The potential use of mapped extent and distribution of habitats as indicators of Good Environmental Status (GES)

The Healthy and Biologically Diverse Seas Evidence Group (HBDSEG) has been tasked with providing the technical advice for the implementation of the Marine Strategy Framework Directive (MSFD) with respect to descriptors linked to biodiversity. A workshop was held in London to address one of the Research and Development (R&D) proposals entitled: ‘Mapping the extent and distribution of habitats using acoustic and remote techniques, relevant to indicators for area/extent/habitat loss.’ The aim of the workshop was to identify, define and assess the feasibility of potential indicators of benthic habitat distribution and extent, and identify the R&D work which could be required to fully develop these indicators. The main points that came out of the workshop were: (i) There are many technical aspects of marine habitat mapping that still need to be resolved if cost-effective spatial indicators are to be developed. Many of the technical aspects that need addressing surround issues of consistency, confidence and repeatability. These areas should be tackled by the JNCC Habitat Mapping and Classification Working Group and the HBDSEG Seabed Mapping Working Group. (ii) There is a need for benthic ecologists (through the HBDSEG Benthic Habitats Subgroup and the JNCC Marine Indicators Group) to finalise the list of habitats for which extent and/or distribution indicators should be considered for development, building upon the recommendations from this report. When reviewing the list of indicators, benthic habitats could also be distinguished into those habitats that are defined/determined primarily by physical parameters (although including biological assemblages) (e.g. subtidal shallow sand) and those defined primarily by their biological assemblage (e.g. seagrass beds). This distinction is important as some anthropogenic pressures may influence the biological component of the ecosystem despite not having a quantifiable effect on the physical habitat distribution/extent. (iii) The scale and variety of UK benthic habitats makes any attempt to undertake comprehensive direct mapping exercises prohibitively expensive (especially where there is a need for repeat surveys for assessment). There is a clear need therefore to develop a risk-based approach that uses indirect indicators (e.g. modelling), such as habitats at risk from pressures caused by current human activities, to develop priorities for information gathering. The next steps that came out of the workshop were: (i) A combined approach should be developed by the JNCC Marine Indicators Group together with the HBDSEG Benthic Habitats Subgroup, which will compile and ultimately synthesise all the criteria used by the three different groups from the workshop. The agreed combined approach will be used to undertake a final review of the habitats considered during the workshop, and to evaluate any remaining habitats in order to produce a list of habitats for indicator development for which extent and/or distribution indicators could be appropriate. (ii) The points of advice raised at this workshop, alongside the combined approach aforementioned, and the final list of habitats for extent and/or distribution indicator development will be used to develop a prioritised list of actions to inform the next round of R&D proposals for benthic habitat indicator development in 2014. This will be done through technical discussions within JNCC and the relevant HBDSEG Subgroups. The preparation of recommendations by these groups should take into account existing work programmes, and consider the limited resources available to undertake any further R&D work.

On the ultrastructure of Gephyrocapsa oceanica (Haptophyta) life stages.

Gephyrocapsa oceanica is a cosmopolitan bloom-forming coccolithophore species belonging to the haptophyte order Isochrysidales and family Noëlaerhabdaceae. Exclusively pelagic, G. oceanica is commonly found in modern oceans and in fossil assemblages. Its sister species Emiliania huxleyi is known to possess a haplo-diplontic life cycle, the non-motile diploid coccolith-bearing cells alternating with haploid cells that are motile and covered by non-mineralized organic scales. Since the cytology and ultrastructure of other members of the Noëlaerhabdaceae has never been reported, it is not clear whether these features are common to the family. Here, we report on the ultrastructure of both the non-motile calcifying stage and the non-calcifying motile stage of G. oceanica. We found no significant ultrastructural differences between E. huxleyi and G. oceanica either in the calcifying diploid stage or the haploid phase. The similarities between these two morphospecies demonstrated a high degree of conservation of cytological features. We discuss the significance of these results in the light of the evolution of the Noelaerhabdaceae.

