Mutational bias of Turnip Yellow Mosaic Virus in the context of host anti-viral gene silencing

Plant Dicer-like (DCL) enzymes exhibit a GC-preference during anti-viral post-transcriptional gene silencing (PTGS), delivering an evolutionary selection pressure resulting in plant viruses with GC-poor genomes. However, some viruses, e.g. Turnip Yellow Mosaic Virus (TYMV, genus Tymovirus) have GC-rich genomes, raising the question as to whether or not DCL derived selection pressure affects these viruses. In this study we analyzed the virus-derived small interfering RNAs from TYMV-infected leaves of Brassica juncea showed that the TYMV population accumulated a mutational bias with AU replacing GC (GC–AU), demonstrating PTGS pressure. Interestingly, at the highly polymorphic sites the GC–AU bias was no longer observed. This suggests the presence of an unknown mechanism preventing mutational drift of the viral population and maintaining viral genome stability, despite the host PTGS pressure

Nucleotide bias of DCL and AGO in plant anti-virus gene silencing

Plant Dicer-like (DCL) and Argonaute (AGO) are the key enzymes involved in anti-virus post-transcriptional gene silencing (AV-PTGS). Here we show that AV-PTGS exhibited nucleotide preference by calculating a relative AV-PTGS efficiency on processing viral RNA substrates. In comparison with genome sequences of dicot-infecting Turnip mosaic virus (TuMV) and monocot-infecting Cocksfoot streak virus (CSV), viral-derived small interfering RNAs (vsiRNAs) displayed positive correlations between AV-PTGS efficiency and G+C content (GC%). Further investigations on nucleotide contents revealed that the vsiRNA populations had G-biases. This finding was further supported by our analyses of previously reported vsiRNA populations in diverse plant-virus associations, and AGO associated Arabidopsis endogenous siRNA populations, indicating that plant AGOs operated with G-preference. We further propose a hypothesis that AV-PTGS imposes selection pressure(s) on the evolution of plant viruses. This hypothesis was supported when potyvirus genomes were analysed for evidence of GC elimination, suggesting that plant virus evolution to have low GC% genomes would have a unique function, which is to reduce the host AV-PTGS attack during infections

Biogeochemical and climate drivers of wetland phosphorus and nitrogen release: implications for nutrient legacies and eutrophication risk

The dynamics and processes of nutrient cycling and release were examined for a lowland wetland‐pond system, draining woodland in southern England. Hydrochemical and meteorological data were analyzed from 1997 to 2017, along with high‐resolution in situ sensor measurements from 2016 to 2017. The results showed that even a relatively pristine wetland can become a source of highly bioavailable phosphorus (P), nitrogen (N), and silicon (Si) during low‐flow periods of high ecological sensitivity. The drivers of nutrient release were primary production and accumulation of biomass, which provided a carbon (C) source for microbial respiration and, via mineralization, a source of bioavailable nutrients for P and N co‐limited microorganisms. During high‐intensity nutrient release events, the dominant N‐cycling process switched from denitrification to nitrate ammonification, and a positive feedback cycle of P and N release was sustained over several months during summer and fall. Temperature controls on microbial activity were the primary drivers of short‐term (day‐to‐day) variability in P release, with subdaily (diurnal) fluctuations in P concentrations driven by water body metabolism. Interannual relationships between nutrient release and climate variables indicated “memory” effects of antecedent climate drivers through accumulated legacy organic matter from the previous year's biomass production. Natural flood management initiatives promote the use of wetlands as “nature‐based solutions” in climate change adaptation, flood management, and soil and water conservation. This study highlights potential water quality trade‐offs and shows how the convergence of climate and biogeochemical drivers of wetland nutrient release can amplify background nutrient signals by mobilizing legacy nutrients, causing water quality impairment and accelerating eutrophication risk

Evidence for increases in vegetation species richness across UK Environmental Change Network sites linked to changes in air pollution and weather patterns

We analysed trends in vegetation monitored at regular intervals over the past two decades (1993–2012)at the twelve terrestrial Environmental Change Network (ECN) sites. We sought to determine the extent to which flora had changed and link any such changes to potential environmental drivers. We observed significant increases in species richness, both at a whole network level, and when data were analysed within Broad Habitat groupings representing the open uplands, open lowlands and woodlands. We also found comparable increases in an indicator of vegetation response to soil pH, Ellenberg R. Species characteristic of less acid soils tended to show more consistent increases in frequency across sites relative to species with a known tolerance for strongly acidic soils. These changes are, therefore, broadly consistent with a response to increases in soil solution pH observed for the majority of ECN sites that, in turn, are likely to be driven by large reductions in acid deposition in recent decades. Increases in species richness in certain habitat groupings could also be linked to increased soil moisture availability in drier lowland sites that are likely to have been influenced by a trend towards wetter summers in recent years, and possibly also to a reduction in soil nitrogen availability in some upland locations. Changes in site management are also likely to have influenced trends at certain sites, particularly with respect to agricultural practices. Our results are therefore indicative of wide-scale responses to major regional-scale changes in air pollution and recent weather patterns, modified by local management effects. The relative consistency of management of ECN sites over time is atypical of much of the wider countryside and it is therefore not appropriate to scale up these observations to infer national scale trends. Nevertheless the results provide an important insight into processes that may be operating nationally. It will now be necessary to test for the ubiquity of these changes using appropriate broader spatial scale survey data

