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Background and aims – A plant’s tolerance of herbivory depends on its ability to endure and compensate for damage so as to lessen the impact that herbivores have on the plant’s performance (e.g. its growth, reproduction, or fitness). While tolerance of herbivory is beneficial to plants, it is rarely complete, and individuals in plant populations tend to vary in their levels of tolerance. The goal of this study was to investigate potential costs associated with tolerance of leaf and floral herbivory in horsenettle (Solanum carolinense), a perennial herbaceous weed that is often subjected to high levels of damage from a diversity of herbivores. Material and methods – We exposed 96 potted individuals across eight genets of horsenettle to factorial treatments of leaf herbivory by lace bugs and simulated floral herbivory by weevils. We quantified tolerance for each plant genet for both types of herbivory in terms of the impact of damage on the number of flowers opened, number of seeds produced, and root biomass (i.e. paternal, maternal, and vegetative tolerance, respectively).Key results – Plant genets ranged widely in their ability to compensate for leaf and flower damage. While there was little evidence for tradeoffs in tolerance through the different routes, there was strong evidence of tradeoffs in genets’ abilities to tolerate herbivore damage to leaves and damage to flowers.Conclusion – Tolerance is a useful defence strategy to cope with damage caused by herbivores, but its evolution may be constrained by concomitant costs and tradeoffs. The evolutionary role of the tradeoffs identified in this study are likely to be greater the more species of herbivores a plant hosts, and the more that herbivore levels vary both spatially and temporally.

Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.

The evolutionary spread of a trait that benefits individuals of one species in their interactions with a second species may be constrained by “ecological costs” if the trait also has detrimental effects on interactions with a third species in the environment. In particular, the identification of ecological costs may help explain why natural plant populations often display less-than-maximal resistance against natural enemies—even when the plant populations possess substantial genetic variation that could serve as raw material for evolving greater resistance. One such resistance trait that confers an obvious fitness advantage, yet is maintained in populations at intermediate levels, is the strategy of resistance-by-ducking displayed by certain species of goldenrods (Solidago). In a ducking individual, the stem temporarily nods near the apex during a time in spring that coincides with the oviposition season of several herbivores. I investigated whether the fitness benefits of ducking in terms of deterring apex-galling insects may be offset by ecological costs posed by a common sap-sucking specialist—the red goldenrod aphid, Uroleucon nigrotuberculatum. In a controlled outdoor experiment, ducking was associated with significantly lower antixenosis (i.e., reduced preference), antibiosis (reduced performance), and indirect resistance against aphids. Specifically, aphids colonized ducking plants at a higher rate than erect-stemmed plants; populations of aphids on bagged ducking plants increased more quickly than on bagged erect-stemmed plants; and aphid populations on erect-stemmed plants were wiped out more quickly by natural enemies than on ducking plants when bags were removed. To the extent that aphid damage reduces goldenrod’s fitness, these ecological costs may be responsible for limiting the ducking trait to intermediate levels in goldenrod populations. Because most plant species are attacked by multiple types of herbivores, ecological costs of resistance mechanisms are likely to be more widespread than is generally appreciated, though their subtlety may make them challenging to identify.

Neisseria meningitidis , the meningococcus, resides exclusively in humans and causes invasive meningococcal disease (IMD). The population of N. meningitidis is structured into stable clonal complexes by limited horizontal recombination in this naturally transformable species. N. meningitidis is an opportunistic pathogen, with some clonal complexes, such as cc53, effectively acting as commensal colonizers, while other genetic lineages, such as cc11, are rarely colonizers but are over-represented in IMD and are termed hypervirulent. This study examined theoretical evolutionary pathways for pathogenic and commensal lineages by examining the prevalence of horizontally acquired genomic islands (GIs) and loss-of-function (LOF) mutations. Using a collection of 4850 genomes from the BIGSdb database, we identified 82 GIs in the pan-genome of 11 lineages (10 hypervirulent and one commensal lineage). A new computational tool, Phaser, was used to identify frameshift mutations, which were examined for statistically significant association with genetic lineage. Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. The 82 GIs, but not the LOF loci, were associated with genetic lineage and invasiveness using the disease carriage ratio metric. These observations have been integrated into a new model that infers the early events of the evolution of the human adapted meningococcus. These pathways are enriched for GIs that are involved in modulating attachment to the host, growth rate, iron uptake and toxin expression which are proposed to increase competition within the meningococcal population for the limited environmental niche of the human nasopharynx. We surmise that competition for the host mucosal surface with the nasopharyngeal microbiome has led to the selection of isolates with traits that enable access to cell types (non-phagocytic and phagocytic) in the submucosal tissues leading to an increased risk for IMD.

The accumulation of petroleum-based plastic waste has become a major issue for the environment. A sustainable and biodegradable solution can be found in Polyhydroxyalkanoates (PHAs), a microbially produced biopolymer. An analysis of the global phylogenetic and ecological distribution of potential PHA producing bacteria and archaea was carried out by mining a global genome repository for PHA synthase (PhaC), a key enzyme involved in PHA biosynthesis. Bacteria from the phylum Actinobacteria were found to contain the PhaC Class II genotype which produces medium-chain length PHAs, a physiology until now only found within a few Pseudomonas species. Further, several PhaC genotypes were discovered within Thaumarchaeota, an archaeal phylum with poly-extremophiles and the ability to efficiently use CO2 as a carbon source, a significant ecological group which have thus far been little studied for PHA production. Bacterial and archaeal PhaC genotypes were also observed in high salinity and alkalinity conditions, as well as high-temperature geothermal ecosystems. These genome mining efforts uncovered previously unknown candidate taxa for biopolymer production, as well as microbes from environmental niches with properties that could potentially improve PHA production. This in silico study provides valuable insights into unique PHA producing candidates, supporting future bioprospecting efforts toward better targeted and relevant taxa to further enhance the diversity of exploitable PHA production systems.

We present a novel method for taxon selection, the aim being to minimize problems arising from highly recombinant species such as Helicobacter pylori. Helicobacter pylori has accompanied modern‐human migration out of Africa and is marked by a phylogeographic strain distribution, which has been exploited to add an extra layer of information about human migrations to that obtained from human sources. However, H. pylori's genome has high sequence heterogeneity combined with a very high rate of recombination, causing major allelic diversification across strains. On the other hand, recombination events that have become preserved in sub‐populations are a useful source of phylogenetic information. This creates a potential problem in selecting representative strains for particular genetic or phylogeographic clusters and generally ameliorating the impact on analyses of extensive low‐level recombination. To address this issue, we perform multiple population structure‐based analyses on core genomes to select exemplar strains, called ‘quintessents’, which exhibit limited recombination. In essence, quintessent strains are representative of their specific phylogenetic clades and can be used to refine the current MLST concatenation‐based population structure classification system. The use of quintessents reduces the noise due to local recombination events, while preserving recombination events that have become fixed in sub‐populations. We illustrate the method with an analysis of core genome concatenations from 185 H. pylori strains, which reveals a recent speciation event resulting from the recombination of strains from phylogeographic clade hpSahul, carried by Aboriginal Australians, and hpEurope, carried by some of the people who arrived in Australia over the past 200 years. The signal is much clearer when based on quintessent strains, but absent from the analysis based on MLST concatenations.

