Participatory methods in planning & political processes: Linking the grassroots & policies for sustainable development

The use of participatory methods has become increasingly popular in agricultural research and development and natural resource management. A range of approaches are being used at the grassroots level in order to involve local citizens and groups in projects. Many of these activities remain peripheral and isolated from conventional development agencies and policies. However, recent efforts are evolving to link participatory approaches into wider planning and policy-making processes and to increase the influence of such methods in resource management initiatives. Main lessons from these innovative participatory experiences in addressing policy issues for sustainable development are summarized.     

A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.     

Environmental genome shotgun sequencing of the Sargasso Sea

We have applied "whole-genome shotgun sequencing" to microbial populations collected en masse on tangential flow and impact filters from seawater samples collected from the Sargasso Sea near Bermuda. A total of 1.045 billion base pairs of nonredundant sequence was generated, annotated, and analyzed to elucidate the gene content, diversity, and relative abundance of the organisms within these environmental samples. These data are estimated to derive from at least 1800 genomic species based on sequence relatedness, including 148 previously unknown bacterial phylotypes. We have identified over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors. Variation in species present and stoichiometry suggests substantial oceanic microbial diversity.     

The Use of Frozen,Food-Grade Blood to Successfully Maintain Colonies of Four Species of Mosquitoes (Diptera: Culicidae)

An essential component of all mosquito-rearing activities is the act of blood-feeding the mosquitoes (Diptera: Culicidae). Many options exist for this purpose including live host animals and a diverse array of artificial-feeding methods. Most of the published artificial-feeding methods involve expensive materials, custom-built devices, or are labor-intensive. All of the previously published methods utilize blood sources, which are either expensive, or difficult to obtain. Additionally, much of the research into artificial blood-feeding methods for mosquitoes has focused on two species: Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse). This article presents a modified artificial blood-feeding method that uses affordable and easily sourced materials, does not require any technical knowledge to assemble, and requires minimal time and effort. The combination of inexpensive aluminum plates, Parafilm and polytetrafluoroethylene tape membranes, an electric germination mat, and frozen, food-grade blood produces exceptional feeding rates and abundant egg production. The method has been used for 2 yr at the Lee County Mosquito Control District to successfully maintain laboratory colonies of four species of mosquito: Ae. aegypti, Ae. albopictus, Aedes taeniorhynchus (Wiedemann), and Culex quinquefasciatus (Say). Variations of this method are reported, which can be used for wild and laboratory colonies of multiple species. This modified method is highly accessible for any small-scale mosquito rearing facility with labor or budgetary constraints.     

An assessment of the genetic integrity of ex situ germplasm collections of three endangered species of Coffea from Madagascar: implications for the management of field germplasm collections

Madagascar has 59 species of Coffea, of which 42 are listed as Critically Endangered, Endangered, or Vulnerable by criteria of the Red List Category system of the World Conservation Union. In an attempt to assess the conservation value of ex situ collections of Malagasy coffee species, a study was undertaken using the field genebank collections maintained at the Kianjavato Coffee Research Station. Three species were selected for this purpose, C. kianjavatensis, C. montis-sacri, and C. vatovavyensis, and for comparative purposes extant, in situ populations of the same species were studied. Parentage analyses of ex situ propagated offspring of C. kianjavatensis and C. montis-sacri were performed to assess if crossing with other Coffea species maintained in the field genebank is compromising the genetic integrity of the collection. For these three species, higher genetic diversity was observed in the ex situ populations compared to the in situ populations, highlighting the importance of preserving the plants currently in ex situ collections. Parentage analyses of seed-propagated offspring of C. kianjavatensis and C. montis-sacri revealed that cross contamination with pollen from other Coffea species in the ex situ field genebank is occurring. These results have significant implications for the conservation management of wild Coffea species and for the management of ex situ genebanks.     

Salt Discharge from an Inland Farm for Marine Shrimp in Alabama

The total salt input in saline well water, mineral amendments, feed, and rainfall and runoff to ponds of an inland shrimp farm in Alabama was 1980.8 tonnes over a 5‐yr period. A residual of 270.4 tonnes of salt remained in pond water and 38.3 tonnes in bottom soil. Only 8.0 tonnes of salt were removed in harvested shrimp. A total of 1588.0 tonnes of salt or 80.2% of the input was lost to the environment with about equal amounts exiting the ponds in seepage and in overflow and harvest effluent. About 4.2% of the salt input (84.1 tonnes) could not be accounted for because of errors in assumptions and measurements. Salt concentration was elevated in a small stream passing through the farm and in the shallow aquifer beneath it. Needham Creek, the receiving water body for runoff and base flow from the farm watershed, had elevated salt concentrations when ponds were partially drained for harvest in the fall. At this time, chloride concentration exceeded 230 mg/L, the maximum concentration allowed by Alabama Department of Environmental Management regulations. Greater water reuse or more gradual release of pond effluent during harvest would reduce the peak in‐stream chloride concentration and avoid noncompliance with the in‐stream chloride criterion.     

