History of Ichnology: Early Ichnology Poems and Their Poets

In the early nineteenth century, the discovery of trace fossils fired the imagination of the discoverers and inspired them to compose unique poems. John Joly of Ireland wrote a poem about the invertebrate trace fossil Oldhamia that had been discovered in rocks around Bray Head. In the United States, the Reverend Edward Hitchcock discovered what he felt were giant bird tracks that later turned out to be reptile tracks. The traces inspired Hitchcock, who published a poem “The Sandstone Bird” in The Knickerbocker magazine under the pseudonym Poetaster. The poem is about a sorceress bringing the great sandstone bird back to life and probably represents the first ichnological poem.     

A Multifaceted Approach to Ichnology

Trace fossils link paleontology and sedimentology in ways that most body fossils cannot achieve. A multifaceted approach to ichnology helps to bridge the gap the biologic and geologic standpoints, to connect different levels of analysis (conceptual framework, explanatory schemata and applications), and to reconcile dichotomic views (e.g., adaptationist vs. interactionist approaches, time's arrow vs, time's cycle perspectives) by integrating the multiple aspects of the science of animal-substrate interactions. In this context, ichnologic investigations provide important links among numerous different fields. Analysis of specific ichnofaunas using this integrated approach may result in important and meaningful contributions to our understanding of paleoecology, sedimentology, sequence stratigraphy, reservoir characterization, biostratigraphy, evolutionary paleoecology, paleoceanography, and paleoclimatology.     

Responses of Very Shallow Marine Ecosystems to Nutrient Enrichment

The success of simple predictive relationships such as the Vollenweider plot in limnology has encouraged marine ecologists to attempt to develop similar models relating pollutant inputs to ecological conditions in estuaries. Most of these efforts have focused on relatively deep (>5?m) river mouth estuaries and embayments where primary production is dominated by phytoplankton. Experimental nutrient enrichment studies of phytoplankton-based mesocosms at the Marine Ecosystems Research Laboratory (MERL) have confirmed that simple Vollenweider type relationships can be found between the rate of input of inorganic nutrients and annual mean chlorophyll concentrations and primary production. However, much of the coastline of the U.S. is characterized by estuarine ecosystems that are very shallow, and where most of the primary production is carried out by angiosperms, such as eelgrass, Zostera marina, epiphytic algae, drift and attached macroalgae, and epibenthic microalgae, rather than by phytoplankton. We have not been able to find useful relationships between nutrient input and the type of plant providing most of the primary production or between nutrient input and the amount of primary production in such shallow lagoon systems. Attempting to adjust nutrient loading for varying hydraulic residence time did not improve the models. Experimental studies using shallow lagoon mesocosms have shown that there is a large variation in the abundance of the various plant forms in these very shallow systems, and that simple Vollenweider models are not likely to emerge for this type of environment. However, it does seem that total system production increases with nutrient enrichment at very low rates of input, and that eelgrass does not persist when exposed to even moderate levels of fertilization. Zostera responds to inorganic nitrogen enrichment and to shading by increasing the rate of leaf elongation and decreasing the allocation of resources to below ground roots and rhizomes. This reduces or eliminates lateral branching of the rhizomes and causes a decline in the density of shoots. Based on mesocosm studies, we propose several indicators of eelgrass health, including the rate of leaf elongation, plant density, and the shoot: root biomass ratio that all deserve further study and field testing.     

Shell Growth in the Marine Environment: Approaches to the Problem of Marginal Calcification

Although marine waters are usually found to be supersaturatedwith respect to both calcite and aragonite, natural precipitationof these carbonate minerals is very restricted. This is apparentlydue to the occupancy and effective removal of lattice sitesby random organic molecules present in natural seawater. Despite this, many marine organisms build external shells orskeletons of calcium carbonate, utilizing various ingeniousmethods to prevent seawater contamination at the growing shellmargin. The periostracum, which apparently evolved as an aidto marginal calcification, has undergone numerous modificationsserving important secondary functions inspecialized groups.     

