Microbial tropicalization driven by a strengthening western ocean boundary current

Western boundary currents (WBCs) redistribute heat and oligotrophic seawater from the tropics to temperate latitudes, with several displaying substantial climate change‐driven intensification over the last century. Strengthening WBCs have been implicated in the poleward range expansion of marine macroflora and fauna, however, the impacts on the structure and function of temperate microbial communities are largely unknown. Here we show that the major subtropical WBC of the South Pacific Ocean, the East Australian Current (EAC), transports microbial assemblages that maintain tropical and oligotrophic (k‐strategist) signatures, to seasonally displace more copiotrophic (r‐strategist) temperate microbial populations within temperate latitudes of the Tasman Sea. We identified specific characteristics of EAC microbial assemblages compared with non‐EAC assemblages, including strain transitions within the SAR11 clade, enrichment of Prochlorococcus, predicted smaller genome sizes and shifts in the importance of several functional genes, including those associated with cyanobacterial photosynthesis, secondary metabolism and fatty acid and lipid transport. At a temperate time‐series site in the Tasman Sea, we observed significant reductions in standing stocks of total carbon and chlorophyll a, and a shift towards smaller phytoplankton and carnivorous copepods, associated with the seasonal impact of the EAC microbial assemblage. In light of the substantial shifts in microbial assemblage structure and function associated with the EAC, we conclude that climate‐driven expansions of WBCs will expand the range of tropical oligotrophic microbes, and potentially profoundly impact the trophic status of temperate waters.     

Effects of planktivore abundance on chlorophyll-a and Secchi depth

We used two analyses to test the hypothesis that planktivore abundances contribute to the residual variations of Secchi depth or chlorophyll-a plotted with respect to mean summer epilimnetic total phosphorus. The first analysis involved 15 lake years of data from six lakes. The data set comprised mark-recapture assessments of piscivore and planktivore numbers and estimates of mean summer chlorophyll-a, total phosphorus and Secchi depth. We found that residual chlorophyll-a variation was not significantly (p>0.05) correlated with planktivore densities, but that planktivore densities did contribute (p<0.02) to the residual variation of Secchi depth on mean total phosphorus. The second analysis included all of the data used in the first plus an additional 13 lake years of data from the literature. These data showed that the percentage of the total fish community comprising planktivores did not significantly (p>0.05) contribute to the residual variation in chlorophyll-a with respect to mean summer total phosphorus. Together, our results suggest that planktivore abundance has a significant cascading impact on water clarity, but no long term statistically significant impact on mean summer chlorophyll-a concentration.     

Repeated H2O2 exposure drives cell cycle progression in an in vitro model of ulcerative colitis

The production of hydrogen peroxide (H₂O₂) drives tumourigenesis in ulcerative colitis (UC). Recently, we showed that H₂O₂ activates DNA damage checkpoints in human colonic epithelial cells (HCEC) through c‐Jun N‐terminal Kinases (JNK) that induces p21^WAF1. Moreover, caspases circumvented the G1/S and intra‐S checkpoints, and cells accumulated in G2/M. The latter observation raised the question of whether repeated H₂O₂ exposures alter JNK activation, thereby promoting a direct passage of cells from G2/M arrest to driven cell cycle progression. Here, we report that increased proliferation of repeatedly H₂O₂‐exposed HCEC cells (C‐cell cultures) was associated with (i) increased phospho‐p46 JNK, (ii) decreased total JNK and phospho‐p54 JNK and (iii) p21^WAF1 down‐regulation. Altered JNK activation and p21^WAF1 down‐regulation were accompanied by defects in maintaining G2/M and mitotic spindle checkpoints through adaptation, as well as by apoptosis resistance following H₂O₂ exposure. This may cause increased proliferation of C‐cell cultures, a defining initiating feature in the inflammation‐carcinoma pathway in UC. We further suggest that dysregulated JNK activation is attributed to a non‐apoptotic function of caspases, causing checkpoint adaptation in C‐cell cultures. Additionally, loss of cell‐contact inhibition and the overcoming of senescence, hallmarks of cancer, contributed to increased proliferation. Furthermore, there was evidence that p54 JNK inactivation is responsible for loss of cell‐contact inhibition. We present a cellular model of UC and suggest a sinusoidal pattern of proliferation, which is triggered by H₂O₂‐induced reactive oxygen species generation, involving an interplay between JNK activation/inactivation, p21^WAF1, c‐Fos, c‐Jun/phospho‐c‐Jun, ATF2/phospho‐ATF2, β‐catenin/TCF4‐signalling, c‐Myc, CDK6 and Cyclin D2, leading to driven cell cycle progression.     

