Treasuring crop wild relative diversity: analysis of success from the seed collecting phase of the ‘Adapting Agriculture to Climate Change’ project

The seed collecting phase of the ‘Adapting Agriculture to Climate Change’ project was, to the best of our knowledge, the most comprehensive crop wild relatives (CWR) collecting and conservation mission to-date and provides priceless genetic diversity for ongoing and future crop breeding efforts. The seed collecting started in 2013 and was concluded in 2019, it was carried out in 22 countries in Africa, Asia, the Americas and Europe, involving CWR taxa of 28 different crop genepools. 3002 target seed accessions of 242 taxa were collected and are currently stored long-term in the countries of collection and, in most of the cases, backed up at the Millennium Seed Bank (UK). Considering also non-target species, 3854 seed accessions were collected. For the genepools of bambara groundnut (Vigna subterranea (L.) Verdc.), barley (Hordeum L.), grass pea (Lathyrus sativus L.), sorghum (Sorghum bicolor (L.) Moench), and wheat (Triticum L.), the collecting phase was highly successful in terms of diversity of both, species and populations. Despite the overall success of the project, in our analysis we discovered several issues that were encountered in the seed collecting. In particular, comparing the initial collecting targets with the seed accessions effectively collected it emerges that: (1) some important crop genepools were characterized by a low collecting success (e.g. banana/plantain (Musa L.), potato (Solanum tuberosum L.), rice (Oryza L.), (2) genepool 1 (the most important for breeding efforts) of some crop genepools was under-collected (e.g. eggplant (Solanum L.) and sorghum), (3) some important centres of plant biodiversity (especially the Indian Subcontinent) were underrepresented in the seed collecting. This analysis can guide further collecting missions in order to fill gaps in the long-term conservation of CWR of great importance for crop improvement.

     

Analysis of Nitrogen Dynamics in the Lye Brook Wilderness Area,Vermont, USA

Nitrogen (N) deposition and its impact on terrestrial and aquatic ecosystems is a concern facing federal land managers at the Lye Brook Wilderness in Vermont and other protected aras throughout the northeastern United States. In this study, we compared N production in soils with N concentrations and outputs in leachates to determine how forest cover types differ in regulating N losses. Also, precipitation inputs and modeled estimates of streamwater outputs were used to calculate a watershed N budget. Most ammonium and nitrate were produced in organic soils with deciduous cover. Softwood stands had low net nitrification rates and minimal N leaching. A comparison of watershed inputs and outputs showed a net gain in total dissolved N (5.5 kg ha^-1 yr^-1) due to an accumulation of dissolved inorganic N. The Lye Brook Wilderness ecosystem has N budgets similar to other forested ecosystems in the region, and appears to be assimilating the accumulating N. However seasonal losses of nitrate observed in mineral soils and streamwater may be early warnings of the initial stages of N saturation.     

Novel “filter pellet” sample preparation strategy for quantitative LA-ICP-MS analysis of filter-bound sediments: a “green chemistry” alternative to sediment fingerprinting in Tanzania’s Ruvu River basin

Journal of Soils and Sediments - The goal of this study was to develop a “green chemistry” alternative sample preparation method for elemental analysis of sediments using laser ablation...     

Persistence of Gunnison’s prairie dog colonies in Arizona, USA

Although the five species of prairie dogs (Cynomys spp.) are recognized as important components of grassland ecosystems in western North America, they have experienced major population declines due to poisoning, outbreaks of sylvatic plague, recreational shooting, and habitat conversion. From May 2000 to October 2001, we investigated 270 colonies of Gunnison’s prairie dog (Cynomys gunnisoni) in Arizona. Because these colonies were classified as active in previous surveys (1987, 1990-1994, 1998), we were able to examine their persistence. Most (70%) of the colonies became inactive between the initial and recent surveys, with colony extinctions spanning our study area. Colony persistence was positively associated with the persistence of the nearest neighboring colony but was not associated with major vegetation type, distance to nearest neighboring colony, or initial size of the colony. The amount of area occupied by individual colonies varied between surveys, sometimes dramatically. We found little evidence that the reduction in active colonies was due to poisoning, recreational shooting, or habitat conversion. Rather, direct and indirect evidence suggest plague is the primary factor negatively impacting Gunnison’s prairie dog populations in Arizona. Currently, there is no way to control or prevent plague outbreaks in Gunnison’s prairie dog populations. To mitigate the effects of localized plague outbreaks on the overall population of this species, we suggest that Gunnison’s prairie dog be reintroduced to public lands throughout its historical range.     

Estimating floristic integrity in tallgrass prairie

Indices are needed in habitat conservation and restoration to provide repeatable measures relevant to conservation goals. A monitoring and research program was established at Nachusa Grasslands in north-central Illinois (USA) to assess progress in tallgrass prairie restoration and reconstruction efforts and evaluate the effectiveness of indices used to measure community-level properties related to vegetation integrity. Indices selected for comparison included standard diversity measures (e.g., Shannon-Weiner Index, Evenness, Species Richness) and indices developed specifically to estimate vegetation integrity. These latter indices included two unweighted diversity indices, the Species Richness Index and Native Richness Index, and two indices weighted by characteristics of species composition, the Floristic Quality Index (FQI) and its component Mean Coefficient of Conservatism (Mean C). A coefficient of conservatism (CC) is an integer ranging from 0 to 10 assigned a priori to each taxon in a regional flora that estimates the fidelity of a species to natural areas (non-native and most ruderal species are assigned 0 or low values, respectively; species known primarily from natural areas are assigned higher values). All indices compared in this study were calculated using vegetation data collected from equal-sized sampling grids stratified across seven prairie units. The units included remnants and plantings representing a wide range of habitat quality. The FQI and Mean C explained the most variation among sites and were most effective at distinguishing recognized qualitative differences indicating they can be more informative than traditional species-diversity measures in assessing floristic integrity within community types. The FQI and Mean C are applicable to both quantitative ecological monitoring and plotless survey methods.     

