Energyscapes: linking the energy system and ecosystem services in real landscapes

The drive for sustainable energy production is leading to increased deployment of land based renewables. Although there is public support, in principle, for renewable energy at a national level, major resistance to renewable energy technologies often occurs at a local level. Within this context, it can be useful to consider the "energyscape" which we initially define as the complex spatial and temporal combination of the supply, demand and infrastructure for energy within a landscape. By starting with a consideration of the energyscape, we can then consider the positive and negative interactions with other ecosystem services within a particular landscape. This requires a multidisciplinary systems-approach that uses existing knowledge of landscapes, energy options, and the different perspectives of stakeholders. The approach is examined in relation to pilot case-study comprising a 155 km2 catchment in Bedfordshire, England

Survival analysis of worker honeybee fungal infection bioassay.

<p>Survival of honeybees following infection by <i>Metarhizium anisopliae</i> s.l. Solid lines show observed mortalities. Lines ending with “+” indicate censored populations. Dashed lines indicate expected decline in populations (dotted lines mark 95% confidence envelopes), estimated by fitting a logistic model of survival.</p

Schematic outline of experimental procedure.

<p>(1) Adult honeybees originated from a single hive with a naturally mated queen. (2) Separate cohorts of ‘house’ and ‘forager’ bees were collected and checked for signs of infection by naturally occurring pathogens. (3) Groups of bees from each cohort were infected with <i>Metarhizium anisopliae</i>, or mock infected. (4) Groups of infected and control bees were split into those destined for bioassay or microarray. (5) Bioassay bees were censused twice daily; at 48 hrs p.i., bees destined for microarray analysis were sacrificed. (6) Bioassays were maintained until all infected bees died, at which point control bioassays were censored.</p

High-throughput sequencing of the honeybee small RNA libraries.

<p>The graphs show depth of coverage at the genomic loci of DWV (red) and VDV-1 (blue). A statistical summary of the reads is given to the right of each group. Only reads unambiguously aligning to DWV or VDV-1 were used (GenBank Accession numbers GU109335 and AY251269 respectively) with no mismatches being tolerated in the 18 nt. seed.</p

Transcriptomic differences between house and forager bees: Summary of candidate immune genes (based on previous homology assignments [34]) differentially expressed in response to infection by <i>M. anisopliae</i> s.l.

<p>Transcriptomic differences between house and forager bees: Summary of candidate immune genes (based on previous homology assignments <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1003083#ppat.1003083-Moore1" target="_blank">[34]</a>) differentially expressed in response to infection by <i>M. anisopliae</i> s.l.</p

Genome wide differential expression associated with honeybee worker type and age.

<p>Venn diagrams of differential probe expression; identified at a significance probability threshold of <i>p</i><(1/number of probes). Circles represent: a) infected with <i>M. anisopliae</i>, compared to uninfected house honeybees; b) infected, compared to uninfected forager honeybees; and c) uninfected house, compared to uninfected forager honeybees.</p

Phylogenetic analysis of the central region of DWV-like virus genome.

<p>PCR amplified cDNA was cloned and sequenced through the region corresponding to positions 4926 to 6255 of the DWV genome (GenBank Accession number AJ489744). The tip labels include GenBank accession numbers and are prefixed as follows: C, NV, VL, VH denote the corresponding honeybee pupae treatment group; Varroa-VH and Varroa-VL indicate sequences from <i>Varroa</i> mites associated with groups VH and VL respectively; “Infested-colony” denotes sequences derived from pupae from the <i>Varroa</i> source colony; DWV, VDV-1, VDV-1-DWV-Rec followed by a place name indicate reference DWV, VDV-1 and VDV-1-DWV recombinant sequences present in GenBank. Sequences derived from the group VH honeybee pupae are highlighted with arrows and sequences from <i>Varroa</i> mites associated with groups VH and VL are indicated with filled or empty squares respectively. Alignments were performed using CLUSTAL <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004230#ppat.1004230-Smyth1" target="_blank">[77]</a>, and the neighbour-joining trees were produced and bootstrapped using the PHYLIP package <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004230#ppat.1004230-Kendziorski1" target="_blank">[78]</a>. Numbers at the nodes represent bootstrap values obtained from 1000 replications shown for the major branches supported by more than 750 replications. The length of branches is proportional to the number of changes. RF1 to RF4 indicate the distinct DWV/VDV-1 recombinant forms as defined by similarity to reference DWV and VDV-1 sequences (GenBank Accession numbers GU109335 and AY251269 respectively) in the CP and NS regions of the sequence., DWV^V indicates virulent form of DWV.</p

