Inhibitory effects of Eucalyptus globulus on understorey plant growth and species richness are greater in non‐native regions

Aim

We studied the novel weapons hypothesis in the context of the broadly distributed tree species Eucalyptus globulus. We evaluated the hypothesis that this Australian species would produce stronger inhibitory effects on species from its non‐native range than on species from its native range.

Location

We worked in four countries where this species is exotic (U.S.A., Chile, India, Portugal) and one country where it is native (Australia).

Time period

2009–2012.

Major taxa studied

Plants.

Methods

We compared species composition, richness and height of plant communities in 20 paired plots underneath E. globulus individuals and open areas in two sites within its native range and each non‐native region. We also compared effects of litter leachates of E. globulus on root growth of seedlings in species from Australia, Chile, the U.S.A. and India.

Results

In all sites and countries, the plant community under E. globulus canopies had lower species richness than did the plant community in open areas. However, the reduction was much greater in the non‐native ranges: species richness declined by an average of 51% in the eight non‐native sites versus 8% in the two native Australian sites. The root growth of 15 out of 21 species from the non‐native range were highly suppressed by E. globulus litter leachates, whereas the effect of litter leachate varied from facilitation to suppression for six species native to Australia. The mean reduction in root growth for Australian plants was significantly lower than for plants from the U.S.A., Chile and India.

Main conclusions

Our results show biogeographical differences in the impact of an exotic species on understorey plant communities. Consistent with the novel weapons hypothesis, our findings suggest that different adaptations of species from the native and non‐native ranges to biochemical compounds produced by an exotic species may play a role in these biogeographical differences.     

An optimised recovery method for thermophilic Campylobacter from liver

Background  

The past three decades have witnessed the rise of Campylobacter enteritis in man from virtual obscurity to notoriety, with present isolation rates superseding those of other enteric pathogens such as Salmonella spp. and Shigella spp. in most developed countries. Although campylobacters are not completely new to applied bacteriology, they have evaded traditional isolation techniques used for the isolation of pure cultures, apart from single isolations that were free from competing organisms. Offals, in particular liver have been decribed as both a source of campylobacters, as well as a route of transmission of this organism to human. Therefore, the aim of this study was to develop an optimum method for the recovery of Campylobacter spp. from porcine liver.     

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

Background  

MicroRNAs (miRNAs) are small regulatory RNAs, some of which are conserved in diverse plant genomes. Therefore, computational identification and further experimental validation of miRNAs from non-model organisms is both feasible and instrumental for addressing miRNA-based gene regulation and evolution. Sugarcane (Saccharum spp.) is an important biofuel crop with publicly available expressed sequence tag and genomic survey sequence databases, but little is known about miRNAs and their targets in this highly polyploid species.     

Fish and fisheries in the Upper Mekong: current assessment of the fish community, threats and conservation

The Mekong flows north to south, through six countries in south–east Asia. Many studies have concentrated on fish and fisheries in the Lower Mekong, which has been identified as one of the largest inland fisheries in the world with an incredibly rich diversity of species. In contrast, fish and fisheries in the Upper Mekong (Lancang River) have remained relatively undocumented. In this paper, we synthesized information on freshwater fish biodiversity and fisheries in the Upper Mekong and documented 173 species and subspecies (including 87 endemic species) among 7 orders, 23 families and 100 genera. We divided the Upper Mekong into 17 sub-basins based on Digital Elevation Model (DEM) and then used fish species data to cluster the sub-basins. Four parts (the headwater, the upper reach, the middle reach and the lower reach) and one lake have distinct fish species communities associated with them. There was a linear relationship between fish species (x) and endemic species (y) as y = 0.5464x − 3.2926. Relationship between species number or endemic species number (y) and mean altitude (x) can be described as y = −54.352 ln(x) + 460.79 or y = −30.381 ln(x) + 253.85, respectively. Fisheries kept as about 6,000 t from 1989 to 1998, and then steadily increased to 10,000 t in 2004. We reviewed the overall threats to the Upper Mekong fish and fisheries, and found that hydrological alteration is the largest threat in the basin, followed by over fishing and the introduction of exotic species. In terms of specific river sections, water pollution was the most serious threat to fishes in the upper reach of the Upper Mekong, whilst migratory fishes in the lower reach of the Upper Mekong are seriously threatened by the construction of cascade dams. The Buyuan River and the Nanla River were identified as important feeding and spawning habitats for upstream migrant species and should be considered as a priority for conservation.     

