Molecular detection of sugarcane striate virus and sugarcane white streak virus and their prevalence in the Miami World Collection of sugarcane and related grasses

Viruses in the genus Mastrevirus (family Geminiviridae), including those infecting sugarcane, have natural geographical ranges almost exclusively restricted to Africa and the Indian Ocean islands off the African coast. Only sugarcane white streak virus (SWSV) in Barbados and sugarcane striate virus (SStrV) in Florida and Guadeloupe are known to infect a few sugarcane varieties in the Western Hemisphere. In this study, PCR assays were developed to detect these two viruses in sugarcane. Five hundred and seventy-one DNA samples from Saccharum species and interspecific hybrids from the Miami World Collection of sugarcane and related grasses were tested for the presence of SStrV and SWSV by PCR. No variety was found infected by SWSV but SStrV was detected in 19 varieties. PCR data were confirmed by sequencing amplified fragments (248 bp). These fragments shared 93%–100% nucleotide identity with SStrV sequences from the GenBank database. SStrV isolates were distributed in six phylogenetic groups, including the four strains of the virus. Most varieties infected by SStrV originated from Asia, thus confirming a previous hypothesis stating that this virus originated from this continent. Absence of SStrV in commercial sugarcane in Florida also suggested that this virus has not been spread in this location, while infected plants have been present for several decades.     

Drivers of fine-scale avian functional diversity with changing land use: an assessment of the effects of eco-estate housing development and management

Landscape Ecology - The effects of changing land use, and especially urbanisation, on species and functional diversity are of global concern. Eco-estates are a form of urban housing development...     

Ripening reduces the shrinkage of processed dredged material

Purpose

The utilization of dredged material in dike construction as a substitute for traditionally used materials is considered as an option to preserve natural resources such as marsh sediments. As a prerequisite for this application, the equivalency with respect to soil physical and mechanical properties of the materials must be assessed. Previous investigations have shown pronounced differences in shrinkage behavior and desiccation cracking between sediments and dredged material. The key objective of the study was to assess whether shrinkage of processed dredged material can be reduced by further processing, i.e., dewatering, which can be referred to as ripening.

Materials and methods

To compare the shrinkage behavior of the materials, three different methods of different scales were applied. Small-scale methods conducted were the standard procedure for the determination of the shrinkage limit and the determination of the coefficient of linear extensibility (COLE_rod). Large-scale shrink-swell experiments were carried out in a specially constructed test system with 90 l capacity for a period of up to 385 days. Here the materials were ripened, i.e., air-dried, until shrinkage almost ceased, and a rewetting-air-drying cycle was conducted. Shrinkage and swelling were determined during the processes by measuring the changes in volume. On the ripened materials, COLE_rod was determined.

Results and discussion

The experiments show that the shrinkage behavior of processed dredged material can be ameliorated by ripening. COLE_rod of the ripened materials were about 20–80% lower than COLE_rod of the un-ripened materials. The large-scale shrink-swell experiments showed that shrinkage in the second drying cycle amounted to less volume than in the first drying cycle and that shrinkage behavior in contrast to the first drying cycle, where pronounced proportional shrinkage was observed, was dominated by structural and residual shrinkage in this cycle.

Conclusions

Ripening of processed dredged material is considered a useful pre-treatment option to ameliorate the shrink-swell behavior of processed dredged material and to obtain a better functional equivalency with traditionally used dike construction materials such as fine-grained marsh sediments.

     

SnToxA,SnTox1, and SnTox3 originated in Parastagonospora nodorum in the Fertile Crescent

The centre of origin of the globally distributed wheat pathogen Parastagonospora nodorum has remained uncertain because only a small number of isolates from the Fertile Crescent were included in earlier population genetic and phylogeographic studies. We isolated and genetically analysed 193 P. nodorum strains from three naturally infected wheat fields distributed across Iran using 11 neutral microsatellite loci. Compared to previous studies that included populations from North America, Europe, Africa, Australia, and China, the populations from Iran had the highest genetic diversity globally and also exhibited greater population structure over smaller spatial scales, patterns typically associated with the centre of origin of a species. Genes encoding the necrotrophic effectors SnToxA, SnTox1, and SnTox3 were found at a high frequency in the Iranian population. By sequencing 96 randomly chosen Iranian strains, we detected new alleles for all three effector genes. Analysis of allele diversity showed that all three effector genes had higher diversity in Iran than in any population included in previous studies, with Iran acting as a hub for the effector diversity that was found in other global populations. Taken together, these findings support the hypothesis that P. nodorum originated either within or nearby the Fertile Crescent with a genome that already encoded all three necrotrophic effectors during its emergence as a pathogen on wheat. Our findings also suggest that P. nodorum was the original source of the ToxA genes discovered in the wheat pathogens Phaeosphaeria avenaria f. sp. tritici 1, Pyrenophora tritici-repentis, and Bipolaris sorokiniana.     

