Divergence and biogeography of the recently evolved Macaronesian red Festuca (Gramineae) species inferred from coalescence-based analyses

Studying the biogeography and the phylogeography of the endemic Macaronesian red Festuca species (Loliinae, Poaceae) is of prime interest in understanding the speciation and colonization patterns of recently evolved groups in oceanic archipelagos. Coalescence‐based analyses of plastid trnLF sequences were employed to estimate evolutionary parameters and to test different species‐history scenarios that model the pattern of species divergence. Bayesian IM estimates of species divergence times suggested that ancestral lineages of diploid Macaronesian and Iberian red fescues could have diverged between 1.2 and 1.57 Ma. When empirical data were compared to coalescence‐based simulated distributions of discordance and p‐distance statistics, two species‐history models were chosen in which the first branching lineage derived in Canarian Festuca agustinii. Its sister lineage could have involved a recent polytomy leading to the Madeiran Festuca jubata, the Azorean Festuca francoi + Festuca petraea and the continental Festuca rivularis lineages (Canarian model) or the sequential branching of lineages leading to F. jubata and finally to the sister clades of F. rivularis and F. francoi + F. petraea (Sequential model). Nested clade phylogeographic analysis (NCPA) and a first adapted host–parasite co‐evolutionary ParaFit method were used to detect the phylogeographic signal. NCPA inferred long‐distance colonizations for the entire diploid red Festuca complex, but allopatric‐fragmentation and isolation‐by‐distance (IBD) patterns were inferred within archipelagos. In addition, the ParaFit method suggested a generalized pattern of a stepping‐stone model at all hierarchical levels. Maximum‐likelihood‐based dispersal‐extinction‐cladogenesis (DEC) models were superimposed on the Sequential model species tree. The three‐independent‐colonization (3IC) model was the best supported biogeographic scenario, concurring with previous analysis based on multilocus AFLP data.     

Computer assisted image analysis to assess colonization of recipient seminiferous tubules by spermatogonial stem cells from transgenic donor mice

Transplantation of spermatogonial stem cells from fertile, transgenic donor mice to the testes of infertile recipients provides a unique system to study the biology of spermatogonial stem cells. To facilitate the investigation of treatment effects on colonization efficiency an analysis system was needed to quantify colonization of recipient mouse seminiferous tubules by donor stem cell‐derived spermatogenesis. In this study, a computer‐assisted morphometry system was developed and validated to analyze large numbers of samples. Donor spermatogenesis in recipient testes is identified by blue staining of donor‐derived spermatogenic cells expressing the E. coli lacZ structural gene. Images of seminiferous tubules from recipient testes collected three months after spermatogonial transplantation are captured, and stained seminiferous tubules containing donor‐derived spermatogenesis are selected for measurement based on their color by color thresholding. Colonization is measured as number, area, and length of stained tubules. Interactive, operator‐controlled color selection and sample preparation accounted for less than 10% variability for all collected parameters. Using this system, the relationship between number of transplanted cells and colonization efficiency was investigated. Transplantation of 10⁴ cells per testis only rarely resulted in colonization, whereas after transplantation of 10⁵ and 10⁶ cells per testis the extent of donor‐derived spermatogenesis was directly related to the number of transplanted donor cells. It appears that about 10% of transplanted spermatogonial stem cells result in colony formation in the recipient testis. The present study establishes a rapid, repeatable, semi‐interactive morphometry system to investigate treatment effects on colonization efficiency after spermatogonial transplantation in the mouse. Mol. Reprod. Dev. 53:142–148, 1999. © 1999 Wiley‐Liss, Inc.     

Towards a balanced view of pike in Ireland: a reply to Ensing

In our recent study of the population genetics of pike (Esox lucius) in Ireland (Pedreschi et al., 2014 , Journal of Biogeography, 41 , 548–560), we reported the existence of two main demographic units and showed that these may correspond to two independent and temporally staggered colonization events, the first of which may have been too old to be caused or assisted by human translocations. Ensing (2015, Journal of Biogeography, doi: 10.1111/jbi.12410 ) first used our genotypic data to explore alternative historical scenarios, then attempted to reconcile the ‘two‐wave’ colonization process of Ireland by pike with translocation activities by humans in Neolithic/Bronze age times. Here we illustrate why the evidence base for Ensing's reconstruction is weak and we outline a realistic strategy to better understand the role of pike in Irish freshwater ecosystems.     