Feeding rates and prey selectivity of planktonic decapod larvae in the Western English Channel

Meroplankton are seasonally important contributors to the zooplankton, particularly at inshore sites, yet their feeding ecology is poorly known relative to holoplankton. While several studies have measured feeding in decapod larvae, few studies have examined the feeding rates of decapod larvae on natural prey assemblages throughout the reproductive season. We conducted 8 feeding experiments with Necora puber, Liocarcinus spp. and Upogebia spp. zoea larvae collected from the L4 monitoring site off Plymouth (50°15.00′N, 4°13.02′W) during spring–summer 2009 and 2010. This period spanned moderate-to-high food availability (0.5–1.6 µg chl-a L−1), but a great range in food composition with small cells <20 µm dominating in 2010. Daily rations averaged 17, 60 and 22 % of body C for the 3 respective decapod species. Clearance rates differed according to prey type, and all 3 decapod genera showed evidence of selection of dinoflagellates. Importantly, small cells including nano- and pico-plankton were ingested, this being demonstrated independently by flow cytometric analysis of the feeding experiments and molecular analysis. PCR-based analysis of the haptophyte portion of the diet revealed ingestion of Isochrysis galbana by decapod larvae in the bottle incubations and Isochrysis galbana and Phaeocystis globosa by decapod larvae collected directly from the field. This study has shown that pico- and nano-sized plankton form an important supplement to the diverse and variable diet of decapod larvae.

Contrasting transcriptome response to thermal stress in two key zooplankton species, Calanus finmarchicus and C. glacialis

Climate change has already led to the range expansion of warm-water plankton assemblages in the northeast Atlantic and the corresponding range contraction of colder-water species. The temperate copepod Calanus finmarchicus is predicted to shift farther northward into polar waters traditionally dominated by the arctic copepod C. glacialis. To identify temperaturemediated changes in gene expression that may be critical for the thermal acclimation and resilience of the 2 Calanus spp., we conducted a whole transcriptome profiling using RNA-seq on an Ion Torrent platform. Transcriptome responses of C. finmarchicus and C. glacialis from Disko Bay, west Greenland, were investigated under realistic thermal stresses (at + 5, +10 and +15°C) for 4 h and 6 d. C. finmarchicus showed a strong response to temperature and duration of stress, involving up-regulation of genes related to protein folding, transcription, translation and metabolism. In sharp contrast, C. glacialis displayed only low-magnitude changes in gene expression in response to temperature and duration of stress. Differences in the thermal responses of the 2 species, particularly the lack of thermal stress response in C. glacialis, are in line with laboratory and field observations and suggest a vulnerability of C. glacialis to climate change.

Depth-related gradients in community structure and relatedness of bivalves and isopods in the Southern Ocean.

Despite increased research over the last decade, diversity patterns in Antarctic deep-sea benthic taxa and their driving forces are only marginally known. Depth-related patterns of diversity and distribution of isopods and bivalves collected in the Atlantic sector of the Southern Ocean are analysed. The data, sampled by epibenthic sledge at 40 deep-sea stations from the upper continental slope to the hadal zone (774 – 6348 m) over a wide area of the Southern Ocean, comprises 619 species of isopods and 81 species of bivalves,. There were more species of isopods than bivalves in all samples, and species per station varied from 2 to 85 for isopods and from 0 to 18 for bivalves. Most species were rare, with 72% of isopod species restricted to one or two stations, and 45% of bivalves. Among less-rare species bivalves tended to have wider distributions than isopods. The species richness of isopods varied with depth, showing a weak unimodal curve with a peak at 2000 – 4000 m, while the richness of bivalves did not. Multivariate analyses indicate that there are two main assemblages in the Southern Ocean, one shallow and one deep. These overlap over a large depth-range (2000 – 4000 m). Comparing analyses based on the Sørensen resemblance measure (presence/absence) and Γ+ (presence/absence incorporating relatedness among species) indicates that rare species tend to have other closely related species within the same depth band. Analysis of relatedness among species indicates that the taxonomic variety of bivalves tends to decline at depth, whereas that of isopods is maintained. This, it is speculated, may indicate that the available energy at depth is insufficient to maintain a range of bivalve life-history strategies

Assessing the conservation status of marine habitats: thoughts from a sandflat on the Isles of Scilly.

Statutory monitoring of the fauna of the ‘mudflats and sandflats not covered by seawater at low tide’ biotope complex on St Martin’s Flats, a part of the Isles of Scilly Complex Special Area of Conservation, was undertaken in 2000, 2004 and 2009. The targets set by Natural England for “characteristic biotopes” were that “composite species, abundance and diversity should not deviate significantly from an established baseline, subject to natural change”. The three specified biotopes could not be distinguished, and instead three assemblages were subjectively defined based on sediment surface features. There were statistically significant natural changes in diversity and species composition between years, especially in the association initially characterized by the razor-clam Ensis, and possible reasons for this are discussed. It is suggested that setting fixed local limits on natural variability is almost always impractical. Two possible approaches to distinguishing between natural and anthropogenic changes are suggested; a change in ecological condition as indicated by AMBI scores, and a significant change in average taxonomic distinctness (Δ+) compared with expectation. The determination of species biomasses as well as abundances might also open more possibilities for assessment. The practice of setting objectives for a marine SAC feature that include the range and number of biotopes cannot be supported, in view the difficulty in ascribing assemblages to recognised biotopes. A more realistic definition of species assemblages might best be gained from examination of the species that consistently make a substantial contribution to the Bray Curtis similarity among samples collected from specific sites.