Glycogen, a randomly branched glucose polymer, provides energy storage in organisms. It forms small β particles which in animals bind to form composite α particles, which give better glucose release. Simulations imply β particle size is controlled only by activities and sizes of glycogen biosynthetic enzymes and sizes of polymer chains. Thus, storing more glucose requires forming more β particles, which are expected to sometimes form α particles. No α particles have been reported in bacteria, but the extraction techniques might have caused degradation. Using milder glycogen extraction techniques on Escherichia coli, transmission electron microscopy and size-exclusion chromatography showed α particles, consistent with this hypothesis for α-particle formation. Molecular density and size distributions show similarities with animal glycogen, despite very different metabolic processes. These general polymer constraints are such that any organism which needs to store and then release glucose will have similar α and β particle structures: a type of convergent evolution.

Background Metronidazole is one of the first-line drugs of choice in the standard triple therapy used to eradicate Helicobacter pylori infection. Hence, the global emergence of metronidazole resistance in Hp poses a major challenge to health professionals. Inactivation of RdxA is known to be a major mechanism of conferring metronidazole resistance in H. pylori. However, metronidazole resistance can also arise in H. pylori strains expressing functional RdxA protein, suggesting that there are other mechanisms that may confer resistance to this drug. Methods We performed whole-genome sequencing on 121 H. pylori clinical strains, among which 73 were metronidazole-resistant. Sequence-alignment analysis of core protein clusters derived from clinical strains containing full-length RdxA was performed. Variable sites in each alignment were statistically compared between the resistant and susceptible groups to determine candidate genes along with their respective amino-acid changes that may account for the development of metronidazole resistance in H. pylori. Results Resistance due to RdxA truncation was identified in 34% of metronidazole-resistant strains. Analysis of core protein clusters derived from the remaining 48 metronidazole-resistant strains and 48 metronidazole-susceptible identified four variable sites significantly associated with metronidazole resistance. These sites included R16H/C in RdxA, D85N in the inner-membrane protein RclC (HP0565), V265I in a biotin carboxylase protein (HP0370) and A51V/T in a putative threonylcarbamoyl-AMP synthase (HP0918). Conclusions Our approach identified new potential mechanisms for metronidazole resistance in H. pylori that merit further investigation.

Background The urea breath test (UBT) is widely used for diagnosing Helicobacter pylori infection. In the Shenzhen Kuichong People’s Hospital, some UBT findings were contradictory to the histology outcomes, therefore this study aimed to assess and compare the diagnostic performance of both 13C- and 14C-UBT assays. Methods We recruited 484 H. pylori-treatment naïve patients, among which 217 and 267 were tested by the 13C-UBT or 14C-UBT, respectively. The cutoff value for H. pylori positivity based on manufacturer’s instruction was 4% delta over baseline (DOB) for the 13C-UBT, and 100 disintegrations per minute (DPM) for the 14C-UBT. Gastric biopsies of the antrum and corpus were obtained during endoscopy for histopathology. Results In patients who were tested using the 13C-UBT kit, histopathology was positive in 136 out of 164 UBT-positive patients (82.9% concordance), and negative in 46 out of 53 UBT-negative cases (86.8% concordance). For the 14C-UBT-tested patients, histopathology was positive for H. pylori in 186 out of 220 UBT-positive patients (84.5% concordance), and negative in 41 out of 47 UBT-negative cases (87.2% concordance). While the 13C-UBT and 14C-UBT each had a high sensitivity level of 95.1% and 96.9%, respectively, their specificity was low, at 62.2% and 54.7%, respectively. By using new optimal cutoff values and including an indeterminate range (3–10.3% DOB for 13C-UBT and 87–237 DPM for 14C-UBT), the specificity values can be improved to 76.7% and 76.9% for the 13C- and 14C-UBT, respectively. Conclusions The establishment of an indeterminate range is recommended to allow for repeated testing to confirm H. pylori infection, and thereby avoiding unnecessary antibiotic treatment. Trial registration: Chinese Clinical Trial Registry, ChiCTR2000041570. Registered 29 December 2020- Retrospectively registered, http://www.chictr.org.cn/edit.aspx?pid=66416&htm=4

Lake Magic is an extremely acidic, hypersaline lake found in Western Australia, with the highest concentrations of aluminum and silica in the world. Previous studies of Lake Magic diversity have revealed that the lake hosts acid- and halotolerant bacterial and fungal species. However, they have not canvassed microbial population dynamics across flooding, evapo-concentration and desiccation stages. In this study, we used amplicon sequencing and potential function prediction on sediment and salt mat samples. We observed that the bacterial and fungal diversity in Lake Magic is strongly driven by carbon, temperature, pH and salt concentrations at the different stages of the lake. We also saw that the fungal diversity decreased as the environmental conditions became more extreme. However, prokaryotic diversity was very dynamic and bacteria dominated archaeal species, both in abundance and diversity, perhaps because bacteria better tolerate the extreme variation in conditions. Bacterial species diversity was the highest during early flooding stage and decreased during more stressful conditions. We observed an increase in acid tolerant and halotolerant species in the sediment, involved in functions such as sulfur and iron metabolism, i.e., species involved in buffering the external environment. Thus, due to activity within the microbial community, the environmental conditions in the sediment do not change to the same degree as conditions in the salt mat, resulting in the sediment becoming a safe haven for microbes, which are able to thrive during the extreme conditions of the evapo-concentration and desiccation stages.

Objectives Drug resistance of Helicobacter pylori is a major clinical problem worldwide. The objective of the present study was to investigate the prevalence of antibiotic-resistant H. pylori in the city of Shenzhen in China, as well as to identify the genetic mutations specifically associated with drug resistance rather than unrelated phylogenetic signals. Methods Antibiotic susceptibility testing was performed on 238 clinical strains successfully isolated from H. pylori-positive dyspeptic patients who underwent gastroscopy at the Department of Gastroenterology in Shenzhen People’s Second Hospital. Following WGS of all strains using Illumina technology, mutation and phylogenetic analyses were performed. Results The resistance rates were 84.9%, 35.3%, 25.2% and 2.1% for metronidazole, clarithromycin, ciprofloxacin and rifampicin, respectively. An A2143G conversion in the 23S rRNA gene was the primary mutation observed in clarithromycin-resistant strains, whilst N87K/I and D91G/N/Y in GyrA were detected in ciprofloxacin-resistant strains. In RdxA, our results demonstrated that only R16H/C and M21A are significant contributors to metronidazole resistance; there were 15 other sites, but these are phylogenetically related and thus unrelated to metronidazole resistance. Conclusions There is a high prevalence of metronidazole, clarithromycin and ciprofloxacin resistance and a low prevalence of rifampicin resistance in H. pylori from Shenzhen, China. Omission of phylogenetically related sites will help to improve identification of sites genuinely related to antibiotic resistance in H. pylori and, we believe, other species.