Sir William Jardine and the Ichnology of Annandale

ABSTRACT

Sir William Jardine was a polymath; he was one of the world's foremost ornithologists, and ichthyologists, as well as a knowledgeable geologist, entomologist and botanist. He was a talented and skilled artist and engraver and a keen hunter and fisherman. He was also the author of the book The Ichnology of Annandale that represents the first book ever published on the subject of ichnology. It was here in this volume that Jardine coined the word ichnology. It is also one of the rarest ichnology publications, as it is believed that only 135–140 copies were ever printed. This volume remains the most lavishly illustrated book in vertebrate ichnology literature. This paper discusses the work of Jardine, the finds from his estate and his role in defining ichnology as a science.     

Patterns of Post-Glacial Genetic Differentiation in Marginal Populations of a Marine Microalga

This study investigates the genetic structure of an eukaryotic microorganism, the toxic dinoflagellate Alexandrium ostenfeldii, from the Baltic Sea, a geologically young and ecologically marginal brackish water estuary which is predicted to support evolution of distinct, genetically impoverished lineages of marine macroorganisms. Analyses of the internal transcribed spacer (ITS) sequences and Amplified Fragment Length Polymorphism (AFLP) of 84 A. ostenfeldii isolates from five different Baltic locations and multiple external sites revealed that Baltic A. ostenfeldii is phylogenetically differentiated from other lineages of the species and micro-geographically fragmented within the Baltic Sea. Significant genetic differentiation (F _ST) between northern and southern locations was correlated to geographical distance. However, instead of discrete genetic units or continuous genetic differentiation, the analysis of population structure suggests a complex and partially hierarchic pattern of genetic differentiation. The observed pattern suggests that initial colonization was followed by local differentiation and varying degrees of dispersal, most likely depending on local habitat conditions and prevailing current systems separating the Baltic Sea populations. Local subpopulations generally exhibited low levels of overall gene diversity. Association analysis suggests predominately asexual reproduction most likely accompanied by frequency shifts of clonal lineages during planktonic growth. Our results indicate that the general pattern of genetic differentiation and reduced genetic diversity of Baltic populations found in large organisms also applies to microscopic eukaryotic organisms.     

Ningaloo Reef: Shallow Marine Habitats Mapped Using a Hyperspectral Sensor

Research, monitoring and management of large marine protected areas require detailed and up-to-date habitat maps. Ningaloo Marine Park (including the Muiron Islands) in north-western Australia (stretching across three degrees of latitude) was mapped to 20 m depth using HyMap airborne hyperspectral imagery (125 bands) at 3.5 m resolution across the 762 km² of reef environment between the shoreline and reef slope. The imagery was corrected for atmospheric, air-water interface and water column influences to retrieve bottom reflectance and bathymetry using the physics-based Modular Inversion and Processing System. Using field-validated, image-derived spectra from a representative range of cover types, the classification combined a semi-automated, pixel-based approach with fuzzy logic and derivative techniques. Five thematic classification levels for benthic cover (with probability maps) were generated with varying degrees of detail, ranging from a basic one with three classes (biotic, abiotic and mixed) to the most detailed with 46 classes. The latter consisted of all abiotic and biotic seabed components and hard coral growth forms in dominant or mixed states. The overall accuracy of mapping for the most detailed maps was 70% for the highest classification level. Macro-algal communities formed most of the benthic cover, while hard and soft corals represented only about 7% of the mapped area (58.6 km²). Dense tabulate coral was the largest coral mosaic type (37% of all corals) and the rest of the corals were a mix of tabulate, digitate, massive and soft corals. Our results show that for this shallow, fringing reef environment situated in the arid tropics, hyperspectral remote sensing techniques can offer an efficient and cost-effective approach to mapping and monitoring reef habitats over large, remote and inaccessible areas.     