Using genetic methods for analysis of fish meals and feeds employed in Greek mariculture

Large quantities of high protein fish meals are needed to sustain cultured species and thus the impact to marine ecosystem has been highly discussed. The aim of this study was to apply a PCR‐cloning methodology for a robust insight into the composition of commercial fish meals and feeds for farmed species of the Greek mariculture, assessing the risk posed by aquaculture to marine ecosystems but also the risk posed by commercial fish feeds to the increase in trophic level of species farmed in Greece. 89% of the sequences were identified to species level and only 11% to genus/family level. Overall, a total of 49 taxa were identified (44 fish species/taxon, five non‐fish species/taxon). Even though small pelagic fish like Engraulis sp. were the main portion, a wide range of species constituted the fish meals and feeds. Plant and animal species were also detected as an alternative protein source. Feed products employed in Greek mariculture still contain large portions of fish meals which increase the mean trophic level of farmed species causing a farming up trend. The results emphasize that such molecular methodologies are needed to certify aquafeeds allowing fish feed producers to demonstrate their commitment to sustainable aquaculture.     

Regional differences in aspen (Populus tremuloides Michx.) seedling response to an established nursery protocol

New Forests - In seedling-based reforestation operations, seed source is known to be an influential variable affecting outplanting success. Adaptive variation among seed sources may also be an...     

Examining horizontal and vertical social ties to achieve social–ecological fit in an emerging marine reserve network

1. Most MPA networks are designed only with ecological processes in mind to increase their conservation utility. However, since MPA networks often involve large geographic areas, they also affect and involve multiple actors, institutions, and policy sectors.
2. A key challenge when establishing an effective MPA network is to align the ‘social system’ with the biophysical MPA network (the ‘ecological system’). This challenge is often denoted as ‘social–ecological fit’.
3. Facilitating collaborative social interactions among various actors and stakeholders (social connectivity) is equally as important as accomplishing ecological connectivity. New analytical approaches are required to effectively examine this ‘social’ dimension of fit.
4. An emerging marine reserve network in Jamaica and the recent invasion of Indo‐Pacific lionfish are used as a case study to: (1) examine the extent to which horizontal and vertical social ties bring local and national actors together to collaborate, coordinate, and share knowledge; and (2) assess the extent to which different attributes and features of such multilevel social networks may enhance or inhibit particular aspects of social–ecological fit.
5. Findings suggest that multilevel linkages have played the greatest role in relation to enhancing fit in the marine reserve network in the context of the recent lionfish invasion. However, the long‐term propensity of the multi‐actor and multilevel networks to enhance social–ecological fit is uncertain given the prevalence of weak social ties, lack of a culture of information sharing and collaboration, and limited financial resources.

     

A review of the biology and status of Cape Fold Ecoregion freshwater fishes

1. Mediterranean climate regions are globally recognized as hotspots of endemism in fishes; however, these unique assemblages are increasingly threatened by human mediated impacts including water abstraction, damming and non‐native species introductions.
2. The Cape Fold aquatic ecoregion (CFR) of South Africa supports an assemblage of range‐restricted endemic freshwater fishes, the majority of which are conservation priorities because they are under severe threat of extinction. Effective conservation and management are constrained by the lack of readily available information on this imperilled group of fishes because research efforts over the last century have been temporally disjointed and relatively uncoordinated.
3. This review provides an exhaustive appraisal of published literature on the taxonomy, biogeography, life history, ecology and physiology of freshwater fishes in the CFR, and the human impacts that affect them. Its aim is to direct future research needs for effective management and conservation of this imperilled group.
4. Only 103 peer‐reviewed articles on CFR fishes were recorded and the majority of available research is on taxonomy and biogeography (40.8%), followed by ecological investigations (22.3%), conservation (19.4%) and human impacts (17.5%).
5. Despite a plethora of studies on taxonomy and biogeography, recent genetic evidence suggests that fish diversity in the CFR has been severely underestimated and requires urgent attention. Human impacts severely threaten the existence of many native CFR fishes and require further study. Information on the biology and ecology of CFR fishes is limited to studies on selected species; of particular note is the lack of physiological information which is particularly pertinent given projected climate change scenarios.

     

Impact of waterlogging and temperature on autumn growth,hardening and freezing tolerance of timothy (Phleum pratense)

Precipitation has generally increased in Norway during the last century, and climate projections indicate a further increase. The growing season has also become longer with higher temperatures, particularly in autumn. Previous studies have shown negative effects of high temperatures and, depending upon temperature conditions, contrasting effects of waterlogging on hardening capacity of timothy. We studied effects of waterlogging on seedlings of timothy (Phleum pratense, cv. Noreng) under three pre-acclimation temperatures: 3°C, 7°C, 12°C, and in autumn natural light in a phytotron at Holt, Tromsø (69°N). After temperature treatments, all plants were cold acclimated at 2°C for three weeks under continued waterlogging treatments. Freezing tolerance was determined by intact plants being frozen in pots at incremental temperature decreases in a programmable freezer. Waterlogging resulted in a higher probability of death after freezing, and a significantly reduced regrowth after three weeks at 18°C, 24 hrs light in a greenhouse. Increasing pre-acclimation temperatures also had a clear negative effect on freezing tolerance, but there was no interaction between temperatures and waterlogging. The results indicate that waterlogging may have negative implications for hardening of timothy and may contribute to reduced winter survival under the projected increase in autumn temperatures and precipitation.