Milling plant and soil material in plastic tubes over-estimates carbon and under-estimates nitrogen concentrations

Background and aims

Milling of plant and soil material in plastic tubes, such as microcentrifuge tubes, over-estimates carbon (C) and under-estimates nitrogen (N) concentrations due to the introduction of polypropylene into milled samples, as identified using Fourier-transform infra-red spectroscopy.

Methods and results

This study compares C and N concentrations of roots and soil milled in microcentrifuge tubes versus stainless steel containers, demonstrating that a longer milling time, greater milling intensity, smaller sample size and inclusion of abrasive sample material all increase polypropylene contamination from plastic tubes leading to overestimation of C concentrations by up to 8 % (0.08 g?g^?1).

Conclusions

Erroneous estimations of C and N, and other analytes, must be assumed after milling in plastic tubes and milling methods should be adapted to minimise such error.     

Soil drainage and phosphorus depletion contribute to retrogressive succession along a New Zealand chronosequence

Background and aims

Models of retrogressive succession have emphasised the role of phosphorus (P) depletion in driving biomass loss on surfaces of increasing geologic age, but the influence of impeded drainage on old surfaces has received much less attention. We tested whether poor drainage contributed to changes in ecosystem properties along a 291,000-year chronosequence in New Zealand (the Waitutu chronosequence).

Methods

Soil and ecosystem properties were measured at 24 evenly distributed points within each of eight 1.5 ha plots located on young, intermediate and old surfaces. Regression analyses tested whether drainage, in addition to P, affected ecosystem functioning. A complementary fertilization experiment tested whether P was indeed limiting on the most nutrient-depleted sites.

Results

Most phosphorus depletion occurred in the early stages of pedogenesis (within 24,000 years), and the older surfaces were similar in soil-P contents, whereas drainage was initially good but became increasingly impeded with surface age. In the fertilizer experiment, species showed positive responses to both nitrogen (N) and P addition on the oldest surfaces, supporting Walker and Syer’s model. However, water table depth was also found to be strongly correlated with plant species composition, forest basal area, light transmission, and litter decomposition when comparisons were made across sites, emphasising that it too has strong influences on ecosystem processes.

Conclusions

Poor drainage influences the process of retrogressive succession along the Waitutu chronosequence. We discuss the implications of our work with regard to other chronosequences, suggesting that topography is likely to have strong influences on retrogressive processes.     

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.     

Aldehyde dehydrogenase (ALDH) superfamily in plants: gene nomenclature and comparative genomics

In recent years, there has been a significant increase in the number of completely sequenced plant genomes. The comparison of fully sequenced genomes allows for identification of new gene family members, as well as comprehensive analysis of gene family evolution. The aldehyde dehydrogenase (ALDH) gene superfamily comprises a group of enzymes involved in the NAD⁺- or NADP⁺-dependent conversion of various aldehydes to their corresponding carboxylic acids. ALDH enzymes are involved in processing many aldehydes that serve as biogenic intermediates in a wide range of metabolic pathways. In addition, many of these enzymes function as ‘aldehyde scavengers’ by removing reactive aldehydes generated during the oxidative degradation of lipid membranes, also known as lipid peroxidation. Plants and animals share many ALDH families, and many genes are highly conserved between these two evolutionarily distinct groups. Conversely, both plants and animals also contain unique ALDH genes and families. Herein we carried out genome-wide identification of ALDH genes in a number of plant species—including Arabidopsis thaliana (thale crest), Chlamydomonas reinhardtii (unicellular algae), Oryza sativa (rice), Physcomitrella patens (moss), Vitis vinifera (grapevine) and Zea mays (maize). These data were then combined with previous analysis of Populus trichocarpa (poplar tree), Selaginella moellindorffii (gemmiferous spikemoss), Sorghum bicolor (sorghum) and Volvox carteri (colonial algae) for a comprehensive evolutionary comparison of the plant ALDH superfamily. As a result, newly identified genes can be more easily analyzed and gene names can be assigned according to current nomenclature guidelines; our goal is to clarify previously confusing and conflicting names and classifications that might confound results and prevent accurate comparisons between studies.     

