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Results for “Spatial niche”

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PubMed2001

Axial differences in community structure of Crenarchaeota and Euryarchaeota in the highly compartmentalized gut of the soil-feeding termite Cubitermes orthognathus.

Methanogenesis represents an important electron sink reaction in the hindgut of soil-feeding termites. This is the first comprehensive analysis of the archaeal community structure within the highly compartmentalized intestinal tract of a humivorous insect, combining clonal analysis and terminal restriction fragment (T-RF) length polymorphism (T-RFLP) fingerprinting of the archaeal communities in the different gut compartments of Cubitermes orthognathus. We found that the morphological and physicochemical heterogeneity of the gut is reflected in a large phylogenetic diversity and pronounced axial differences in the composition of the archaeal gut microbiota, notably among those clones or ribotypes that could be assigned to methanogenic taxa. Comparative analysis of the relative frequencies of different archaeal lineages among the small-subunit rRNA gene (SSU rDNA) clones and their corresponding T-RF indicated that the archaeal community in the anterior, extremely alkaline hindgut compartment (P1) consists mainly of members of the Methanosarcinaceae, whereas Methanobacteriaceae and Methanomicrobiales predominate in the subsequent, more posterior compartments (P3/4a and P4b). The relative abundance of Thermoplasmales increased towards the rectum (P5). SSU rDNA sequences representing Crenarchaeota, which have not yet been reported to occur in the intestinal tracts of arthropods, were detected in all gut sections. We discuss how the spatial distribution of methanogenic populations may be linked to axial heterogeneity in the physicochemical gut conditions and to functional adaptations to their respective ecological niches.

Animals↗

PubMed2025

A single-cell spatial transcriptomic census of human skin anatomy.

The skin is the largest human organ and a site of significant disease burden, yet its cellular and molecular organization across the body are largely undefined. Here, we construct a spatially-resolved single-cell atlas of 1.2 million cells from normal adult human skin to localize 45 cell types across 15 anatomic sites. We define principles of organ-wide cell composition, including axes of cell diversity and specialization, and distinguish site-enriched cell types. Each body site is comprised of 10 multicellular neighborhoods that define cell-cell communication. Notably, we identify a perivascular neighborhood enriched for immune-stromal crosstalk with features resembling a homeostatic immune niche similar to skin-associated lymphoid tissue. Finally, mapping these neighborhoods onto skin disease reveals pathogenic neighborhood disruptions, including pan-disease immune alterations in the perivascular neighborhood. We present a framework charting the skin's multiscale spatial organization across a molecular to macroanatomic scale. This work advances our understanding of organ-wide skin cellular organization and communication, and its architectural disruption in disease.

Journal Article↗

PubMed2004

Dormant propagule banks integrate spatio-temporal heterogeneity in cladoceran communities.

The dynamics of populations of short-lived organisms are very patchy, both in space and time. The production of dormant propagules, however, results in an effective increase in generation time. We hypothesize that prolonged dormancy, together with variable regeneration niches, result in integration of temporal variability in community structure. In addition, in aquatic habitats, mechanisms such as sediment focussing can contribute to the integration of spatial variability. We tested the hypothesis that dormant propagule banks integrate spatial and temporal variation in active zooplankton communities. This was done by comparing cladoceran species richness and the community structure of hatchling assemblages retrieved from propagule bank samples collected on a single occasion with assemblages encountered in active community samples covering spatial variation (littoral and pelagic zone), diel (day and night), intra-year (May-October) and inter-year variation (1996-2000). The egg bank community structure differed significantly from the active community structure, but the dissimilarity decreased as spatial and temporal variation was better covered by the active community samples. Furthermore, the identification of all fully grown hatchlings ( n=214) yielded an equally high number of species ( n=22) to that occurring in all active community samples together (a total of 1,730 individuals were analysed). We conclude that the analysis of dormant propagules may form a cost-efficient alternative tool to the analysis of active community samples for an integrated assessment of cladoceran communities.

Adaptation, Physiological↗

PubMed1997

The 'sniffer-patch' technique for detection of neurotransmitter release.

