Environmental and spatial characterisation of bacterial community composition in soil to inform sampling strategies

Soil physicochemical properties and microbial communities are highly heterogeneous and vary widely over spatial scales, necessitating careful consideration of sampling strategies to provide representative and reproducible soil samples across field sites. To achieve this, the study aimed to establish appropriate sampling methodology and to determine links between the variability of parameters, utilising two sampling strategies. The first (design 1) involved extracting 25 cores from random locations throughout the field and pooling them into five sets of five cores. The second (design 2) involved a further 25 cores within five 1 m² sub-plots. Sub-samples from each sub-plot were pooled in order to determine between and within sub-plot variability. All samples were analysed independently and as pooled sub-samples. Results indicate that pooling spatially separated samples significantly reduced the variability in pH, compared to individual samples. Pooling samples from a small area resulted in lower within sub-plot variability than between sub-plots for pH and bacterial community composition assessed by terminal-restriction fragment length polymorphism analysis. Following multivariate statistical analysis, a large amount of variation in community composition was explained by soil pH, which is remarkable given the relatively small size of the sampling area and minor differences in pH. Moisture content was also important in determining bacterial communities in the random design (design 1). In the 1 m² sub-plot design (design 2), the spatial location of the plots explained a large degree of the variation in bacterial community composition between plots, which was due to spatial autocorrelation of pH and possible additional environmental parameters. This study emphasises the importance of sampling design for obtaining representative samples from soil.     

A comparison of indexes to estimate corn S uptake and S mineralization in the field

The development of simple predictors of sulfur (S) mineralization and its correlation with field-derived data may help improving corn S availability diagnosis. The objectives of this study were (1) to compare methods to estimate soil S mineralization, (2) to develop a model to predict soil S mineralization from S mineralization indexes and edaphic variables, and (3) to predict field-grown corn S uptake (S_uptake) and apparent S mineralization (S_min-app) from different S mineralization indexes and edaphic-climatic variables. We evaluated 26 experimental sites where we measured edaphic variables as soil organic C (SOC), organic C in the particulate fraction (C-PF), S mineralization potential (S_min-10wk), S mineralized during a short-term (7 days) aerobic incubation + initial inorganic S (S_min-7d?+?S_inorg), and N mineralized during a short-term (7 days) anaerobic incubation (N_an). Additionally, 18 field experiments were carried out to quantify S_uptake and S_min-app. The C-PF, S_min-7d?+?S_inorg, N_an, and SOC were variables significantly correlated with S_min-10wk (r?=?0.89, 0.89, 0.88, and 0.85, respectively). We developed a simple model to predict S_min-10wk from selected edaphic variables (S_min-10wk?=?0.038*N_an?+?0.106*SOC?+?0.74; R_a² =?0.87). The S_min-10wk, C-PF, and S_min-7d?+?S_inorg showed a liner-plateau association with S_uptake (R²?=?0.73, 0.53, and 0.48, respectively). We modified the method to estimate S_min-app to account for S losses (S_{min-app (modified)}) and developed a model to predict S_{min-app (modified)} from C-PF (S_{min-app (modified)}?=?4.65*C-PF?+?9.86; R²?=?0.62) or S_min-10wk (S_{min-app (modified)}?=?3.0*S_min-10wk?+?7.4; R²?=?0.54). Our results demonstrate that S mineralization indexes can be used to predict corn S availability under field conditions.     

Analysis of tree interactions in a mixed Mediterranean pine stand using competition indices

