Passive flow through an unstalked intertidal ascidian: Orientation and morphology enhance suspension feeding in Pyura stolonifera

Passive flow is believed to increase the gains and reduce the costs of active suspension feeding. We used a mixture of field and laboratory experiments to evaluate whether the unstalked intertidal ascidian Pyura stolonifera exploits passive flow. We predicted that its orientation to prevailing currents and the arrangement of its siphons would induce passive flow due to dynamic pressure at the inhalant siphon, as well as by the Bernoulli effect or viscous entrainment associated with different fluid velocities at each siphon, or by both mechanisms. The orientation of P. stolonifera at several locations along the Sydney-Illawarra coast (Australia) covering a wide range of wave exposures was nonrandom and revealed that the ascidians were con- sistently oriented with their inhalant siphons directed into the waves or backwash. Flume experiments using wax mod- els demonstrated that the arrangement of the siphons could induce passive flow and that passive flow was greatest when the inhalant siphon was oriented into the flow. Field exper- iments using transplanted animals confirmed that such an orientation resulted in ascidians gaining food at greater rates, as measured by fecal production, than when oriented perpendicular to the wave direction. We conclude that P. stolonifera enhances suspension feeding by inducing pas- sive flow and is, therefore, a facultatively active suspension feeder. Furthermore, we argue that it is likely that many other active suspension feeders utilize passive flow and, therefore, measurements of their clearance rates should be made under appropriate conditions of flow to gain ecolog- ically relevant results.

Sperm environment affects offspring quality in broadcast spawning marine invertebrates

The provisioning of offspring can have far-reaching consequences for later life in a wide range of organisms and generally this provisioning is thought to be under maternal influence or control. In experiments with a broadcast-spawning ascidian, we found that the size of offspring was determined by egg size and the abundance of sperm present during fertilization. Larger eggs were fertilized at low sperm concentrations, whilst smaller eggs were successfully fertilized at high sperm concentrations. These differences in fertilized egg size resulted in differences in the development rate, hatching success and mean size of the subsequent larvae. Our results suggest that, in contrast to females that reproduce by other mating systems, free-spawning mothers lack some control over the provisioning of offspring. Furthermore, because males can alter the sperm environment, they can exert paternal (non-genetic) control over key offspring characteristics.

Fungal Planet description sheets: 371-399

Novel species of fungi described in the present study include the following from Australia: Neoseptorioides eucalypti gen. & sp. nov. from Eucalyptus radiata leaves, Phytophthora gondwanensis from soil, Diaporthe tulliensis from rotted stem ends of Theobroma cacao fruit, Diaporthe vawdreyi from fruit rot of Psidium guajava, Magnaporthiopsis agrostidis from rotted roots of Agrostis stolonifera and Semifissispora natalis from Eucalyptus leaf litter. Furthermore, Neopestalotiopsis egyptiaca is described from Mangifera indica leaves (Egypt), Roussoella mexicana from Coffea arabica leaves (Mexico), Calonectria monticola from soil (Thailand), Hygrocybe jackmanii from littoral sand dunes (Canada), Lindgomyces madisonensis from submerged decorticated wood (USA), Neofabraea brasiliensis from Malus domestica (Brazil), Geastrum diosiae from litter (Argentina), Ganoderma wiiroense on angiosperms (Ghana), Arthrinium gutiae from the gut of a grasshopper (India), Pyrenochaeta telephoni from the screen of a mobile phone (India) and Xenoleptographium phialoconidium gen. & sp. nov. on exposed xylem tissues of Gmelina arborea (Indonesia). Several novelties are introduced from Spain, namely Psathyrella complutensis on loamy soil, Chlorophyllum lusitanicum on nitrified grasslands (incl. Chlorophyllum arizonicum comb. nov.), Aspergillus citocrescens from cave sediment and Lotinia verna gen. & sp. nov. from muddy soil. Novel foliicolous taxa from South Africa include Phyllosticta carissicola from Carissa macrocarpa, Pseudopyricularia hagahagae from Cyperaceae and Zeloasperisporium searsiae from Searsia chirindensis. Furthermore, Neophaeococcomyces is introduced as a novel genus, with two new combinations, N. aloes and N. catenatus. Several foliicolous novelties are recorded from La Réunion, France, namely Ochroconis pandanicola from Pandanus utilis, Neosulcatispora agaves gen. & sp. nov. from Agave vera-cruz, Pilidium eucalyptorum from Eucalyptus robusta, Strelitziana syzygii from Syzygium jambos (incl. Strelitzianaceae fam. nov.) and Pseudobeltrania ocoteae from Ocotea obtusata (Beltraniaceae emend.). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Rapid changes in the vegetation of a shallow pond in Epping Forest, related to recent droughts