A wide variety of techniques have been employed for the detection and measurement of neurotransmitter release from biological preparations. Whilst many of these methods offer impressive levels of sensitivity, few are able to combine sensitivity with the necessary temporal and spatial resolution required to study quantal release from single cells. One detection method that is seeing a revival of interest and has the potential to fill this niche is the so-called 'sniffer-patch' technique. In this article, specific examples of the practical aspects of using this technique are discussed along with the procedures involved in calibrating these biosensors to extend their applications to provide quantitative, in addition to simple qualitative, measurements of quantal transmitter release.

Animals↗

PubMed2005

Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.

Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such "ubiquitous dispersal" has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological "species" will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.

Journal Article↗

PubMed2025

Ovarian development is driven by early spatiotemporal priming of the coelomic epithelium.

Ovarian organogenesis requires the coordinated specification of supporting and steroidogenic cell lineages from multipotent coelomic epithelium (CE) progenitors. A longstanding question is whether the CE contains transcriptionally distinct, spatially organized progenitor subpopulations with predetermined lineage biases, or whether specification into supporting and steroidogenic lineages occurs only after delamination and integration into the bipotential gonad. The developmental origins of granulosa cells and the emergence of ovarian steroidogenic/stromal progenitors (SPs) also remain poorly defined. Here, we show that CE cells covering the fetal mouse ovary are transcriptionally heterogeneous and spatially organized into subdomains already primed toward supporting or steroidogenic fates. CE priming is dynamic, with transient coexistence of supporting- and steroidogenic-biased CE progenitors before resolving into a predominantly supporting-biased CE. Local delamination of these primed cells seeds intragonadal niches where pre-granulosa cells and SPs mirror the spatio-temporal arrangements of CE-primed progenitors. We further demonstrate a dual origin for the supporting lineage, with granulosa cells deriving from both the CE and supporting-like cells (SLCs). In parallel, we show that SPs arise from steroidogenic-primed CE cells, expand to represent 52% of ovarian somatic cells at birth, persist into adulthood and contribute to both theca and steroidogenic stromal cells. Together, these findings reveal transcriptionally and spatially distinct CE subpopulations that shape somatic lineage emergence with important implications for ovarian pathophysiology.

Ovarian development↗

PubMed2004

Seasonal sexual segregation in two Thalassarche albatross species: competitive exclusion, reproductive role specialization or foraging niche divergence?

Sexual segregation by micro- or macrohabitat is common in birds, and usually attributed to size-mediated dominance and exclusion of females by larger males, trophic niche divergence or reproductive role specialization. Our study of black-browed albatrosses, Thalassarche melanophrys, and grey-headed albatrosses, T. chrysostoma, revealed an exceptional degree of sexual segregation during incubation, with largely mutually exclusive core foraging ranges for each sex in both species. Spatial segregation was not apparent during brood-guard or post-guard chick rearing, when adults are constrained to feed close to colonies, providing no evidence for dominance-related competitive exclusion at the macrohabitat level. A comprehensive morphometric comparison indicated considerable species and sexual dimorphism in wing area and wing loading that corresponded, both within and between species, to broad-scale habitat preferences relating to wind strength. We suggest that seasonal sexual segregation in these two species is attributable to niche divergence mediated by differences in flight performance. Such sexual segregation may also have implications for conservation in relation to sex-specific overlap with commercial fisheries.

Animals↗

PubMed2004

Analysis of size distribution and areal cell density of ammonia-oxidizing bacterial microcolonies in relation to substrate microprofiles in biofilms.