The success of assisted colonization and assisted gene flow depends on phenology

Global warming will jeopardize the persistence and genetic diversity of many species. Assisted colonization, or the movement of species beyond their current range boundary, is a conservation strategy proposed for species with limited dispersal abilities or adaptive potential. However, species that rely on photoperiodic and thermal cues for development may experience conflicting signals if transported across latitudes. Relocating multiple, distinct populations may remedy this quandary by expanding genetic variation and promoting evolutionary responses in the receiving habitat – a strategy known as assisted gene flow. To better inform these policies, we planted seeds from latitudinally distinct populations of the annual legume, Chamaecrista fasciculata, in a potential future colonization site north of its current range boundary. Plants were exposed to ambient or elevated temperatures via infrared heating. We monitored several life history traits and estimated patterns of natural selection to determine the adaptive value of plastic responses. To assess the feasibility of assisted gene flow between phenologically distinct populations, we counted flowers each day and estimated the degree of temporal isolation between populations. Increased temperatures advanced each successive phenological trait more than the last, resulting in a compressed life cycle for all but the southern‐most population. Warming altered patterns of selection on flowering onset and vegetative biomass. Population performance was dependent on latitude of origin, with the northern‐most population performing best under ambient conditions and the southern‐most performing most poorly, even under elevated temperatures. Among‐population differences in flowering phenology limited the potential for genetic exchange among the northern‐ and southern‐most populations. All plastic responses to warming were neutral or adaptive; however, photoperiodic constraints will likely necessitate evolutionary responses for long‐term persistence, especially when involving populations from disparate latitudes. With strategic planning, our results suggest that assisted colonization and assisted gene flow may be feasible options for preservation.     

Interaction of landscape and life history attributes on genetic diversity,neutral divergence and gene flow in a pristine community of salmonids

Landscape genetics holds promise for the forecasting of spatial patterns of genetic diversity based on key environmental features. Yet, the degree to which inferences based on single species can be extended to whole communities is not fully understood. We used a pristine and spatially structured community of three landlocked salmonids (Salvelinus fontinalis, Salmo salar, and Salvelinus alpinus) from Gros Morne National Park (Newfoundland, Canada) to test several predictions on the interacting effects of landscape and life history variation on genetic diversity, neutral divergence, and gene flow (m, migration rate). Landscape factors consistently influenced multispecies genetic patterns: (i) waterfalls created strong dichotomies in genetic diversity and divergence between populations above and below them in all three salmonids; (ii) contemporary m decreased with waterway distance in all three species, while neutral genetic divergence (θ) increased with waterway distance, albeit in only two taxa; (iii) river flow generally produced downstream‐biased m between populations when waterfalls separated these, but not otherwise. In contrast, we expected differential life history to result in a hierarchy of neutral divergence (S. salar > S. fontinalis > S. alpinus) based on disparities in dispersal abilities and population size from previous mark‐recapture studies. Such hierarchy additionally matched varying degrees of spatial genetic structure among species revealed through individual‐based analyses. We conclude that, whereas key landscape attributes hold power to predict multispecies genetic patterns in equivalent communities, they are likely to interact with species‐specific life history attributes such as dispersal, demography, and ecology, which will in turn affect holistic conservation strategies.     

