The devil is in the detail: Discrepancy between soil organic carbon stocks estimated from regional and local data sources in Flanders,Belgium

Storage of soil organic carbon (SOC) is an essential function of ecosystems underpinning the delivery of multiple services to society. Regional SOC stock estimates often rely on data collected during land‐use‐specific inventory schemes with varying sampling depth and density. Using such data requires techniques that can deal with the associated heterogeneity. As the resulting SOC assessments are not calibrated for the local scale, they could suffer from oversimplification of landscape processes and heterogeneity. This might especially be the case for sandy regions where typical historical land use practices and soil development processes determine SOC storage. The aims of this study were (a) to combine four land‐use‐specific SOC stock assessments to estimate the total stock in Flanders, Belgium, and (b) to evaluate the applicability of this regional‐scale estimate at the local scale. We estimated the SOC stock in the upper 100 cm of the unsealed area in Flanders (887,745 ha) to be 111.67 Mt OC, or 12.6 ± 5.65 kg OC m^?2 on average. In general, soils under (semi‐) natural land‐use types, for example forests, store on average more organic carbon than under agriculture. However, overall agricultural soils store the largest amounts of SOC due to their vast spatial extent. Zooming in on a sandy location study (13.55 km²) revealed the poor performance of the regional estimates, especially where Histosols occurred. Our findings show that a greater spatial sampling density is required when SOC stock estimates are needed to inform carbon‐aware land management rather than to provide for regional reporting.     

Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction

Reference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree‐based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single‐Step approach (SSGBLUP) using both. For a scenario with no‐selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single‐Step approach to obtain accurate and unbiased prediction of GEBV.     

Deficit irrigation as an on-farm strategy to maximize crop water productivity in dry areas

Deficit irrigation (DI) has been widely investigated as a valuable and sustainable production strategy in dry regions. By limiting water applications to drought-sensitive growth stages, this practice aims to maximize water productivity and to stabilize - rather than maximize - yields. We review selected research from around the world and we summarize the advantages and disadvantages of deficit irrigation. Research results confirm that DI is successful in increasing water productivity for various crops without causing severe yield reductions. Nevertheless, a certain minimum amount of seasonal moisture must be guaranteed. DI requires precise knowledge of crop response to drought stress, as drought tolerance varies considerably by genotype and phenological stage. In developing and optimizing DI strategies, field research should therefore be combined with crop water productivity modeling.     

Efficacy of a novel virulence gene-deleted Salmonella Typhimurium vaccine for protection against Salmonella infections in growing piglets

We have previously developed a novel attenuated Salmonella Typhimurium (S. Typhimurium) ΔcpxR Δlon vaccine. This study was carried out to examine whether this vaccine could effectively protect growing piglets against Salmonella infection. Attenuated S. Typhimurium secreting the B subunit of Escherichia coli heat-labile enterotoxin was also used as a mucosal adjuvant. Pregnant sows in groups A and B were primed and boosted with the vaccine and mucosal adjuvant, whereas sows in groups C, D and E received PBS. Piglets in groups A and C were intramuscularly primed with formalin-inactivated vaccine and orally boosted with live vaccine, while piglets in groups B, D and E received PBS. Piglets in groups A, B, C, and D were challenged with a wild type virulent S. Typhimurium at the 11th weeks of age. Colostrum sIgA and IgG titers in vaccinated groups A and B sows were approximately 50 and 40 times higher than those of non-vaccinated groups C, D and E sows (P < 0.001). Serum IgG titers of group A piglets were also significantly higher than those of groups D and E piglets during the study (P < 0.001). Furthermore, no clinical signs were observed in group A piglets during the entire experimental period after the challenge, while diarrhea was observed in many of the piglets in groups B, C, and D. No Salmonella was isolated from fecal samples of the groups A and C piglets on day 14 after challenge, whereas the challenge strain was isolated from several piglets in groups B and D. These results indicate that vaccination of the piglets with the vaccine and mucosal adjuvant in addition to vaccination of their sows induced effective protection against Salmonella infections in the growing piglets.     

Camera-trapping forest-woodland wildlife of western Uganda reveals how gregariousness biases estimates of relative abundance and distribution

Camera traps are increasingly used to estimate relative abundance and distribution of wildlife. These methods are powerful and efficient ways to inventory multiple species simultaneously and count rare, secretive individuals across landscapes. However the estimation methods demand assumptions about relative capture probability that may not hold well for gregarious animals. We present results from the first systematic, camera-trap study in forest-woodland, western Uganda. Within a landscape of seven protected areas with globally important biodiversity, we detected >36 species of large mammals and birds in 8841 camera-trap days. Species photographed in groups of two or more individuals produced higher estimates of relative abundance and wider distribution than species photographed as single individuals. We propose these findings reflect higher detectability for animals that forage or travel in groups. We discuss how capture-recapture theory should be adapted to account for both non-independence among individuals in groups and for the interaction between individual and temporal variation in capture probability. We also identify several species that deserve greater conservation attention in Uganda and beyond. Among them, leopards were unexpectedly rare, especially when compared to the sympatric African golden cat. We recommend against a recent policy on leopard trophy hunting, at least in western Uganda.     