National‐scale analyses of habitat associations of Marsh Tits Poecile palustris and Blue Tits Cyanistes caeruleus: two species with opposing population trends in Britain

Capsule Marsh Tits were strongly associated with both the amount and species diversity of woodland understorey; Blue Tits were associated with large trees and deadwood.

Aims To gather quantitative information on the habitat requirements of Marsh Tits, in comparison with those of Blue Tits, across a large number of sites in England and Wales, and secondly to evaluate the range of habitat conditions likely to encourage the presence, and increase the abundance of, each species.

Methods Counts of birds were made at each of 181 woods across England and Wales, and habitat data were collected from the same locations in each woodland. Marsh Tit and Blue Tit presence and abundance were related to habitat characteristics, interspecific competition and deer impact.

Results Shrub cover and species diversity were important for the presence and abundance of Marsh Tits, across their geographical range in Britain. Blue Tits were associated with large trees and deadwood.

Conclusion Our results support the hypothesis that changes in woodland management, leading to canopy closure and a decline in the understorey available, could have had an impact on Marsh Tits, and may have led to the observed population decline. These same changes were also consistent with population increase in Blue Tits.     

Drivers of low breeding success in the Lesser Spotted Woodpecker Dendrocopos minor in England: testing hypotheses for the decline

Capsule The breeding success of Lesser Spotted Woodpeckers Dendrocopos minor is now lower in England than previously reported and also lower than found in studies elsewhere in Europe.

Aims To quantify the breeding success and identify the causes of nest failure. To test the hypotheses that breeding success is related to aspects of food limitation and parental care, and inclement weather during the nesting period, or to interactions with Great Spotted Woodpeckers.

Methods Nests were monitored in three regions of England, recording survival and causes of failure. We measured aspects of food limitation and parental care, rainfall and Great Spotted Woodpecker interactions at nests, to explore whether there was any evidence that these factors were related to breeding success. We compared results to other studies from the UK and continental Europe.

Results Nest survival was 52%. The average number of chicks produced from successful nests was 2.8. Chick-stage daily nest survival was positively related to provisioning rates, indicating that food supply may be limiting. The most common cause of nest failure was presumed starvation of chicks after the disappearance of an adult. Some females ceased visiting nests, leaving provisioning solely to the male. This behaviour has been reported elsewhere in Europe, but in the present study males were unable to compensate fully by increasing their provisioning rates, leading to poor nest survival. Provisioning rates and chick-stage daily nest survival were negatively associated with rainfall. Nest predation by Great Spotted Woodpeckers occurred but was a less frequent cause of failure. Aggressive interactions were recorded between the two woodpecker species but these were unrelated to breeding parameters.

Conclusions Low breeding success is most probably related to food shortages in the breeding period. Simple population modelling using parameters from the present study and from published work shows that if the low productivity that we have observed is replicated throughout Britain, it would be sufficient to account for the observed population decline. However, the possibility that survival rates are also low cannot be ruled out.     

