High temporal resolution modelling of environmentally-dependent seabird ammonia emissions: description and testing of the GUANO model

Many studies in recent years have highlighted the ecological implications of adding reactive nitrogen (Nr) to terrestrial ecosystems. Seabird colonies represent a situation with concentrated sources of Nr, through excreted and accumulated guano, often occurring in otherwise nutrient-poor areas. To date, there has been little attention given to modelling N flows in this context, and particularly to quantifying the relationship between ammonia (NH3) emissions and meteorology. This paper presents a dynamic mass-flow model (GUANO) that simulates temporal variations in NH3 emissions from seabird guano. While the focus is on NH3 emissions, the model necessarily also treats the interaction with wash-off as far as this affects NH3. The model is validated using NH3 emissions measurements from seabird colonies across a range of climates, from sub-polar to tropical. In simulations for hourly time-resolved data, the model is able to capture the observed dependence of NH3 emission on environmental variables. With temperature and wind speed having the greatest effects on emission for the cases considered. In comparison with empirical data, the percentage of excreted nitrogen that volatilizes as NH3 is found to range from 2% to 67% (based on measurements), with the GUANO model providing a range of 2%–82%. The model provides a tool that can be used to investigate the meteorological dependence of NH3 emissions from seabird guano and provides a starting point to refine models of NH3 emissions from other sources

Measurement of ammonia emissions from temperate and sub-polar seabird colonies

The chemical breakdown of marine derived reactive nitrogen transported to the land as seabird guano represents a significant source of ammonia (NH3) in areas far from other NH3 sources. Measurements made at tropical and temperate seabird colonies indicate substantial NH3 emissions, with emission rates larger than many anthropogenic point sources. However, several studies indicate that thermodynamic processes limit the amount of NH3 emitted from guano, suggesting that the percentage of guano volatilizing as NH3 may be considerably lower in colder climates. This study undertook high resolution temporal ammonia measurements in the field and coupled results with modelling to estimate NH3 emissions at a temperate puffin colony and two sub-polar penguin colonies (Signy Island, South Orkney Islands and Bird Island, South Georgia) during the breeding season. These emission rates are then compared with NH3 volatilization rates from other climates. Ammonia emissions were calculated using a Lagrangian atmospheric dispersion model, resulting in mean emissions of 5 μg m-2 s-1 at the Isle of May, 12 μg m-2 s-1 at Signy Island and 9 μg m-2 s-1 at Bird Island. The estimated percentage of total guano nitrogen volatilized was 5% on the Isle of May, 3% on Signy and 2% on Bird Island. These values are much smaller than the percentage of guano nitrogen volatilized in tropical contexts (31-65%). The study confirmed temperature, wind speed and water availability have a significant influence on the magnitude of NH3 emissions, which has implications for reactive nitrogen in both modern remote regions and pre-industrial atmospheric composition and ecosystem interactions

Characteristics of freshly deposited sand and finer sediments along an island-braided, gravel-bed river: the roles of water, wind and trees