A fine-scale in situ spatial organization of ammonia-oxidizing bacteria (AOB) in biofilms was investigated by combining molecular techniques (i.e., fluorescence in situ hybridization (FISH) and 16S rDNA-cloning analysis) and microelectrode measurements. Important parameters of AOB microcolonies such as size distribution and areal cell density of the microcolonies were determined and correlated with substrate microprofiles in the biofilms. In situ hybridization with a nested 16S rRNA-targeted oligonucleotide probe set revealed two different populations of AOB, Nitrosomonas europaea-lineage and Nitrosospira multiformis-lineage, coexisting in an autotrophic nitrifying biofilm. Nitrosospira formed looser microcolonies, with an areal cell density of 0.51 cells microm(-2), which was half of the cell density of Nitrosomonas (1.12 cells microm(-2)). It is speculated that the formation of looser microcolonies facilitates substrate diffusion into the microcolonies, which might be a survival strategy to low O(2) and NH(4) (+) conditions in the biofilm. A long-term experiment (4-week cultivation at different substrate C/N ratios) revealed that the size distribution of AOB microcolonies was strongly affected by better substrate supply due to shorter distance from the surface and the presence of organic carbon. The microcolony size was relatively constant throughout the autotrophic nitrifying biofilm, while the size increased by approximately 80% toward the depth of the biofilm cultured at the substrate C/N = 1. A short-term ( approximately 3 h) organic carbon addition experiment showed that the addition of organic carbon created interspecies competition for O(2) between AOB and heterotrophic bacteria, which dramatically decreased the in situ NH(4) (+)-uptake activity of AOB in the surface of the biofilms. This result might explain the spatial distribution of AOB microcolony size in the biofilms cultured at the substrate C/N = 1. These experimental results suggest O(2) and organic carbon were the main factors controlling the spatial organization and activity of AOB in biofilms. These findings are significantly important to further improve mathematical models used to describe how the slow-growing AOB develop their niches in biofilms and how that configuration affects nitrification performance in the biofilm.

Ammonia↗

PubMed2007

Macroevolutionary dynamics in environmental space and the latitudinal diversity gradient in New World birds.

Correlations between species richness and climate suggest non-random occupation of environmental space and niche evolution through time. However, the evolutionary mechanisms involved remain unresolved. Here, we partition the occupation of environmental space into intra- and inter-clade components to differentiate a model based on pure conservation of ancestral niches with higher diversification rates in the tropics, and an adaptive radiation model based on shifts in adaptive peaks at the family level allowing occupation of temperate regions. We examined these mechanisms using within- and among-family skewness components based on centroids of 3560 New World bird species across four environmental variables. We found that the accumulation of species in the tropics is a result of both processes. The components of adaptive radiation have family level skewness of species' distributions strongly structured in space, but not phylogenetically, according to the integrated analyses of spatial filters and phylogenetic eigenvectors. Moreover, stronger radiation components were found for energy variables, which are often used to argue for direct climatic effects on diversity. Thus, the correspondence between diversity and climate may be due to the conservation of ancestral tropical niches coupled with repeated broad shifts in adaptive peaks during birds' evolutionary history more than by higher diversification rates driven by more energy in the tropics.

Adaptation, Physiological↗

PubMed2002

Occupancy frequency distributions: patterns, artefacts and mechanisms.

Numerous hypotheses have been proposed to explain the shape of occupancy frequency distributions (distributions of the numbers of species occupying different numbers of areas). Artefactual effects include sampling characteristics, whereas biological mechanisms include organismal, niche-based and meta-population models. To date, there has been little testing of these models. In addition, although empirically derived occupancy distributions encompass an array of taxa and spatial scales, comparisons between them are often not possible because of differences in sampling protocol and method of construction. In this paper, the effects of sampling protocol (grain, sample number, extent, sampling coverage and intensity) on the shape of occupancy distributions are examined, and approaches for minimising artefactual effects recommended. Evidence for proposed biological determinants of the shape of occupancy distributions is then examined. Good support exists for some mechanisms (habitat and environmental heterogeneity), little for others (dispersal ability), while some hypotheses remain untested (landscape productivity, position in geographic range, range size frequency distributions), or are unlikely to be useful explanations for the shape of occupancy distributions 'species specificity and adaptation to habitat, extinction-colonization dynamics). The presence of a core (class containing species with the highest occupancy) mode in occupancy distributions is most likely to be associated with larger sample units, and small homogenous sampling areas positioned well within and towards the range centers of a sufficient proportion of the species in the assemblage. Satellite (class with species with the lowest occupancy) modes are associated with sampling large, heterogeneous areas that incorporate a large proportion of the assemblage range. However, satellite modes commonly also occur in the presence of a core mode, and rare species effects are likely to contribute to the presence of a satellite mode at most sampling scales. In most proposed hypotheses, spatial scale is an important determinant of the shape of the observed occupancy distribution. Because the attributes of the mechanisms associated with these hypotheses change with spatial scale, their predictions for the shape of occupancy distributions also change. To understand occupancy distributions and the mechanisms underlying them, a synthesis of pattern documentation and model testing across scales is thus needed. The development of null models, comparisons of occupancy distributions across spatial scales and taxa, documentation of the movement of individual species between occupancy classes with changes in spatial scale, as well as further testing of biological mechanisms are all necessary for an improved understanding of the distribution of species and assemblages within their geographic ranges.