Vascular Occlusions in Grapevines with Pierce’s Disease Make Disease Symptom Development Worse

Vascular occlusions are common structural modifications made by many plant species in response to pathogen infection. However, the functional role(s) of occlusions in host plant disease resistance/susceptibility remains controversial. This study focuses on vascular occlusions that form in stem secondary xylem of grapevines (Vitis vinifera) infected with Pierce’s disease (PD) and the impact of occlusions on the hosts’ water transport and the systemic spread of the causal bacterium Xylella fastidiosa in infected vines. Tyloses are the predominant type of occlusion that forms in grapevine genotypes with differing PD resistances. Tyloses form throughout PD-susceptible grapevines with over 60% of the vessels in transverse sections of all examined internodes becoming fully blocked. By contrast, tylose development was mainly limited to a few internodes close to the point of inoculation in PD-resistant grapevines, impacting only 20% or less of the vessels. The extensive vessel blockage in PD-susceptible grapevines was correlated to a greater than 90% decrease in stem hydraulic conductivity, compared with an approximately 30% reduction in the stems of PD-resistant vines. Despite the systemic spread of X. fastidiosa in PD-susceptible grapevines, the pathogen colonized only 15% or less of the vessels in any internode and occurred in relatively small numbers, amounts much too small to directly block the vessels. Therefore, we concluded that the extensive formation of vascular occlusions in PD-susceptible grapevines does not prevent the pathogen’s systemic spread in them, but may significantly suppress the vines’ water conduction, contributing to PD symptom development and the vines’ eventual death.Pierce’s disease (PD) of grapevines (Vitis vinifera), currently jeopardizing the wine and table grape industries in the southern United States and California, as well as in many other countries, is a vascular disease caused by the xylem-limited bacterium Xylella fastidiosa (Hopkins, 1989; Varela et al., 2001). The pathogen is transmitted mostly via xylem sap-feeding sharpshooters (e.g. Homalodisca vitripennis; Redak et al., 2004) and inhabits, proliferates, and spreads within the vessel system of a host grapevine (Fry and Milholland, 1990a; Hill and Purcell, 1995). PD symptom development in grapevines depends on the interactions between the pathogen and the host vine’s xylem tissue, through which the pathogen may achieve its systemic spread (Purcell and Hopkins, 1996; Krivanek and Walker, 2005; Pérez-Donoso et al., 2010; Sun et al., 2011). Since the path for this spread is the host’s xylem system, xylem tissue and its vessels have become the major focus for studying potential X. fastidiosa-host vine interactions at the cellular or tissue levels (Fry and Milholland, 1990b; Stevenson et al., 2004a; Sun et al., 2006, 2007; Thorne et al., 2006).One major issue related to this host-pathogen interaction is the relationship of a vine’s xylem anatomy to the X. fastidiosa population’s spread. Sun et al. (2006) did a detailed anatomical analysis of the stem secondary xylem, especially the vessel system. Stevenson et al. (2004b) described xylem connection patterns between a stem and the attached leaves. Other studies reported the presence of open continuous vessels connecting stems and leaves, which represent conduits that might facilitate the pathogen’s stem-to-leaf movement (Thorne et al., 2006; Chatelet et al., 2006, 2011). Chatelet et al. (2011) also suggested that vessel size and ray density were the two xylem features that were most relevant to the restriction of X. fastidiosa’s movement. These studies indicate the importance of understanding the grapevine’s xylem anatomy in order to characterize the grapevine host’s susceptibility or resistance to PD.Another focus of PD-related xylem studies is the tylose, a developmental modification that has important impacts on a vessel’s role in water transport and, potentially, its availability as a path for X. fastidiosa’s systemic spread through a vine. Tyloses are outgrowths into a vessel lumen from living parenchyma cells that are adjacent to the vessel and can transfer solutes into the transpiration stream via vessel-parenchyma (V-P) pit pairs (Esau, 1977). Tylose development involves the expansion of the portions of the parenchyma cell’s wall that are shared with the neighboring vessels, specifically the so-called pit membranes (PMs). Intensive tylose development may eventually block the affected vessel (Sun et al., 2006). Since tyloses occur in the vessel system of PD-infected grapevines (Esau, 1948; Mollenhauer and Hopkins, 1976; Stevenson et al., 2004a; Krivanek et al., 2005) that is also the avenue of X. fastidiosa’s spread and water transport, a great deal of effort has been made to understand tyloses and their possible relations to grapevine PD as well as to diseases caused by other vascular system-localized pathogens. One major aspect is to clarify the process of tylose development