Over the past two decades there has been a growing interest in the geomorphological mosaic along large floodplain rivers where channel dynamics are seen to drive habitat-patch creation and turnover and to contribute to high biological diversity. This has required a new perspective on fluvial geomorphology that focuses on biological scales of space and time. This study examines the spatial pattern of surface fine sediment accumulations along a reach of a large gravel-bed river, the Tagliamento River in NE Italy; an area with a moist Mediterranean climate and seasonal flow regime. The study investigates changes in sediment characteristics during the summer low-flow period between April and September. Focussing on five areas representing a gradient from open, bar-braided to wooded island-braided morphologies, the paper demonstrates the importance of riparian vegetation and aeolian–fluvial interactions. Significant contrasts in particle size distributions and organic content of freshly deposited sand and finer sediments were found between sampling areas, geomorphological settings, and sampling dates. In particular, wooded floodplain and established islands supported consistently finer sediment deposits than both open bar surfaces and the lee of pioneer islands, and in September significantly finer sediments were also found in deposits located in the lee of pioneer islands than on open bar surfaces. Overall, the September samples had a greater variability in particle size characteristics than those obtained from the same sites in April, with a general coarsening of the D5 (φ) (i.e., the coarse tail of the particle size distribution). Also in September, crusts of fine sediment (30 μm < D50 < 64 μm) had formed on the surface of some of the open bar and pioneer island deposits within the more open sampling areas along the study reach. These crusts possessed similar particle size characteristics to aeolian crusts found in more arid environments. They were significantly finer than April samples and September subcrust samples obtained from the same sites and had similar particle size characteristics to some samples taken from wooded floodplain, established island surfaces and the lee of pioneer islands that were not crusted. Local climatological and river level data confirm significant wind and rainfall events during a period of consistently low river levels between the April and September sampling periods. These support deflation, deposition and rain wash of finer sediment during the summer, with windblown sediments being deposited on bar surfaces and in the lee of pioneer islands where wood and young trees provide foci for accelerated sedimentation and island growth as well as on marginal floodplains and established islands. We conclude that along braided rivers in moist settings but with a distinct dry season, aeolian reworking of sediment deposits may have a more important role in driving habitat dynamics than previously considered

Sub-Antarctic marine aerosol: significant contributions from biogenic sources

Biogenic influences on the composition and characteristics of aerosol were investigated on Bird Island (54°00' S, 38°03' W) in the South Atlantic during November and December 2010. This remote marine environment is characterised by large seabird and seal colonies. The chemical composition of the submicron particles, measured by an aerosol mass spectrometer (AMS), was 21% non-sea-salt sulfate, 2% nitrate, 8% ammonium, 22% organics and 47% sea salt including sea salt sulfate. A new method to isolate the sea spray signature from the high-resolution AMS data was applied. Generally, the aerosol was found to be less acidic than in other marine environments due to the high availability of ammonia, from local fauna emissions. By positive matrix factorisation five different organic aerosol (OA) profiles could be isolated: an amino acid/amine factor (AA-OA, 18% of OA mass), a methanesulfonic acid OA factor (MSA-OA, 25%), a marine oxygenated OA factor (M-OOA, 41%), a sea spray OA fraction (SS-OA, 7%) and locally produced hydrocarbon-like OA (HOA, 9%). The AA-OA was dominant during the first two weeks of November and found to be related with the hatching of penguins in a nearby colony. This factor, rich in nitrogen (N : C ratio = 0.13), has implications for the biogeochemical cycling of nitrogen in the area as particulate matter is often transported over longer distances than gaseous N-rich compounds. The MSA-OA was mainly transported from more southerly latitudes where phytoplankton bloomed. The bloom was identified as one of three sources for particulate sulfate on Bird Island, next to sea salt sulfate and sulfate transported from South America. M-OOA was the dominant organic factor and found to be similar to marine OA observed at Mace Head, Ireland. An additional OA factor highly correlated with sea spray aerosol was identified (SS-OA). However, based on the available data the type of mixture, internal or external, could not be determined. Potassium was not associated with sea salt particles during 19% of the time, indicating the presence of biogenic particles in addition to the MSA-OA and AA-OA factors