Eubacterial communities in different soil macroaggregate environments and cropping systems

Different positions within soil macroaggregates, and macroaggregates of different sizes, have different chemical and physical properties which could affect microbial growth and interactions among taxa. The hypothesis that these soil aggregate fractions contain different eubacterial communities was tested using terminal restriction fragment length polymorphism (T-RFLP) of the 16S ribosomal gene. Communities were characterized from two field experiments, located at the Kellogg Biological Station (KBS), MI, USA and the Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA. Three soil management regimes at each site were sampled and management was found to significantly affect T-RFLP profiles. The soil aggregate erosion (SAE) method was used to isolate aggregate regions (external and internal regions). Differences between eubacterial T-RFLP profiles of aggregate exteriors and interiors were marginally significant at KBS (accounting for 12.5% of total profile variance), and not significant at OARDC. There were no significant differences among macroaggregate size classes at either site. These results are in general agreement with previous studies using molecular methods to examine microbial communities among different soil macroaggregate size fractions, although further study of communities within different aggregate regions is warranted. Analysis of individual macroaggregates revealed large inter-aggregate variability in community structure. Hence the tertiary components of soil structure, e.g. arrangement of aggregates in relation to shoot residue, roots, macropores, etc., may be more important than aggregate size or intra-aggregate regions in the determination of the types of microbial communities present in aggregates. Direct microscopic counts were also used to examine the bacterial population size in aggregate regions at KBS. The proportion of bacterial cells with biovolumes >0.18 μm³ was higher in aggregate interiors than in exteriors, indicating potentially higher activity in that environment. This proportion was significantly related to percent C of the samples, while total bacterial cell counts were not.     

Organic C and N stabilization in a forest soil: Evidence from sequential density fractionation

In mineral soil, organic matter (OM) accumulates mainly on and around surfaces of silt- and clay-size particles. When fractionated according to particle density, C and N concentration (per g fraction) and C/N of these soil organo-mineral particles decrease with increasing particle density across soils of widely divergent texture, mineralogy, location, and management. The variation in particle density is explained potentially by two factors: (1) a decrease in the mass ratio of organic to mineral phase of these particles, and (2) variations in density of the mineral phase. The first explanation implies that the thickness of the organic accumulations decreases with increasing particle density. The decrease in C/N can be explained at least partially by especially stable sorption of nitrogenous N-containing compounds (amine, amide, and pyrrole) directly to mineral surfaces, a phenomenon well documented both empirically and theoretically. These peptidic compounds, along with ligand-exchanged carboxylic compounds, could then form a stable inner organic layer onto which other organics could sorb more readily than onto the unconditioned mineral surfaces (“onion” layering model).To explore mechanisms underlying this trend in C concentration and C/N with particle density, we sequentially density fractionated an Oregon andic soil at 1.65, 1.85, 2.00, 2.28, and 2.55 g cm⁻³ and analyzed the six fractions for measures of organic matter and mineral phase properties.All measures of OM composition showed either: (1) a monotonic change with density, or (2) a monotonic change across the lightest fractions, then little change over the heaviest fractions. Total C, N, and lignin phenol concentration all decreased monotonically with increasing density, and ¹⁴C mean residence time (MRT) increased with particle density from ca. 150 years to >980 years in the four organo-mineral fractions. In contrast, C/N, ¹³C and ¹⁵N concentration all showed the second pattern. All these data are consistent with a general pattern of an increase in extent of microbial processing with increasing organo-mineral particle density, and also with an “onion” layering model.X-ray diffraction before and after separation of magnetic materials showed that the sequential density fractionation (SDF) isolated pools of differing mineralogy, with layer-silicate clays dominating in two of the intermediate fractions and primary minerals in the heaviest two fractions. There was no indication that these differences in mineralogy controlled the differences in density of the organo-mineral particles in this soil. Thus, our data are consistent with the hypothesis that variation in particle density reflects variation in thickness of the organic accumulations and with an “onion” layering model for organic matter accumulation on mineral surfaces. However, the mineralogy differences among fractions made it difficult to test either the layer-thickness or “onion” layering models with this soil. Although SDF isolated pools of distinct mineralogy and organic-matter composition, more work will be needed to understand mechanisms relating the two factors.     

Fungal diseases of rabbits.

Although fungal diseases in rabbits are reported, they are encountered infrequently in clinical practice. The most common fungal disease is a superficial dermatophytosis, with deep mycotic infections being rare. Rabbits can be asymptomatic carriers of dermatophytes and should be considered a potential source of zoonotic exposure. Treatment protocols often are based on common small animal regimes. Rabbits also have normal gastrointestinal yeast that often is found on routine fecal examinations.