itself, in which an open vessel may be gradually sealed (Sun et al., 2006, 2008). Our investigations of the initiation of tylose formation in grapevines have identified ethylene as an important factor (Pérez-Donoso et al., 2007; Sun et al., 2007). In terms of the relationship of tyloses to grapevine PD, studies have so far led to several controversial viewpoints that are discussed below (Mollenhauer and Hopkins, 1976; Fry and Milholland, 1990b; Stevenson et al., 2004a; Krivanek et al., 2005). However, more convincing evidence is still needed to support any of them.Another issue potentially relevant to PD symptom development is the possibility that X. fastidiosa cells and/or their secretions contribute to the blockage of water transport in host vines. The bacteria secrete an exopolysaccharide (Roper et al., 2007a) that contributes to the formation of cellular aggregates. Accumulations of X. fastidiosa cells embedded in an exopolysaccharide matrix (occasionally identified as biofilms, gums, or gels) have been reported in PD-infected grapevines (Mollenhauer and Hopkins, 1974; Fry and Milholland, 1990a; Newman et al., 2003; Stevenson et al., 2004b). However, a more detailed investigation is still needed to clarify if and to what extent these aggregates affect water transport in infected grapevines.The xylem tissue in which X. fastidiosa spreads can be classified as primary xylem or secondary xylem, being derived from procambium or vascular cambium, respectively. Primary xylem is located in and responsible for material transport and structural support in young organs (i.e. leaves, young stems, and roots), while secondary xylem is the conductive and supportive tissue in more mature stems and roots (Esau, 1977). It should be noted that most of the earlier experimental results have been based on examinations of leaves (petioles or veins) or young stems of grapevines, which contain mostly primary xylem with little or no secondary xylem. However, X. fastidiosa’s systemic spread generally occurs after introduction during the insect vector’s feeding from an internode of one shoot. The pathogen then moves upward along that shoot and also downward toward the shoot base. The downward movement allows the bacteria to enter the vine’s other shoots via the shared trunk and then move upward (Stevenson et al., 2004a; Sun et al., 2011). These upward and downward bacterial movements occur through stems that contain significant amounts of secondary xylem but relatively dysfunctional primary xylem. Secondary and primary xylem show some major differences in the structure and arrangement of their cell components (Esau, 1977). In terms of the vessel system that is the path of X. fastidiosa’s spread, the secondary xylem has a large number of much bigger vessels with scalariform (ladder-like) PMs (and pit pairs) as the sole intervessel (I-V) PM type, compared with the primary xylem, which contains only a limited number of smaller vessels with multiple types of I-V PMs (Esau, 1948; Sun et al., 2006). Vessels in secondary xylem are also different from those in primary xylem in forming vessel groups and in the number of parenchyma cells associated with a vessel (as seen in transverse sections of xylem tissue). These features of secondary xylem can affect the initial entry and subsequent I-V movement of the pathogen and the formation of vascular occlusions, respectively, in stems containing significant amounts of secondary xylem. Recently, the X. fastidiosa population size only in stems with secondary xylem was found to correlate with the grapevine’s resistance to PD (Baccari and Lindow, 2011), indicating an important role of stem secondary xylem in determining a host vine’s disease resistance. Despite these facts, little is known about the pathogen-grapevine interactions in the stem secondary xylem and their possible impacts on disease development.This study addresses X. fastidiosa-grapevine interactions in stem secondary xylem and examines the resulting impacts on overall vine physiology, with a primary focus on vine water transport. We have made use of grapevine genotypes displaying different PD resistances and explored whether differences in the pathogen’s induction of vascular occlusions occur among the genotypes and, if so, how the differences impact X. fastidiosa’s systemic spread. Our overall, longer-term aim is to elucidate the functional role of vascular occlusions in PD development, an understanding that we view to be essential for identifying effective approaches for controlling this devastating disease.     

Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family

Background

It is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5''-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.

Results

Phylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5''-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.

Conclusions

Like the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5''-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1584-3) contains supplementary material, which is available to authorized users.