Over much of Britain, 1995 and 1996 have been perceived as drought years. To evaluate the impact that local climatic conditions are having upon successional changes in higher vegetation (macrophytes), Speakmans Pond in Epping Forest was surveyed and mapped in 1996. The results are related to previous vegetation surveys carried out in 1989 and 1991. In 1989 the dominant marginal vegetation was floating sweet-grass Glyceria fluitans, which also covered a major part of the main body of the pond. Other abundant species included soft rush Juncus effusus, reed mace Typha latifolia and yellow flag Iris pseudocorus. A small (central) area of open water contained bladderwort Utricularia vulgaris and white water-lily Nymphaea alba. A similar plant coverage was found in 1991, with a dominance of floating sweet-grass along the shallow eastern edge. A marked change in the pond was found during the 1996 survey of vegetation in July, when the pool was dry. The major plant cover now consisted of creeping bent Agrostis stolonifera, with isolated clumps of Yorkshire fog Holcus lanatus around the edges; both are terrestrial grasses found on land surrounding the pond. Rushes (Juncus) had increased their distribution round the margins of the pond, and the patch of yellow flag noted in 1989 and 1991 was not found in 1996. The deeper trenches were also dry, but a small patch of white water-lily remained adjacent to one of the trenches.

Diversity of functional groups in the vegetation sandy seashore of the Grande, Anclitas and Caguamas Cays (Jardines de la Reina Archipelago, Cuba)

Sandy shores are known to be extreme ecosystems where the vegetation has evolved many morphological and physiological adaptations for its survival. With the aim of identify possible relationships between the vegetation´s functional diversity with abiotic factors and its corresponding quantification, we collected data on the abundance and richness of the sandy coast vegetation complex in Grande, Anclitas and Caguamas keys. Its flora is largely characterized by the dominance of hemicryptophytes and chamaephytes plants with nanophyllous leaves and displaying dispersal syndromes such as zoochory and anemochory. However, the functional groups´ richness, in the present study, varies from one key to another. Functional diversity is similar between the wet and dry seasons, and its spatial variation is influenced by the interplay of the set of abiotic factors herein studied.

Prospección del recurso Caracol (Thais Chocolata) en el litoral de Moquegua y Tacna. Julio 1997

Presenta los resultados de la evaluación de los bancos naturales del recurso caracol (Thais chocolata) situados en Cocotea y Llostay (departamentos de Moquegua y Tacna), encontrándose que el recurso tiene como hábitat preferente las comunidades de Aulacomya ater (chorales) y Pyura chilensis (cochizales). En relación a los resultados obtenidos durante la prospección de 1996, se afirma que el recurso sigue sometido a la sobreexplotación por lo que se sugiere adoptar medidas regulativas para no causar un colapso pesquero.

Étude de l’interaction entre le champignon mycorhizien Glomus irregulare et les bactéries du sol