Background and aims – For a more complete understanding of the eco-evolutionary dynamics of plant-herbivore interactions, it is important to know the genetic mechanisms that control defence traits, as well as the levels of genetic variation for these traits in plant populations. Here, I present results of a study of the occurrence and pattern of inheritance of the recently discovered trait of ‘resistance-by-ducking’ in the goldenrod Solidago gigantea (Asteraceae).Methods – I grew maternal families of seedlings from fruits collected in a large field population of S. gigantea in southwestern Virginia, USA. I determined stem phenotype (ducking or erect) for 704 plants across 36 maternal families.Key results – Of the 704 plants, 72% had ducking stems and 28% had erect stems. Employing bootstrapping with Hardy-Weinberg principles, I found that the pattern of inheritance was consistent with stem phenotype being controlled by a major gene, with the ducking morph being recessive to the erect morph. The allele frequencies for stem phenotype in the source population were estimated to be 0.85 ducking and 0.15 erect alleles.Conclusions – These findings not only help inform ecological studies of ducking in S. gigantea, but they lay the groundwork for comparative studies of similar goldenrod species whose populations have differing proportions of ducking stems. For example, in all previous studies on populations of S. altissima, ducking stems have been the minority morph, occurring at a frequency of less than 20%. These results suggest that ducking may be costlier in S. altissima, while S. gigantea may face different ecological pressures, or has somehow overcome some of the costs of ducking.

While herbivores can have a wide range of impacts on their host plants, instances in which herbivore damage is truly beneficial are rare. Thus, it was surprising that damage by the potato stalk borer (PSB) was associated with increased fitness of its native host plant (horsenettle) in a recent field study, particularly because this insect can have such severe negative effects on potato crops. A controlled experiment with potted horsenettle was conducted to investigate the impact of damage by PSB to see if it has any negative impacts on the plants, or whether horsenettle truly overcompensates for its damage. Damage by PSB had negligible impact on sexual reproduction and potential future vegetative propagation through root production in this experiment. Additionally, PSB damage did not exacerbate the negative fitness impact of heavy leaf damage by the eggplant lace bug. The lack of positive impacts in the potted horsenettle study suggests that selection for decreased resistance to PSB in the field study was due to correlated selection for increased plant vigor, rather than to overcompensation. That is, when given options, PSB females may preferentially oviposit on larger, healthier plants that are likely to be better hosts for their larvae. An important implication of these results is that a wild weed’s high tolerance of a natural herbivore can compound the weed’s potential to serve as a reservoir from which the herbivore can switch to closely related agricultural plants that are not tolerant of its damage.

Glycogen is conventionally considered as a transient energy reserve that can be rapidly synthesized for glucose accumulation and mobilized for ATP production. However, this conception is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies noticed that glycogen with small average chain length gc in bacteria has the potential to degrade slowly, which might prolong bacterial environment survival. This phenomenon was previously examined and later formulated as the durable energy storage mechanism hypothesis. Although recent research has been warming to the hypothesis, experimental validation is still missing at current stage. In this review, we summarized recent progress of the hypothesis, provided a supporting mathematical model, and explored the technical pitfalls that shall be avoided in glycogen study.

Background Helicobacter pylori is a Gram-negative bacterium which mainly causes peptic ulcer disease in human, but is also the predominant cause of stomach cancer. It has been coevolving with human since 120,000 years and, according to Multi-locus sequence typing (MLST), H. pylori can be classified into seven major population types, namely, hpAfrica1, hpAfrica2, hpNEAfrica, hpEastAsia, hpAsia2, hpEurope and hpSahul. Helicobacter pylori harbours a large number of restriction-modification (R-M) systems. The methyltransferase (MTase) unit plays a significant role in gene regulation and also possibly modulates pathogenicity. The diversity in MTase can act as geomarkers to correlate strains with the phylogeographic origins. This paper describes the complete genome sequence and methylome of gastric pathogen H. pylori belonging to the population hpNEAfrica. Results In this paper, we present the complete genome sequence and the methylome profile of H. pylori hpNEAfrica strain HP14039, isolated from a patient who was born in Somalia and likely to be infected locally during early childhood prior to migration. The genome of HP14039 consists of 1,678,260 bp with 1574 coding genes and 38.7% GC content. The sequence analysis showed that this strain lacks the cag pathogenicity island. The vacA gene is of S2M2 type. We have also identified 15 methylation motifs, including WCANHNNNNTG and CTANNNNNNNTAYG that were not previously described. Conclusions We have described the complete genome of H. pylori strain HP14039. The information regarding phylo-geography, methylome and associated metadata would help scientific community to study more about hpNEAfrica population type. Electronic supplementary material The online version of this article (10.1186/s13099-019-0284-y) contains supplementary material, which is available to authorized users.

Metabolism of energy reserves are essential for bacterial functions such as pathogenicity, metabolic adaptation, and environmental persistence, etc. Previous bioinformatics studies have linked gain or loss of energy reserves such as glycogen and polyphosphate (polyP) with host-pathogen interactions and bacterial virulence based on a comparatively small number of bacterial genomes or proteomes. Thus, understanding the distribution patterns of energy reserves metabolism across bacterial species provides a shortcut route to look into bacterial lifestyle and physiology theoretically. So far, five major energy reserves have been identified in bacteria due to their effective capacity to support bacterial persistence under nutrient deprivation conditions, which include wax ester (WE), triacylglycerol (TAG), polyhydroxyalkanoates (PHA), polyphosphate, and glycogen. Although unknown pathways directly involved in energy reserves keep being discovered with the continuous endeavour of molecular microbiologists and it is currently rather clear about the enzymes related with the metabolism of energy reserves, there is a lack of systematic study of the pathway or key enzyme distributions of the five energy reserves in bacteria from an evolutionary point of view. With the fast development of sequencing technology, abundant bacterial proteomes are available in public database now. In this study, we sourced 8214 manually reviewed bacterial reference proteomes from UniProt database and used statistical models to search homologous sequences of key enzymes related with energy reserves. The distribution patterns of the pathways for energy reserves metabolism are visualized in taxonomy-based phylogenetic trees. According to the study, it was revealed that specific pathways and enzymes are associated with certain types of bacterial groups, which provides evolutionary insights into the understanding of their origins and functions. In addition, the study also confirmed that loss of energy reserves is correlated with bacterial genome reduction. Through this analysis, a much clearer picture about energy reserves metabolism in bacteria is present, which could serve a guide for further theoretical and experimental analyses of energy reserves metabolism in bacteria.

