A case study of biofilter activation and microbial nitrification in a marine recirculation aquaculture system for rearing Atlantic salmon (Salmo salar L.)

Marine recirculation aquaculture system (RAS) is a prominent technology within fish farming. However, the nitrifying bacteria in the biofilter have low growth rates, which can make the biofilter activation a long and delicate process with periods of low nitrification rates and variations in water quality. More knowledge on the microbial development in biofilters is therefore needed in order to understand the rearing conditions that favour optimal activation of the biofilters. In this case study, we investigated the activation of two biofilters in a marine RAS for Atlantic salmon post‐smolt associated with either high or low stocking densities of fish by monitoring the microbial communities and chemical composition. The results showed that the microbial communities in both biofilters were similar during the first rearing cycle, despite variations in the water quality. Nitrifying bacteria were established in both biofilters; however, the biofilter associated with low stocking density had the highest relative abundance of ammonia‐oxidizing Nitrosococcus (1.0%) and nitrite‐oxidizing Nitrospira (2.1%) at the end of the first rearing cycle, while the relative abundance of ammonia‐oxidizing Nitrosomonas (2.3%–2.9%) was similar in both biofilters. Our study showed that low fish stocking density during the first rearing cycle provided low and steady concentrations of ammonium, nitrite and organic load, which can stimulate rapid development of a nitrifying population in new marine RAS biofilters.     

Structure of the advanced regeneration community in tropical rain forest fragments of Los Tuxtlas, Mexico

We characterized the tree seedling community within seven forest fragments of different size (3-640 ha) at Los Tuxtlas, Mexico. We considered individual density, species richness, diversity, composition and functional group (shade tolerant, non-pioneer-light demander and pioneer species). We recorded 8038 individuals, belonging to 128 species and 40 morphospecies. Overall, shade-tolerant species had the highest density and diversity followed by non-pioneer-light demanders and pioneer species. Mean individual density per plot was not related to fragment size, but mean species richness per plot, total observed species richness and diversity were inversely related to fragment size, with the smallest fragments having the highest values. Species composition comparisons highlighted low similarity among fragments. Furthermore, larger fragments shared more species with the smallest fragments than between each other. Our results show that the largest fragments do not always hold the highest species richness; that small fragments comprise of high seedling species diversity, and represent a high regeneration potential for tree native species in the study landscape.     

High levels of spatial heterogeneity in the biodiversity of soil prokaryotes on Signy Island, Antarctica

In a previous study, soil bacterial diversity at environmentally distinct locations on Signy Island was examined using denaturing gradient gel electrophoresis (DGGE) profiling, and a range of chemical variables in soils was determined in order to describe variations between them. The dominant bacterial communities of all locations were found to be significantly different, although higher levels of similarity were observed between locations with similar physico-chemical characteristics, such as at penguin rookeries, seal wallows and vegetated soils. Extending this study, here soil prokaryote biodiversity was compared between 15 distinct locations in order to elucidate any interaction between four general habitat types on Signy Island (South Orkney Islands, maritime Antarctic) and any influence of previous human impacts at these sites. Specific sites were selected to represent the range of different soil environments present and to cover a range of environmental factors present in the maritime Antarctic which are known to influence bacterial community composition in soils elsewhere. A diverse prokaryote community is described, again with the majority of excised and sequenced bands belonging to the Bacteroidetes. Although DGGE profiling identified significant differences in prokaryotic biodiversity between all sampling sites, aggregations of banding patterns were also apparent across the different soil environments examined. Correlations between specific DGGE profiles and 10 selected soil parameters suggested that much of this variation could be explained by differences in the levels of environmental disturbance and soil pH. In particular, a greater proportion of variation in soil bacterial diversity was explained by differences in soil properties at human-disturbed locations than at undisturbed locations, with higher explanatory values by edaphic factors in the former and soil metal content in the later. In general, our data indicate that small-scale variation is an important factor in understanding patterns of prokaryotic distributions in soil habitats in the maritime Antarctic environment.     

Molecular markers for promoting agro-biodiversity conservation: a case study from Italy. How cowpea landraces were saved from extinction

Landraces (LRs) are crop populations that are locally grown by farmers; they have a strategic role to play in rebuilding healthy and complex agro-ecosystems, but are at risk of extinction. This paper outlines how some LRs were rescued with the support of modern techniques such as molecular markers. Cowpea LRs from Umbria, Italy, were initially characterized for morphological, organoleptic and genetic traits and reintroduced among farmers. These activities led to an expansion of the area under LR based cowpea cultivation and increased farmers’ income. To encourage further LR cultivation a request for the Protected Designation of Origin (PDO) status has been promoted. Investigations were carried out to determine if it is possible to certify that the product actually belongs to the traditional agricultural and cultural context of the cultivation area. The genetic diversity and phylogenetic relationships among local LRs, other LRs, commercial varieties, and other taxa were investigated with five AFLP markers. Although genetic diversity is limited, genetic analysis showed that Umbrian cowpea LRs can be distinguished from commercial varieties, LRs from abroad and other taxa. There is a tight phylogenetic connection among Umbrian LRs. These data confirmed the available historical and sociological data and were included in the PDO specification. AFLP markers can be used to monitor the origin of seed lots that are on the market; this protects the rights of both consumers and farmers. This case study could be a resource for planning activities for the future on-farm conservation of other LRs in different countries.     