Relationships between biodiversity and the stability of marine ecosystems: comparisons at a European scale using meta-analysis.

The relationship between biodiversity and stability of marine benthic assemblages was investigated using existing data sets (n = 28) covering various spatial (m-km) and temporal (1973-2006) scales in different benthic habitats (emergent rock, rock pools and sedimentary habitats) through meta-analyses. Assemblage stability was estimated by measuring temporal variances of species richness, total abundance (density or % cover) and community species composition and abundance structure (using multivariate analyses). Positive relationships between temporal variability in species number and richness were generally observed at both quadrat (<1 m2) and site (100 m2) scales, while no relationships were observed by multivariate analyses. Positive relationships were also observed at the scale of site between temporal variability in species number and variability in community structure with evenness estimates. This implies that the relationship between species richness or evenness and species richness variability is slightly positive and depends on the scale of observation, suggesting that biodiversity per se is important for the stability of ecosystems. Changes within community assemblages in terms of structure are, however, generally independent of biodiversity, suggesting no effect of diversity, but the potential impact of individual species, and/or environmental factors. Except for sedimentary and rock pool habitats, no relationship was observed between temporal variation of the aggregated variable of total abundances and diversity at either scale. Overall our results emphasise that relationships depend on scale of measurements, type of habitats and the marine systems (North Atlantic and Mediterranean) considered.

Validations and descriptions of European syntaxa of vegetation dominated by lichens, bryophytes and algae

Fourty-two high-rank syntaxa and seven associations of the thallophyte system of syntaxa are either described as new or validated in this paper. Among those, there are the following nine classes: Aspicilietea candidae, Caulerpetea racemosae, Desmococcetea olivacei, Entophysalidetea deustae, Gloeocapsetea sanguineae, Mesotaenietea berggrenii, Naviculetea gregariae, Porpidietea zeoroidis, Roccelletea phycopsis. Eleven orders and ten alliances as well as three associations are described or validated: the Aspicilietalia verruculosae (incl. Aspicilion mashiginensis and Teloschistion contortuplicati), the Caulerpetalia racemosae (incl. Caulerpion racemosae), the Desmococcetalia olivacei (incl. Desmococcion olivacei), the Dirinetalia massiliensis, the Fucetalia vesiculosi (incl. Ascophyllion nodosi), the Gloeocapsetalia sanguineae, the Lecideetalia confluescentis (incl. Lecideion confluescentis), the Mesotaenietalia berggrenii (incl. Mesotaenion berggrenii, Mesotaenietum berggrenii and Chloromonadetum nivalis), the Naviculetalia gregariae (incl. Oscillatorion limosae and Oscillatorietum limosae), the Porpidietalia zeoroidis (incl. Porpidion zeoroidis), and the Roccelletalia fuciformis (incl. Paralecanographion grumulosae). Further, five orders, seven alliances and four associations, classified in known classes, were described as well. These include: the Bacidinetalia phacodis, the Agonimion octosporae and the Dendrographetalia decolorantis (all in the Arthonio radiatae-Lecidelletea elaeochromae), the Staurothelion solventis (in the Aspicilietea lacustris), the Pediastro duplicis-Scenedesmion quadricaudae and the Pediastro duplicis-Scenedesmetum quadricaudae (both in the Asterionelletea formosae), the Peccanion coralloidis and the Peltuletalia euplocae (both in the Collematetea cristati), the Laminarion hyperboreae, the Saccorhizo polyschidi-Laminarietum and the Alario esculenti-Himanthalietum elongatae (all in the Cystoseiretea crinitae), the Delesserietalia sanguinei, the Delesserion sanguinei and the Delesserietum sanguineae (all in the Lithophylletea soluti), as well as the the Rinodino confragosae-Rusavskietalia elegantis and the Rhizocarpo geographici-Rusavskion elegantis (both in the Rhizocarpetea geographici).