Antimicrobial Activity of Marine Bacterial Symbionts Retrieved from Shallow Water Hydrothermal Vents

Marine sponges and other sessile macro-organisms were collected at a shallow water hydrothermal site in Eyjafjörður, Iceland. Bacteria were isolated from the organisms using selective media for actinomycetes, and the isolates were screened for antimicrobial activity. A total of 111 isolates revealed antimicrobial activity displaying different antimicrobial patterns which indicates production of various compounds. Known test strains were grown in the presence of ethyl acetate extracts from one selected isolate, and a clear growth inhibition of Staphylococcus aureus was observed down to 0.1 % extract concentration in the medium. Identification of isolates shows different species of Actinobacteria with Streptomyces sp. playing the largest role, but also members of Bacilli, Alphaproteobacteria and Gammaproteobacteria. Sponges have an excellent record regarding production of bioactive compounds, often involving microbial symbionts. At the hydrothermal vents, however, the majority of active isolates originated from other invertebrates such as sea anemones or algae. The results indicate that antimicrobial assays involving isolates in full growth can detect activity not visible by other methods. The macro-organisms inhabiting the Eyjafjörður hydrothermal vent area host diverse microbial species in the phylum Actinobacteria with antimicrobial activity, and the compounds responsible for the activity will be subject to further research.     

History of Ichnology: The Misconceived Footprints of Rhynchosaurs

In 1842 Richard Owen described a Triassic reptile from Grinshill, Shropshire, which he named Rhynchosaurus articeps. He suggested that footprints found in the same beds were those of this fossil. However, the footprints were characterised by a backward-pointing toe and so were of the type now known as Rotodactylus. Huxley (1877), Woodward (1907), and Benton (1990) have subsequently shown that the five digits of Rhynchosaurus point forward and so could not have left these footprints. In 1896 Beasley classified the Triassic footprints found in Cheshire, his type D prints being those earlier assigned to rhynchosaurs. His D1 prints were named Rhynchosauroides articeps by Maidwell (1911). However, these D1 prints, which come from a lower horizon in the Anisian, are consistently too small to match Owen's fossil. Beasley's D3 form, now named Synaptichnium pseudosuchoides Nopcsa, is more likely to represent the footprints of Rhynchosaurus articeps, although further research and study of more complete trackways will be necessary to clarify whether these are the footprints of Archosauromorphs, such as rhynchosaurs or possibly those of Archosauriformes, for example, erythrosuchids or proterosuchids. Maidwell's Rhynchosauroides rectipes and Rhynchosauroides membranipes, originally believed to be distinct ichnospecies, are more likely to be synonyms, their apparent differences reflecting variations in the substrate traversed.     

Wave Glider Monitoring of Sediment Transport and Dredge Plumes in a Shallow Marine Sandbank Environment

As human pressure on the marine environment increases, safeguarding healthy and productive seas increasingly necessitates integrated, time- and cost-effective environmental monitoring. Employment of a Wave Glider proved very useful for the study of sediment transport in a shallow sandbank area in the Belgian part of the North Sea. During 22 days, data on surface and water-column currents and turbidity were recorded along 39 loops around an aggregate-extraction site. Correlation with wave and tidal-amplitude data allowed the quantification of current- and wave-induced advection and resuspension, important background information to assess dredging impacts. Important anomalies in suspended particulate matter concentrations in the water column suggested dredging-induced overflow of sediments in the near field (i.e., dynamic plume), and settling of finer-grained material in the far field (i.e., passive plume). Capturing the latter is a successful outcome to this experiment, since the location of dispersion and settling of a passive plume is highly dependent on the ruling hydro-meteorological conditions and thus difficult to predict. Deposition of the observed sediment plumes may cause habitat changes in the long-term.     

Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.     

Presence of Nitrate-Accumulating Sulfur Bacteria and Their Influence on Nitrogen Cycling in a Shallow Coastal Marine Sediment

