Restricted Niche Research Articles

How to not inflate population estimates? Spatial density distribution of white-lipped peccaries in a continuous Atlantic forest

In a world with poor biological inventorying and rapid land-use change, predicting the spatial distribution of species is fundamental for the effective management and conservation of threatened taxa. However, on a regional scale, predicting the distribution of rare terrestrial mammals is often unreliable and/or impractical, especially in tropical forests. We apply a recently developed analytic process that integrates density estimation (kernel smoothing), niche-analysis and geostatistics (regression-kriging) to model the occupancy and density distribution of a threatened population of white-lipped peccaries Tayassu pecari in a Brazilian Atlantic forest. Locations (n=45) within a protected area of the Serra-do-Mar state park were obtained from diurnal line transect census (233 km), camera-trapping (751 camera-trap days) and surveys (>626 km) conducted by park rangers. Niche modelling (environmental niche-factor analysis and MAXENT) revealed a restricted niche compared with the available habitat as defined by seven environmental variables. From the occupancy model obtained from regression-kriging, we found that 72% of a 170 km2 protected area is likely to be used by peccaries. We demonstrate that the distribution of large mammals can be restricted within continuous areas of Atlantic forest and therefore population estimates based on the size of protected areas can be overestimated. Our findings suggest that the generation of realized density distributions should become the norm rather than the exception to enable conservation managers and researchers to extrapolate abundance and density estimates across continuous habitats and protected areas.

Diurnal habitat suitability for a Mediterranean steppeland bird, identified by Ecological Niche Factor Analysis

Context The negative effects of agricultural intensification and policies, use of pesticides, fertilisers and mechanised harvesting on several populations of pseudo-steppe birds have increasingly required more detailed and effective habitat suitability models. Distribution models of farmland species are prone to incur recordings of false absence data. Ecological Niche Factor Analysis (ENFA) allows identification of environmental predictors of species distribution by using presence data only. Aims We quantified the diurnal habitat preferences and niche width of one steppe species, the stone curlew (Burhinus oedicnemus), with unfavourable conservations status in a Mediterranean area and reclassified a map with respect to habitat suitability classes according to the resulting distribution model. Methods Ecological Niche Factor Analysis was used with GIS cartography customised with habitat and anthropogenic variables recorded during field surveys carried out in four study plots (~500 ha) and at different spatial scales. Key results The stone curlew selected areas with low vegetation cover, such as fields following artichoke harvesting and tillage, close to rural buildings and unpaved roads. In contrast, the stone curlew avoided areas with high vegetation cover and areas highly disturbed by human-induced fires. The occurrence of natural vegetation was neither preferred nor avoided. The most robust model was based on a large-scale analysis (200 m from the bird location points), according to which the optimal area for stone curlew distribution during its breeding season was restricted to 1% of the entire study area. Conclusions Two uncorrelated factors, ‘marginality’ and ‘tolerance’, described the stone curlew’s niche in the area. The first index indicated selection for habitats that were marginal with respect to those available in the area, whereas the second indicated a species with a medium–wide environmental niche. In particular, the stone curlew occupied a much more restricted niche (low tolerance) in relation to individual variables. The use of customised databases at a large scale of analysis was found to more effectively reveal ecological requirements of this marginal and specialised species. Implications Our results allowed us to indicate practical land management actions for the stone curlew, such as prevention of human-induced fires and increase of pastoral activities. Our results indicated a potentially positive role of little-disturbed service roads along rural buildings in stone curlew distribution, which warrants further research. In addition, studies are needed to verify the presence of an ecological trap in artichoke fields, their preferred habitat. As we showed for the stone curlew, niche analyses conducted at a large scale using customised databases could greatly improve habitat suitability models of farmland species.

Effect of competition on niche dynamics of syntopic grazing ungulates: contrasting the predictions of habitat selection models using stable isotope analysis