“Islands” in Holocene forests: implications for forest openness, landscape clearance and “culture-steppe” species

Human activity has undoubtedly had a major impact on Holocene forested ecosystems, with the concurrent expansion of plants and animals associated with cleared landscapes and pasture, also known as 'culture-steppe'. However, this anthropogenic perspective may have underestimated the contribution of autogenic disturbance (e.g. wind-throw, fire), or a mixture of autogenic and anthropogenic processes, within early Holocene forests. Entomologists have long argued that the north European primary forest was probably similar in structure to pasture woodland. This idea has received support from the conservation biologist Frans Vera, who has recently strongly argued that the role of large herbivores in maintaining open forests in the primeval landscapes of Europe has been seriously underestimated. This paper reviews this debate from a fossil invertebrate perspective and looks at several early Holocene insect assemblages. Although wood taxa are indeed important during this period, species typical of open areas and grassland and dung beetles, usually associated with the dung of grazing animals, are persistent presences in many early woodland faunas. We also suggest that fire and other natural disturbance agents appear to have played an important ecological role in some of these forests, maintaining open areas and creating open vegetation islands within these systems. More work, however, is required to ascertain the role of grazing animals, but we conclude that fossil insects have a significant contribution to make to this debate. This evidence has fundamental implications in terms of how the palaeoecological record is interpreted, particularly by environmental archaeologists and palaeoecologists who may be more interested in identifying human-environment interactions rather than the ecological processes which may be preserved within palaeoecological records.

Pinus and Prostomis: a dendrochronological and palaeoentomological study of a study of a mid-Holocene woodland in Eastern England

Tree-ring analysis of sub-fossil Pinus sylvestris L. and Quercus sp. and their associated sub-fossil insect assemblages from tree rot holes have been used to study a prehistoric forest buried in the basal peats at Tyrham Hall Quarry, Hatfield Moors SSSI, in the Humberhead Levels, eastern England. The site provided a rare opportunity to examine the date, composition, age structure and entomological biodiversity of a mid-Holocene Pinus-dominated forest. The combined approaches of dendrochronology and palaeoentomology have enabled a detailed picture of the forest to be reconstructed, within a precise time frame. The Pinus chronology has been precisely dated to 2921- 2445 BC against the English Quercus master curve and represents the first English Pinus chronology to be dendrochronologically dated. A suite of important xylophilous (wood-loving) beetles that are today very rare and four species that no longer live within the British Isles were also recovered, their disappearance associated with the decline in woodland habitats as well as possible climate change. The sub-fossil insects indicate that the characteristic species of the site's modern-day fauna were already in place 4000 years ago. These findings have important implications in terms of maintaining long-term invertebrate biodiversity of mire sites.

Novel frenatins from the skin of the Australasian Giant White-lipped tree frog, Litoria infrafrenata: cloning of precursor cDNAs and identification in defensive skin secretion.

The Australasian anuran amphibian genus Litoria, contains many phenotypically-diverse species as a result of radial evolution of an ancestral species into different biotopes much in the manner of the indigenous marsupial mammals. In common with members of the Central/South American genus Phyllomedusa, their specialized skin granular glands are factories for the production of a plethora of biologically-active peptides. Here we report a more detailed study of those present in the defensive skin secretion of the Australasian giant white-lipped tree frog, Litoria infrafrenata, and, for the first time, we have identified three novel frenatins by deduction of primary structures from cDNAs that were cloned from a library constructed from lyophilized skin secretion using a recently-developed technique. All open-reading frames consisted of a putative signal peptide and an acidic pro-region followed by a single copy of a frenatin peptide. Processed peptides corresponding in molecular mass to the deduced molecular masses of frenatins (named 1.1, 3, 3.1 and 4.1) were identified in the same secretion sample using HPLC and mass spectroscopy. The application of this technique thus permits parallel peptidomic and transcriptomic analyzes on the same lyophilized skin secretion sample circumventing sacrifice of specimens from endangered herpetofauna.

The smooth muscle pharmacology of maximakinin, a receptor-selective, bradykinin-related nonadecapeptide from the venom of the Chinese toad, Bombina maxima.

Structural homologues of vertebrate regulatory peptides found in defensive skin secretions of anuran amphibians often display enhanced bioactivity and receptor binding when compared with endogenous mammalian peptide ligands. Maximakinin, a novel N-terminally extended bradykinin (DLPKINRKGPRPPGFSPFR) from the skin venom of a Chinese toad (Bombina maxima), displays such activity enhancement when compared with bradykinin but is additionally highly selective for mammalian arterial smooth muscle bradykinin receptors displaying a 50-fold increase in molar potency in this smooth muscle type. In contrast, a 100-fold decrease in molar potency was observed at bradykinin receptors in intestinal and uterine smooth muscle preparations. Maximakinin has thus evolved as a “smart” defensive weapon in the toad with receptor/tissue selective targeting. Natural selection of amphibian skin venom peptides for antipredator defence, through inter-species delivery by an exogenous secretory mode, produces subtle structural stabilisation modifications that can potentially provide new insights for the design of selectively targeted peptide therapeutics.