Doxycycline-regulated gene expression in the opportunistic fungal pathogen Aspergillus fumigatus

Background  

Although Aspergillus fumigatus is an important human fungal pathogen there are few expression systems available to study the contribution of specific genes to the growth and virulence of this opportunistic mould. Regulatable promoter systems based upon prokaryotic regulatory elements in the E. coli tetracycline-resistance operon have been successfully used to manipulate gene expression in several organisms, including mice, flies, plants, and yeast. However, the system has not yet been adapted for Aspergillus spp.     

Identification of the family of aquaporin genes and their expression in upland cotton (<Emphasis Type="Italic">Gossypium hirsutum</Emphasis>L.)

Background  

Cotton (Gossypium spp.) is produced in over 30 countries and represents the most important natural fiber in the world. One of the primary factors affecting both the quantity and quality of cotton production is water. A major facilitator of water movement through cell membranes of cotton and other plants are the aquaporin proteins. Aquaporin proteins are present as diverse forms in plants, where they function as transport systems for water and other small molecules. The plant aquaporins belong to the large major intrinsic protein (MIP) family. In higher plants, they consist of five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). Although a great deal is known about aquaporins in plants, very little is known in cotton.     

Identification of an unusual <Emphasis Type="Italic">Brucella</Emphasis> strain (BO2) from a lung biopsy in a 52 year-old patient with chronic destructive pneumonia

Background  

Brucellosis is primarily a zoonotic disease caused by Brucella species. There are currently ten Brucella spp. including the recently identified novel B. inopinata sp. isolated from a wound associated with a breast implant infection. In this study we report on the identification of an unusual Brucella-like strain (BO2) isolated from a lung biopsy in a 52-year-old patient in Australia with a clinical history of chronic destructive pneumonia.     

The Escherichia coli BarA-UvrY two-component system is a virulence determinant in the urinary tract

Background  

The Salmonella enterica BarA-SirA, the Erwinia carotovora ExpS-ExpA, the Vibrio cholerae BarA-VarA and the Pseudomonas spp GacS-GacA all belong to the same orthologous family of two-component systems as the Escherichia coli BarA-UvrY. In the first four species it has been demonstrated that disruption of this two-component system leads to a clear reduction in virulence of the bacteria. Our aim was to determine if the Escherichia coli BarA-UvrY two-component system is connected with virulence using a monkey cystitis model.     

<Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> inhibits <Emphasis Type="Italic">in-vitro Candida</Emphasis> biofilm development

Background  

Elucidation of the communal behavior of microbes in mixed species biofilms may have a major impact on understanding infectious diseases and for the therapeutics. Although, the structure and the properties of monospecies biofilms and their role in disease have been extensively studied during the last decade, the interactions within mixed biofilms consisting of bacteria and fungi such as Candida spp. have not been illustrated in depth. Hence, the aim of this study was to evaluate the interspecies interactions of Pseudomonas aeruginosa and six different species of Candida comprising C. albicans, C. glabrata, C. krusei, C. tropicalis, C. parapsilosis, and C. dubliniensis in dual species biofilm development.     

British species that are present in Australia have different traits from British species that are not present in Australia

Aim

Introduced species spreading to natural ecosystems is a leading cause of environmental change and a key feature of the Anthropocene. While there have been many studies of the traits of introduced and invasive species, less is known about the traits that affect a species' chances of reaching and establishing in new areas. We asked whether British species that are present in Australia have different traits to British species that are not present in Australia.

Location

Great Britain and Australia.

Methods

We compiled a list of all vascular plant species from Great Britain and divided them into those that are present in Australia (395 species) and those that are not present in Australia (1171 species). We compiled data for each species' seed mass, seedbank longevity, maximum plant height, flower size, flower colour and geographical extent in the British Isles. We conducted independent sample t-tests for continuous variables and Chi-squared tests for categorical variables to determine differences between groups.

Results

We found British species present in Australia have, on average, larger geographic extents in the British Isles, longer periods of seed bank longevity (mean ~3 months as opposed to ~3 weeks), and maximum heights that are on average 36% taller than British species that are not present in Australia. However, British species present in Australia did not have significantly different flower size, flower colour or seed mass from British species that are not present in Australia.