Use of ELISA and GUS‐transformed strains to study competition between pathogenic and non‐pathogenic Fusarium oxysporum for root colonization

To characterize the ability of different strains of Fusarium oxysporum to colonize roots, and to analyze competition for root colonization between pathogenic and non‐pathogenic strains of F. oxysporum, it was necessary to develop specific labelling techniques for quantification of root colonization. Two methods were selected: the production of polyclonal antibodies, and the use of GUS‐transformed strains of F. oxysporum. The polyclonal antibodies recognized infected plants, and gave a minimum reaction with healthy plants, but were not specific for individual strains of F. oxysporum. These antibodies enabled total density of F. oxysporum to be assessed on roots, by ELISA. Metabolic activity of the root population of GUS‐marked strains was assessed by measuring the glucuronidase activity. Strains showed a diversity in their ability to colonize roots: patterns of root colonization were similar, but the intensity and the speed of colonization differed according to the plant—fungus combination used. Results demonstrated competition between the pathogenic and the non‐pathogenic strains for root colonization. In the presence of the non‐pathogenic strain Fo 47, the competition seems to be reciprocal, affecting both the pathogen and non‐pathogenic strain. Other non‐pathogenic strains reduced root colonization by the pathogenic strain, but some strains did not reduce the metabolic activity of the pathogen, suggesting that different mechanisms are involved in the interaction between pathogenic and non‐pathogenic F. oxysporum.     

Post‐fire bryophyte establishment in a continental bog

Questions : What is the mechanism of bog ground layer colonization post‐fire? Is species colonization stochastic or does facilitation occur? Location : Boreal bog peatland near Crow Lake, Alberta, Canada. Methods : Diaspore‐addition treatments were applied in 2003 to autoclaved peat samples from high and low microtopographic positions within a recently burned bog. Colonization was assessed within the plots in 2005 and compared to control plots to determine treatment success and patterns of colonization. Results : A significant degree of ground layer colonization was found two years after fire, with Polytrichum strictum dominating the site. Colonization was greater in low (wet) plots, although only P. strictum and Sphagnum angustifolium had significant colonization. No effect of diaspore addition was observed and Sphagnum was only found in conjunction with P. strictum. Conclusions : Environmental conditions and species life history strategy are more important than diaspore availability for post‐fire colonization. True mosses (e.g. P. strictum) appearto facilitate Sphagnum colonization.     

Development of an in vitro colonization model to investigate Staphylococcus aureus interactions with airway epithelia

Staphylococcus aureus is a bacterial pathogen responsible for a wide range of diseases and is also a human commensal colonizing the upper respiratory tract. Strains belonging to the clonal complex group CC30 are associated with colonization, although the colonization state itself is not clearly defined. In this work, we developed a co‐culture model with S. aureus colonizing the apical surface of polarized human airway epithelial cells. The S. aureus are grown at the air–liquid interface to allow an in‐depth evaluation of a simulated colonization state. Exposure to wild‐type, S. aureus bacteria or conditioned media killed airway epithelial cells within 1 day, while mutant S. aureus strains lacking alpha‐toxin (hla) persisted on viable cells for at least 2 days. Recent S. aureus CC30 isolates are natural hla mutants, and we observed that these strains displayed reduced toxicity toward airway epithelial cells. Quantitative real‐time polymerase chain reaction of known virulence factors showed the expression profile of S. aureus grown in co‐culture correlates with results from previous human colonization studies. Microarray analysis indicated significant shifts in S. aureus physiology in the co‐culture model toward lipid and amino acid metabolism. The development of the in vitro colonization model will enable further study of specific S. aureus interactions with the host epithelia.     

Efficient rhizosphere colonization by Pseudomonas fluorescens f113 mutants unable to form biofilms on abiotic surfaces

Motility is a key trait for rhizosphere colonization by Pseudomonas fluorescens. Mutants with reduced motility are poor competitors, and hypermotile, more competitive phenotypic variants are selected in the rhizosphere. Flagellar motility is a feature associated to planktonic, free‐living single cells, and although it is necessary for the initial steps of biofilm formation, bacteria in biofilm lack flagella. To test the correlation between biofilm formation and rhizosphere colonization, we have used P. fluorescens F113 hypermotile derivatives and mutants affected in regulatory genes which in other bacteria modulate biofilm development, namely gacS (G), sadB (S) and wspR (W). Mutants affected in these three genes and a hypermotile variant (V35) isolated from the rhizosphere were impaired in biofilm formation on abiotic surfaces, but colonized the alfalfa root apex as efficiently as the wild‐type strain, indicating that biofilm formation on abiotic surfaces and rhizosphere colonization follow different regulatory pathways in P. fluorescens. Furthermore, a triple mutant gacSsadBwspR (GSW) and V35 were more competitive than the wild‐type strain for root‐tip colonization, suggesting that motility is more relevant in this environment than the ability to form biofilms on abiotic surfaces. Microscopy showed the same root colonization pattern for P. fluorescens F113 and all the derivatives: extensive microcolonies, apparently held to the rhizoplane by a mucigel that seems to be plant produced. Therefore, the ability to form biofilms on abiotic surfaces does not necessarily correlates with efficient rhizosphere colonization or competitive colonization.     

