Evaluation of a photosynthesis-based biogenic isoprene emission scheme in JULES and simulation of isoprene emissions under present-day climate conditions

We have incorporated a semi-mechanistic isoprene emission module into the JULES land-surface scheme, as a first step towards a modelling tool that can be applied for studies of vegetation – atmospheric chemistry interactions, including chemistry-climate feedbacks. Here, we evaluate the coupled model against local above-canopy isoprene emission flux measurements from six flux tower sites as well as satellite-derived estimates of isoprene emission over tropical South America and east and south Asia. The model simulates diurnal variability well: correlation coefficients are significant (at the 95 % level) for all flux tower sites. The model reproduces day-to-day variability with significant correlations (at the 95 % confidence level) at four of the six flux tower sites. At the UMBS site, a complete set of seasonal observations is available for two years (2000 and 2002). The model reproduces the seasonal pattern of emission during 2002, but does less well in the year 2000. The model overestimates observed emissions at all sites, which is partially because it does not include isoprene loss through the canopy. Comparison with the satellite-derived isoprene-emission estimates suggests that the model simulates the main spatial patterns, seasonal and inter-annual variability over tropical regions. The model yields a global annual isoprene emission of 535 ± 9 TgC yr−1 during the 1990s, 78 % of which from forested areas.

BAECC: a field campaign to elucidate the impact of Biogenic Aerosols on Clouds and Climate

Observations obtained during an 8-month deployment of AMF2 in a boreal environment in Hyytiälä, Finland, and the 20-year comprehensive in-situ data from SMEAR-II station enable the characterization of biogenic aerosol, clouds and precipitation, and their interactions. During “Biogenic Aerosols - Effects on Clouds and Climate (BAECC)”, the U.S. Department of Energy’s Atmospheric Radiation Measurement (ARM) Program deployed the ARM 2nd Mobile Facility (AMF2) to Hyytiälä, Finland, for an 8-month intensive measurement campaign from February to September 2014. The primary research goal is to understand the role of biogenic aerosols in cloud formation. Hyytiälä is host to SMEAR-II (Station for Measuring Forest Ecosystem-Atmosphere Relations), one of the world’s most comprehensive surface in-situ observation sites in a boreal forest environment. The station has been measuring atmospheric aerosols, biogenic emissions and an extensive suite of parameters relevant to atmosphere-biosphere interactions continuously since 1996. Combining vertical profiles from AMF2 with surface-based in-situ SMEAR-II observations allow the processes at the surface to be directly related to processes occurring throughout the entire tropospheric column. Together with the inclusion of extensive surface precipitation measurements, and intensive observation periods involving aircraft flights and novel radiosonde launches, the complementary observations provide a unique opportunity for investigating aerosol-cloud interactions, and cloud-to-precipitation processes, in a boreal environment. The BAECC dataset provides opportunities for evaluating and improving models of aerosol sources and transport, cloud microphysical processes, and boundary-layer structures. In addition, numerical models are being used to bridge the gap between surface-based and tropospheric observations.

Rainforest Aerosols as Biogenic Nuclei of Clouds and Precipitation in the Amazon

The Amazon is one of the few continental regions where atmospheric aerosol particles and their effects on climate are not dominated by anthropogenic sources. During the wet season, the ambient conditions approach those of the pristine pre-industrial era. We show that the fine submicrometer particles accounting for most cloud condensation nuclei are predominantly composed of secondary organic material formed by oxidation of gaseous biogenic precursors. Supermicrometer particles, which are relevant as ice nuclei, consist mostly of primary biological material directly released from rainforest biota. The Amazon Basin appears to be a biogeochemical reactor, in which the biosphere and atmospheric photochemistry produce nuclei for clouds and precipitation sustaining the hydrological cycle. The prevailing regime of aerosol-cloud interactions in this natural environment is distinctly different from polluted regions.

Stereochemical transfer to atmospheric aerosol particles accompanying the oxidation of biogenic volatile organic compounds

Asymmetric emission profiles of the stereoisomers of plant-derived volatile organic compounds vary with season, geography, plant type, and stress factors. After oxidation of these compounds in the atmosphere, the low-vapor pressure products ultimately contribute strongly to the particle-phase material of the atmosphere. In order to explore the possibility of stereochemical transfer to atmospheric aerosol particles during the oxidation of biogenic volatile organic compounds, second-order coherent vibrational spectra were recorded of the particle-phase organic material produced by the oxidation of different stereoisomeric mixes of alpha-pinene. The spectra show that the stereochemical configurations are not scrambled but instead are transferred from the gas-phase molecular precursors to the particle-phase molecules. The spectra also show that oligomers formed in the particle phase have a handed superstructure that depends strongly and nonlinearly on the initial stereochemical composition of the precursors. Because the stereochemical mix of the precursors for a material can influence the physical and chemical properties of that material, our findings suggest that chirality is also important for such properties of plant-derived aerosol particles. Citation: Ebben, C. J., S. R. Zorn, S.-B. Lee, P. Artaxo, S. T. Martin, and F. M. Geiger (2011), Stereochemical transfer to atmospheric aerosol particles accompanying the oxidation of biogenic volatile organic compounds, Geophys. Res. Lett., 38, L16807, doi: 10.1029/2011GL048599.

