Polyketide Synthases in the Microbiome of the Marine Sponge Plakortis halichondrioides: A Metagenomic Update

Sponge-associated microorganisms are able to assemble the complex machinery for the production of secondary metabolites such as polyketides, the most important class of marine natural products from a drug discovery perspective. A comprehensive overview of polyketide biosynthetic genes of the sponge Plakortis halichondrioides and its symbionts was obtained in the present study by massively parallel 454 pyrosequencing of complex and heterogeneous PCR (Polymerase Chain Reaction) products amplified from the metagenomic DNA of a specimen of P. halichondrioides collected in the Caribbean Sea. This was accompanied by a survey of the bacterial diversity within the sponge. In line with previous studies, sequences belonging to supA and swfA, two widespread sponge-specific groups of polyketide synthase (PKS) genes were dominant. While they have been previously reported as belonging to Poribacteria (a novel bacterial phylum found exclusively in sponges), re-examination of current genomic sequencing data showed supA and swfA not to be present in the poribacterial genome. Several non-supA, non-swfA type-I PKS fragments were also identified. A significant portion of these fragments resembled type-I PKSs from protists, suggesting that bacteria may not be the only source of polyketides from P. halichondrioides, and that protistan PKSs should receive further investigation as a source of novel polyketides.     

Variation in morphology and seed production of snow clover [<Emphasis Type="Italic">Trifolium pratense</Emphasis> L. subsp. <Emphasis Type="Italic">nivale</Emphasis> (Koch) Arcang.] germplasm from the Rhaetian Alps,Italy

A recent approach to restoration of degraded mountain landscapes (e.g. ski slopes) recommend to sow seed mixtures including ‘site-specific’ species, i.e. native germplasm adapted to the prevailing conditions and ecologically compatible with the area of intervention. To better exploit the potential of these species and enhance their spread in revegetation projects, deeper knowledge is needed, however, on the existing variation in their germplasm, particularly for economically useful traits such as seed yield. Snow clover is one of the recommended ‘site-specific’ legumes. This study evaluated 12 populations of snow clover, collected in three valleys of the Rhaetian Alps, Italy, to assess their variation and highlight any promising material. The evaluation encompassed a mountain and a lowland site, to verify the behaviour of the germplasm also in one environment markedly different from that of origin. Differences among valleys were observed for flower colour, growth habit and type, flowering time and susceptibility to mildew, although the overall pattern of phenotypic diversity was similar among valleys. Some effect of the evaluation site on the expression of morphological and seed production traits, and on the overall diversity, was also evident. Furthermore, the lowland site experienced very high plant mortality towards the end of the first growing season. Individual populations proved a valuable source of variation for seed production. Some populations, in particular, were worth of attention for a possible selection of high-seed-yielding snow clover cultivars. An assessment of the mating system suggested a lack of self-tripping or an almost absolute self-incompatibility in snow clover.     

A framework for results‐based management in fisheries

We present a framework for results‐based management (RBM) of commercial fisheries. The core idea of RBM is to reduce micromanagement by delegating management responsibility to resource users. The RBM framework represents an industrial organization approach to co‐management and comprises three defining processes, conducted by three independent “agents”: (i) an “authority” defines specific and measurable and achievable objectives (outcome targets, OTs) for the utilization of fisheries resources, (ii) resource user organizations (termed “operators”) take responsibility for achieving these OTs and provide documentation that (iii) allows independent “auditors” to evaluate the achievement of OTs. Using incentive mechanisms, notably deregulation, RBM grants operators the flexibility to develop and implement innovative and cost‐effective ways to achieve OTs. The feasibility of implementing RBM in five European fisheries was investigated in cooperation with relevant stakeholders through artificial planning processes and computer simulations. The operators involved were enthusiastic, and new management plans were drafted based on the framework. These included socioeconomic OTs in addition to traditional stock objectives, encompassing an ecosystem approach. Several issues are in need of further research to consolidate the approach and prepare the ground for practical implementation, including: the specification of the legal and regulatory framework required to underpin RBM, details of transitional arrangements when shifting towards RBM (including cost‐sharing) and the development of necessary organizational capacity for operators. Initially, we therefore envisage the framework being applied to high‐value single‐species fisheries, with a limited number of participants, which are adequately represented by a competent organization.     

