Woody cover and birds

Major influences on biodiversity in general and on species distributions in particular have occurred on South African landscapes over time as a result of human activities and climate change. Landscapes in southern Africa are not only a product of changes in climate, but they are also a product of the changes brought about by people and their land management practices. In recent decades, bush encroachment has increased dramatically throughout the Savanna Biome of South Africa. Bush encroachment is a vegetation dynamic of global interest. It refers to the thickening or increase of woody vegetation (trees and shrubs) at the expense of grasses and/or herbaceous vegetation. In many areas across South Africa, systems that were once open grassland have become dense thickets dominated by trees and shrubs. Bush encroachment is driven by global factors like increasing carbon dioxide (CO2) levels in the atmosphere as well as local factors like grazing pressures and fire management practices. In Africa, it has long been recognized that there is an influence of vegetation patterns and structure on the distribution and abundance of birds. Changes in habitats due to an increase or decrease in woody cover has been linked to changes in bird diversity and community structure. This thesis looks at what impacts bush encroachment has had on bird distributions in eastern South Africa, with a special focus on the Kruger National Park as well as Palearctic migrants. Chapter 2 of the thesis develops a new quantitative method to relate bird distributions to woody cover. The algorithm is experimental, and an important aspect of the chapter is to investigate whether the results obtained coincide with expectations. The approach first estimates the proportion of the bird species in an area which occur in each woody cover category in a region. It also calculates the proportion of the area of the region which is in each woody cover category. It then uses Jacobs Index to provide an estimate of the extent of preference/avoidance of each species for each woody cover category, on a scale that runs from +1 (the entire population of the species is in that woody cover category) to –1 (none of the population of the species is in that woody cover category). The method is tested on a region consisting of three one-degree grid cells spanning Mpumalanga, Limpopo and Gauteng which include a diversity of woody cover categories, from grassland (no woody cover) to savanna to dense woodland. Chapter 3 applies this approach to the birds of the Kruger National Park, examining which species have distributions which can, and which cannot, be explained to a greater or lesser extent by a preference for a particular range of woody covers. Bird species are selected for close monitoring for ecological management purposes of the Kruger National Park. Chapter 4 considers a set of 10 bird species, all of which are migrants to South Africa from Eurasia, and occur to a large extent during their non-breeding period within the savanna biome of South Africa. For each species, the extent of increase in relative abundance between the first and second bird atlas projects in the region (SABAP1 and SABAP2) is estimated. In most cases, the change of relative abundance can be explained in terms of bush encroachment. The likely provenance of these species in Eurasia is considered; for most species, this area lies in southwestern Asia, i.e. the Ukraine and adjacent Russia. Changes in habitat in this region are also considered and help to improve the understanding of how the populations in South Africa have changed

Science fiction in the public library : essence and selection

The selection of science fiction was researched to determine how science fiction should be evaluated and selected in the context of the public library. The first sub-problem to be researched concerned the cultural, societal and literary origins of this genre, after which its distinct phases of development were studied as well as the characteristic essence of science fiction which would affect its selection per se, specifically whether conventional literary criteria are suitable for the evaluation of items of science fiction during selection. The next sub-problem focused on, was whether theory can explain the process of fiction selection, The succeeding sub-problem was to empirically Study current practice in science fiction selection. Survey research was conducted amongst selected major urban/regional public library services in the USA. Final research results indicated that science fiction is a sophisticated, multi-textured genre which differs significantly from fellow popular genres, Science fiction is viewed by some critics as being on the cusp of post-modernism, a significant body of work in contemporary literature, and a supreme expression of late capitalism. Research further showed that no satisfactory evaluative criteria exist. It was also established that theory of fiction selection is not always capable of explaining or guiding the process of fiction selection. There is no model for the selection of science fiction. Finn guiding principles for science fiction selection could be formulated by the aid of this study. The study concluded with a specially-designed model for the selection of science fiction (including a scorecard with specially-compiled criteria for evaluating items), as well as a suggested core collection. A structured approach should be followed by the science fiction selector. The guiding principles and core collection which were formulated in this study, the set of special criteria as well as the model, together demonstrate that the selection of science fiction can be structured, controlled and guided within established parameters.Information ScienceD. Lit. et Phil. (Information Science