Adaptation, Physiological↗

PubMed2002

A novel theory to explain species diversity in landscapes: positive frequency dependence and habitat suitability.

Theories to explain the diversity of species have required that individual species occupy unique niches and/or vary in their response to environmental factors. Positive interactions within a species, although common in communities, have not been thought to maintain species diversity because in non-spatial models the more abundant species always outcompetes the rarer species. Here, we show, using a stochastic spatial model, that positive intraspecific interactions such as those caused by positive frequency dependence and/or priority effects, can maintain species diversity if interactions between individuals are primarily local and the habitat contains areas that cannot be colonized by any species, such as boulders or other physical obstructions. When intraspecific interactions are primarily neutral, species diversity will eventually erode to a single species. When the landscape is homogeneous (i.e. does not contain areas that cannot be colonized by any species), the presence of strong intraspecific interactions will not maintain diversity.

Ecosystem↗

PubMed2004

Potential of multivariate quantitative methods for delineation and visualization of ecoregions.

Multivariate clustering based on fine spatial resolution maps of elevation, temperature, precipitation, soil characteristics, and solar inputs has been used at several specified levels of division to produce a spectrum of quantitative ecoregion maps for the conterminous United States. The coarse ecoregion divisions accurately capture intuitively-understood regional environmental differences, whereas the finer divisions highlight local condition gradients, ecotones, and clines. Such statistically generated ecoregions can be produced based on user-selected continuous variables, allowing customized regions to be delineated for any specific problem. By creating an objective ecoregion classification, the ecoregion concept is removed from the limitations of human subjectivity, making possible a new array of ecologically useful derivative products. A red-green-blue visualization based on principal components analysis of ecoregion centroids indicates with color the relative combination of environmental conditions found within each ecoregion. Multiple geographic areas can be classified into a single common set of quantitative ecoregions to provide a basis for comparison, or maps of a single area through time can be classified to portray climatic or environmental changes geographically in terms of current conditions. Quantified representativeness can characterize borders between ecoregions as gradual, sharp, or of changing character along their length. Similarity of any ecoregion to all other ecoregions can be quantified and displayed as a "representativeness" map. The representativeness of an existing spatial array of sample locations or study sites can be mapped relative to a set of quantitative ecoregions, suggesting locations for additional samples or sites. In addition, the shape of Hutchinsonian niches in environment space can be defined if a multivariate range map of species occurrence is available.

Color↗

PubMed2005

Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand.

Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of approximately 50-65 degrees C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42-53 degrees C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.

China↗

PubMed2005

Ecological factors influencing tetraploid speciation in snow buttercups (Ranunculus Adoneus): niche differentiation and tetraploid establishment.

Chromosome doubling plays an important role in generating new species of flowering plants. However, reproductive incompatibilities between newly formed tetraploid plants and their diploid progenitors are expected to create a significant barrier to the persistence and establishment of neopolyploid populations. Ecological differentiation can reduce this barrier via prezygotic isolation arising from spatial separation. Alternatively, superior viability or fecundity of neotetraploid plants might compensate for the reproductive cost of incompatible pollen from diploid neighbors. The performance of plants of both cytotypes can be assessed in their respective habitats through reciprocal transplants, although such experiments have not been used previously in the study of tetraploid speciation. We used a series of seed and seedling transplant experiments to assess ecological differentiation and competitive ability during early establishment phases for tetraploid and diploid forms of the snow buttercup (Ranunculus adoneus). At two sites, seeds from diploids and tetraploids had similar germination probabilities. Tetraploid snow buttercup seedlings had a significant growth advantage in a controlled environment chamber experiment. However, in the field diploid and tetraploid buttercup seedlings did not differ consistently in survival or growth, nor did the two cytotypes show reciprocal advantages in performance, as expected if ecological differentiation has occurred. At the seed and seedling stages, neither niche differentiation nor tetraploid competitive superiority appears sufficient to explain neotetraploid success in the presence of their diploid progenitors.