Nitrate flux between sediment and water, nitrate concentration profile at the sediment-water interface, and in situ sediment denitrification activity were measured seasonally at the innermost part of Tokyo Bay, Japan. For the determination of sediment nitrate concentration, undisturbed sediment cores were sectioned into 5-mm depth intervals and each segment was stored frozen at −30°C. The nitrate concentration was determined for the supernatants after centrifuging the frozen and thawed sediments. Nitrate in the uppermost sediment showed a remarkable seasonal change, and its seasonal maximum of up to 400 μM was found in October. The directions of the diffusive nitrate fluxes predicted from the interfacial concentration gradients were out of the sediment throughout the year. In contrast, the directions of the total nitrate fluxes measured by the whole-core incubation were into the sediment at all seasons. This contradiction between directions indicates that a large part of the nitrate pool extracted from the frozen surface sediments is not a pore water constituent, and preliminary examinations demonstrated that the nitrate was contained in the intracellular vacuoles of filamentous sulfur bacteria dwelling on or in the surface sediment. Based on the comparison between in situ sediment denitrification activity and total nitrate flux, it is suggested that intracellular nitrate cannot be directly utilized by sediment denitrification, and the probable fate of the intracellular nitrate is hypothesized to be dissimilatory reduction to ammonium. The presence of nitrate-accumulating sulfur bacteria therefore may lower nature's self-purification capacity (denitrification) and exacerbate eutrophication in shallow coastal marine environments.     

200 kHz Commercial Sonar Systems Generate Lower Frequency Side Lobes Audible to Some Marine Mammals

The spectral properties of pulses transmitted by three commercially available 200 kHz echo sounders were measured to assess the possibility that marine mammals might hear sound energy below the center (carrier) frequency that may be generated by transmitting short rectangular pulses. All three sounders were found to generate sound at frequencies below the center frequency and within the hearing range of some marine mammals, e.g. killer whales, false killer whales, beluga whales, Atlantic bottlenose dolphins, harbor porpoises, and others. The frequencies of these sub-harmonic sounds ranged from 90 to 130 kHz. These sounds were likely detectable by the animals over distances up to several hundred meters but were well below potentially harmful levels. The sounds generated by the sounders could potentially affect the behavior of marine mammals within fairly close proximity to the sources and therefore the exclusion of echo sounders from environmental impact analysis based solely on the center frequency output in relation to the range of marine mammal hearing should be reconsidered.     

Microbial Iron Mats at the Mid-Atlantic Ridge and Evidence that Zetaproteobacteria May Be Restricted to Iron-Oxidizing Marine Systems

Chemolithoautotrophic iron-oxidizing bacteria play an essential role in the global iron cycle. Thus far, the majority of marine iron-oxidizing bacteria have been identified as Zetaproteobacteria, a novel class within the phylum Proteobacteria. Marine iron-oxidizing microbial communities have been found associated with volcanically active seamounts, crustal spreading centers, and coastal waters. However, little is known about the presence and diversity of iron-oxidizing communities at hydrothermal systems along the slow crustal spreading center of the Mid-Atlantic Ridge. From October to November 2012, samples were collected from rust-colored mats at three well-known hydrothermal vent systems on the Mid-Atlantic Ridge (Rainbow, Trans-Atlantic Geotraverse, and Snake Pit) using the ROV Jason II. The goal of these efforts was to determine if iron-oxidizing Zetaproteobacteria were present at sites proximal to black smoker vent fields. Small, diffuse flow venting areas with high iron(II) concentrations and rust-colored microbial mats were observed at all three sites proximal to black smoker chimneys. A novel, syringe-based precision sampler was used to collect discrete microbial iron mat samples at the three sites. The presence of Zetaproteobacteria was confirmed using a combination of 16S rRNA pyrosequencing and single-cell sorting, while light micros-copy revealed a variety of iron-oxyhydroxide structures, indicating that active iron-oxidizing communities exist along the Mid-Atlantic Ridge. Sequencing analysis suggests that these iron mats contain cosmopolitan representatives of Zetaproteobacteria, but also exhibit diversity that may be uncommon at other iron-rich marine sites studied to date. A meta-analysis of publically available data encompassing a variety of aquatic habitats indicates that Zetaproteobacteria are rare if an iron source is not readily available. This work adds to the growing understanding of Zetaproteobacteria ecology and suggests that this organism is likely locally restricted to iron-rich marine environments but may exhibit wide-scale geographic distribution, further underscoring the importance of Zetaproteobacteria in global iron cycling.