Draft genome sequence of Pseudomonas moraviensis R28-S

We report the draft genome sequence of Pseudomonas moraviensis R28-S, isolated from the municipal wastewater treatment plant of Moscow, ID. The strain carries a native mercury resistance plasmid, poorly maintains introduced IncP-1 antibiotic resistance plasmids, and has been useful for studying the evolution of plasmid host range and stability

Bacterial evolution: Resistance is a numbers game

Plasmids are well known for spreading antibiotic-resistance genes between bacterial strains. Recent experiments show that they can also act as catalysts for evolutionary innovation, promoting rapid evolution of novel antibiotic resistance

Draft genome sequence of Pseudomonas sp. nov. H2

We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in Moscow, ID, USA. The strain is most closely related to Pseudomonas putida. However, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains IncP-1 plasmids

Mobile compensatory mutations promote plasmid survival

The global dissemination of plasmids encoding antibiotic resistance represents an urgent issue for human health and society. While the fitness costs for host cells associated with plasmid acquisition are expected to limit plasmid dissemination in the absence of positive selection of plasmid traits, compensatory evolution can reduce this burden. Experimental data suggest that compensatory mutations can be located on either the chromosome or the plasmid, and these are likely to have contrasting effects on plasmid dynamics. Whereas chromosomal mutations are inherited vertically through bacterial fission, plasmid mutations can be inherited both vertically and horizontally and potentially reduce the initial cost of the plasmid in new host cells. Here we show using mathematical models and simulations that the dynamics of plasmids depends critically on the genomic location of the compensatory mutation. We demonstrate that plasmid-located compensatory evolution is better at enhancing plasmid persistence, even when its effects are smaller than those provided by chromosomal compensation. Moreover, either type of compensatory evolution facilitates the survival of resistance plasmids at low drug concentrations. These insights contribute to an improved understanding of the conditions and mechanisms driving the spread and the evolution of antibiotic resistance plasmids. IMPORTANCE Understanding the evolutionary forces that maintain antibiotic resistance genes in a population, especially when antibiotics are not used, is an important problem for human health and society. The most common platform for the dissemination of antibiotic resistance genes is conjugative plasmids. Experimental studies showed that mutations located on the plasmid or the bacterial chromosome can reduce the costs plasmids impose on their hosts, resulting in antibiotic resistance plasmids being maintained even in the absence of antibiotics. While chromosomal mutations are only vertically inherited by the daughter cells, plasmid mutations are also provided to bacteria that acquire the plasmid through conjugation. Here we demonstrate how the mode of inheritance of a compensatory mutation crucially influences the ability of plasmids to spread and persist in a bacterial population

The influence of the accessory genome on bacterial pathogen evolution

Bacterial pathogens exhibit significant variation in their genomic content of virulence factors. This reflects the abundance of strategies pathogens evolved to infect host organisms by suppressing host immunity. Molecular arms-races have been a strong driving force for the evolution of pathogenicity, with pathogens often encoding overlapping or redundant functions, such as type III protein secretion effectors and hosts encoding ever more sophisticated immune systems. The pathogens’ frequent exposure to other microbes, either in their host or in the environment, provides opportunities for the acquisition or interchange of mobile genetic elements. These DNA elements accessorise the core genome and can play major roles in shaping genome structure and altering the complement of virulence factors. Here, we review the different mobile genetic elements focusing on the more recent discoveries and highlighting their role in shaping bacterial pathogen evolution