Dans cette étude, nous avons isolé et cultivé des bactéries intimement liées aux spores du champignon mycorhizien Glomus irregulare prélevées dans la rhizosphère de plants d’Agrostis stolonifera L. récoltés dans un sol naturel. Le séquençage des 29 morphotypes isolés a révélé la présence de seulement sept taxons bactériens (Variovorax paradoxus, Microbacterium ginsengiosoli, Sphingomonas sp., Bacillus megaterium, B. simplex, B. cereus et Kocuria rhizophila). Des isolats de chacun de ces sept taxons ont ensuite été cultivés in vitro sur le mycélium de G. irregulare afin d’observer par microscopie leur capacité à croitre et à s’attacher au mycélium en absence d’éléments nutritifs autres que ceux fournis par le champignon. Tous les isolats, sauf B. cereus, ont été capables de bien croitre dans le système expérimental et de s’attacher au mycélium en formant des structures ressemblant à des biofilms sur la surface du champignon. Toutefois, B. simplex formait ces structures plus rapidement, soit en 15 jours, alors que les autres isolats les ont formés après 30 jours (K. rhizophila et B. megaterium) ou 45 jours (V. paradoxus, M. ginsengiosoli et Sphingomonas sp.). D’autre part, la technique PCR-DGGE a permis d’analyser la diversité bactérienne associée aux spores. La diversité des taxons associés aux spores de G. irregulare qu’il a été possible d’isoler et de cultiver in vitro a été nettement moindre que celle qui était présente sur la surface des spores, alors que la biodiversité bactérienne totale du sol a été encore beaucoup plus élevée. Les bactéries associées aux champignons mycorhiziens jouent probablement un rôle important dans la capacité des plantes à résister aux stress biotiques et abiotiques auxquels elles sont soumises.