The global distribution of ammonia emissions from seabird colonies

Seabird colonies represent a significant source of atmospheric ammonia (NH3) in remote maritime systems, producing a source of nitrogen that may encourage plant growth, alter terrestrial plant community composition and affect the surrounding marine ecosystem. To investigate seabird NH3 emissions on a global scale, we developed a contemporary seabird database including a total seabird population of 261 million breeding pairs. We used this in conjunction with a bioenergetics model to estimate the mass of nitrogen excreted by all seabirds at each breeding colony. The results combined with the findings of mid-latitude field studies of volatilization rates estimate the global distribution of NH3 emissions from seabird colonies on an annual basis. The largest uncertainty in our emission estimate concerns the potential temperature dependence of NH3 emission. To investigate this we calculated and compared temperature independent emission estimates with a maximum feasible temperature dependent emission, based on the thermodynamic dissociation and solubility equilibria. Using the temperature independent approach, we estimate global NH3 emissions from seabird colonies at 404 Gg NH3 per year. By comparison, since most seabirds are located in relatively cold circumpolar locations, the thermodynamically dependent estimate is 136 Gg NH3 per year. Actual global emissions are expected to be within these bounds, as other factors, such as non-linear interactions with water availability and surface infiltration, moderate the theoretical temperature response. Combining sources of error from temperature (±49%), seabird population estimates (±36%), variation in diet composition (±23%) and non-breeder attendance (±13%), gives a mid estimate with an overall uncertainty range of NH3 emission from seabird colonies of 270 [97–442] Gg NH3 per year. These emissions are environmentally relevant as they primarily occur as “hot-spots” in otherwise pristine environments with low anthropogenic emissions

Genetic analysis of a plasmid encoding haemocin production in Haemophilus paragallinarum

The full sequence of plasmid p250, isolated from Haemophilus paragallinarum strain HP250, has been obtained. The plasmid contains seven ORFs: a putative integrase, a putative replication protein (repB) and five ORFs similar to those from the haemocin (bacteriocin) hmcDCBAI operon from Haemophilus influenzae. Of 19 other non-plasmid-containing H. paragallinarum strains screened (11 serovar reference strains and 8 field isolates), 17 strains produced haemocin and were resistant to killing by strain HP250. These strains, unlike strain HP250, have a chromosomally encoded haemocin operon. A number of other members of the family Pasteurellaceae were tested for haemocin sensitivity. Pasteurella avium, Pasteurella volantium and Pasteurella species A, all non-pathogenic bacteria found in the respiratory tract of chickens suffering from respiratory diseases, were sensitive to H. paragallinarum haemocin. However, amongst the pathogenic Pasteurellaceae, 50 % of P. multocida isolates and all five isolates of Pasteurella haemolytica tested were sensitive to the haemocin. Given the prevalence of haemocin production in H. paragallinarum strains, it may play a role in aiding colonization by inhibiting other Gram-negative bacteria that are associated with the respiratory tract in chickens. The origin of replication from plasmid p250 has been used to generate an Escherichia coli–H. paragallinarum shuttle vector which may be useful in genetically manipulating H. paragallinarum

Genetic analysis of a plasmid encoding haemocin production in Haemophilus paragallinarum

The full sequence of plasmid p250, isolated from Haemophilus paragallinarum strain HP250, has been obtained. The plasmid contains seven ORFs: a putative integrase, a putative replication protein (repB) and five ORFs similar to those from the haemocin (bacteriocin) hmcDCBAI operon from Haemophilus influenzae. Of 19 other non-plasmid-containing H. paragallinarum strains screened (11 serovar reference strains and 8 field isolates), 17 strains produced haemocin and were resistant to killing by strain HP250. These strains, unlike strain HP250, have a chromosomally encoded haemocin operon. A number of other members of the family Pasteurellaceae were tested for haemocin sensitivity. Pasteurella avium, Pasteurella volantium and Pasteurella species A, all non-pathogenic bacteria found in the respiratory tract of chickens suffering from respiratory diseases, were sensitive to H. paragallinarum haemocin. However, amongst the pathogenic Pasteurellaceae, 50 % of P. multocida isolates and all five isolates of Pasteurella haemolytica tested were sensitive to the haemocin. Given the prevalence of haemocin production in H. paragallinarum strains, it may play a role in aiding colonization by inhibiting other Gram-negative bacteria that are associated with the respiratory tract in chickens. The origin of replication from plasmid p250 has been used to generate an Escherichia coli–H. paragallinarum shuttle vector which may be useful in genetically manipulating H. paragallinarum