Background: Theories of density-dependent habitat selection provide two solutions for co-existence of competing species. The niche compression hypothesis predicts that species reduce their respective niche breadths in response to inter-specific competition. Alternatively, if the species have similar resource preferences, the subordinate species may be forced to expand its niche to incorporate secondary resources. Aim: Determine whether grazing ungulate species partition the resource by compression or expansion of dietary niches. Organisms: Black wildebeest (Connochaetes gnou) and blue wildebeest (C. taurinus). Methods: Stable carbon and nitrogen isotope analysis of faeces. Isotopic niche breadths are compared across allopatric and sympatric wildebeest populations in South African grasslands. Results: Stable carbon and nitrogen isotope niche breadths of the two wildebeest species were virtually identical. In sympatry, however, black wildebeest had a narrower δ13C niche breadth (indicating almost exclusive use of C4 grass), whereas blue wildebeest had a wider δ13C niche breadth (indicating significant contributions from C3 sources). Blue wildebeest also had a wider δ15N niche breadth than sympatric black wildebeest. Moreover, the δ13C niche breadths of sympatric black wildebeest and blue wildebeest were narrower and wider, respectively, than those of allopatric populations of either species. Conclusions: Isotope niche dynamics across allopatric and sympatric populations arise due to the combined effects of competition and habitat heterogeneity on resource use. Although results for black wildebeest resemble niche compression, this hypothesis cannot explain patterns observed in blue wildebeest. Expansion of the blue wildebeest niche, and restricted niche breadth of black wildebeest, is consistent with predictions of a shared preference model in which black wildebeest are the dominant competitor. When competition is operating, differences in the way species use secondary resources can have an important role in structuring grazer assemblages.

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

BackgroundAdherent and invasive Escherichia coli (AIEC) are commonly found in ileal lesions of Crohn's Disease (CD) patients, where they adhere to intestinal epithelial cells and invade into and survive in epithelial cells and macrophages, thereby gaining access to a typically restricted host niche. Colonization leads to strong inflammatory responses in the gut suggesting that AIEC could play a role in CD immunopathology. Despite extensive investigation, the genetic determinants accounting for the AIEC phenotype remain poorly defined. To address this, we present the complete genome sequence of an AIEC, revealing the genetic blueprint for this disease-associated E. coli pathotype.ResultsWe sequenced the complete genome of E. coli NRG857c (O83:H1), a clinical isolate of AIEC from the ileum of a Crohn's Disease patient. Our sequence data confirmed a phylogenetic linkage between AIEC and extraintestinal pathogenic E. coli causing urinary tract infections and neonatal meningitis. The comparison of the NRG857c AIEC genome with other pathogenic and commensal E. coli allowed for the identification of unique genetic features of the AIEC pathotype, including 41 genomic islands, and unique genes that are found only in strains exhibiting the adherent and invasive phenotype.ConclusionsUp to now, the virulence-like features associated with AIEC are detectable only phenotypically. AIEC genome sequence data will facilitate the identification of genetic determinants implicated in invasion and intracellular growth, as well as enable functional genomic studies of AIEC gene expression during health and disease.

The Population Structure of Acinetobacter baumannii: Expanding Multiresistant Clones from an Ancestral Susceptible Genetic Pool

Outbreaks of hospital infections caused by multidrug resistant Acinetobacter baumannii strains are of increasing concern worldwide. Although it has been reported that particular outbreak strains are geographically widespread, little is known about the diversity and phylogenetic relatedness of A. baumannii clonal groups. Sequencing of internal portions of seven housekeeping genes (total 2,976 nt) was performed in 154 A. baumannii strains covering the breadth of known diversity and including representatives of previously recognized international clones, and in 19 representatives of other Acinetobacter species. Restricted amounts of diversity and a star-like phylogeny reveal that A. baumannii is a genetically compact species that suffered a severe bottleneck in the recent past, possibly linked to a restricted ecological niche. A. baumannii is neatly demarcated from its closest relative (genomic species 13TU) and other Acinetobacter species. Multilocus sequence typing analysis demonstrated that the previously recognized international clones I to III correspond to three clonal complexes, each made of a central, predominant genotype and few single locus variants, a hallmark of recent clonal expansion. Whereas antimicrobial resistance was almost universal among isolates of these and a novel international clone (ST15), isolates of the other genotypes were mostly susceptible. This dichotomy indicates that antimicrobial resistance is a major selective advantage that drives the ongoing rapid clonal expansion of these highly problematic agents of nosocomial infections.

Niche use and resource partitioning of Arctic charr, European whitefish and grayling in a subarctic lake

Arctic charr and European whitefish are common species in northern Europe, but have a parapatric distribution pattern and rarely coexist in substantial densities within the same lake. Whitefish is considered to be the strongest competitor, usually causing competitive relegation or exclusion of co-occurring charr. Some exceptions do however occur, and the present study addresses niche utilization and resource partitioning of an Arctic charr population coexisting with whitefish and grayling in a subarctic lake. There was a distinct resource partitioning with respect to habitat and diet utilization of the three species. Grayling were exclusively caught in shallow near-shore areas, feeding chiefly on surface insects and Trichoptera larvae. Whitefish dominated in all lake habitats, feeding predominantly on small-sized planktonic and benthic crustaceans. Arctic charr were mainly found along the benthic profile, feeding predominantly on insects and snails and showing a low dietary overlap with whitefish which appeared to have monopolised the zooplankton resources. The highly restricted trophic niche of Arctic charr suggests a severe competitive impact due to the presence of whitefish, but the coexistence of the two species may be facilitated by the presence of grayling.