Technologies for biological containment of GM and Non-GM crops

International Perspective The development of GM technology continues to expand into increasing numbers of crops and conferred traits. Inevitably, the focus remains on the major field crops of soybean, maize, cotton, oilseed rape and potato with introduced genes conferring herbicide tolerance and/or pest resistance. Although there are comparatively few GM crops that have been commercialised to date, GM versions of 172 plant species have been grown in field trials in 31 countries. European Crops with Containment Issues Of the 20 main crops in the EU there are four for which GM varieties are commercially available (cotton, maize for animal feed and forage, and oilseed rape). Fourteen have GM varieties in field trials (bread wheat, barley, durum wheat, sunflower, oats, potatoes, sugar beet, grapes, alfalfa, olives, field peas, clover, apples, rice) and two have GM varieties still in development (rye, triticale). Many of these crops have hybridisation potential with wild and weedy relatives in the European flora (bread wheat, barley, oilseed rape, durum wheat, oats, sugar beet and grapes), with escapes (sunflower); and all have potential to cross-pollinate fields non-GM crops. Several fodder crops, forestry trees, grasses and ornamentals have varieties in field trials and these too may hybridise with wild relatives in the European flora (alfalfa, clover, lupin, silver birch, sweet chestnut, Norway spruce, Scots pine, poplar, elm, Agrostis canina, A. stolonifera, Festuca arundinacea, Lolium perenne, L. multiflorum, statice and rose). All these crops will require containment strategies to be in place if it is deemed necessary to prevent transgene movement to wild relatives and non-GM crops. Current Containment Strategies A wide variety of GM containment strategies are currently under development, with a particular focus on crops expressing pharmaceutical products. Physical containment in greenhouses and growth rooms is suitable for some crops (tomatoes, lettuce) and for research purposes. Aquatic bioreactors of some non-crop species (algae, moss, and duckweed) expressing pharmaceutical products have been adopted by some biotechnology companies. There are obvious limitations of the scale of physical containment strategies, addressed in part by the development of large underground facilities in the US and Canada. The additional resources required to grow plants underground incurs high costs that in the long term may negate any advantage of GM for commercial productioNatural genetic containment has been adopted by some companies through the selection of either non-food/feed crops (algae, moss, duckweed) as bio-pharming platforms or organisms with no wild relatives present in the local flora (safflower in the Americas). The expression of pharmaceutical products in leafy crops (tobacco, alfalfa, lettuce, spinach) enables growth and harvesting prior to and in the absence of flowering. Transgenically controlled containment strategies range in their approach and degree of development. Plastid transformation is relatively well developed but is not suited to all traits or crops and does not offer complete containment. Male sterility is well developed across a range of plants but has limitations in its application for fruit/seed bearing crops. It has been adopted in some commercial lines of oilseed rape despite not preventing escape via seed. Conditional lethality can be used to prevent flowering or seed development following the application of a chemical inducer, but requires 100% induction of the trait and sufficient application of the inducer to all plants. Equally, inducible expression of the GM trait requires equally stringent application conditions. Such a method will contain the trait but will allow the escape of a non-functioning transgene. Seed lethality (‘terminator’ technology) is the only strategy at present that prevents transgene movement via seed, but due to public opinion against the concept it has never been trialled in the field and is no longer under commercial development. Methods to control flowering and fruit development such as apomixis and cleistogamy will prevent crop-to-wild and wild-to-crop pollination, but in nature both of these strategies are complex and leaky. None of the genes controlling these traits have as yet been identified or characterised and therefore have not been transgenically introduced into crop species. Neither of these strategies will prevent transgene escape via seed and any feral apomicts that form are arguably more likely to become invasives. Transgene mitigation reduces the fitness of initial hybrids and so prevents stable introgression of transgenes into wild populations. However, it does not prevent initial formation of hybrids or spread to non-GM crops. Such strategies could be detrimental to wild populations and have not yet been demonstrated in the field. Similarly, auxotrophy prevents persistence of escapes and hybrids containing the transgene in an uncontrolled environment, but does not prevent transgene movement from the crop. Recoverable block of function, intein trans-splicing and transgene excision all use recombinases to modify the transgene in planta either to induce expression or to prevent it. All require optimal conditions and 100% accuracy to function and none have been tested under field conditions as yet. All will contain the GM trait but all will allow some non-native DNA to escape to wild populations or to non-GM crops. There are particular issues with GM trees and grasses as both are largely undomesticated, wind pollinated and perennial, thus providing many opportunities for hybridisation. Some species of both trees and grass are also capable of vegetative propagation without sexual reproduction. There are additional concerns regarding the weedy nature of many grass species and the long-term stability of GM traits across the life span of trees. Transgene stability and conferred sterility are difficult to trial in trees as most field trials are only conducted during the juvenile phase of tree growth. Bio-pharming of pharmaceutical and industrial compounds in plants Bio-pharming of pharmaceutical and industrial compounds in plants offers an attractive alternative to mammalian-based pharmaceutical and vaccine production. Several plantbased products are already on the market (Prodigene’s avidin, β-glucuronidase, trypsin generated in GM maize; Ventria’s lactoferrin generated in GM rice). Numerous products are in clinical trials (collagen, antibodies against tooth decay and non-Hodgkin’s lymphoma from tobacco; human gastric lipase, therapeutic enzymes, dietary supplements from maize; Hepatitis B and Norwalk virus vaccines from potato; rabies vaccines from spinach; dietary supplements from Arabidopsis). The initial production platforms for plant-based pharmaceuticals were selected from conventional crops, largely because an established knowledge base already existed. Tobacco and other leafy crops such as alfalfa, lettuce and spinach are widely used as leaves can be harvested and no flowering is required. Many of these crops can be grown in contained greenhouses. Potato is also widely used and can also be grown in contained conditions. The introduction of morphological markers may aid in the recognition and traceability of crops expressing pharmaceutical products. Plant cells or plant parts may be transformed and maintained in culture to produce recombinant products in a contained environment. Plant cells in suspension or in vitro, roots, root cells and guttation fluid from leaves may be engineered to secrete proteins that may be harvested in a continuous, non-destructive manner. Most strategies in this category remain developmental and have not been commercially adopted at present. Transient expression produces GM compounds from non-GM plants via the utilisation of bacterial or viral vectors. These vectors introduce the trait into specific tissues of whole plants or plant parts, but do not insert them into the heritable genome. There are some limitations of scale and the field release of such crops will require the regulation of the vector. However, several companies have several transiently expressed products in clinical and pre-clinical trials from crops raised in physical containment.