Neutral detergent fiber increases endogenous ileal losses but has no effect on ileal digestibility of amino acids in growing pigs

Two experiments were conducted to determine the effect of neutral detergent fiber (NDF) on endogenous amino acids and protein ileal losses; and also apparent ileal digestibility (AID), and standardized ileal digestibility (SID) of amino acids and crude protein. Sixteen barrows were fed four protein‐free diets containing graded NDF levels in Experiment 1. NDF was a mixture of sugarcane bagasse and corn leaves (SBCL). Twenty‐four barrows were fed diets with soybean protein concentrate (SPC) or casein as protein sources and SBCL or corncobs (CC) as NDF sources in Experiment 2. In Experiment 1, a linear increase (P < 0.05) in endogenous amino acid and protein ileal losses was observed with increased NDF levels, except for arginine, histidine, methionine and proline. In Experiment 2, protein (P < 0.001) and NDF (P < 0.01) sources significantly affected AID of dry matter, which was higher in casein diets (71.7%) and CC diets (70.7%). Protein and NDF sources significantly affected (P < 0.05) SID of crude protein, which was higher in casein diets (92.8%) and CC diets (92.7%). NDF source had no effect (P > 0.05) on SID of amino acids. Overall, this study showed that NDF increased endogenous amino acid and protein ileal losses, but did not affect ileal digestibility of amino acids.     

Use of an N-tester chlorophyll meter to tune a late third nitrogen application to wheat under humid Mediterranean conditions

In Northern Spain, winter wheat is usually fertilized with 180–220 kg N/ha split in two applications. To reduce this rate, a strategy was tested which comprised three nitrogen (N)-applications, the latter being tuned to the nutritional needs of the crop using a chlorophyll meter. N-fertilization experiments were performed on winter wheat (Soissons variety). Treatments consisted of three N-broadcasts of 40, 60, and either 0, 40, 60, or 80 kg N/ha respectively applied at Zadoks scale growth stages 21, 30, and 37. An over-fertilized treatment of 220 kg N/ha was included for normalization of chlorophyll-meter values. Chlorophyll-meter readings were performed at growth stage 37, before fertilization. When normalized chlorophyll-meter values were below 92%, yield and grain protein contents attained with 40+60+0 kg N/ha could be respectively enhanced with third applications of 60 or 80 kg N/ha and 40 kg N/ha.     

How local stakeholders perceive agroforestry systems: an Italian perspective

This paper reports the results of a study conducted in Italy, within the AGFORWARD (2014–2017) project, aimed at promoting innovative agroforestry practices in Europe. Agroforestry offers a means for maintaining food production whilst addressing some of the negative environmental effects of intensive agriculture. This study aims to elicit the positive and negative points of view and perceptions of local stakeholders in Italy in relation to three types of agroforestry systems. The Participatory Research and Network Development was implemented in three workshops conducted in Sardinia, Umbria, and Veneto regions, and applied adopting a common methodological protocol. Qualitative data were obtained using open discussions with stakeholders on key issues, challenges and innovations. Quantitative data were obtained from stakeholders completing questionnaires during the workshops. A statistical analysis was applied to elicit the differences in stakeholders’ positive and negative perceptions in relation to production, management, environment and socio-economy aspects. Although the participants in the study came from different geographical and socioeconomic contexts with varied educational and cultural backgrounds, the different professional groups (farmers, policy-makers and researchers) and the three workshops generally shared similar perceptions of the benefits and constraints. The effects of agroforestry on production and the environment were generally perceived as positive, whilst those related to management were generally negative. The process of bringing the groups together seemed to be an effective means for identifying the key research gaps that need to be addressed in order to promote the uptake and maintenance of agroforestry.     

Phenolic Compounds Determined by LC-MS/MS and <Emphasis Type="Italic">In Vitro</Emphasis> Antioxidant Capacity of Brazilian Fruits in Two Edible Ripening Stages

The aim of this study was to investigate the free individual phenolics and the in vitro antioxidant capacity of blackberry, acerola, yellow guava, guabiju, jambolan and jabuticaba fruits in two edible stages. Of the thirty-three phenolics investigated by liquid chromatography - tandem mass spectrometry (LC-MS/MS), twenty-five were quantified and the major ones were catechin, isoquercitrin, epicatechin and gallic acid. The highest values for the total phenolic content (in dry matter) were observed for acerola (83.6 to 97.7 mg gallic acid equivalents g^?1 DM) and blackberry (18.9 to 28.3 mg gallic acid equivalents g^?1 DM); however, acerola, jabuticaba, and blackberry showed the highest antioxidant capacities (134.6 to 1120.4 mg Trolox equivalents g^?1 for 2,2-diphenyl-1-picrylhydrazyl and 43.6 to 501.8 μmol Trolox equivalents g^?1 for ferric reducing antioxidant power). For most fruits, the antioxidant capacity decreased during the ripening, possibly due to a decrease in the concentration of most of the phenolics.