Caecal transcriptome analysis of colonized and non-colonized chickens within two genetic lines that differ in caecal colonization by Campylobacter jejuni

Campylobacter jejuni is one of the most common causes of human bacterial enteritis worldwide. The molecular mechanisms of the host responses of chickens to C. jejuni colonization are not well understood. We have previously found differences in C. jejuni colonization at 7‐days post‐inoculation (pi) between two genetic broiler lines. However, within each line, not all birds were colonized by C. jejuni (27.5% colonized in line A, and 70% in line B). Therefore, the objective of the present experiments was to further define the differences in host gene expression between colonized and non‐colonized chickens within each genetic line. RNA isolated from ceca of colonized and non‐colonized birds within each line was applied to a chicken 44K Agilent microarray for the pair comparison. There were differences in the mechanisms of host resistant to C. jejuni colonization between line A and line B. Ten times more differentially expressed genes were observed between colonized and non‐colonized chickens within line B than those within line A. Our study supports the fact that the MAPK pathway is important in host response to C. jejuni colonization in line B, but not in line A. The data indicate that inhibition of small GTPase‐mediated signal transduction could enhance the resistance of chickens to C. jejuni colonization and that the tumour necrosis factor receptor superfamily genes play important roles in determining C. jejuni non‐colonization in broilers.     

The microRNA miR171h modulates arbuscular mycorrhizal colonization of Medicago truncatula by targeting NSP2

Most land plants live symbiotically with arbuscular mycorrhizal fungi. Establishment of this symbiosis requires signals produced by both partners: strigolactones in root exudates stimulate pre‐symbiotic growth of the fungus, which releases lipochito‐oligosaccharides (Myc‐LCOs) that prepare the plant for symbiosis. Here, we have investigated the events downstream of this early signaling in the roots. We report that expression of miR171h, a microRNA that targets NSP2, is up‐regulated in the elongation zone of the root during colonization by Rhizophagus irregularis (formerly Glomus intraradices) and in response to Myc‐LCOs. Fungal colonization was much reduced by over‐expressing miR171h in roots, mimicking the phenotype of nsp2 mutants. Conversely, in plants expressing an NSP2 mRNA resistant to miR171h cleavage, fungal colonization was much increased and extended into the elongation zone of the roots. Finally, phylogenetic analyses revealed that miR171h regulation of NSP2 is probably conserved among mycotrophic plants. Our findings suggest a regulatory mechanism, triggered by Myc‐LCOs, that prevents over‐colonization of roots by arbuscular mycorrhizal fungi by a mechanism involving miRNA‐mediated negative regulation of NSP2.     

Arbuscular mycorrhizal fungi benefit from 7 years of free air CO2 enrichment in well-fertilized grass and legume monocultures