Genetic diversity,structure and fruit trait associations in Greek sweet cherry cultivars using microsatellite based (SSR/ISSR) and morpho-physiological markers

It is important to couple phenotypic analysis with genetic diversity for germplasm conservation in gene bank collections. The use of molecular markers supports the study of genetic marker-trait associations of biological and agronomic interest on diverse genetic material. In this report, 19 Greek traditional sweet cherry cultivars and two international cultivars, which were used as controls, were grown in Greece and characterized for 17 morpho-physiological traits, 15 simple sequence repeat (SSR) loci and 10 inter simple sequence repeat (ISSR) markers. To our knowledge, this is the first report on molecular genetic diversity studies in sweet cherry in Greece. Principal component analysis (PCA) of nine qualitative and eight quantitative morphological parameters explain over 77.33% of total variability in the first five axes. The SSR markers yielded a combined matching probability ratio (MPR) of 9.569 × e−12. The 15 SSR loci produced a total of 92 alleles. Ten ISSR primers generated 91 bands, with an average of 9.1 bands per primer. Expected heterozygosity (gene diversity) values of 15 SSR loci and 10 ISSR markers averaged at 0.683 and 0.369, respectively. Based on stepwise multiple regression analysis (MRA), SSR alleles were found associated with harvest time and fruit polar diameter. Furthermore, three ISSR markers were correlated with fruit harvest and soluble solids and four ISSR markers were correlated with fruit skin color. Stepwise MRA identified six SSR alleles associated with harvest time with a high correlation (P < 0.001), with linear associations with high F values. Hence, data analyzed by the use of MRA could be useful in marker-assisted breeding programs when no other genetic information is available.     

Influence of foetal calf serum supplementation during in vitro embryo culture in Iberian red deer

Nowadays, the use of foetal calf serum (FCS) during in vitro embryo culture is very controversial. Whilst some authors have encouraged its use, others reject it because of its harmful effects. Although in vitro embryo production in red deer is a promising assisted reproductive technique, it is still in its infancy and a great effort is needed to update the protocols used. The aim of this study was to assess whether FCS supplementation in red deer embryo culture medium is necessary to produce blastocyst and, if so, when is the best time to add it in terms of blastocyst production and quality. In vitro blastocysts were cultured with FCS added at 24, 48 or 96 hours post‐insemination (hpi). In addition, a treatment without FCS was used as control. Six hundred and ninety‐four cumulus–oocyte complexes were collected for in vitro fertilization. Cleavage rate was examined at 48 hpi, and blastocyst yield was recorded on days 6, 7 and 8. FCS had no influence on cleavage and blastocyst rate for any of the treatments studied. However, the number of cells was higher (p = .025) in those blastocysts cultured with FCS from 48 hpi compared with FCS‐free culture media (93.88 ± 7.76 vs. 54.11 ± 8.36). In conclusion, the addition of FCS to the embryo culture medium at 48 hpi improves the quality of red deer blastocyst, although it does not affect the percentage of embryos obtained.     

Testing the effectiveness of conservation management within biosphere reserves: the case of the Mexican deer mouse (Peromyscus mexicanus) as a bioindicator

Biosphere reserves are protected areas whose purpose is to combine conservation and sustainable development. However, their effectiveness has not been tested sufficiently, especially from an ecological and genetic approach. In this sense, the Peromyscus genus represents an excellent bioindicator to address these questions, due to its short life and high evolutionary rate and fecundity. For conservation managers, genetic structure can increase the rate of loss of genetic diversity because alleles exclusive of a subpopulation are more likely to disappear as a consequence of genetic drift in comparison with a panmictic population. Here we analyzed the abundance, movement distances, morphology/morphometry and genetic structure of 3 populations of Mexican deer mouse (Peromyscus mexicanus) located in different protected zones of La Tigra National Park (Honduras). Our results are consistent among the 3 approaches and showed the highest values of abundance, morphometry and genetic diversity in the population located at the core zone, whereas non‐statistically significant differences were found between buffer and transition zone populations, suggesting suitable effectiveness of conservation management in the core zone but a lack of ecological buffering function of the other zones. In addition, the low movement distances and high genetic structure among the studied populations provide evidence of poor conservation management in the buffer and transition zone. Thus, we discuss the utility of the novel methodology used in this work, combining morphometry, abundance and genetics, in testing the effectiveness of conservation strategies in biosphere reserves, and the value of the Peromyscus genus as a bioindicator.