The future of biomass energy: A Fermi-calculation perspective

It is argued: (i) that the harvesting of terrestrial solar radiation to perform useful work is at least an order of magnitude more efficient when carried out by solar-thermal or solar-photovoltaic processes than when carried out by way of biomass conversion and (ii) that, therefore, biomass energy is unlikely to compete successfully with inanimately harvested solar energy—except of course in restricted niche applications.

Alien aquatic macroinvertebrates along the lateral dimension of a large floodplain

Floodplains are simultaneously among the most species-rich and the most threatened ecosystems. Alien aquatic macroinvertebrates contribute to this threat but remain scarcely studied in the lateral dimension of floodplains. We modelled the realized ecological niches of the alien species occurring in 24 floodplain channels of the Rhone River. Environmental variables depicting the ecological niches were associated to the lateral hydrological connectivity and light availability, both being modified during floodplain restoration works. Eight alien species were observed and they demonstrated either ubiquity or a restricted niche, with no link to the date of introduction. For most of them, the main river channel appeared as an important dispersal route in the lateral dimension of the floodplain. An increase of both lateral connectivity and light availability favoured most of the modelled species. Consequently, we recommend that sector-scale restoration programmes preserve varying levels of lateral connectivity for floodplain channels to prevent the expansion of alien aquatic macroinvertebrates.

Exploring habitat use by cheetahs using ecological niche factor analysis

AbstractUnderstanding the basis of habitat choice having important implications for explaining the distribution of organisms, as well as helping to differentiate between habitats of different quality for effective management. In this study, the effects of sex, age and reproductive status on habitat use patterns of cheetahs Acinonyx jubatus in the Serengeti plains were explored using Ecological Niche Factor Analysis (ENFA). Our results showed that gender and territoriality did not affect patterns of habitat use. However, females tended to be more specialized when they were young than when they were older, displaying a more restricted ecological niche. Likewise, older females without cubs were more specialized than the same adult females with young cubs. This result did not hold for younger females. Altogether, the ENFA approach allowed us to (1) use the large amount of incidental sighting data collected over 12 years on cheetah spatial distribution; (2) identify the importance of reproductive status and age on the relationship between animals and their habitat; (3) further demonstrate that ENFA is applicable in a wide range of situations, including for exploring individual variation in niche definition.

Is the endangeredApium repens(Jacq.) Lag. rare because of a narrow regeneration niche?

AbstractThe conservation of rare plant species is an important aspect of global biodiversity protection, but in many cases these species and the reasons why they are rare are poorly understood. The perennial umbelliferApium repensis generally regarded to be a rare species all over its European range. We hypothesized that its rarity might be caused by a restricted regeneration niche, that is, highly specific requirements for sexual regeneration, low seed dispersal potential and low endurance capacity of seeds in the ground. We conducted several experimental investigations on its germination ecology, hydrochorous dispersal potential and soil seed bank properties.Apium repensshowed high germination success under a variety of abiotic conditions. Either light or cold‐wet stratification was necessary to stimulate germination. Seeds were able to float for more than 50 days when protected from precipitation, and soil seed bank sampling revealed that at least some seeds ofA. repenswere contained in soil depths of up to 10 cm. Overall, our findings do not support the hypothesis that the rarity ofA. repensis caused by highly specific requirements for its sexual regeneration. Nonetheless, its germination ecology should be considered when designing conservation measures for this endangered species.

Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation.

Clavibacter michiganensis subsp. sepedonicus is a plant-pathogenic bacterium and the causative agent of bacterial ring rot, a devastating agricultural disease under strict quarantine control and zero tolerance in the seed potato industry. This organism appears to be largely restricted to an endophytic lifestyle, proliferating within plant tissues and unable to persist in the absence of plant material. Analysis of the genome sequence of C. michiganensis subsp. sepedonicus and comparison with the genome sequences of related plant pathogens revealed a dramatic recent evolutionary history. The genome contains 106 insertion sequence elements, which appear to have been active in extensive rearrangement of the chromosome compared to that of Clavibacter michiganensis subsp. michiganensis. There are 110 pseudogenes with overrepresentation in functions associated with carbohydrate metabolism, transcriptional regulation, and pathogenicity. Genome comparisons also indicated that there is substantial gene content diversity within the species, probably due to differential gene acquisition and loss. These genomic features and evolutionary dating suggest that there was recent adaptation for life in a restricted niche where nutrient diversity and perhaps competition are low, correlated with a reduced ability to exploit previously occupied complex niches outside the plant. Toleration of factors such as multiplication and integration of insertion sequence elements, genome rearrangements, and functional disruption of many genes and operons seems to indicate that there has been general relaxation of selective pressure on a large proportion of the genome.