Management intervention affects river-bound spatial dynamics of elephants

The potential consequences of growing elephant populations are a cause of debate and concern in many African conservation areas. Even though space use of elephants is central to understanding their biodiversity consequences, few studies explicitly consider how different management strategies influence elephants’ spatial utilization of landscapes. Here we study elephant’s spatial dispersion patterns in relation to different sized rivers under different management regimes by analyzing aerial census data collected annually during the mid dry-season between 1985 and 2007 across the 19,485 km² Kruger National Park. We found that different sized rivers can be used as a simple proxy for elephant density gradients in the dry-season. This has implications for stratifying and designing elephant impact monitoring programmes in semi-arid savannas. Furthermore, we found that dry-season elephant densities increased around rivers in a period after culling was stopped and large-scale artificial water provision reduced. Most importantly, these localized density increases were not spatially homogeneous, with culling and water provision having a greater suppressing effect on the localized densities around larger rivers than around smaller rivers and areas far removed from rivers. Assuming a positive correlation between elephant density and elephant impact, the impact of elephants around larger rivers has increased disproportionably compared to areas around smaller rivers and areas far removed from rivers since management stopped culling and reduced large-scale water provision. Since areas around the larger rivers have unique functional, structural and compositional characteristics, they should receive specific attention in impact monitoring programmes and elephant management policies. Furthermore, we recommend that if artificial waterholes are provided in semi-arid systems, it should not be located close to rivers that are mostly dry nor in areas far from rivers as this may compromise the spatio-temporal refugia that these areas afford aspects of biodiversity that are sensitive to continuous elephant impact.     

Sequence analysis of 43-year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed

Plantain virus X was first recognized by the ICTV as a species in the genus Potexvirus in 1982. However, because no sequence was available for plantain virus X (PlVX), abolishing the species was proposed to the Flexiviridae working group of the ICTV in 2015. This initiated efforts to sequence the original isolates from Plantago lanceolata samples. Here we report the full-genome sequencing of two original isolates of PlVX, which demonstrate that the virus is synonymous to Actinidia virus X, a species previously reported from kiwifruit (Actinidia sp.) and blackcurrant (Ribes nigrum). PlVX was previously noted to be widespread in the UK in P. lanceolata. This report additionally presents novel data on the distribution and diversity of PlVX, collected at the same site as the original UK isolates, and from three independent surveys, two in the Netherlands and one in Belgium. This study also includes two new host records for PlVX, Browallia americana and Capsicum annuum (sweet pepper), indicating the virus is more widespread and infects a broader range of hosts than previously reported. This stresses the importance of surveys of noncultivated species to gain insight into viral distribution and host range. This study also demonstrates the value of generating sequence data for isolates retained in virus collections. Additionally, it demonstrates the potential value in prepublication data sharing for giving context to virus detections such as the four independent studies here which, when combined, give greater clarity to the identity, diversity, distribution, and host range of plantain virus X.     

Characterization, Genetic Structure, and Pathogenicity of Rhizoctonia spp. Associated with Rice Sheath Diseases in India

ABSTRACT Isolates of Rhizoctonia spp. were obtained from rice in India during 2000-2003. Characterization by conventional techniques and polymerase chain reaction showed that from 110 isolates, 99 were R. solani and 11 were R. oryzae-sativae. Of 99 isolates identified as R. solani, 96 were AG1-IA, 1 was AG1-IB, and 2 were AG1-IC. Amplified fragment length polymorphism (AFLP) analyzes were used to determine genetic relationships in Rhizoctonia pathogen populations collected from different geographic regions. Cluster analysis based on the AFLP data separated isolates belonging to the three different intraspecific groups of R. solani AG1 and differentiated R. solani from R. oryzae-sativae. Analysis of molecular variance (AMOVA) revealed that geographic region was the dominant factor determining population structure of R. solani AG1-1A; host cultivar had no significant effect. Pathogenicity tests on Oryza sativa cv. Zenith revealed that isolates of R. solani AG1-1A and AG1-1B were more virulent than R. solani AG1-IC and R. oryzae-sativae isolates.     

Rates and patterns of landscape change in the Central Sikhote-alin Mountains,Russian Far East

We used Landsat imagery and GIS to quantify the rates and patterns of landscape change between 1972 and 1992 for a 734,126 ha forested study area in the central Sikhote-alin Mountains of the Russian Far East. The study area includes a portion of the Sikhote-alinskiy Biosphere Reserve which is a part of the United Nations international Man and the Biosphere (MAB) reserve network. Wildfire is a major disturbance agent throughout the area and timber harvesting outside the reserve is also important. Maximum likelihood classification of the satellite imagery identified four broad cover types (hardwood, conifer, mixed and non-forest) in 1992 and changes among them between 1972 and 1992. We used multi-temporal principal components analysis to describe the magnitude and direction of landscape change for six watersheds that represent a range of ecological histories and disturbance regimes. Overall, forest cover declined from 90.4% in 1972 to 77.2% in 1992. The disturbance rate was more than twice as high in conifer than in hardwood forests. The rate of disturbance outside the reserve was three times that inside. While the rates of disturbance are not markedly higher than those recorded from other temperate forests, there has recently been a large alteration in the disturbance regime which will lead to a general transformation of forest composition and structure in the study area if the trend continues.