Contingency tables of numbers of up- and down-regulated differentially expressed genes for house and forager honeybees treated with the entomopathogen <i>M. anisopliae</i> s.l.

<p>Contingency tables of numbers of up- and down-regulated differentially expressed genes for house and forager honeybees treated with the entomopathogen <i>M. anisopliae</i> s.l.</p

Differential expression of the honeybee immune-related genes in response to oral DWV and <i>Varroa</i> mite feeding.

a<p>Honeybee gene ID according to the <i>Apis mellifera</i> Official Gene Set 1 <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004230#ppat.1004230-Vinciotti1" target="_blank">[30]</a>. Honeybee immune-related genes included in the analysis were either those described in <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004230#ppat.1004230-Ashburner1" target="_blank">[33]</a> or the honeybee homologues of the Drosophila melanogaster genes associated with Gene Ontology Biological Process term “Immune System Process” GO:0002376.</p>b<p>Drosophila melanogaster homologue showing highest similarity in BLAST.</p>c<p>Drosophila melanogaster gene name according to FlyBase.</p>d<p>Pathway or category of gene if known (Toll - Toll signalling pathway; SP - serine protease; Scav - Scavenger receptor A; Notch - Notch signalling pathway; JNK - JNK signalling pathway; J-ST - JAK-STAT signalling pathway; IG - IG Superfamily Genes; GATA - GATA transcription factor), Immune - Immune system process gene.</p

Changes in the strain composition of DWV complexes in honeybee pupae following direct injection of virus.

<p>Levels of the DWV- and VDV-1 CP-coding RNA determined by qRT-PCR (left panel) in the virus preparations used for injection, and (right panel) in pupae following incubation for 3 days. (A) Left panel: ΔCt values for the DWV-type and VDV-1-type CP were obtained by subtracting Ct values for the corresponding CP from Ct for the total DWV-like viruses quantified using “Universal” primers to the NS gene. Right panel: Ct values for the DWV-type and VDV-1-type CP. Six pupae were used for each virus-injected group, three pupae were used for each of the buffer-injected and non-injected control groups. Bars show mean value with standard error. Letters above the bars represent statistically significant groupings according to pairwise <i>t</i>-test comparisons for VDV-1 CP (<i>p</i>-value <0.01). (B) High-throughput sequencing of the virus preparations from the honeybees of group C (left), and the virus accumulated in the pupae injected with 20 ng of the virus preparation (right), 3 days post injection. The graphs show depth of coverage at genomic loci in DWV (red) and VDV-1 (blue) determined by high-throughput sequencing of viral RNA aligning to the DWV and VDV-1 sequences (GenBank Accession numbers GU109335 and AY251269 respectively). Only reads unambiguously aligning to DWV or VDV-1 sequences were used, with up to 3 mismatches tolerated in the 18 nt. seed region. The percentages of DWV, VDV-1 and the DWV-VDV-1 recombinants predicted by MosaicSolver <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004230#ppat.1004230-Wood1" target="_blank">[40]</a> are shown below. The pileup graphs for DWV and VDV-1 are shown, respectively, in red and dark blue. The CP-coding region of the virus C preparation and the virus C-injected pupae, which shows a decrease of DWV coverage compared to the injected virus, is highlighted in yellow.</p