Testing palaeo-environmental proxies in Jurassic belemnites: Mg/Ca, Sr/Ca, Na/Ca, δ 18O and δ 13C

We test the hypothesis that the noise in belemnite records through time results from changing climate. We do so by comparing palaeo-proxies (Mg/Ca, Sr/Ca, Na/Ca, δ 18O, δ 13C) in two species of Toarcian belemnites, Acrocoelites ( Odontobelus) vulgaris (14 specimens) and Acrocoelites ( Acrocoelites) subtenuis (10 specimens), deposited in a period of time that was short relative to the timescale of climate change. The specimens are interpreted to have been regurgitated from the stomach of a marine predator and so were deposited together in a geological instant of Early Jurassic time. In A. ( O.) vulgaris, isotopic and elemental palaeo-proxies group tightly, suggesting that this belemnite occupied a restricted environmental niche. In A. ( A.) subtenuis, elemental and isotopic compositions spread more widely, suggesting that this species occupied a greater range of habitats. Possible sexual dimorphism in A. ( O.) vulgaris is reflected in bimodal Mg/Ca and differing intra-rostral distribution of Mg in putative dimorphs; concentrations decline by 30% from apical line to rim in specimens with high Mg/Ca, but are largely invariant radially in specimens with lower Mg/Ca. Sexual dimorphism in A. ( A.) subtenuis yields a bimodality in size, Mg/Ca, and intra-rostral distribution of Mg; larger specimens have a higher Mg/Ca, and Mg concentrations that increase along radial traverses from apical line to rim, whilst the smaller specimens show a mid-rostral minimum in Mg concentration. Radial profiles of concentrations for Sr and Na vary little in all forms. Toarcian belemnites of these species thus show strong biofractionation effects on Mg/Ca, and little or no observable biofractionation of Sr/Ca or Na/Ca. It follows that much of the noise in belemnite records results from biofractionation, and from a cosmopolitan life-style of some belemnite species, rather than climate-change. For Toarcian belemnites, we suggest that Sr/Ca is the best indicator of palaeo-temperature.

The bacterial species definition in the genomic era.

The bacterial species definition, despite its eminent practical significance for identification, diagnosis, quarantine and diversity surveys, remains a very difficult issue to advance. Genomics now offers novel insights into intra-species diversity and the potential for emergence of a more soundly based system. Although we share the excitement, we argue that it is premature for a universal change to the definition because current knowledge is based on too few phylogenetic groups and too few samples of natural populations. Our analysis of five important bacterial groups suggests, however, that more stringent standards for species may be justifiable when a solid understanding of gene content and ecological distinctiveness becomes available. Our analysis also reveals what is actually encompassed in a species according to the current standards, in terms of whole-genome sequence and gene-content diversity, and shows that this does not correspond to coherent clusters for the environmental Burkholderia and Shewanella genera examined. In contrast, the obligatory pathogens, which have a very restricted ecological niche, do exhibit clusters. Therefore, the idea of biologically meaningful clusters of diversity that applies to most eukaryotes may not be universally applicable in the microbial world, or if such clusters exist, they may be found at different levels of distinction.

Patterns of resource exploitation in four coexisting globeflower fly species (Chiastocheta sp.)

Life history and spatio-temporal patterns of resource utilisation were characterised in four Chiastocheta (Diptera: Anthomyiidae) species, whose larvae compete as seed predators on Trollius europaeus fruits. Interspecific co-occurrence was observed in 80% of the resource patches (= Trollius fruits) in the two communities studied. Isolated larvae from all species had a similar food intake, but differed in development time and size at emergence Different species exhibit contrasting resource exploitation strategies with specific mining patterns and a partial temporal shift. Two species exhibited particularly singular strategies. C. rotundiventris escaped from strong interactions with other species because it was the first species to develop and the only one to exploit the central pith of Trollius fruits. The key role of this species as the main pollinator of the host-plant appears to be a by-product of constraints imposed by occupying a restricted niche. Although the resource is ephemeral due to seed dispersal, C. dentifera, the last species to oviposit, is not disadvantaged because it has a short development time and rapid food intake. The different patterns can partly explain the stability of Chiastocheta communities, but do not prevent competition to occur at high larval densities. (c) 2006 Elsevier SAS. All rights reserved.