Main Conclusions

British species that are present in Australia and British species that are not present in Australia differ in several traits. These differences likely result from a combination of factors including introduction biases, environmental filters during establishment and stochasticity. Our results suggest that humans may be consciously and unconsciously selecting species for introduction. Some of the traits that are associated with an increased chance of a species being transported to/establishing in a new range also contribute to invasiveness. Thus, anthropogenic introduction biases could contribute to an increased risk of ecosystem invasion.     

Genetic diversity of peanut (Arachis hypogaea L.) and its wild relatives based on the analysis of hypervariable regions of the genome

Background  

The genus Arachis is native to a region that includes Central Brazil and neighboring countries. Little is known about the genetic variability of the Brazilian cultivated peanut (Arachis hypogaea, genome AABB) germplasm collection at the DNA level. The understanding of the genetic diversity of cultivated and wild species of peanut (Arachis spp.) is essential to develop strategies of collection, conservation and use of the germplasm in variety development. The identity of the ancestor progenitor species of cultivated peanut has also been of great interest. Several species have been suggested as putative AA and BB genome donors to allotetraploid A. hypogaea. Microsatellite or SSR (Simple Sequence Repeat) markers are co-dominant, multiallelic, and highly polymorphic genetic markers, appropriate for genetic diversity studies. Microsatellite markers may also, to some extent, support phylogenetic inferences. Here we report the use of a set of microsatellite markers, including newly developed ones, for phylogenetic inferences and the analysis of genetic variation of accessions of A. hypogea and its wild relatives.     

Allopatric speciation in ticks: genetic and reproductive divergence between geographic strains of Rhipicephalus (Boophilus) microplus

Background  

The cattle tick, Rhipicephalus (Boophilus) microplus, economically impact cattle industry in tropical and subtropical regions of the world. The morphological and genetic differences among R. microplus strains have been documented in the literature, suggesting that biogeographical and ecological separation may have resulted in boophilid ticks from America/Africa and those from Australia being different species. To test the hypothesis of the presence of different boophilid species, herein we performed a series of experiments to characterize the reproductive performance of crosses between R. microplus from Australia, Africa and America and the genetic diversity of strains from Australia, Asia, Africa and America.     

Biotic interactions influence the projected distribution of a specialist mammal under climate change

Aim

To measure the effects of including biotic interactions on climate‐based species distribution models (SDMs) used to predict distribution shifts under climate change. We evaluated the performance of distribution models for an endangered marsupial, the northern bettong (Bettongia tropica), comparing models that used only climate variables with models that also took into account biotic interactions.

Location

North‐east Queensland, Australia.

Methods

We developed separate climate‐based distribution models for the northern bettong, its two main resources and a competitor species. We then constructed models for the northern bettong by including climate suitability estimates for the resources and competitor as additional predictor variables to make climate + resource and climate + resource + competition models. We projected these models onto seven future climate scenarios and compared predictions of northern bettong distribution made by these differently structured models, using a ‘global’ metric, the I similarity statistic, to measure overlap in distribution and a ‘local’ metric to identify where predictions differed significantly.

Results

Inclusion of food resource biotic interactions improved model performance. Over moderate climate changes, up to 3.0 °C of warming, the climate‐only model for the northern bettong gave similar predictions of distribution to the more complex models including interactions, with differences only at the margins of predicted distributions. For climate changes beyond 3.0 °C, model predictions diverged significantly. The interactive model predicted less contraction of distribution than the simpler climate‐only model.

Main conclusions

Distribution models that account for interactions with other species, in particular direct resources, improve model predictions in the present‐day climate. For larger climate changes, shifts in distribution of interacting species cause predictions of interactive models to diverge from climate‐only models. Incorporating interactions with other species in SDMs may be needed for long‐term prediction of changes in distribution of species under climate change, particularly for specialized species strongly dependent on a small number of biotic interactions.     

An <Emphasis Type="Italic">in silico</Emphasis> analysis of the mitochondrial protein import apparatus of plants

Background  

An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species.     

Evolution of the leukotoxin promoter in genus Mannheimia

Background  

The Mannheimia species encompass a wide variety of bacterial lifestyles, including opportunistic pathogens and commensals of the ruminant respiratory tract, commensals of the ovine rumen, and pathogens of the ruminant integument. Here we present a scenario for the evolution of the leukotoxin promoter among representatives of the five species within genus Mannheimia. We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence.     

