Colonization,mouse-style

Several recent papers, including one in BMC Evolutionary Biology, examine the colonization history of house mice. As well as background for the analysis of mouse adaptation, such studies offer a perspective on the history of movements of the humans that accidentally transported the mice.     

Oral Colonization of Fungi

Opportunistic microbes are able to exist as commensals or pathogens depending on local environmental conditions. The bacterial microbiome at mucosal sites (gut, oral and vaginal) has been well characterized but there has been less focus on the fungal component of the microbiome, the “mycobiome”, especially of the oral mucosa. Genomic characterization studies have shown that Candida species are the most prevalent fungal species in the mycobiomes of the murine gut and human oral cavity, with C. albicans being the most abundant fungal species in the oral cavity. In this review, we outline recent advances in the characterization of the oral mycobiome, how different Candida species colonize, invade and infect the oral cavity, and how epithelial surfaces play a key role in antifungal activity and discriminate between commensal and pathogenic Candida.     

Streptococcus Adherence and Colonization

Summary: Streptococci readily colonize mucosal tissues in the nasopharynx; the respiratory, gastrointestinal, and genitourinary tracts; and the skin. Each ecological niche presents a series of challenges to successful colonization with which streptococci have to contend. Some species exist in equilibrium with their host, neither stimulating nor submitting to immune defenses mounted against them. Most are either opportunistic or true pathogens responsible for diseases such as pharyngitis, tooth decay, necrotizing fasciitis, infective endocarditis, and meningitis. Part of the success of streptococci as colonizers is attributable to the spectrum of proteins expressed on their surfaces. Adhesins enable interactions with salivary, serum, and extracellular matrix components; host cells; and other microbes. This is the essential first step to colonization, the development of complex communities, and possible invasion of host tissues. The majority of streptococcal adhesins are anchored to the cell wall via a C-terminal LPxTz motif. Other proteins may be surface anchored through N-terminal lipid modifications, while the mechanism of cell wall associations for others remains unclear. Collectively, these surface-bound proteins provide Streptococcus species with a “coat of many colors,” enabling multiple intimate contacts and interplays between the bacterial cell and the host. In vitro and in vivo studies have demonstrated direct roles for many streptococcal adhesins as colonization or virulence factors, making them attractive targets for therapeutic and preventive strategies against streptococcal infections. There is, therefore, much focus on applying increasingly advanced molecular techniques to determine the precise structures and functions of these proteins, and their regulatory pathways, so that more targeted approaches can be developed.     

Gastrointestinal Colonization of Fungi

The human gastrointestinal tract is colonized with trillions of commensal microbes, and disturbances in the equilibrium of the gut microbiota have now been shown to be associated with a number of human diseases. Fungi, particularly Candida spp., are normal, harmless residents of the human gut, but in certain instances can cause invasive infections and inflammatory disorders. This paper will review the fungal diversity in the human gut, host and fungal factors that regulate GI colonization, and how these factors play into the pathogenesis of human disease.     

Inhibition of Fungal Colonization by Pseudoalteromonas tunicata Provides a Competitive Advantage during Surface Colonization

The marine epiphytic bacterium Pseudoalteromonas tunicata produces a range of extracellular secondary metabolites that inhibit an array of common fouling organisms, including fungi. In this study, we test the hypothesis that the ability to inhibit fungi provides P. tunicata with an advantage during colonization of a surface. Studies on a transposon-generated antifungal-deficient mutant of P. tunicata, FM3, indicated that a long-chain fatty acid-coenzyme A ligase is involved in the production of a broad-range antifungal compound by P. tunicata. Flow cell experiments demonstrated that production of an antifungal compound provided P. tunicata with a competitive advantage against a marine yeast isolate during surface colonization. This compound enabled P. tunicata to disrupt an already established fungal biofilm by decreasing the number of yeast cells attached to the surface by 66% ± 9%. For in vivo experiments, the wild-type and FM3 strains of P. tunicata were used to inoculate the surface of the green alga Ulva australis. Double-gradient denaturing gradient gel electrophoresis analysis revealed that after 48 h, the wild-type P. tunicata had outcompeted the surface-associated fungal community, whereas the antifungal-deficient mutant had no effect on the fungal community. Our data suggest that P. tunicata is an effective competitor against fungal surface communities in the marine environment.     

Colonization history in Fennoscandian rodents

Fennoscandia probably constitutes one of the best places on earth to study faunal history. During the height of the most recent glacial period Fennoscandia was completely covered with ice. Thus, the majority of extant species must originate from ancestors who survived the latest glaciation in non-glaciated areas outside Fennoscandia. Moreover, the geography and geological history of Fennoscandia suggests that post-glacial recolonization by land mammals must have been restricted to specific routes in time and space. Phylogeographic surveys of mitochondrial DNA (mtDNA) variation in Fennoscandian rodents have demonstrated that glacial history and patterns of post-glacial colonization have played a major role in shaping present day patterns of genetic differentiation within species. Thus, the genetic imprints of historical demographic conditions and vicariant geographic events have been retained within species and can be used to infer the history of populations. The field vole (Microtus agrestis) is used to illustrate these data and processes. Comparisons are made with phylogeographic surveys of the bank vole (Clethrionomys glareolus) , the eastern house mouse (Mus musculus) and the wood lemming (Myopus schisticolor) as well as a few other species for which less extensive studies have been performed. The main patterns of post-glacial colonization of Fennoscandia by rodents are described. The effects of timing and patterns of colonization on contemporary population genetic structure and levels of genetic variation are discussed. Specifically, the effects of hybridization and introgression as well as founder events and bottlenecks are explored.     