Trends and variability in weather and atmospheric deposition at UK Environmental Change Network sites (1993–2012)

We characterised temporal trends and variability in key indicators of climate and atmospheric deposition chemistry at the twelve terrestrial UK Environmental Change Network (ECN) sites over the first two decades of ECN monitoring (1993–2012) using various statistical approaches. Mean air temperatures for the monitoring period were approximately 0.7 °C higher than those modelled for 1961–1990, but there was little evidence for significant change in air temperature over either the full monthly records or within individual seasons. Some upland ECN sites, however, warmed significantly over the first decade before cooling in the second. Summers at most sites became progressively wetter, and extremes in daily rainfall increased in magnitude. Average wind speeds in winter and spring declined at the majority of sites. Directional trends in summer precipitation could be linked to an atypically prolonged negative deviation in the summer North Atlantic Oscillation (NAO) Index. Several aspects of air quality improved markedly. Concentrations and fluxes of sulphate in precipitation declined significantly and substantially across the network, particularly during the earlier years and at the most polluted sites in the south and east. Precipitation concentrations of nitrate and ammonium, and atmospheric concentrations of nitrogen dioxide also decreased at most sites. There was less evidence for reductions in the loads of wet deposited nitrogen species, while trends in atmospheric ammonia concentration varied in direction and strength between sites. Reductions in acid deposition are likely to account for widespread gradual increases in the pH of soil water at ECN sites, representing partial recovery from acidification. Overall, therefore, ECN sites have experienced marked changes in atmospheric chemistry and weather regimes over the last two decades that might be expected to have exerted detectable effects on ecosystem structure and function. While the downward trend in acid deposition is unlikely to be reversed, it is too early to conclude whether the trend towards wetter summers simply represents a phase in a multi-decadal cycle, or is indicative of a more directional shift in climate. Conversely, the first two decades of ECN now provide a relatively stable long-term baseline with respect to air temperature, against which effects of anticipated future warming on these ecosystems should be able to be assessed robustly

Meta-analysis of multidecadal biodiversity trends in Europe

Local biodiversity trends over time are likely to be decoupled from global trends, as local processes may compensate or counteract global change. We analyze 161 long-term biological time series (15-91 years) collected across Europe, using a comprehensive dataset comprising similar to 6,200 marine, freshwater and terrestrial taxa. We test whether (i) local long-term biodiversity trends are consistent among biogeoregions, realms and taxonomic groups, and (ii) changes in biodiversity correlate with regional climate and local conditions. Our results reveal that local trends of abundance, richness and diversity differ among biogeoregions, realms and taxonomic groups, demonstrating that biodiversity changes at local scale are often complex and cannot be easily generalized. However, we find increases in richness and abundance with increasing temperature and naturalness as well as a clear spatial pattern in changes in community composition (i.e. temporal taxonomic turnover) in most biogeoregions of Northern and Eastern Europe. The global biodiversity decline might conceal complex local and group-specific trends. Here the authors report a quantitative synthesis of longterm biodiversity trends across Europe, showing how, despite overall increase in biodiversity metric and stability in abundance, trends differ between regions, ecosystem types, and taxa.peerReviewe

Evidence for targeting common siRNA hotspots and GC preference by plant Dicer-like proteins

Small interfering (si)RNAs isolated from Brassica juncea leaves infected by Turnip mosaic virus (TuMV) were characterized by cloning and sequencing. The TuMV siRNA population was dominated by 21 and 22-nt long species originated mainly from the same siRNA hotspots, indicating operational similarity between the plant Dicer-like (DCL) enzymes. Robust GC bias was observed for TuMV siRNAs versus the virus genome, indicating that DCL was more likely to target GC-rich regions. Furthermore, dicot micro-(mi)RNAs displayed higher GC% than their DCL1 substrate RNAs, implicating that the GC bias may be ancient, therefore may be important for the RNAi technology

Detection of Cereal yellow dwarf virus using small interfering RNAs and enhanced infection rate with Cocksfoot streak virus in wild cocksfoot grass (Dactylis glomerata)

Small RNA sequences were obtained from leaf extracts of wild Dactylis glomerata (cocksfoot grass) using deep sequencing (454 Life Sciences, Roche Diagnostics), and were screened against virus sequences in GenBank using a local BLASTn search program (BioEdit). Putative small interfering (si)RNAs complementary in sequence to Cereal yellow dwarf virus (CYDV, genus Luteovirus) genomes were identified. Primer sequences were made against the “high scoring” siRNA sequences and RT-PCR was used to amplify a 438 bp CYDV fragment in total RNA extracts from D. glomerata leaves. Sequencing of the RT-PCR product confirmed the occurrence of a previously undescribed CYDV population with phylogenetic affinity to CYDV-RPS. In D. glomerata the CYDV infection rates were 42.3% (n = 78) in 2008 and 50.0% (n = 48) in 2009. Specific RT-PCR tests also showed that this D. glomerata population harboured Cocksfoot streak virus (CSV, genus Potyvirus). Dual infections by these viruses were observed in 20.5–22.9% of all plants tested in 2008–2009. Interestingly, infections of either CYDV or CSV enhanced the occurrence of the other virus in individual grasses. Opportunities are discussed for using siRNA sequencing approaches in virus survey and other ecology studies under field conditions