Freshwater mussels in Mediterranean-climate regions: Species richness,conservation status,threats, and Conservation Actions Needed

1. The five global Mediterranean-climate regions are experiencing alarming rates of freshwater biodiversity loss. Although freshwater mussels are recognized as important functional components in aquatic ecosystems, and are among the most threatened faunal groups globally, there has been no synthesis of the plight of this group within these regions.
2. Data from the International Union for Conservation of Nature (IUCN) Red List were reviewed to compare the conservation status, threats, and conservation actions needed for freshwater mussel species occurring in Mediterranean-climate regions (med-mussels) with those of other freshwater mussel species globally. The first comprehensive catalogue of med-mussel species was compiled using existing taxonomic literature.
3. There are 41 med-mussel species, 30 of which occur in the Mediterranean basin. Many regions have just a single species, and regions where multiple species occur generally only have between one and four species per river basin. Med-mussel species are almost twice as likely to be ‘Imperilled’, are affected by 2.4 times more threats, and require 3.5 times more conservation actions than non-med mussels. In many cases, the exact threats have not been identified.
4. In combination with low species richness, this level of imperilment means that Mediterranean-climate regions are at risk of losing the benefits that mussels provide to broader ecosystem functioning. The conservation of med-mussels can be improved by increasing our knowledge of species distributions, including the identification of cryptic species and significant management units, through population genetic work. In addition, recognizing the potential of ‘novel’ habitats and refuge areas could augment the management of this important functional group.

     

Mitochondrial genome sequences illuminate maternal lineages of conservation concern in a rare carnivore

Background

When a specimen belongs to a species not yet represented in DNA barcode reference libraries there is disagreement over the effectiveness of using sequence comparisons to assign the query accurately to a higher taxon. Library completeness and the assignment criteria used have been proposed as critical factors affecting the accuracy of such assignments but have not been thoroughly investigated. We explored the accuracy of assignments to genus, tribe and subfamily in the Sphingidae, using the almost complete global DNA barcode reference library (1095 species) available for this family. Costa Rican sphingids (118 species), a well-documented, diverse subset of the family, with each of the tribes and subfamilies represented were used as queries. We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria.

Results

A liberal tree-based criterion assigned 83% of queries accurately to genus, 74% to tribe and 90% to subfamily, compared to a strict tree-based criterion, which assigned 75% of queries accurately to genus, 66% to tribe and 84% to subfamily, with a library containing 100% of available species (but excluding the species of the query). The greater number of true positives delivered by more relaxed criteria was negatively balanced by the occurrence of more false positives. This effect was most sharply observed with libraries of the lowest completeness where, for example at the genus level, 32% of assignments were false positives with the liberal criterion versus < 1% when using the strict. We observed little difference (< 8% using the liberal criterion) however, in the overall accuracy of the assignments between the lowest and highest levels of library completeness at the tribe and subfamily level.

Conclusions

Our results suggest that when using a strict tree-based criterion for higher taxon assignment with DNA barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage.     

Antibacterial activity of marine and black band disease cyanobacteria against coral-associated bacteria

Black band disease (BBD) of corals is a cyanobacteria-dominated polymicrobial disease that contains diverse populations of heterotrophic bacteria. It is one of the most destructive of coral diseases and is found globally on tropical and sub-tropical reefs. We assessed ten strains of BBD cyanobacteria, and ten strains of cyanobacteria isolated from other marine sources, for their antibacterial effect on growth of heterotrophic bacteria isolated from BBD, from the surface mucopolysaccharide layer (SML) of healthy corals, and three known bacterial coral pathogens. Assays were conducted using two methods: co-cultivation of cyanobacterial and bacterial isolates, and exposure of test bacteria to (hydrophilic and lipophilic) cyanobacterial cell extracts. During co-cultivation, 15 of the 20 cyanobacterial strains tested had antibacterial activity against at least one of the test bacterial strains. Inhibition was significantly higher for BBD cyanobacteria when compared to other marine cyanobacteria. Lipophilic extracts were more active than co-cultivation (extracts of 18 of the 20 strains were active) while hydrophilic extracts had very limited activity. In some cases co-cultivation resulted in stimulation of BBD and SML bacterial growth. Our results suggest that BBD cyanobacteria are involved in structuring the complex polymicrobial BBD microbial community by production of antimicrobial compounds.