Accordingly, plant roots in dry environments have fewer soil water source options, so xylem water and bulk soil water will trend towards similar isotopic compositions.Despite our unique data set and our observations, several open questions remain: a) Biophysical processes: Recent research shows that various complex bio-physical processes in the soil plant-atmosphere continuum may help explain why xylem water at the VeWa sites cannot be fully explained by soil water sources . As noted above, one possibility is that exchange between the soil liquid and vapour phase is complex and may affect root water uptake. This may be either through roots being able to access a fractionated vapour phase and/or condensation onto soil surfaces from the soil atmosphere increasing the likelihood that plants take up water depleted in heavier isotopes, especially deuterium. Both recent field and modelling studies have highlighted the plausibility of such mechanisms, but mechanistic studies to test such a hypothesis are limited and urgently needed. Similarly, the complex interactions in the symbiotic relationship between mycorrhiza and plant roots cause uptake of more 2 H- and 18O-depleted water compared to bulk soil water. In particular, widespread arbuscular mycorrhizal fungi which penetrate the cortical cells in the roots of vascular plants may be an effective mechanism that can facilitate fractionation of root water uptake . This occurs as part of the complex symbiosis of nutrient exchange that also affects plant-water relationships and is focused in the upper soil horizons.

Such mycorrhizal interactions are particularly important in nutrient poor minerogenic northern soils,blueberry production and may have strong effects at sites like Bruntland Burn, Dorset and Krycklan. Again, more specific process-based studies are required to test this hypothesis in contrasting soil-plant systems. Finally, diffusion and evaporation through bark may be important biophysical processes, especially during winter when there is no transpiration . This is potentially a factor in northern regions where winter conditions preclude transpiration but can expose vegetation to arid conditions with high wind speeds and low humidity at sites like Dry Creek and Wolf Creek . Isotope transport through bark may explain why the gymnosperms at Dry Creek showed much greater overlap with the isotopic composition of soil water sampled over a range of antecedent intervalsin spring compared with Bruntland Burn, Dorset, and Krycklan where there was very little overlap. However, this inter-site difference was less pronounced for angiosperms . b) Extraction of vegetation and soil water: We do not fully know what kind of vegetation water is mobilized by the cryogenic extraction, although it is usually assumed to characterise xylem water. However, it is likely that some of the water that gets extracted is part of live cells subject to potentially fractionating biophysical processes that are independent of the hydrological cycle. Zhao et al. saw large differences between xylem sap, extracted with a syringe, and twig water extracted via cryogenic extraction with the former being more enriched in 2 H compared to the latter. In such cases, differences in the ratio of cell water to xylem water, which would depend on soil wetness, could have an effect on the differences between the isotopic composition of plant water and cryogenically extracted water . Barbeta et al. support this interpretation and call for more specific characterisation of what is assumed to be extracted xylem water. Very recent experimental work by Chen et al. showed that cryogenic extraction can enhance deuterium exchange with organically bound water and contribute to the deuterium depletion.

Moreover, they showed the effect can be greatest under more moisture-limited conditions which may explain the tendency for more negative swexcess values as sites become drier. Physiological and biochemical differences between angiosperms and gymnosperms may also contribute to differences in extraction effects . As with vegetation water extraction, differences from contrasting soil extraction techniques may explain some of the mis-match between observed xylem water and soil sources. For example, the similarities between soil and xylem water at Dry Creek involved cryogenic extraction of soils, whereas all other sites used equilibration. However, at Bruntland Burn cryogenic and equilibration methods gave similar results for peaty soils, and reasonable agreement with xylem water . Extraction focusing on small-scale moisture isotope dynamics at the root – soil interface may be needed, including scalable methods to explore the phase change/mycorrhizal mechanisms suggested above. Our findings, based on bulk soil field measurements, underline the major difficulties associated with relating potential water sources to plant water stable isotope compositions. Even under controlled laboratory conditions, Orlowski et al. could not confidently link relate the soil water to root crown isotopic compositions, but reported similar 2 H depletion as we found in Dandelions growing on sandy soils. c) Differences between angiosperms vs gymnosperms: A clear finding of our study is that the extracted xylem waters of angiosperms and gymnosperms have a very different isotopic composition at most sites, with gymnosperms generally showing a greater degree of fractionation. In this regard, several hypotheses could be tested. Firstly, root networks and root-mycorrhizal networks of different species may be able to access different pore sizes. For example, gymnosperms may have greater potential to mobilize water that has undergone some fractionation during the interactions among water, gas, and solid phases of the soil. Secondly, storage and mixing of water within plant tissues may be greater in softwood gymnosperms, as suggested in recent modelling work . The generally slower metabolism and transpiration rates for gymnosperms might exacerbate this mechanism.