The Magdalenian Colonization of Southern Germany

Although the topics of migration and colonization have received renewed archaeological attention in recent years, their relevance to the deep past of hunter-gatherer archaeology has been debated. The Magdalenian colonization of southern Germany after the last glacial maximum, ca. 15,000-13,000 B.P., presents a case study in which many of the debated issues can be explored. Environmental change and relative demographic pressure played a causal role in population movements, leading to a gradual, discontinuous expansion from the Franco-cantabrian refugium. Active social strategies to overcome the risks facing frontier groups helped maintain remarkable uniformity in material culture across hundreds of kilometers, despite shifts in subsistence and settlement patterns required in the newly occupied areas, [archaeology. Palaeolithic, Europe, migration]     

Evaluating Five Models of Human Colonization

Five patterns for the human colonization of unoccupied regions are tested for viability by the use of a new stochastic band simulation program, called ETHNOPOP ©, that incorporates four demographic variables: (1) sex ratio at birth, (2) distribution of sibships, (3) maternal risk of giving birth, and (4) risk of death; as well as three cultural variables: (1) marriage choice, (2) polygyny, and (3) marriage pool. It was discovered that small colonizing bands initially undergo a Stochastic Crisis because of a demographic version of the Sewall Wright Effect, followed most often by a Malthusian Takeoff in population size if fertility rates are high enough. Of the models tested, it was discovered that the "string of pearls" model, in which bands are arrayed along a stream or coastline, is the most viable colonizing pattern, and that the "outpost" model, in which a band has no contiguous bands, and the "beachhead" model, in which a group of bands are clustered against a body of water, should be subsumed under the "pulse" model, in which successive waves of colonists enter a previously unoccupied area, [colonization, modeling, simulation, sex ratio, fertility]     

Colonization and succession in deep-sea ecosystems

Experimental studies reveal generally slow but variable colonization rates in deep-sea soft bottoms. Species successions following biological disturbance appear to be complex and unpredictable, potentially playing a role in structuring these diverse communities. In contrast, physical processes probably play a prominent role in the rapid species turnovers observed at hydrothermal vents. Better information concerning disturbance regimes, recruitment processes and resource utilization is required to elaborate successional mechanisms in both soft-bottom and vent environments.     

Colonization in an abandoned East-Mediterranean vineyard

Abstract. Previous studies on secondary succession in abandoned agricultural land in the Mediterranean area were carried out by the chronosequence method, including data from different sites. A unique opportunity to study secondary succession arose from a situation in which different parts of one homogeneous East-Mediterranean vineyard were abandoned for 5, 8, 15 and 35 yr, and did not suffer from any disturbance subsequently. Most of the perennial species that colonized the abandoned vineyard were fleshy fruited species, which apparently were dispersed by birds from the surrounding maquis into the vineyard. These bird-dispersed species were the first to be established, and were the dominant plant group according to dispersal modes. The abandoned vine plants and their supporting columns provided the birds with perching and feeding sites, enhancing the arrival of bird-dispersed species regardless of their life forms. Under these conditions the most important attribute that affected vegetation dynamics was seed dispersal mode. Trees were among the first to colonize in the vineyard, implying that no facilitation was needed for their establishment. Annual plant species were the only species to disappear during succession. Almost all perennial species which had arrived persisted in the vineyard, and no replacement of perennial species was found. The rate of succession was rapid, as expressed by the short time (8–15 yr) needed for the stabilization of species composition, for growth to average height of late succession trees, and for reaching high cover of the invading perennial species in the abandoned vineyard. The secondary succession described above differs from that in the western Mediterranean by the absence of perennial species replacement and its rapid rate. The possible causes are discussed.     

Colonization Credit in Restored Wet Heathlands

Although human‐driven landscape modification is generally characterized by habitat destruction and fragmentation, it may also result in the creation of new habitat patches, providing conditions conducive to spontaneous colonization. In this article, we propose the concept of “colonization credit” (i.e., the number of species yet to colonize a patch, following landscape changes) as a framework to evaluate the success of colonization, in terms of species richness, in new/restored habitats, taking into account the spatial structure of landscapes. The method mirrors similar approaches used to estimate extinction debt in the context of habitat fragmentation, that is, comparisons, between old and new habitat patches, of the relationships among spatial patch metrics and patch species richness. We applied our method to the case of spontaneous colonization of newly created habitat patches suitable for wet heathland plant communities in South Belgium. Colonization credit was estimated for the total species richness, the specialist species richness, and the species richness of three emergent groups (EGs) of specialist species, delineated on the basis of dispersal traits. No significant colonization credit was identified either in patches created 25–55 years ago or in those created within the past 25 years, with the exception of species from our first EG (mostly anemochorous species with long‐term persistent seed bank). However, the differential response of species in that first EG could not be explained through their characteristic life history traits. The results of this study are encouraging and suggest that deliberate, directed restoration activities could yield positive developments in a relatively short period of time.     