Glycogen is conventionally viewed as a transient energy reserve that can be rapidly synthesized for glucose accumulation or mobilized for ATP production and blood glucose homeostasis in higher organisms. However, this understanding is not completely applicable to prokaryotes due to glycogen structural heterogeneity. A number of studies have noted that glycogen with short average chain lengthgcin bacteria has the potential to degrade slowly, which might prolong bacterial survival in the environment and thus enhance potential for transmission to new hosts. This phenomenon has been examined over the past few years and called the durable energy storage mechanism hypothesis (DESM). In this updated bibliography, we summarize recent progress and provide a mathematical model of glycogen as a durable energy reserve.

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

In bacteria, glycogen plays important roles in carbon and energy storage. Its structure has recently been linked with bacterial environmental durability. Among the essential genes for bacterial glycogen metabolism, the glgB-encoded branching enzyme GBE plays an essential role in forming α-1,6-glycosidic branching points, and determines the unique branching patterns in glycogen. Previously, evolutionary analysis of a small sets of GBEs based on their N-terminal domain organization revealed that two types of GBEs might exist: (1) Type 1 GBE with both N1 and N2 (also known as CBM48) domains and (2) Type 2 GBE with only the N2 domain. In this study, we initially analyzed N-terminal domains of 169 manually reviewed bacterial GBEs based on hidden Markov models. A previously unreported group of GBEs (Type 3) with around 100 amino acids ahead of the N1 domains was identified. Phylogenetic analysis found clustered patterns of GBE types in certain bacterial phyla, with the shorter, Type 2 GBEs predominantly found in Gram-positive species, while the longer Type 1 GBEs are found in Gram-negative species. Several in vitro studies have linked N1 domain with transfer of short oligosaccharide chains during glycogen formation, which could lead to small and compact glycogen structures. Compact glycogen degrades more slowly and, as a result, may serve as a durable energy reserve, contributing to the enhanced environmental persistence for bacteria. We were therefore interested in classifying GBEs based on their N-terminal domain via large-scale sequence analysis. In addition, we set to understand the evolutionary patterns of different GBEs through phylogenetic analysis at species and sequence levels. Three-dimensional modeling of GBE N-termini was also performed for structural comparisons. A further study of 9,387 GBE sequences identified 147 GBEs that might belong to a possibly novel group of Type 3 GBE, most of which fall into the phylum of Actinobacteria. We also attempted to correlate glycogen average chain length (ACL) with GBE types. However, no significant conclusions were drawn due to limited data availability. In sum, our study systematically investigated bacterial GBEs in terms of domain organizations from evolutionary point of view, which provides guidance for further experimental study of GBE N-terminal functions in glycogen structure and bacterial physiology.

Inorganic polyphosphate (polyP) is a linear polymer of orthophosphate residues. It is reported to be present in all life forms. Experimental studies showed that polyP plays important roles in bacterial durability and virulence. Here we investigated the relationships of polyP with bacterial durability and virulence theoretically. Bacterial lifestyle, environmental persistence, virulence factors (VFs), and species evolution are all included in the analysis. The presence of seven genes involved in polyP metabolism (ppk1, ppk2, pap, surE, gppA, ppnK, and ppgK) and 2595 core VFs were verified in 944 bacterial reference proteomes for distribution patterns via HMMER. Proteome size and VFs were compared in terms of gain and loss of polyP pathway. Literature mining and phylogenetic analysis were recruited to support the study. Our analyzes revealed that the presence of polyP metabolism is positively correlated with bacterial proteome size and the number of virulence genes. A potential relationship of polyP in bacterial lifestyle and environmental durability is suggested. Evolutionary analysis shows that polyP genes are randomly lost along the phylogenetic tree. In sum, based on our theoretical analysis, we confirmed that bacteria with polyP metabolism are associated with high environmental durability and more VFs.

Background Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates. Results Population structure analysis of the 59 isolates together with 72 isolates from an international collection, revealed six population groups suggesting that N. gonorrhoeae is a weakly clonal species. Two distinct population groups, Aus1 and Aus2, represented 63% of WA isolates and were mostly composed of the remote community isolates that carried no chromosomal AMR genotypes. In contrast, the Western Australian metropolitan isolates were frequently multi-drug resistant and belonged to population groups found in the international database, suggesting international transmission of the isolates. Conclusions Our study suggests that the population structure of N. gonorrhoeae is distinct between the communities in remote and metropolitan WA. Given the high rate of AMR in metropolitan regions, ongoing surveillance is essential to ensure the enduring efficacy of the empiric gonorrhoea treatment in remote WA.

Reproductive isolation and speciation in herbivorous insects may be accomplished via shifts between host-plant resources: either plant species or plant organs. The intimate association between gall-inducing insects and their host plants makes them particularly useful models in the study of speciation. North American goldenrods (Asteraceae: Solidago and Euthamia) support a rich fauna of gall-inducing insects. Although several of these insects have been the subject of studies focusing on speciation and tritrophic interactions, others remain unstudied and undescribed. Among the latter are at least seven species of the large, cosmopolitan gall midge genus Asphondylia Loew (Diptera: Cecidomyiidae), the taxonomy and biology of which are elucidated here for the first time using morphological, molecular, and life-history data. We describe Asphondylia pseudorosa sp. nov., Asphondylia rosulata sp. nov., and Asphondylia silva sp. nov., and redescribe Asphondylia monacha Osten Sacken, 1869 and Asphondylia solidaginis Beutenmuller, 1907, using morphological characters of adults, immature stages, and galls, as well as sequence data from both nuclear and mitochondrial genes. A neotype is designated for A. solidaginis, the type series of which is considered lost. We also provide information on the life history of all species, including a description of two inquilinous cecidomyiids commonly found in the galls, Clinodiplosis comitis sp. nov. and Youngomyia podophyllae (Felt, 1907), and on parasitoid wasps associated with the gall midges. Asphondylia johnsoni Felt, 1908, which was described from an unknown gall on an unknown Solidago host, is assigned to nomina dubia. Our phylogenetic analyses show that some of the Asphondylia species associated with goldenrods induce two different types of galls during their life cycle, some exhibit host alterations, and some do both. In the absence of reliable morphological differences, recognising species boundaries and deciphering host associations of species must rely heavily on molecular data. Our analysis suggests that radiation in this group has been recent and occurred through shifts among host plants. © 2015 The Linnean Society of London