Genomic taxonomy of vibrios

Background  

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i. e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.     

Rapid global expansion of invertebrate fisheries: trends, drivers, and ecosystem effects

Background

Worldwide, finfish fisheries are receiving increasing assessment and regulation, slowly leading to more sustainable exploitation and rebuilding. In their wake, invertebrate fisheries are rapidly expanding with little scientific scrutiny despite increasing socio-economic importance.

Methods and Findings

We provide the first global evaluation of the trends, drivers, and population and ecosystem consequences of invertebrate fisheries based on a global catch database in combination with taxa-specific reviews. We also develop new methodologies to quantify temporal and spatial trends in resource status and fishery development. Since 1950, global invertebrate catches have increased 6-fold with 1.5 times more countries fishing and double the taxa reported. By 2004, 34% of invertebrate fisheries were over-exploited, collapsed, or closed. New fisheries have developed increasingly rapidly, with a decrease of 6 years (3 years) in time to peak from the 1950s to 1990s. Moreover, some fisheries have expanded further and further away from their driving market, encompassing a global fishery by the 1990s. 71% of taxa (53% of catches) are harvested with habitat-destructive gear, and many provide important ecosystem functions including habitat, filtration, and grazing.

Conclusions

Our findings suggest that invertebrate species, which form an important component of the basis of marine food webs, are increasingly exploited with limited stock and ecosystem-impact assessments, and enhanced management attention is needed to avoid negative consequences for ocean ecosystems and human well-being.     

Genetic and phenotypic diversity in <Emphasis Type="Italic">Burkholderia</Emphasis>: contributions by prophage and phage-like elements

Background  

Burkholderia species exhibit enormous phenotypic diversity, ranging from the nonpathogenic, soil- and water-inhabiting Burkholderia thailandensis to the virulent, host-adapted mammalian pathogen B. mallei. Genomic diversity is evident within Burkholderia species as well. Individual isolates of Burkholderia pseudomallei and B. thailandensis, for example, carry a variety of strain-specific genomic islands (GIs), including putative pathogenicity and metabolic islands, prophage-like islands, and prophages. These GIs may provide some strains with a competitive advantage in the environment and/or in the host relative to other strains.     

Human inflammatory bowel disease does not associate with Lawsonia intracellularis infection

Background  

There is increasing evidence that bacterial infection of the intestinal mucosa may contribute to the pathogenesis of inflammatory bowel diseases (IBD). In pigs, an obligate intracellular bacterium, Lawsonia intracellularis (LI), was shown to cause proliferative enteropathy (PE) of which some forms display histological and clinical similarities to human IBD. Since LI-similar Desulfovibrio spp. may infect human cells, we hypothesized that LI might be associated with the development of human IBD.     

Immigrant and native? The case of the swamp foxtail Cenchrus purpurascens in Australia

Aim

Spring wetlands in arid regions of Australia provide habitat for many highly endemic organisms, including fish, molluscs, crustaceans and plants, but these unique ecosystems have been under pressure since the arrival of Europeans about 250 years ago. Arguments over whether particular plant species are long‐term spring inhabitants or recent immigrants are confounding efforts to conserve spring flora. One such example is the swamp foxtail, Cenchrus purpurascens, a grass that is variably listed in the literature as being native to Australian wetlands or as being an introduced weedy species from Asia.

Location

Australia, China and Korea.

Methods

We use DNA sequences of the nuclear ITS and the chloroplast DNA regions trnL‐F and matK, complemented with newly designed simple sequence repeat (SSR) markers, to assess the native status of C. purpurascens in Australia and determine whether there is genetic differentiation among spring populations.

Results

We find that, although there has been gene flow between Asia and Australia in the geological past, the populations are now strongly differentiated: C. purpurascens has probably been present in Australia through the Pleistocene. In Australia, there is also strong genetic differentiation among populations from different springs, and between springs and non‐springs populations, indicating long‐term occupancy of some springs sites.

Main conclusions

Cenchrus purpurascens was present in Australia well before European colonization of the continent. The level of genetic differentiation among populations enhances the existing conservation values of Elizabeth Springs, Edgbaston, Doongmabulla and Carnarvon Gorge springs complexes within the Great Artesian Basin.