Adaptation, Biological↗

PubMed2000

Spatial distribution of protists in the presence of macroaggregates in a marine system.

The spatial distribution of marine protistan communities in the presence of organic macroaggregates, formed from natural seawater, was studied in several microcosm experiments. The presence of macroaggregates had two main effects. First, the size of the communities of bacteria, flagellates and ciliates increased, as these communities were three orders of magnitude higher in the aggregates than in the microcosm water. In addition, it brought the diversification on the niches accessible to planktonic microorganisms, as three phases were formed: water, aggregates and aggregate-water interphase. Some of the detected protistan taxa were only found in the water, and therefore they can be considered as truly free-swimming protists. Others quickly colonised the aggregates, and finally, some of them showed a preference for the aggregate-water interphase. We discuss this spatial structuring of the protistan community on the basis of their feeding strategies and structural and behavioural characteristics.

Journal Article↗

PubMed2006

Phylogeny and the hierarchical organization of plant diversity.

R. H. Whittaker's idea that plant diversity can be divided into a hierarchy of spatial components from alpha at the within-habitat scale through beta for the turnover of species between habitats to gamma along regional gradients implies the underlying existence of alpha, beta, and gamma niches. We explore the hypothesis that the evolution of alpha, beta, and gamma niches is also hierarchical, with traits that define the alpha niche being labile, while those defining beta and gamma niches are conservative. At the alpha level we find support for the hypothesis in the lack of close significant phylogenetic relationship between meadow species that have similar alpha niches. In a second test, alpha niche overlap based on a variety of traits is compared between congeners and noncongeners in several communities; here, too, there is no evidence of a correlation between alpha niche and phylogeny. To test whether beta and gamma niches evolve conservatively, we reconstructed the evolution of relevant traits on evolutionary trees for 14 different clades. Tests against null models revealed a number of instances, including some in island radiations, in which habitat (beta niche) and elevational maximum (an aspect of the gamma niche) showed evolutionary conservatism.

Biodiversity↗

PubMed2005

Brainy but not too brainy: starting and stopping neuroblast divisions in Drosophila.

Drosophila neuroblasts are similar to mammalian neural stem cells in that they self-renew and have the potential to generate many different types of neurons and glia. They have already proved useful for uncovering asymmetric division components and now look set to provide insights into how stem cell divisions are initiated and terminated during neural development. In particular, some of the humoral factors and short-range 'niche' signals that modulate neuroblast activity during postembryonic development have been identified. In addition, recent studies have begun to reveal how the total number of cells generated by a single neuroblast is regulated by spatial and temporal cues from Hox proteins and a transcription-factor series linked to cell cycle progression.

Animals↗

PubMed2026

Patient-derived models of prostate cancer: Capturing tumour complexity from initiation to metastasis.

Prostate cancer is a growing global health challenge. To identify new ways to improve patient care, researchers need a variety of preclinical models that faithfully recapitulate human tumours across the disease continuum, from initiation to metastasis. These complementary models include primary cultures of prostate epithelial cells (PrECs), co-cultures, patient-derived explants (PDEs), patient-derived organoids (PDOs) and patient-derived xenografts (PDXs). Collectively, these models enable researchers to study tumour biology and therapeutic responses in clinically relevant contexts. Yet, there is still a need to improve the fidelity of preclinical models to human tumours by integrating diverse cell types from the tumour microenvironment and mimicking biomechanical features. By improving culture methods with matrix components that resemble the tumour microenvironment and new formulations of media that imitate human plasma, in vitro models will more accurately reflect human physiology, nutrient availability, and metabolism. In time this may reduce the reliance on animal testing through organ-on-chip and related techniques. These more complex models are suited to more detailed experimental readouts, including single-cell and spatial analyses. Intravital imaging also enables dynamic visualisation of cell-cell interactions and treatment responses in vivo. Collectively, these approaches are facilitating a shift towards sophisticated models that capture patients' tumour heterogeneity, different cellular niches, and provide opportunities to carefully study tumorigenesis, metastasis, lineage plasticity, and therapy resistance. In this review, we discuss the current progress and future directions for patient-derived models of prostate cancer, highlighting how they can be generated, refined, characterised and shared to accelerate the worldwide effort in translational research.

Humans↗