The intriguing sit-and-wait hypothesis predicts that bacterial durability in the external environment is positively correlated with their virulence. Since its first proposal in 1987, the hypothesis has been spurring debates in terms of its validity in the field of bacterial virulence. As a special case of the vector-borne transmission versus virulence tradeoff, where vector is now replaced by environmental longevity, there are only sporadic studies over the last three decades showing that environmental durability is possibly linked with virulence. However, no systematic study of these works is currently available and epidemiological analysis has not been updated for the sit-and-wait hypothesis since the publication of Walther and Ewald’s (2004) review. In this article, we put experimental evidence, epidemiological data and theoretical analysis together to support the sit-and-wait hypothesis. According to the epidemiological data in terms of gain and loss of virulence (+/-) and durability (+/-) phenotypes, we classify bacteria into four groups, which are: sit-and-wait pathogens (++), vector-borne pathogens (+-), obligate-intracellular bacteria (--), and free-living bacteria (-+). After that, we dive into the abundant bacterial proteomic data with the assistance of bioinformatics techniques in order to investigate the two factors at molecular level thanks to the fast development of high-throughput sequencing technology. Sequences of durability-related genes sourced from Gene Ontology and UniProt databases and virulence factors collected from Virulence Factor Database are used to search 20 corresponding bacterial proteomes in batch mode for homologous sequences via the HMMER software package. Statistical analysis only identified a modest, and not statistically significant correlation between mortality and survival time for eight non-vector-borne bacteria with sit-and-wait potentials. Meanwhile, through between-group comparisons, bacteria with higher host-mortality are significantly more durable in the external environment. The results of bioinformatics analysis correspond well with epidemiological data, that is, non-vector-borne pathogens with sit-and-wait potentials have higher number of virulence and durability genes compared with other bacterial groups. However, the conclusions are constrained by the relatively small bacterial sample size and non-standardized experimental data.

Premise of the study Despite the fact that herbivores can be highly detrimental to their host plants' fitness, plant populations often maintain genetic variation for resistance to their natural enemies. Investigating the various costs (e.g., allocation tradeoffs, autotoxicity, and ecological costs) that may prevent plants from evolving to their fullest potential resistance has been a productive strategy for shedding insight into the eco-evolutionary dynamics of plant-herbivore communities. Methods Recent studies have shown that some individuals of goldenrod (Solidago spp.) evade apex-attacking herbivores by a temporary nodding of their stem (i.e., resistance-by-ducking). Although ducking provides an obvious fitness benefit to these individuals, nonducking (erect) morphs persist in goldenrod populations. In this study, I investigated potential costs of ducking in Solidago gigantea in terms of tradeoffs involving growth and reproduction in a common garden experiment using field-collected seeds. Key results The S. gigantea population contained substantial genetic variation for stem morph, with 28% erect and 72% ducking stems. In the absence of herbivory, ducking plants were taller, had thicker stems, and produced an average of 20% more seeds than erect plants. Conclusions This study suggests that resistance-by-ducking, instead of being costly, actually comes with additional, nondefense-related benefits. These results support the conclusion that the factors that constrain the evolution of resistance in plant populations are likely to be more subtle and complex than simple tradeoffs in resource allocation.

Plant populations frequently maintain submaximal levels of resistance to natural enemies, even in the presence of substantial genetic variation for resistance. Identifying constraints on the evolution of increased resistance has been a major goal of researchers of plant-herbivore interactions. In a glasshouse study, we measured relative costs and benefits of resistance of tall goldenrod (Solidago altissima) to the gall-inducing tephritid Eurosta solidaginis. We exposed multiple ramets of 26 goldenrod genets to nutrient or shade stress and to oviposition by E. solidaginis. The presence of a gall cost a ramet an average of 1743 seeds, but the cost differed 10-fold across environments. Plant genets varied widely for an induced 'hypersensitive' response in which meristem cells become necrotic and kill E. solidaginis hatchlings before gall induction. There was no evidence that this highly effective resistance trait carried an allocation cost. However, the response carried a risk of autotoxicity, as necrosis killed the apex of 37% of the ungalled ramets. On average, a damaged apex cost each ramet 5015 seeds. Autotoxicity may constrain the resistance of S. altissima to an intermediate level, and variation in environmental conditions may alter the relative costs and benefits of resistance and tolerance, thus maintaining genetic variation within goldenrod populations.

Algorithmic prediction of RNA secondary structure has been an area of active inquiry since the 1970s. Despite many innovations since then, our best techniques are not yet perfect. The workhorses of the RNA secondary structure prediction engine are recursions first described by Zuker and Stiegler in 1981. These have well understood caveats; a notable flaw is the ad-hoc treatment of multi-loops, also called helical-junctions, that persists today. While several advanced models for multi-loops have been proposed, it seems to have been assumed that incorporating them into the recursions would lead to intractability, and so no algorithms for these models exist. Some of these models include the classical model based on Jacobson–Stockmayer polymer theory, and another by Aalberts and Nadagopal that incorporates two-length-scale polymer physics. We have realized practical, tractable algorithms for each of these models. However, after implementing these algorithms, we found that no advanced model was better than the original, ad-hoc model used for multi-loops. While this is unexpected, it supports the praxis of the current model.

Helicobacter pylori, responsible for chronic ulcers and most stomach cancers, infects half of the world&rsquo, s population. The Urea Breath Test (UBT) is one of the most accurate and reliable non-invasive methods for diagnosing active H. pylori infection. The objective was to use longitudinal, population-wide UBT data for Western Australia to look for H. pylori-related disease patterns. We collected 95,713 UBT results from 77,552 individuals for the years 2010&ndash, 2015, likely representing all of the UBT samples analysed in Western Australia. Data collected also included sex, age and residential postcode. Other data reported here were inferred via a comparison with the 2011 Australian Census using a specially written Python program. While women appear to have more H. pylori-related disease than men, there is no difference in the disease rates once women&rsquo, s higher rates of presentation for testing are taken into account. On the other hand, while the treatment strategy for H. pylori infection is generally very effective in Western Australia, failure of the first-line treatment is significantly more common in women than men. Migrants and Aboriginal Australians have elevated rates of H. pylori-related disease, while the rate for non-Aboriginal Australian-born West Australians is very low. However, no significant associations were found with other socio-economic indicators. We conclude that, for some people, H. pylori-related disease is not a solved problem.

Background We investigated the effects of gastric Helicobacter pylori infection on the daytime and overnight human oral microbiota. Methods Twenty four volunteers were recruited. Ten tested positive for H. pylori infection by the Carbon-14 Urea Breath Test, and the rest were negative. Two oral swabs were collected: one immediately after waking up in the morning and before brushing teeth, and another in the evening before teeth-brushing. DNA extract acquired from each swab was subjected to Illumina sequencing of 16S rRNA gene amplicons. The microbial abundance and composition were analysed in relation to H. pylori infection status. Results Helicobacter pylori-positive individuals had significant changes in the alpha and beta diversities in the daytime samples in comparison to those who were H. pylori negative. To identify which taxa could be significantly affected within the cohorts in the daytime, we employed the LEfSe method. When compared against UBT-negative samples, significantly higher abundances were detected in both Pseudomonas and Roseomonas, while Fusobacterium, Solobacterium, Haemophilus and Streptococcus were significantly decreased in the UBT-positive samples. Discussion Our data demonstrated that H. pylori infection affects the human daytime oral microbiota. The hitherto undocumented changes of several bacterial genera due to H. pylori infection require more studies to examine their potential health effects on affected individuals.

Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (∼170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.

Although plants are generally attacked by a community of several species of herbivores, relatively little is known about the strength of natural selection for resistance in multiple-herbivore communities-particularly how the strength of selection differs among herbivores that feed on different plant organs or how strongly genetic correlations in resistance affect the evolutionary responses of the plant. Here, we report on a field study measuring natural selection for resistance in a diverse community of herbivores of Solanum carolinense. Using linear phenotypic-selection analyses, we found that directional selection acted to increase resistance to seven species. Selection was strongest to increase resistance to fruit feeders, followed by flower feeders, then leaf feeders. Selection favored a decrease in resistance to a stem borer. Bootstrapping analyses showed that the plant population contained significant genetic variation for each of 14 measured resistance traits and significant covariances in one-third of the pairwise combinations of resistance traits. These genetic covariances reduced the plant's overall predicted evolutionary response for resistance against the herbivore community by about 60%. Diffuse (co)evolution was widespread in this community, and the diffuse interactions had an overwhelmingly constraining (rather than facilitative) effect on the plant's evolution of resistance.

Multiple sequence alignment (MSA) is a crucial first step in the analysis of genomic and proteomic data. Commonly occurring sequence features, such as deletions and insertions, are known to affect the accuracy of MSA programs, but the extent to which alignment accuracy is affected by the positions of insertions and deletions has not been examined independently of other sources of sequence variation. We assessed the performance of 6 popular MSA programs (ClustalW, DIALIGN-T, MAFFT, MUSCLE, PROBCONS, and T-COFFEE) and one experimental program, PRANK, on amino acid sequences that differed only by short regions of deleted residues. The analysis showed that the absence of residues often led to an incorrect placement of gaps in the alignments, even though the sequences were otherwise identical. In data sets containing sequences with partially overlapping deletions, most MSA programs preferentially aligned the gaps vertically at the expense of incorrectly aligning residues in the flanking regions. Of the programs assessed, only DIALIGN-T was able to place overlapping gaps correctly relative to one another, but this was usually context dependent and was observed only in some of the data sets. In data sets containing sequences with non-overlapping deletions, both DIALIGN-T and MAFFT (G-INS-I) were able to align gaps with near-perfect accuracy, but only MAFFT produced the correct alignment consistently. The same was true for data sets that comprised isoforms of alternatively spliced gene products: both DIALIGN-T and MAFFT produced highly accurate alignments, with MAFFT being the more consistent of the 2 programs. Other programs, notably T-COFFEE and ClustalW, were less accurate. For all data sets, alignments produced by different MSA programs differed markedly, indicating that reliance on a single MSA program may give misleading results. It is therefore advisable to use more than one MSA program when dealing with sequences that may contain deletions or insertions, particularly for high-throughput and pipeline applications where manual refinement of each alignment is not practicable.

Biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. However, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. In addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. A decision must therefore be made about which gene, or gene combinations, should be used to compute a tree. Deflated Cladistic Information based on Total Entropy (dCITE) is proposed as an easily computed metric for measuring the cladistic information in multiple sequence alignments representing a range of taxa, without the need to first compute the corresponding trees. dCITE scores can be used to rank candidate genes or decide whether input sequences provide insufficient cladistic information, making artefactual polytomies more likely. The dCITE method can be applied to protein, nucleotide or encoded phenotypic data, so can be used to select which data-type is most appropriate, given the choice. In a series of experiments the dCITE method was compared with related measures. Then, as a practical demonstration, the ideas developed in the paper were applied to a dataset representing species from the order Campylobacterales; trees based on sequence combinations, selected on the basis of their dCITE scores, were compared with a tree constructed to mimic Multi-Locus Sequence Typing (MLST) combinations of fragments. We see that the greater the dCITE score the more likely it is that the computed phylogenetic tree will be free of artefactual polytomies. Secondly, cladistic information saturates, beyond which little additional cladistic information can be obtained by adding additional sequences. Finally, sequences with high cladistic information produce more consistent trees for the same taxa.

Motivation Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. Results A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support. Availability DotKnot-PW and the RNA structure test set are available at the web site http://dotknot.csse.uwa.edu.au/pw. Contact janaspe@csse.uwa.edu.au Supplementary information Supplementary data are available at Bioinformatics online.

Glycogen is conventionally viewed as an energy reserve that can be rapidly mobilized for ATP production in higher organisms. However, several studies have noted that glycogen with short average chain length in some bacteria is degraded very slowly. In addition, slow utilization of glycogen is correlated with bacterial viability, that is, the slower the glycogen breakdown rate, the longer the bacterial survival time in the external environment under starvation conditions. We call that a durable energy storage mechanism (DESM). In this review, evidence from microbiology, biochemistry, and molecular biology will be assembled to support the hypothesis of glycogen as a durable energy storage compound. One method for testing the DESM hypothesis is proposed.

Although plant breeding systems are evolutionarily labile, a shift from one system to another can involve formidable ecological obstacles. In order for gynodioecy to evolve from hermaphroditism, the carriers of a male-sterility mutation (i.e., females) must overcome two major hurdles: females must attract pollinators without offering pollen as a reward, and they must produce enough seeds to compensate for the loss of reproduction through the paternal route. We investigated the relative performance of female and hermaphroditic plants in a greenhouse study of Mimulus guttatus originating from a largely hermaphroditic population. Females had larger floral displays than did hermaphrodites, with 5% wider corollas and 34% more flowers open at one time. They also produced 22% more flowers over a lifetime and 25% more ovules per ovary than hermaphrodites, giving females 1.53 times more maternal reproductive potential. In a related experiment, bumblebees visited female plants just as frequently as hermaphroditic p...

Pseudoknots are an essential feature of RNA tertiary structures. Simple H-type pseudoknots have been studied extensively in terms of biological functions, computational prediction, and energy models. Intramolecular kissing hairpins are a more complex and biologically important type of pseudoknot in which two hairpin loops form base pairs. They are hard to predict using free energy minimization due to high computational requirements. Heuristic methods that allow arbitrary pseudoknots strongly depend on the quality of energy parameters, which are not yet available for complex pseudoknots. We present an extension of the heuristic pseudoknot prediction algorithm DotKnot, which covers H-type pseudoknots and intramolecular kissing hairpins. Our framework allows for easy integration of advanced H-type pseudoknot energy models. For a test set of RNA sequences containing kissing hairpins and other types of pseudoknot structures, DotKnot outperforms competing methods from the literature. DotKnot is available as a web server under http://dotknot.csse.uwa.edu.au.