Rising atmospheric carbon dioxide partial pressure (pCO₂) and nitrogen (N) deposition are important components of global environmental change. In the Swiss free air carbon dioxide enrichment (FACE) experiment, the effect of altered atmospheric pCO₂ (35 vs. 60 Pa) and the influence of two different N‐fertilization regimes (14 vs. 56 g N m^?2 a^?1) on root colonization by arbuscular mycorrhizal fungi (AMF) and other fungi (non‐AMF) of Lolium perenne and Trifolium repens were studied. Plants were grown in permanent monoculture plots, and fumigated during the growth period for 7 years. At elevated pCO₂ AMF and non‐AMF root colonization was generally increased in both plant species, with significant effects on colonization intensity and on hyphal and non‐AMF colonization. The CO₂ effect on arbuscules was marginally significant (P=0.076). Moreover, the number of small AMF spores (≤100 μm) in the soils of monocultures (at low‐N fertilization) of both plant species was significantly increased, whereas that of large spores (>100 μm) was increased only in L. perenne plots. N fertilization resulted in a significant decrease of root colonization in L. perenne, including the AMF parameters, hyphae, arbuscules, vesicles and intensity, but not in T. repens. This phenomenon was probably caused by different C‐sink limitations of grass and legume. Lacking effects of CO₂ fumigation on intraradical AMF structures (under high‐N fertilization) and no response to N fertilization of arbuscules, vesicles and colonization intensity suggest that the function of AMF in T. repens was non‐nutritional. In L. perenne, however, AM symbiosis may have amended N nutrition, because all root colonization parameters were significantly increased under low‐N fertilization, whereas under high‐N fertilization only vesicle colonization was increased. Commonly observed P‐nutritional benefits from AMF appeared to be absent under the phosphorus‐rich soil conditions of our field experiment. We hypothesize that in well‐fertilized agricultural ecosystems, grasses benefit from improved N nutrition and legumes benefit from increased protection against pathogens and/or herbivores. This is different from what is expected in nutritionally limited plant communities.     

Salicylic acid prevents Trichoderma harzianum from entering the vascular system of roots

Trichoderma is a soil‐borne fungal genus that includes species with a significant impact on agriculture and industrial processes. Some Trichoderma strains exert beneficial effects in plants through root colonization, although little is known about how this interaction takes place. To better understand this process, the root colonization of wild‐type Arabidopsis and the salicylic acid (SA)‐impaired mutant sid2 by a green fluorescent protein (GFP)‐marked Trichoderma harzianum strain was followed under confocal microscopy. Trichoderma harzianum GFP22 was able to penetrate the vascular tissue of the sid2 mutant because of the absence of callose deposition in the cell wall of root cells. In addition, a higher colonization of sid2 roots by GFP22 compared with that in Arabidopsis wild‐type roots was detected by real‐time polymerase chain reaction. These results, together with differences in the expression levels of plant defence genes in the roots of both interactions, support a key role for SA in Trichoderma early root colonization stages. We observed that, without the support of SA, plants were unable to prevent the arrival of the fungus in the vascular system and its spread into aerial parts, leading to later collapse.     

Use of rare‐earth elements in the phyllosphere colonizer Methylobacterium extorquens PA1

Until recently, rare‐earth elements (REEs) had been thought to be biologically inactive. This view changed with the discovery of the methanol dehydrogenase XoxF that strictly relies on REEs for its activity. Some methylotrophs only contain xoxF, while others, including the model phyllosphere colonizer Methylobacterium extorquens PA1, harbor this gene in addition to mxaFI encoding a Ca²⁺‐dependent enzyme. Here we found that REEs induce the expression of xoxF in M. extorquens PA1, while repressing mxaFI, suggesting that XoxF is the preferred methanol dehydrogenase in the presence of sufficient amounts of REE. Using reporter assays and a suppressor screen, we found that lanthanum (La³⁺) is sensed both in a XoxF‐dependent and independent manner. Furthermore, we investigated the role of REEs during Arabidopsis thaliana colonization. Element analysis of the phyllosphere revealed the presence of several REEs at concentrations up to 10 μg per g dry weight. Complementary proteome analyses of M. extorquens PA1 identified XoxF as a top induced protein in planta and a core set of La³⁺‐regulated proteins under defined artificial media conditions. Among these was a REE‐binding protein that is encoded next to a gene for a TonB‐dependent transporter. The latter was essential for REE‐dependent growth on methanol indicating chelator‐assisted uptake of REEs.     