Adaptive modulation of antibiotic resistance through intragenomic coevolution

Bacteria gain antibiotic resistance genes by horizontal acquisition of mobile genetic elements (MGEs) from other lineages. Newly acquired MGEs are often poorly adapted causing intragenomic conflicts; these are resolved by either compensatory adaptation - of the chromosome or the MGE - or reciprocal coadaptation. The footprints of such intragenomic coevolution are present in bacterial genomes, suggesting an important role promoting genomic integration of horizontally acquired genes, but direct experimental evidence of the process is limited. Here we show adaptive modulation of tetracycline resistance via intragenomic coevolution between Escherichia coli and the multidrug resistant plasmid RK2. Tetracycline treatments, including monotherapy or combination therapies with ampicillin, favoured de novo chromosomal resistance mutations coupled with mutations on RK2 impairing the plasmid-encoded tetracycline efflux pump. These mutations together provided increased tetracycline resistance at reduced cost. Additionally, the chromosomal resistance mutations conferred cross-resistance to chloramphenicol. Reciprocal coadaptation was not observed under ampicillin-only or no antibiotic selection. Intragenomic coevolution can create genomes comprising multiple replicons that together provide high-level, low-cost resistance, but the resulting co-dependence may limit the spread of coadapted MGEs to other lineages

Clinically Relevant Plasmid-Host Interactions Indicate that Transcriptional and Not Genomic Modifications Ameliorate Fitness Costs of Klebsiella pneumoniae Carbapenemase-Carrying Plasmids

The rapid dissemination of antimicrobial resistance (AMR) around the globe is largely due to mobile genetic elements, such as plasmids. They confer resistance to critically important drugs, including extended-spectrum beta-lactams, carbapenems, and colistin. Large, complex resistance plasmids have evolved alongside their host bacteria. However, much of the research on plasmid-host evolution has focused on small, simple laboratory plasmids in laboratory-adapted bacterial hosts. These and other studies have documented mutations in both host and plasmid genes which occur after plasmid introduction to ameliorate fitness costs of plasmid carriage. We describe here the impact of two naturally occurring variants of a large AMR plasmid (pKpQIL) on a globally successful pathogen. In our study, after pKpQIL plasmid introduction, no changes in coding domain sequences were observed in their natural host, Klebsiella pneumoniae. However, significant changes in chromosomal and plasmid gene expression may have allowed the bacterium to adapt to the acquisition of the AMR plasmid. We hypothesize that this was sufficient to ameliorate the associated fitness costs of plasmid carriage, as pKpQIL plasmids were maintained without selection pressure. The dogma that removal of selection pressure (e.g., antimicrobial exposure) results in plasmid loss due to bacterial fitness costs is not true for all plasmid/host combinations. We also show that pKpQIL impacted the ability of K. pneumoniae to form a biofilm, an important aspect of virulence. This study used highly relevant models to study the interaction between AMR plasmids and pathogens and revealed striking differences from results of studies done on laboratory-adapted plasmids and strains

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

Plasmids can mediate horizontal gene transfer of antibiotic resistance, virulence genes, and other adaptive factors across bacterial populations. Here, we analyze genomic composition and pairwise sequence identity for over 10,000 reference plasmids to obtain a global map of the prokaryotic plasmidome. Plasmids in this map organize into discrete clusters, which we call plasmid taxonomic units (PTUs), with high average nucleotide identity between its members. We identify 83 PTUs in the order Enterobacterales, 28 of them corresponding to previously described archetypes. Furthermore, we develop an automated algorithm for PTU identification, and validate its performance using stochastic blockmodeling. The algorithm reveals a total of 276 PTUs in the bacterial domain. Each PTU exhibits a characteristic host distribution, organized into a six-grade scale (I-VI), ranging from plasmids restricted to a single host species (grade I) to plasmids able to colonize species from different phyla (grade VI). More than 60% of the plasmids in the global map are in groups with host ranges beyond the species barrier.This work was funded by grant BFU2017-86378-P from the Spanish MINEC