directed against Gram-negative bacteria including oyster and human pathogens that may confer a beneficial defense mechanism to the host but also represents an untapped source of new antibiotics. The alterins’ mechanisms of action have been deciphered: after binding to lipopolysaccharides (LPS), alterins provoke a membrane depolarization and permeabilization leading to bacterial lysis. As hCg-6 and hCg-42 produced a set of natural derivatives, the structure/activity relationship linked to the carbon tail is clarified. We showed that the hydrocarbon tail determines the LPS-binding properties of alterins and consequently their antibacterial activities. Its length and saturation seem to play a major role in this interaction.     

Monitoring potato seed lots to control blackleg in fields in Switzerland and southern Germany

Potato blackleg is a seedborne disease that can cause significant economic losses for growers. Disease development depends mainly on two drivers, namely seed inoculum and local climatic conditions. To better establish the relationship between these two drivers, blackleg development was monitored in Swiss field trials at multiple locations from 2010 to 2013 involving three sets of naturally infected seed lots planted in each of three locations. The seed lot itself was thereby the most important factor explaining differences in disease development, rather than environmental factors. In a further on-farm project conducted at various locations in Switzerland and southern Germany from 2013 to 2015, the implementation of a seed-testing procedure was investigated. A total of 177 seed lots were tested for natural latent infection with soft rot Pectobacteriaceae and the corresponding blackleg incidence was tracked in 242 fields. The reliability of the relationship between latent infection and field incidence was found to be strongly linked to the bacterial species. Dickeya spp. field infection could be predicted with an acceptable reliability, whereas Pectobacterium carotovorum subsp. brasiliense, even when detected as latent tuber infection, was not consistently expressed as visual blackleg. Moreover, commonly found mixed latent infections with several bacterial species made it even harder to predict which bacteria would cause blackleg symptoms. Finally, variability in the reliability of seed testing may also be explained by differences in local farming practices. These trials over several years with naturally infected potato seed highlight the usefulness and limits of seed testing to manage blackleg.     

Characterization of single nucleotide polymorphism in Tunisian grapevine genome and their potential for population genetics and evolutionary studies

In this study, two gene fragments corresponding to the VvMYBA1 and VvMYBA2 loci were sequenced on a sample of grapes including cultivated and wild accessions originating from Tunisia, Germany and France. A total of 42 SNPs were detected in the sequenced fragments giving an average of 1 SNP every 33 bp. High level of polymorphism was observed in the samples either in cultivated or wild accessions. Pattern of nucleotide diversity indicates a non departure from neutrality expectations for wild grapevine sample for gene VvMYBA1 and VvMYBA2 and for cultivated sample for gene VvMYBA1. However, a linkage to a selective sweep was revealed for cultivated grapevine gene pool in gene VvMYBA2. A genetic structure of the studied sample according to accession taxonomic status was revealed by the UPGMA clustering with a considerable overlap. This result was confirmed by significant but low genetic differentiation values between cultivated and wild sample. The number of migrants Nm based on sequence data information between Tunisian cultivars and Tunisian wild accessions showed a low level of gene flow between those germplasms. This finding indicates that Tunisian cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced during historical times. However, the possibility that some cultivars derived from ancestral events of local domestication or cross hybridization with native wild plants was not completely excluded for Tunisian grapevine accessions.     

Immunological reversal of autoimmune diabetes without hematopoietic replacement of beta cells

Type 1 diabetes mellitus results from the autoimmune destruction of the beta cells of the pancreatic islets of Langerhans and is recapitulated in the nonobese diabetic strain of mice. In an attempt to rescue islet loss, diabetic mice were made normoglycemic by islet transplantation and immunization with Freund's complete adjuvant along with multiple injections of allogeneic male splenocytes. This treatment allowed for survival of transplanted islets and recovery of endogenous beta cell function in a proportion of mice, but with no evidence for allogeneic splenocyte-derived differentiation of new islet beta cells. Control of the autoimmune disease at a crucial time in diabetogenesis can result in recovery of beta cell function.     

Analysis of grape Vitis vinifera L. DNA in must mixtures and experimental mixed wines using microsatellite markers

Because wine quality highly relies on the varietal composition of the must, the development of methods allowing the authentication of varieties in musts and wines would be of great value as a guarantee of quality. Microsatellite markers have already been applied to the authentication of grape juices (Faria, M. A.; Magalh?es, R.; Ferreira, M. A.; Meredith, C. P.; Ferreira Monteiro, F. J. Agric. Food Chem. 2000, 48, 1096-1100) and to the analysis of experimental wines (Siret, R.; Boursiquot, J. M.; Merle, M. H.; Cabanis, J. C.; This, P. J. Agric Food Chem. 2000, 48, 5035-5040). In the present paper, we accessed the usefulness of this technology for the analysis of must and wine mixtures. The detection limit of DNA mixtures was first estimated on DNA extracted from leaves: 4% of a foreign DNA can be detected. Analysis of must and wine mixtures (Chardonnay B/Clairette B and Syrah N/Grenache N) was performed on experimental fermentations. DNA was extracted along the fermentation process and analyzed using five microsatellite loci. The 70:30 (v/v) mixtures were successfully analyzed until the end of the fermentation. The applications of these results to commercial purposes are discussed.