Role of the Phosphatidylserine Receptor TIM-1 in Enveloped-Virus Entry

The cell surface receptor T cell immunoglobulin mucin domain 1 (TIM-1) dramatically enhances filovirus infection of epithelial cells. Here, we showed that key phosphatidylserine (PtdSer) binding residues of the TIM-1 IgV domain are critical for Ebola virus (EBOV) entry through direct interaction with PtdSer on the viral envelope. PtdSer liposomes but not phosphatidylcholine liposomes competed with TIM-1 for EBOV pseudovirion binding and transduction. Further, annexin V (AnxV) substituted for the TIM-1 IgV domain, supporting a PtdSer-dependent mechanism. Our findings suggest that TIM-1-dependent uptake of EBOV occurs by apoptotic mimicry. Additionally, TIM-1 enhanced infection of a wide range of enveloped viruses, including alphaviruses and a baculovirus. As further evidence of the critical role of enveloped-virion-associated PtdSer in TIM-1-mediated uptake, TIM-1 enhanced internalization of pseudovirions and virus-like proteins (VLPs) lacking a glycoprotein, providing evidence that TIM-1 and PtdSer-binding receptors can mediate virus uptake independent of a glycoprotein. These results provide evidence for a broad role of TIM-1 as a PtdSer-binding receptor that mediates enveloped-virus uptake. Utilization of PtdSer-binding receptors may explain the wide tropism of many of these viruses and provide new avenues for controlling their virulence.     

Highly Sensitive Real-Time In Vivo Imaging of an Influenza Reporter Virus Reveals Dynamics of Replication and Spread

The continual public health threat posed by the emergence of novel influenza viruses necessitates the ability to rapidly monitor infection and spread in experimental systems. To analyze real-time infection dynamics, we have created a replication-competent influenza reporter virus suitable for in vivo imaging. The reporter virus encodes the small and bright NanoLuc luciferase whose activity serves as an extremely sensitive readout of viral infection. This virus stably maintains the reporter construct and replicates in culture and in mice with near-native properties. Bioluminescent imaging of the reporter virus permits serial observations of viral load and dissemination in infected animals, even following clearance of a sublethal challenge. We further show that the reporter virus recapitulates known restrictions due to host range and antiviral treatment, suggesting that this technology can be applied to studying emerging influenza viruses and the impact of antiviral interventions on infections in vivo. These results describe a generalizable method to quickly determine the replication and pathogenicity potential of diverse influenza strains in animals.     

Polyomavirus Large T Antigen Binds Symmetrical Repeats at the Viral Origin in an Asymmetrical Manner

Polyomaviruses have repeating sequences at their origins of replication that bind the origin-binding domain of virus-encoded large T antigen. In murine polyomavirus, the central region of the origin contains four copies (P1 to P4) of the sequence G(A/G)GGC. They are arranged as a pair of inverted repeats with a 2-bp overlap between the repeats at the center. In contrast to simian virus 40 (SV40), where the repeats are nonoverlapping and all four repeats can be simultaneously occupied, the crystal structure of the four central murine polyomavirus sequence repeats in complex with the polyomavirus origin-binding domain reveals that only three of the four repeats (P1, P2, and P4) are occupied. Isothermal titration calorimetry confirms that the stoichiometry is the same in solution as in the crystal structure. Consistent with these results, mutation of the third repeat has little effect on DNA replication in vivo. Thus, the apparent 2-fold symmetry within the DNA repeats is not carried over to the protein-DNA complex. Flanking sequences, such as the AT-rich region, are known to be important for DNA replication. When the orientation of the central region was reversed with respect to these flanking regions, the origin was still able to replicate and the P3 sequence (now located at the P2 position with respect to the flanking regions) was again dispensable. This highlights the critical importance of the precise sequence of the region containing the pentamers in replication.     

Genome Scale Evolution of Myxoma Virus Reveals Host-Pathogen Adaptation and Rapid Geographic Spread

The evolutionary interplay between myxoma virus (MYXV) and the European rabbit (Oryctolagus cuniculus) following release of the virus in Australia in 1950 as a biological control is a classic example of host-pathogen coevolution. We present a detailed genomic and phylogeographic analysis of 30 strains of MYXV, including the Australian progenitor strain Standard Laboratory Strain (SLS), 24 Australian viruses isolated from 1951 to 1999, and three isolates from the early radiation in Britain from 1954 and 1955. We show that in Australia MYXV has spread rapidly on a spatial scale, with multiple lineages cocirculating within individual localities, and that both highly virulent and attenuated viruses were still present in the field through the 1990s. In addition, the detection of closely related virus lineages at sites 1,000 km apart suggests that MYXV moves freely in geographic space, with mosquitoes, fleas, and rabbit migration all providing means of transport. Strikingly, despite multiple introductions, all modern viruses appear to be ultimately derived from the original introductions of SLS. The rapidity of MYXV evolution was also apparent at the genomic scale, with gene duplications documented in a number of viruses. Duplication of potential virulence genes may be important in increasing the expression of virulence proteins and provides the basis for the evolution of novel functions. Mutations leading to loss of open reading frames were surprisingly frequent and in some cases may explain attenuation, but no common mutations that correlated with virulence or attenuation were identified.