Colonization of new habitats by earthworms

Summary In this paper a simple model is used to study the dispersal of earthworm populations into new habitats. Simple models do not describe processes accurately, but can help gain insight into the functioning of ecosystems or processes in ecosystems. Using information on reproduction, survival and dispersal at the level of the individual, the velocity of earthworm population expansion was calculated. Dispersal of earthworms can be active or passive. The parameters of active and passive dispersal were calculated from field experiments in one of the Dutch polders. Parameters of reproduction and survival were estimated from published data. The effects of processes at the individual level on the velocity of population expansion were studied for two species (Aporrectodea caliginosa and Lumbricus rubellus). The model shows that passive transport has a major influence on the velocity of population expansion, which is strongly increased even if this transport involves only a very small part of the population. At a high level of passive transport, however, death induced by this mode of dispersal can have a negative influence on population expansion. In the discussion it is indicated that optimising growth conditions of the earthworms might be the easiest way to promote population expansion. However, promoting dispersal by passive mechanisms can also be very important.Communication no. 36 of the Dutch Programme on Soil Ecology of Arable Farming Systems     

Colonization rules and spatial distributions in ecology

Because they are intuitive and mathematically straight-forward, colonization rules are often used to model spatial patterns in ecology. Colonization rules assign individuals to categories according to the locations of previous colonists. In this note, a compact introduction to colonization rules in ecology is presented with implications for autocorrelation and spatial distributions. I use the colonization rule approach to unify a diverse set of spatial and species diversity analyses, exploring future extensions to incorporate greater realism.     

Colonization of artificial bare areas by microorganisms

The Botanical Review -     

Colonization of hospitalized patients with yeast-like organisms

The pharyngeal, fecal and skin carrier rates of yeast-like organisms was determined in 126 patients on the day of admission to a larger Veterans Administration Hospital. None of these patients had been hospitalized or received anti-microbial agents during the previous year Candida and Torulopsis species were most common. A small percentage of patients were carriers of various species belonging to the genera Trichosporon, Rhodotorula, Saccharomyces, Leucosporidium and Endomycopsis. Fifty of the original 126 patients remained hospitalized for a sufficient duration to permit repeat cultures on days 7 and 14. Twenty-five of these patients served as controls and did not receive antibiotics; the other 25 received at least a 4-day course of antibiotic therapy for an underlying infection. Although there was no significant difference in the carrier rates in these 2 groups, organisms other than Candida continued to be isolated from the 50 patients who remained hospitalized for 2 weeks.     

Historical Archaeologies of Global Capitalism and Colonization

The Historical Archaeology of Buenos Aires:. City at the End of the World. Daniel Schavelzon. New York: Kluwer Academic/Plenum Publishers, 2000. 187 pp.
Domestic Architecture and Power: The Historical Archaeology of Colonial Ecuador. Ross W. Jamieson. New York: Kluwer Academic/Plenum Publishers, 2000. 244 pp.
Historical Archaeology in Wachovia: Excavating Eighteenth- Century Bethabara and Moravian Pottery. Stanley South. New York: Kluwer Academic/Plenum Publishers, 1999. 442 pp.
Historical Archaeology of the Ottoman Empire: Breaking New Ground. Uzi Baram and Lynda Carroll. eds. New York: Kluwer Academic/Plenum Publishers, 2000. 272 pp.     

Enhancing Soybean Rhizosphere Colonization by Rhizobium japonicum

A study was conducted to seek means to increase the colonization of the rhizosphere of soybeans (Glycine max L. Merrill) by Rhizobium japonicum. For this purpose, a strain of R. japonicum that was resistant to benomyl, streptomycin, and erythromycin was used. The numbers of R. japonicum rose quickly in the first 2 days after soybean seeds were planted in soil and then rapidly fell. The decline was slower if the seeds were coated with benomyl. This fungicide reduced the numbers of bacteria and protozoa in the rhizosphere, but the effect became less or disappeared as the plants grew. In sterile soil inoculated with R. japonicum and a mixture of microorganisms, the numbers of R. japonicum were usually lower if protozoa were present than if they were absent. Nodulation and plant yield were increased by the addition of benomyl to soybean seeds sown in sterile soil inoculated with R. japonicum and a mixture of microorganisms. The addition of streptomycin and erythromycin to soil stimulated the growth of R. japonicum but inhibited other bacteria in the presence or absence of soybeans. The data indicate that colonization can be increased by the use of antimicrobial agents and R. japonicum strains resistant to those inhibitors.