Distribution patterns and interactions of cestodes in the spiral intestine of the narrownose smooth-hound shark, Mustelus schmitti Springer, 1939 (Chondrichthyes, Carcharhiniformes)

AbstractThe distribution patterns and the cestode species interactions within the spiral intestine of 20 specimens of Mustelus schmitti from coastal waters off Mar del Plata, Argentina were studied. Six cestode species were found: Tetraphyllideans Calliobothrium barbarae, C. australis, C. lunae and Orygmatobothrium schmittii, diphyllidean Echinobothrium notoguidoi and trypanorhynch Eutetrarhynchus vooremi. The most common number of parasite species per host was 3. Brillouin’s diversity index ranged from 0.1 to 1.2 Berger-Parker dominance index indicated that C. barbarae was the dominant species, followed by O. schmittii and C. australis. Calliobothrium barbarae, C. australis and O. schmittii presented a broad distribution along the spiral intestine, whereas C. lunae, E. notoguidoi and E. vooremi showed a more restricted niche breadth. In general, the Renkonen’s index showed no evidence of niche overlap in the range of distribution of the different species. In most of the infracommunities, intraspecific aggregation was stronger than interspecific aggregation, indicating that competition may play a little role. The distribution patterns of the Calliobothrium specimens concurs with the predictions of attachment sites for Calliobothrium species made by previous authors.

Neuston: Its definition with a historical review regarding its concept and community structure

Since NAUMANN (1917) introduced the term neuston, various criteria and descriptions have been used to identify the habitat and its populations. Dissimilar methods of collection protocols have contributed to these different interpretations. To more fully identify the restricted ecological niche occupied by this unique community, papers from the original and more recent freshwater and marine neuston studies are discussed along with the common sampling methods for neuston. Characteristics of the neuston habitat are also presented, with definitions for neuston, epineuston, and hyponeuston. Attachment to the surface layer by its floral or faunal populations is not considered a requirement, and the neuston community includes organisms that move directly on or below the water surface. The depth of the neuston (hyponeuston) community below the water's surface can be determined by noting statistically significant changes within the populations with increasing depth below the surface layer. This depth would be expected to change diurnally and seasonally, and also to differ between freshwater and marine habitats. The horizontal patchiness of the neuston should also be anticipated and resolved through an adequate sampling protocol.

Vernacular Literacy in the Touo Language of the Solomon Islands

The Touo language is a non-Austronesian language spoken on Rendova Island (Western Province, Solomon Islands). First language speakers of Touo are typically multilingual, and are likely to speak other (Austronesian) vernaculars, as well as Solomon Island Pijin and English. There is no institutional support of literacy in Touo: schools function in English, and church-based support for vernacular literacy focuses on the major Austronesian languages of the local area. Touo vernacular literacy exists in a restricted niche of the linguistic ecology, where it is utilised for symbolic rather than communicative goals. Competing vernacular orthographic traditions complicate the situation further.

The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Molecular hijacking and intracellular chaos

Molecular hijacking and intracellular chaos

Food resource partitioning and competition among alvinellid polychaetes of Juan de Fuca Ridge hydrothermal vents

Biotic communities in highly variable, frequently perturbed habitats are usually ex- pected to be structured mainly by abiotic factors. In the highly variable deep-sea hydrothermal vent environment, physical and chemical factors are known to play an important role in limiting the dis- tribution and abundance of species, but the importance of biotic interactions remains largely unre- solved. The high density and biomass attained by the vent macrofauna suggest that resource parti- tioning and competition may be significant in these communities. This study of food resource utilisation at northeast Pacific deep-sea hydrothermal vents uses an approach based on stable carbon and nitrogen isotope analyses to characterise trophic interactions between the 3 dominant alvinellid polychaetes, Paralvinella palmiformis, P. sulfincola, and P. pandorae. We also examine size structure in sympatric and allopatric populations of P. palmiformis and P. pandorae. Results indicate that food resource partitioning occurs both intra- and interspecifically in P. palmiformis and P. sulfincola, and we advocate that this process contributes to explaining their co-existence at very high densities. In contrast, P. pandorae has a much more restricted trophic niche, overlaps P. palmiformis in diet and is much smaller in size when found in sympatry with P. palmiformis. P. pandorae is the most likely of the 3 species to be affected by intra- and/or interspecific competition for food, and this may explain the drastic change in the population size structure observed between successive years. Our work indi- cates that within the limits imposed by environmental conditions, biotic interactions such as food resource partitioning and competition can be significant factors structuring deep-sea hydrothermal vent communities.