Studying species interactions in mixed forests allows us to assess their potential benefits and adapt current silvicultural tools developed in monospecific stands to multi-specific stands. We analyzed tree interactions in a Pinus halepensis Mill. and Pinus pinea L. mixed plantation using individual tree neighborhood models and competition indices that accounted for symmetric and asymmetric competition, to analyze whether the growth of each species was better explained by symmetric or asymmetric competition. We also split the competition indices into their intra- and interspecific forms, to test for competition effects on growth change based on competitor identity. Finally, we analyzed whether P. halepensis and P. pinea trees had different growth responses to competition. When calculating competition indices, we explored how spatial information and size of competitor trees contributed to the quantification of the process. Competition measurements were optimized to more precisely describe interactions. Results showed that the inclusion of competition indices generated important improvements in growth models. The main mode of competition was symmetric, which could be related to water restrictions typical of the Mediterranean climate. Considering competitor identity did not improve the growth models, while measurement without discriminating competitors by species generated more parsimonious models. P. halepensis and P. pinea trees had similar growth responses to competition, indicating that the two species cope with competition in similar ways. However, P. pinea showed lower average growth than P. halepensis in the period analyzed. Results suggest that preventing the onset of intense interspecific competition processes could help slow down the long-term replacement of P. pinea by P. halepensis and could have benefits for silvicultural management in systems with two species that share ecological niches but are capable of generating different goods and services.     

Escherichia coli and selected veterinary and zoonotic pathogens isolated from environmental sites in companion animal veterinary hospitals in southern Ontario

Hospital-based infection control in veterinary medicine is emerging and the role of the environment in hospital-acquired infections (HAI) in veterinary hospitals is largely unknown. This study was initiated to determine the recovery of Escherichia coli and selected veterinary and zoonotic pathogens from the environments of 101 community veterinary hospitals. The proportion of hospitals with positive environmental swabs were: E. coli--92%, Clostridium difficile--58%, methicillin-resistant Staphylococcus aureus (MRSA)--9%, CMY-2 producing E. coli--9%, methicillin-resistant Staphylococcus pseudintermedius--7%, and Salmonella--2%. Vancomycin-resistant Enterococcus spp., canine parvovirus, and feline calicivirus were not isolated. Prevalence of antimicrobial resistance in E. coli isolates was low. Important potential veterinary and human pathogens were recovered including Canadian epidemic strains MRSA-2 and MRSA-5, and C. difficile ribotype 027. There is an environmental reservoir of pathogens in veterinary hospitals; therefore, additional studies are required to characterize risk factors associated with HAI in companion animals, including the role of the environment.     

Spatial heterogeneity in statistical power to detect changes in lake area in Alaskan National Wildlife Refuges

Over the past 50 years, the number and size of high-latitude lakes have decreased throughout many regions; however, individual lake trends have been variable in direction and magnitude. This spatial heterogeneity in lake change makes statistical detection of temporal trends challenging, particularly in small analysis areas where weak trends are difficult to separate from inter- and intra-annual variability. Factors affecting trend detection include inherent variability, trend magnitude, and sample size. In this paper, we investigated how the statistical power to detect average linear trends in lake size of 0.5, 1.0 and 2.0 %/year was affected by the size of the analysis area and the number of years of monitoring in National Wildlife Refuges in Alaska. We estimated power for large (930–4,560 sq km) study areas within refuges and for 2.6, 12.9, and 25.9 sq km cells nested within study areas over temporal extents of 4–50 years. We found that: (1) trends in study areas could be detected within 5–15 years, (2) trends smaller than 2.0 %/year would take >50 years to detect in cells within study areas, and (3) there was substantial spatial variation in the time required to detect change among cells. Power was particularly low in the smallest cells which typically had the fewest lakes. Because small but ecologically meaningful trends may take decades to detect, early establishment of long-term monitoring will enhance power to detect change. Our results have broad applicability and our method is useful for any study involving change detection among variable spatial and temporal extents.     

Parentage assignment in Haliotis midae L.: a precursor to future genetic enhancement programmes for South African abalone

The establishment and evaluation of family lines using pedigree information provides an advanced understanding of the variability that exists for complex, economically valuable traits and is a necessary step in the execution of an effective breeding programme. The aim of this study was to assign parentage to mass‐spawned Haliotis midae juveniles using species‐specific microsatellite markers. Screening of wild abalone individuals revealed that the nine loci selected complied with the minimum requirements for parentage analyses: a null allele frequency <5% as well as a high number and frequency of alleles per locus. A total of 598 individuals were genotyped (198 breeding individuals and 400 F1 progeny) from two farms, with parentage results yielding 91% and 90% successful assignment for Farms A and B respectively. This study, therefore, provided the necessary pedigree information required for controlled breeding of individual adult abalone and indicated the usefulness of the panel of microsatellite markers selected for parentage assignment.