While storms can have obvious ecological impacts on plants, plants’ potential to respond evolutionarily to selection for increased resistance to storm damage has received little study. We took advantage of a thunderstorm with strong wind and hail to examine genetic variation for resistance to stem breakage in the herbaceous perennial Solidago altissima. The storm broke the apex of nearly 10% of 1883 marked ramets in a common-garden plot containing 26 genets of S. altissima. Plant genets varied 20-fold in resistance to breakage. Stem height was strongly correlated with resistance to breakage, with taller stems being significantly more susceptible. A stem’s growth form (erect versus nodding) had no detectable effect on its resistance to breakage. Therefore, we rejected the hypothesis that a function of the nodding, or “candy-cane,” morphology is protection of the apex from storm damage. The significant genetic variation in S. altissima for stem breakage suggests that this plant has the capacity to respond to selection imposed by storms e particularly through changes in mean stem height. Tradeoffs between breakage resistance and competition for light and pollinators may act to maintain a large amount of genetic variation in stem height.

Interactions between plants and herbivores are considered “diffuse” if the ecological interactions between two species, or their evolutionary responses, differ depending on the presence of a third species. I looked for evidence of diffuse interactions among horsenettle (Solanum carolinense) and two common herbivores. Plants experimentally protected from lace bugs (Gargaphia solani) were twice as susceptible to attack from flea beetles (Epitrix fuscula) once transplanted into the field. Thus, the selective benefit to horsenettle of resistance against lace bugs in nature would likely be diminished by increased attack from flea beetles. Moreover, the relative rank among horsenettle genotypes for resistance against flea beetles was changed by prior exposure to lace bugs. Thus, the genetic expression of resistance to flea beetles would depend on the “lace bug environment.” By affecting selective pressures or response to selection, these sorts of diffuse interactions in a plant-herbivore community can slow the host plant’s evolution of resistance to its herbivores.

In most populations of Solidago altissima, a small proportion of plants have a growth pattern in which the stem bends early in the season so that the apex is pointing downward (i.e., a ‘‘candy-cane’’ stem) then straightens up again later in the season. The majority of plants, however, do not show this pattern. Instead their stems remain erect from emergence through flowering and senescence. It has recently been shown that the candy-cane stems are a result of a ducking strategy that reduces the risk of attack by apex-attacking herbivores. With such a resistance advantage, it is unclear why the candy-cane morphology is always in the minority, and why the erect morphology persists at all in S. altissima populations. In this study, we tested the hypothesis that the advantage of ducking is inversely frequency dependent and thus will not be an effective resistance strategy when ducking plants are in the majority. In a series of trials, we introduced gall flies (Eurosta solidaginis) into enclosures with relatively low (15%) and relatively high (85%) frequencies of candy-cane versus erect stems. Candy-cane stems were more resistant than erect stems regardless of relative frequency; thus, the hypothesis was rejected. Overall, attack rates were lower for both stem types in the high candy-cane frequency groups than in the low candy-cane frequency groups. This frequency-dependent attack rate suggests that erect-stemmed plants gain ‘‘associational resistance’’ by having a majority of candy-cane neighbors, while candy-cane plants suffer from ‘‘associational susceptibility’’ when surrounded by erect-stemmed neighbors.

Apical meristem damage (AMD) is a common result of herbivory. AMD can have dramatically variable effects on plant architecture and fitness, ranging from a total loss of reproductive capacity to overcompensation. We explored the influence of environmental stresses and meristem limitation on tolerance of AMD by applying the limiting resource model (LRM) of plant tolerance to 17 previously published studies and a new empirical study on Solidago altissima. In the S. altissima experiment, AMD released axillary meristems from apical dominance, and fertilizer addition enabled plants to take full advantage of the lateral branches. AMD caused a 58% reduction in seed production in nutrient-stressed plants but only a 6% reduction in seed production in fertilized plants. In 12 of the 18 studies reviewed, tolerance was greater in the high-resource (or low-competition) treatment; in two, tolerance was greater in the low-resource treatment; and in four, resource level did not affect tolerance of AMD. The results of 15 studies (83%) were consistent with LRM predictions. Overcompensation was observed in six studies, and it occurred only in the high-resource treatments in five of these studies, as would be expected from applying the LRM.

A main tenet of sex-allocation theory is that environmental stress should lead to increased maleness because reproducing through pollen is generally cheaper than producing fruits and seeds. Though this prediction has held for many species, it has been little tested for gynomonoecious plants, in which individuals produce both female and perfect flowers. We exposed eight ramets of each of 22 genets of a gynomonoecious goldenrod, Solidago altissima (Asteraceae), to a factorial combination of nutrient stress and herbivory by the gall-inducer Eurosta solidaginis (Tephritidae). Nutrient stress alone increased relative femaleness: Stressed ramets produced fewer flowers total and a higher ratio of ray (female) flowers to disk (perfect) flowers. Galling caused no change in fertilized ramets, but the combination of nutrient stress and galling caused an increase in relative maleness: Nutrient-stressed, galled ramets produced fewer flowers total and had a higher disk to ray ratio. In addition to being phenotypically plastic, floral-sex ratio had a great deal of genetic variation, with a broad-sense heritability of 0.68. While the floral-sex ratio responses of gynomonoecious plants may be more complicated than for plants of other breeding systems, they offer the potential to test and refine the already rich body of sex-allocation theory.

Interspecific competition (or facilitation) between herbivores sharing a host plant species can result in negative (or positive) correlations in damage levels, independent of a plant’s genetic covariance in resistance to the herbivores. Just like genetic correlations in resistance to herbivory, these “environmental correlations” in damage may affect the evolution of resistance in the host plant. In a field study of 960 ramets and 40 genets of the herbaceous plant Solanum carolinense, I looked for evidence of such environmental correlations in damage caused by 11 species of herbivores, including 10 insects and 1 mammal. There were 28 significant correlations in damage levels between species (21 negative and 7 positive) after plant genetic influences on resistance were statistically removed. Negative environmental correlations were more likely between species that fed upon the same type of plant organs than between those that fed on different types of organs, and the magnitudes of the correlations were inversely proportional to the abundance of the organ types. Taken together, these results offer strong evidence that competition is largely responsible for the pattern of environmental correlations in damage. Environmental correlations were just as common as genetic correlations in resistance, but the environmental correlations tended to be lower in magnitude, were more likely to be negative, and were more evenly spread out among the herbivore community than the genetic correlations. Damage levels by all 11 species were negatively correlated with damage by at least one other species. Thus the selective advantage a plant would receive from increased resistance any of these herbivores would be partially negated by increased damage by competing herbivores. As a result, competition has the potential to be an important constraint on the evolution of resistance in S. carolinense.