Such differences may also contribute to what water is extracted in the laboratory. Interestingly, Amin et al. showed little difference between angiosperms and gymnosperm xylem waters for cold and temperate environments in their meta-analysis, whereas angiosperms in arid regions were offset in δ2 H compared to gymnosperms. Understanding the mechanisms of adaptive evolution in pathogenic bacteria is central to long-term disease control. One major focus of research into adaptive bacterial evolution has been lateral gene transfer , usually defined as the transfer of genes across species boundaries . Until recently, discussions of LGT focused on the transfer of novel genes, as exemplified by the discovery of the plasmid-mediated transfer across species of the genes coding for penicillin resistance ; however, with the increasing availability of genomic sequence data, it has become apparent that the transfer of homologous gene copies is also widespread . These two kinds of exchange, the transfer of novel genes or novel alleles, are fundamentally different. The acquisition of novel genes can result in the acquisition of a completely new trait that has already been refined in other taxa by natural selection . It can determine critical traits such as virulence, antibiotic resistance,blueberry in container and ecological niche , even though most of the material transferred appears to be evolutionarily transient . In contrast the acquisition of novel alleles is analogous to the effect of sexual reproduction in eukaryotes: it increases the genetic variance that natural selection can act on but does not, in itself, result in a qualitative change in the ecology of the recipient . Due to these fundamental differences, we favor reserving the term “LGT” for the transfer of novel genes, using the term “inter-specific” or “inter sub-specific homologous recombination” for the transfer of alleles; however, both processes, if successful, lead to genetic “introgression,” a term commonly used to describe the spread of genetic material across taxonomic boundaries in plants and animals and now increasingly used to describe the analogous process in bacteria . Homologous recombination is almost ubiquitous among bacteria, although the degree to which it occurs varies widely among species . It involves the replacement of a stretch of DNA sequence in one individual’s genome by a homologous sequence from another individual of the same species following any of the 3 mechanisms of DNA transfer . It typically involves short pieces of DNA . Given the prevalence of homologous recombination, it is generally assumed that it is beneficial, in some cases enabling bacteria to enhance their resistance to antibiotics and avoid host defenses or perhaps promoting adaptation to novel environments . Analogy with the assumed benefits maintaining sexual recombination in metazoans strongly supports this view. This is to be expected even if the benefits are large and common. Homologous recombination typically falls off rapidly with genetic distance , so a well-established population will usually reflect the mixing of relatively similar alleles.

This mixing can be easily detected by the lack of clonality between genes and quantified using evolutionary models ; however, detection of recombination breaks within genes is more problematic. The approaches currently used have very limited power; although the introgression test has improved this situation . Another approach is to test loci sequenced from 2 or more taxa and use the genetic partitioning program STRUCTURE . Alleles that cannot be confidently allocated to one or more of the taxa are likely to be mosaics generated by recombination . To link recombination to adaptive change, it is useful to study a system in which recombination is limited, recognizable, and likely to lead to novel adaptation. Arnold et al. recently made an interesting link between the acquisition of novel adaptations in bacteria via LGT and that via hybridization in metazoans. Excellent examples of how inter specific introgression can result in adaptation to new environments in higher plants are given in the work of Rieseberg and colleagues on the effects of introgression in sunflower species . However, it is not only metazoans that hybridize: bacterial homologous recombination can sometimes result in inter specific introgression . Inter specific hybridization of this kind is likely to be relatively rare, suggesting that the ideal study system is one with a significant frequency of homologous recombination between well-defined groups within a species . This level of study appears most likely to provide valuable insights into recombination-related adaptive change in pathogens. For example, Didelot et al. showed that two human-pathogenic forms of Salmonella entericaare relatively dissimilar across about 75% of their genomes but show marked convergence across the rest. They concluded that this similarity reflects adaptation to the human host, driven by homologous recombination and selection. Similarly, Sheppard et al. proposed that human activity has probably led to an increase in recombination between Campylobacter jejuni and Campylobacter coli and may have also created novel environments that have favored the evolution of hybrids. Another species in which homologous recombination between closely related but distinct taxa has been documented is the plant pathogenic bacterium Xylella fastidiosa . X. fastidiosa is a xylem-limited bacterium that is transmitted by xylem-feeding insects, typically leaf hoppers, and is divided into four subspecies: fastidiosa, sandyi, multiplex, and pauca . These subspecies have diverged genetically by 1 to 3%, apparently due to their geographical isolation over about the last 20,000 to 50,000 years . This isolation has now broken down, due presumably to human activity . The cooccurrence of the previously allopatric subspecies has resulted in inter subspecific homologous recombination , recombination that can be detected relatively easily due to the preexisting genetic divergence of the subspecies . Consistent with these observations, recent experimental work has confirmed that X. fastidiosa is transformationally competent and that some isolates carry a conjugative plasmid . X. fastidiosa is known to infect a wide range of hosts, causing scorch and dwarfing diseases . In citrus, it causes citrus variegated chlorosis , a disease restricted to South America, and in grapevines in the United States and Central America, it causes Pierce’s disease. In the United States, it also causes disease in almond, apricot, plum, peach, alfalfa, pecan, and blueberry. However, individual X. fastidiosa strains are not generalists. The different subspecies infect a characteristic and largely nonoverlapping range of plant hosts, and even within subspecies, different genotypes show differences in host specificity . For example, in the South American X. fastidiosa subsp. pauca, citrus isolates do not typically grow in coffee and vice versa , and in X. fastidiosa subsp. multiplex, Nunney et al. found associations between the genotype and host plant. In their study of X. fastidiosa subsp. multiplex, Nunney et al. used the multilocus sequence typing protocol of Yuan et al. to categorize 143 isolates. The MLST protocol is valuable for gaining insight into the evolutionary history and genetic diversity of taxa . MLST groups isolates into sequence types , where each ST defines a unique set of alleles across the loci used . Based on 8 loci, 31 of these isolates were identified as IHR forms , and 2 isolates were considered “intermediate” , while the remaining 110 non-IHR isolates showed no evidence of introgression.