Endemic Cyprus Warbler Sylvia melanothorax and colonizing Sardinian Warbler Sylvia melanocephala show different habitat associations

Anthropogenic habitat change and assisted colonization are promoting range expansions of some widespread species with potential consequences for endemic fauna. The recent colonization of Cyprus by breeding Sardinian Warblers Sylvia melanocephala has raised concerns that it might be displacing the closely related and endemic Cyprus Warbler Sylvia melanothorax. Habitat associations of both species were examined using models of abundance within the 95% density kernel of the Sardinian Warbler’s range and also outside this range for Cyprus Warbler. Within the Sardinian Warbler’s range, the two species were associated with subtly different scrub habitats. Outside the Sardinian Warbler’s range, the Cyprus Warbler differed again in its habitat association, but this probably resulted from marked differences in habitat extent and availability in different parts of the island rather than from competitive displacement, as none of the habitat or land‐use elements differentially associated with Cyprus Warblers was positively associated with Sardinian Warbler occurrence. This suggests that the Sardinian Warbler has exploited a different niche, rather than displacing the endemic species, and has perhaps benefitted from changing land‐use patterns, particularly recent fallows and abandoned agriculture, in contrast to the stronger association of Cyprus Warblers with semi‐natural scrub.     

Non‐native acylated homoserine lactones reveal that LuxIR quorum sensing promotes symbiont stability

Quorum sensing, a group behaviour coordinated by a diffusible pheromone signal and a cognate receptor, is typical of bacteria that form symbioses with plants and animals. LuxIR‐type N‐acyl L‐homoserine (AHL) quorum sensing is common in Gram‐negative Proteobacteria, and many members of this group have additional quorum‐sensing networks. The bioluminescent symbiont Vibrio fischeri encodes two AHL signal synthases: AinS and LuxI. AinS‐dependent quorum sensing converges with LuxI‐dependent quorum sensing at the LuxR regulatory element. Both AinS‐ and LuxI‐mediated signalling are required for efficient and persistent colonization of the squid host, Euprymna scolopes. The basis of the mutualism is symbiont bioluminescence, which is regulated by both LuxI‐ and AinS‐dependent quorum sensing, and is essential for maintaining a colonization of the host. Here, we used chemical and genetic approaches to probe the dynamics of LuxI‐ and AinS‐mediated regulation of bioluminescence during symbiosis. We demonstrate that both native AHLs and non‐native AHL analogues can be used to non‐invasively and specifically modulate induction of symbiotic bioluminescence via LuxI‐dependent quorum sensing. Our data suggest that the first day of colonization, during which symbiont bioluminescence is induced by LuxIR, is a critical period that determines the stability of the V. fischeri population once symbiosis is established.     

Colonization of disturbed Scots pine trees by bark‐ and wood‐boring beetles

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Pneumocystis jirovecii colonization is associated with enhanced Th1 inflammatory gene expression in lungs of humans with chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a complex disease, the pathogenesis of which remains incompletely understood. Colonization with Pneumocystis jirovecii may play a role in COPD pathogenesis; however, the mechanisms by which such colonization contributes to COPD are unknown. The objective of this study was to determine lung gene expression profiles associated with Pneumocystis colonization in patients with COPD to identify potential key pathways involved in disease pathogenesis. Using COPD lung tissue samples made available through the Lung Tissue Research Consortium (LTRC), Pneumocystis colonization status was determined by nested PCR. Microarray gene expression profiles were performed for each sample and the profiles of colonized and non‐colonized samples compared. Overall, 18 participants (8.5%) were Pneumocystis‐colonized. Pneumocystis colonization was associated with fold increase in expression of four closely related genes: INF‐γ and the three chemokine ligands CXCL9, CXCL10, and CXCL11. These ligands are chemoattractants for the common cognate receptor CXCR3, which is predominantly expressed on activated Th1 T‐lymphocytes. Although these ligand–receptor pairs have previously been implicated in COPD pathogenesis, few initiators of ligand expression and subsequent lymphocyte trafficking have been identified: our findings implicate Pneumocystis as a potential trigger. The finding of upregulation of these inflammatory genes in the setting of Pneumocystis colonization sheds light on infectious‐immune relationships in COPD.