Corner Inlet and Nooramunga Habitat Mapping Project – Part 2 : High resolution mapping and change detection analysis using 2011 Rapid Eye Satellite Image compared to 2009 ALOS Satellite Image

Building on a habitat mapping project completed in 2011, Deakin University was commissioned by Parks Victoria (PV) to apply the same methodology and ground-truth data to a second, more recent and higher resolution satellite image to create habitat maps for areas within the Corner Inlet and Nooramunga Marine and Coastal Park and Ramsar area. A ground-truth data set using in situ video and still photographs was used to develop and assess predictive models of benthic marine habitat distributions incorporating data from both RapidEye satellite imagery (corrected for atmospheric and water column effects by CSIRO) and LiDAR (Light Detection and Ranging) bathymetry. This report describes the results of the mapping effort as well as the methodology used to produce these habitat maps.

Overall accuracies of habitat classifications were good, with error rates similar to or better than the earlier classification (>73 % and kappa values > 0.58 for both study localities). The RapidEye classification failed to accurately detect Pyura and reef habitat classes at the Corner Inlet locality, possibly due to differences in spectral frequencies. For comparison, these categories were combined into a ‘non-seagrass’ category, similar to the one used at the Nooramunga locality in the original classification. Habitats predicted with highest accuracies differed from the earlier classification and were Posidonia in Corner Inlet (89%), and bare sediment (no-visible seagrass class) in Nooramunga (90%). In the Corner Inlet locality reef and Pyura habitat categories were not distinguishable in the repeated classification and so were combined with bare sediments. The majority of remaining classification errors were due to the misclassification of Zosteraceae as bare sediment and vice versa. Dominant habitats were the same as those from the 2011 classification with some differences in extent. For the Corner Inlet study locality the no-visible seagrass category remained the most extensive (9059 ha), followed by Posidonia (5,513 ha) and Zosteraceae (5,504 ha). In Nooramunga no-visible seagrass (6,294 ha), Zosteraceae (3,122 ha) and wet saltmarsh (1,562 ha) habitat classes were most dominant.

Change detection analyses between the 2009 and 2011 imagery were undertaken as part of this project, following the analyses presented in Monk et al. (2011) and incorporating error estimates from both classifications. These analyses indicated some shifts in classification between Posidonia and Zosteraceae as well as a general reduction in the area of Zosteraceae. Issues with classification of mixed beds were apparent, particularly in the main Posidonia bed at Nooramunga where a mosaic of Zosteraceae and Posidonia was seen that was not evident in the ALOS classification. Results of a reanalysis of the 1998-2009 change detection illustrating effects of binning of mixed beds is also provided as an appendix.

This work has been successful in providing baseline maps at an improved level of detail using a repeatable method meaning that any future changes in intertidal and shallow water marine habitats may be assessed in a consistent way with quantitative error assessments. In wider use, these maps should also allow improved conservation planning, advance fisheries and catchment management, and progress infrastructure planning to limit impacts on the Inlet environment.

Effects of flooding on coastal vegetation and salt marshes

This thesis examines the effects of flooding on coastal and salt marsh vegetation. I conducted a field experiment in Bellocchio Lagoon to test the effects of different inundation periods (Level 1 = 0.468 or 11.23 hours; Level 2 = 0.351 or 8.42 hours; Level 3 = 0.263 or 6.312 hours; Level 4 = 0.155 or 3.72 hours; Level 5 = 0.082 or 1.963 hours; Level 6 = 0.04 or 0.96 hours) on the growth responses and survival of the salt marsh grass Spartina maritima in summer 2011 and 2012. S. maritima grew better at intermediate inundation times (0,351 hours; 0,263 hours, 0,115 hours; 0,082 hours), while growth and survival were reduced at greater inundation periods (0,468 hours). The differences between the 2011 and 2012 experiment were mainly related to differences in the initial number of shoots (1 and 5, respectively in 2011 and 2012). In the 2011 experiment a significant lower number of plants was present in the levels 1 and 6, the rhizomes reached the max pick in level 4, weights was major in level 4, spike length reached the pick in level 3 while leaf length in level 2. In the 2012 experiment the plants in level 6 all died, the rhizomes were more present in level 3, weights was major in level 3, spike length reached the pick in level 3, as well as leaf length. I also conducted a laboratory experiment which was designed to test the effects of 5 different inundation periods (0 control, 8, 24, 48, 96 hours) on the survival of three coastal vegetation species Agrostis stolonifera, Trifolium repens and Hippopae rhamnoides in summer 2012. The same laboratory experiment was repeated in the Netherlands. In Italy, H. rhamnoides showed a great survival in the controls, a variable performance in the other treatments and a clear decrease in treatment 4. Conversely T. repens and A. stolonifera only survive in the control. In the Netherlands experiment there was a greater variability responses for each species, still at the end of the experiment survival was significantly smaller in treatment 4 (96 h of seawater inundation) for all the three species. The results suggest that increased flooding can affect negatively the survival of both saltmarsh and coastal plants, limiting root system extension and leaf growth. Flooding effect could lead to further decline and fragmentation of the saltmarshes and coastal vegetation, thereby reducing recovery (and thus resilience) of these systems once disturbed. These effects could be amplified by interactions with other co-occurring human impacts in these systems, and it is therefore necessary to identify management options that increase the resilience of these systems.