Evidence of poor correspondence between an insect herbivore's oviposition preferences and the performance of its offspring has generally been attributed either to maladaptive behavior of the insect mother or inadequate measurement by the researcher. In contrast, we hypothesize that many cases of "bad mothers" in herbivores may be a byproduct of the hierarchical way natural selection works on resistance in host plants. Epistatic selection on the components of resistance (i.e., antixenosis and antibiosis) may generate negative genetic correlations between the resistance components, which could counteract the efforts of herbivores to oviposit on the best hosts for the performance of their offspring. In common garden and greenhouse experiments, we measured aspects of antixenosis and antibiosis resistance in 26 genets of tall goldenrod, Solidago altissima, against two common herbivores: the gall-inducing fly Eurosta solidaginis and the spittlebug Philaenus spumarius. Goldenrod antixenosis and antibiosis were positively correlated against E. solidaginis and negatively correlated against P. spumarius. Analogously, population-wide preference-performance correlations were positive for the gall flies and negative for the spittlebugs. Several natural history differences between the two insects could make gall flies better mothers, including better synchrony of the phenologies of the flies and the host plant, the much narrower host range of the gall flies than the spittlebugs, and the more sedentary lifestyle of the gall fly larvae than the spittlebug nymphs. If these results are typical in nature, then negative genetic correlations in antixenosis and antibiosis in plants may often result in zero or negative population-wide correlations between preference and performance in herbivores, and thus may be an important reason why herbivorous insects often appear to be bad mothers.

I studied interactions between the herbaceous weed Solanum carolinense (horsenettle) and its herbivore community in northern Virginia from 1996–2002. Thirty-two species regularly fed on the plant, including 31 insects from 6 taxonomic orders and Microtus pennsylvanicus (meadow vole). An intensive field experiment on 960 horsenettle individuals in 2001 revealed high levels of damage to all parts of the plants. Two chrysomelid beetles—Epitrix fuscula (eggplant flea beetle) and Leptinotarsa juncta (false potato beetle)—damaged leaves on nearly every plant. Roughly half of the flowers were destroyed by herbivores, with Anthonomus nigrinus (potato bud weevil) destroying 30%. Nearly three-fourths of the fruits were damaged by three species: the tephritid fly Zonosemata electa (pepper maggot), false potato beetle, and meadow vole. The weevil Trichobaris trinotata (potato stalk borer) bored in stems of 73% of the plants, and the most damaging root feeder was the moth Synanthedon rileyana (Riley's clearwi...

Summary • As part of a study of the ecological and evolutionary dynamics of herbivore resistance in Solanum carolinense (horsenettle), potential genetic constraints to the evolution of resistance to 11 of its most common herbivores were investigated. • Leaf, flower, fruit, and stem herbivory were measured in a field experiment involving 24 ramets of each of 40 horsenettle genets. • The experimental plant population contained significant genetic variation for resistance to all 11 species of herbivore. For only one species was there an indication of a genotype-by-environment interaction in the expression of resistance that might constrain its evolution. Genetic correlations in resistance to different species were common but not universal, with seven negative and 12 positive correlations out of the 55 pairwise species comparisons. Correlations were independent of plant part fed upon. • The evolution of the resistance of horsenettle to most of its diverse community of herbivores does not appear to be prevented by a lack of genetic variation or by genotype-by-environment interactions in resistance. Negative genetic correlations in resistance to different herbivores may play a small role in slowing the evolution of resistance, but positive correlations may play at least as large a role in facilitating its evolution.

Research into late embryogenesis abundant (LEA) proteins has been ongoing for more than 20 years but, although there is a strong association of LEA proteins with abiotic stress tolerance particularly dehydration and cold stress, for most of that time, their function has been entirely obscure. After their initial discovery in plant seeds, three major groups (numbered 1, 2 and 3) of LEA proteins have been described in a range of different plants and plant tissues. Homologues of groups 1 and 3 proteins have also been found in bacteria and in certain invertebrates. In this review, we present some new data, survey the biochemistry, biophysics and bioinformatics of the LEA proteins and highlight several possible functions. These include roles as antioxidants and as membrane and protein stabilisers during water stress, either by direct interaction or by acting as molecular shields. Along with other hydrophilic proteins and compatible solutes, LEA proteins might also serve as "space fillers" to prevent cellular collapse at low water activities. This multifunctional capacity of the LEA proteins is probably attributable in part to their structural plasticity, as they are largely lacking in secondary structure in the fully hydrated state, but can become more folded during water stress and/or through association with membrane surfaces. The challenge now facing researchers investigating these enigmatic proteins is to make sense of the various in vitro defined functions in the living cell: Are the LEA proteins truly multi-talented, or are they still just misunderstood?

Although it is widely acknowledged that a plant's tolerance of herbivore damage depends on resource availability in the plant's environment, there is no consensus on whether higher resource levels lead to greater or to lower tolerance. The prevailing model, the compensatory continuum hypothesis (CCH), predicts that tolerance of herbivory should be greater in high-resource or low-competition conditions. The main rival hypothesis, the growth rate model (GRM), makes the opposite prediction: tolerance of herbivory should be greater in more stressful conditions. The tolerance predictions of a recently introduced model, the limiting resource model (LRM), are more flexible and depend on the type of resource and herbivore under consideration. We reviewed 48 studies (from 40 published articles) of plant tolerance of leaf damage in conditions differing in levels of light, inorganic nutrients, water stress, or competition. The results of 31%, 48%, and 95% of the studies were consistent with the predictions of the CCH, GRM, and LRM, respectively. Thus, by considering which resource is primarily affected by herbivory and which resource is limiting a plant's fitness, the LRM offers a substantial advance in predicting how tolerance will be affected by environmental differences in resource availability.

While a plant’s capacity to tolerate damage by herbivores can be studied as a single trait, it is important to recognize that tolerance is generally a result of the combined action of several different traits. Here, we report on a pair of experiments to identify mechanisms for tolerating floral herbivory in Solanum carolinense, an andromonoecious perennial herb that regularly suffers from high levels of florivory. We measured the effect of actual and simulated florivory on host-plant fitness and assessed which plant traits exhibited plasticity in response to florivory. In addition, for each of nine plant genets, we calculated tolerance indices and determined which traits were genetically correlated with tolerance. Traits that served to help S. carolinense tolerate florivory in terms of sexual reproduction included initiating more inflorescences, aborting fewer buds prior to anthesis and fewer ovaries after fertilization, and increasing the ratio of perfect:male flowers. In addition, the greater the levels of florivory, the more the plants allocated to root growth, which may promote tolerance through greater potential future reproduction. The plant population contained significant genetic variation for tolerance itself and for nearly all of the putative tolerance mechanisms, which suggests that S. carolinense has the potential to evolve greater tolerance through a variety of different routes in response to natural selection.