Geophysical imaging of stimulated microbial biomineralization

Understanding how microorganisms influence the physical and chemical properties of the subsurface is hindered by our inability to observe microbial dynamics in real time and with high spatial resolution. Here, we investigate the use of noninvasive geophysical methods to monitor biomineralization at the laboratory scale during stimulated sulfate reduction under dynamic flow conditions. Alterations in sediment characteristics resulting from microbe-mediated sulfide mineral precipitation were concomitant with changes in complex resistivity and acoustic wave propagation signatures. The sequestration of zinc and iron in insoluble sulfides led to alterations in the ability of the pore fluid to conduct electrical charge and of the saturated sediments to dissipate acoustic energy. These changes resulted directly from the nucleation, growth, and development of nanoparticulate precipitates along grain surfaces and within the pore space. Scanning and transmission electron microscopy (SEM and TEM) confirmed the sulfides to be associated with cell surfaces, with precipitates ranging from aggregates of individual 3-5 nm nanocrystals to larger assemblages of up to 10-20 m in diameter. Anomalies in the geophysical data reflected the distribution of mineral precipitates and biomass over space and time, with temporal variations in the signals corresponding to changes in the aggregation state of the nanocrystalline sulfides. These results suggest the potential for using geophysical techniques to image certain subsurface biogeochemical processes, such as those accompanying the bioremediation of metal-contaminated aquifers.

Numerical analysis of surface and fossil pollen spectra from northern Fennoscandia

Aim Determination of the main directions of variance in an extensive data base of annual pollen deposition, and the relationship between pollen data from modified Tauber traps and palaeoecological data. Location Northern Finland and Norway. Methods Pollen analysis of annual samples from pollen traps and contiguous high-resolution samples from a peat sequence. Numerical analysis (principal components analysis) of the resulting data. Results The main direction of variation in the trap data is due to the vegetation region in which each trap is located. A secondary direction of variation is due to the annual variability of pollen production of some of the tree taxa, especially Betula and Pinus. This annual variability is more conspicuous in ‘absolute’ data than it is in percentage data which, at this annual resolution, becomes more random. There are systematic differences, with respect to peat-forming taxa, between pollen data from traps and pollen data from a peat profile collected over the same period of time. Main conclusions Annual variability in pollen production is rarely visible in fossil pollen samples because these cannot be sampled at precisely a 12-month resolution. At near-annual resolution sampling, it results in erratic percentage values which do not reflect changes in vegetation. Profiles sampled at near annual resolution are better analysed in terms of pollen accumulation rates with the realization that even these do not record changes in plant abundance but changes in pollen abundance. However, at the coarser temporal resolution common in most fossil samples it does not mask the origin of the pollen in terms of its vegetation region. Climate change may not be recognizable from pollen assemblages until the change has persisted in the same direction sufficiently long enough to alter the flowering (pollen production) pattern of the dominant trees.

Novel brevinins from Chinese piebald odorous frog (Huia schmackeri) skin deduced from cloned biosynthetic precursors

Antimicrobial peptides represent the most characterized and diverse class of peptides within the defensive skin secretions of anuran amphibians. With an ever expanding database of primary structures, the current accepted rules for nomenclature have become increasingly difficult to apply to peptides whose primary structural attributes are either unique or that fall between those that define existing groups. An additional factor that adds to the confusion is the regular re-classification or revision of existing taxa. In the present study, we have identified five new antimicrobial peptide homologs in the defensive skin secretion of the Chinese piebald odorous frog, Huia schmackeri (formerly Rana (Odorrana) schmackeri), by cloning of their respective biosynthetic precursors. As these peptides are obvious homologs of the brevinin-1 and brevinin-2 families we have named these in accordance: (1) brevinin-1HS1, (2) brevinin-2HS1, (3) brevinin-2HS2, (4) brevinin-2HS3 and (5) brevinin-1HS2. The reasons for adopting these names are discussed. It is clear that with an ever-increasing number of amphibian skin antimicrobial peptides appearing in the literature that a consistent nomenclature scheme needs to be established.