Molecular phylogenesis of Mediterranean Octocorals

In order to support the conservation of the Mediterranean octocorals improvements on information regarding their taxonomic units and phylogenetic relationships are strongly needed. In the present thesis work, phylogenetic analyses based on the mitochondrial mtMSH and 16S genes were performed including 15 Mediterranean octocorals species on the 56 recognized to date. Moreover, an extended datasets with Atlanto/Pacific congeners Octocorallia species was implemented to clarify their phylogenetic relationships and estimate the divergence times of the Mediterranean species. Results indicated that: 1) there are similarity and differences among molecular and morphological traits depending on the taxonomical level considered; 2) the molecular phylogeny of the Mediterranean octocorals retrace the previous relationships based on wide octocorals analyses; and 3) the divergence time among Mediterranean and Atlanto/Pacific species varies depending on analysed taxa. At higher taxonomic level, the Mediterranean trees supported the division of the Mediterranean Octocorallia into one major clade (Alcyoniina-Holaxonia) plus two unresolved branch including the single species available of Scleraxonia and Stolonifera respectively. This topology was better supported including the Atlanto/Pacific congeners species. The molecular evidence suggested that Alcyonium palmatum and Corallium rubrum species are the youngest with a divergence time estimated around 4 MYA. Particularly, C. rubrum results were in agreement with the hypothesis that recent orogenesis process of the Mediterranean Sea promoted the allopatric speciation of this specie. Increasing the sample design and implementing the emerging next-generation genomic-sequencing technologies, further studies would be able to improve the understanding of the Mediterranean octocorals phylogenetic relationships and evolution.

Innovative techniques for sport turf managing: Agronomic and phyisiological implications

The growing substrate of the putting greens is considered a key factor for a healthy turf ecosystem. Actually detailed study on the effects of growth promoting bacteria and biostimulants on a professional sport turf are very limited. This thesis aimed to study the effectiveness of different microorganisms and biostimulants in order to improve the knowledge relative to the relationship between the beneficial microflora and root apparatus of sport turfs. The research project was divided in three principal steps: Initially, commercial products based on biostimulants and microorganisms were tested on a Lolium perenne L. essence grown in a controlled-environment. The principal evaluations were the study of the habitus of plants, biomass production and length of leaves and roots. Were studied the capacity of colonization of microorganisms within root tissues and rhizosphere. In the second step were developed two different biostimulant solutions based on effective microorganisms, mycorrhizae and humic acids. This test was conducted both on an Agrostis stolonifera putting green (Modena Golf & Country Club) in a semi-field condition and within a growth chamber on a Lolium perenne L. essence. Fungicide and chemicals applications were suspended in order to assess the effectiveness of the inoculants for nutrition and control of pests. In the last step, different microorganism mixes and biostimulants were tested on an experimental putting green in the Turf Research Center (TRC) (Virginia Tech, United States) in a real managing situation. The effects of different treatments were studied maintaining all chemicals and mechanicals managements scheduled during a sport season. Both growth-chamber and field results confirmed the capacity of microorganisms based biostimulants to promote the physiologic conditions of the plants, improve the growth of the roots and enhance the aesthetic performance of the turf. Molecular analysis confirmed the capacity of microorganisms to colonize the root tissues.