The imaging science journal

White syndromes (WS) are among the most prevalent coral diseases, and are responsible for reef demise on the Great Barrier Reef. The disease manifests as a clear differentiation between tissue and exposed skeleton and results in rapid tissue loss. Fluorescence in situ hybridisation (FISH) was used in conjunction with histology and transmission electron microscopy (TEM) to investigate bacterial communities and cell death associated with WS. No evidence of bacterial communities or microbial association (using six bacterial probes, TEM and histopathology) was evident within the lesion or adjacent tissues, despite the presence of dense possible secondary invaders in the exposed skeletal regions. Despite widespread reference to necrosis in coral disease literature, there was no evidence of necrosis in any WS lesion or the adjacent tissues in this study. However, in situ end labelling, light microscopy and TEM of WS and healthy coral tissue sections showed evidence of extensive programmed cell death (PCD) exclusively in WS. This study provides the first evidence of intrinsic or PCD as a primary mechanism of cell death in WS, and may provide some explanation for the failure to isolate pathogens from over 80% of identified coral diseases, many of which show similar lesion patterns and WS characteristics

Measurement of ammonia emissions from tropical seabird colonies

The excreta (guano) of seabirds at their breeding colonies represents a notable source of ammonia (NH3) emission to the atmosphere, with effects on surrounding ecosystems through nitrogen compounds being thereby transported from sea to land. Previous measurements in temperate UK conditions quantified emission hotspots and allowed preliminary global upscaling. However, thermodynamic processes and water availability limit NH3 formation from guano, which suggests that the proportion of excreted nitrogen that volatilizes as NH3 may potentially be higher at tropical seabird colonies than similar colonies in temperate or sub-polar regions. To investigate such differences, we measured NH3 concentrations and environmental conditions at two tropical seabird colonies during the breeding season: a colony of 20,000 tern spp. and noddies on Michaelmas Cay, Great Barrier Reef, and a colony of 200,000 Sooty terns on Ascension Island, Atlantic Ocean. At both sites time-integrated NH3 concentrations and meteorological parameters were measured. In addition, at Ascension Island, semi-continuous hourly NH3 concentrations and micrometeorological parameters were measured throughout the campaign. Ammonia emissions, quantified using a backwards Lagrangian atmospheric dispersion model, were estimated at 21.8 μg m−2 s−1 and 18.9 μg m−2 s−1 from Michaelmas Cay and Ascension Island, respectively. High temporal resolution NH3 data at Ascension Island estimated peak hourly emissions up to 377 μg NH3 m2 s−1. The estimated percentage fraction of total guano nitrogen volatilized was 67% at Michaelmas Cay and 32% at Ascension Island, with the larger value at the former site attributed to higher water availability. These values are much larger than published data for sub-polar locations, pointing to a substantial climatic dependence on emission of atmospheric NH3 from seabird colonies

Molecular analysis of a haemagglutinin of Haemophilus paragallinarum

The gene encoding a haemagglutinin of H. paragallinarum, hagA, has been identified and the full-length nucleotide sequence determined. A 39 kDa protein, recognized by an anti-haemagglutinin monoclonal antibody, mAb4D, was purified from H. paragallinarum strain 0083 and the N-terminal sequence obtained. The full-length nucleotide sequence was obtained by inverse PCR and the deduced amino acid sequence of the protein encoded was shown to be similar to other outer-membrane proteins of closely related organisms in the HAP group (Haemophilus, Actinobacillus, Pasteurella), especially the P5 protein of Haemophilus influenzae. The hagA gene was cloned into a His-tag expression vector and overexpressed in Escherichia coli strain M15(pREP4). The identity of the purified recombinant protein as a H. paragallinarum haemagglutinin was confirmed by haemagglutination of chicken red blood cells and reactivity, in a Western blot, with the monoclonal antibody specific for the serovar A haemagglutinin