Mass spectral characterization of submicron biogenic organic particles in the Amazon Basin

Submicron atmospheric particles in the Amazon Basin were characterized by a high-resolution aerosol mass spectrometer during the wet season of 2008. Patterns in the mass spectra closely resembled those of secondary-organic-aerosol (SOA) particles formed in environmental chambers from biogenic precursor gases. In contrast, mass spectral indicators of primary biological aerosol particles (PBAPs) were insignificant, suggesting that PBAPs contributed negligibly to the submicron fraction of particles during the period of study. For 40% of the measurement periods, the mass spectra indicate that in-Basin biogenic SOA production was the dominant source of the submicron mass fraction, contrasted to other periods (30%) during which out-of-Basin organic-carbon sources were significant on top of the baseline in-Basin processes. The in-Basin periods had an average organic-particle loading of 0.6 mu g m(-3) and an average elemental oxygen-to-carbon (O:C) ratio of 0.42, compared to 0.9 mu g m(-3) and 0.49, respectively, during periods of out-of-Basin influence. On the basis of the data, we conclude that most of the organic material composing submicron particles over the Basin derived from biogenic SOA production, a finding that is consistent with microscopy observations made in a concurrent study. This source was augmented during some periods by aged organic material delivered by long-range transport. Citation: Chen, Q., et al. (2009), Mass spectral characterization of submicron biogenic organic particles in the Amazon Basin, Geophys. Res. Lett., 36, L20806, doi: 10.1029/2009GL039880.

Relative roles of biogenic emissions and Saharan dust as ice nuclei in the Amazon basin

Some aerosol particles, known as ice nuclei, can initiate ice formation in clouds, thereby influencing precipitation, cloud dynamics and the amount of incoming and outgoing solar radiation. In the absence of biomass burning, aerosol mass concentrations in the Amazon basin are low(1). Tropical forests emit primary biological particles directly into the atmosphere; secondary organic aerosols form from the emission and oxidation of biogenic gases(2). In addition, particles derived from biomass burning in central Africa, marine aerosols, and windblown dust from North Africa(3-5) often reach the central part of the Amazon basin during the wet season. The contribution of these aerosol sources to ice nucleation in the region is uncertain. Here we present observations of the concentration and elemental composition of ice nuclei in the Amazon basin during the wet season. Using transmission electron microscopy combined with energy-dispersive X-ray spectroscopy, we show that ice nuclei are primarily composed of carbonaceous material and dust. We show that biological particles dominate the carbonaceous fraction, whereas import of Saharan dust explains the intermittent appearance of dust-containing nuclei. We conclude that ice-nucleus concentration and abundance can be explained almost entirely by local emissions of biological particles supplemented by import of Saharan dust. Using a simple model, we tentatively suggest that the contribution of local biological particles to ice nucleation is increased at higher atmospheric temperatures, whereas the contribution of dust particles is increased at lower temperatures.

Determination of anthropogenic and biogenic compounds on atmospheric aerosol collected in urban, biomass burning and forest areas in Sao Paulo, Brazil

This study was conducted at three sites of different characteristics in Sao Paulo State Sao Paulo (SPA), Piracicaba (PRB) and Mate Atlantica Forest (MAT) PM(10), n-alkanes. pristane and phytane, PAHs, water-soluble ions and biomass burning tracers like levoglucosan and retene, were determined in quartz fiber filters. Samplings occurred on May 8th to August 8th, 2007 at the MAT site; on August 15th to 29th in 2007 and November 10th to 29th in 2008 at the PRB site and, March 13th to April 4th in 2007 and August 7th to 29th in 2008 at the SPA site Aliphatic compounds emitted biogenically were less abundant at the urban sites than at the forest site, and its distribution showed the influence of tropical vascular plants Air mass transport front biomass burning regions is likely to impact the sites with specific molecular markers The concentrations of all species were variable and dependent of seasonal changes In the most dry and polluted seasons, n-alkane and canon total concentrations were similar between the megacity and the biomass burning site PAHs and inorganic ion abundances were higher at Sao Paulo than Piracicaba, yet, the site influenced by biomass burning seems lobe the most impacted by the organic anion abundance in the atmosphere Pristane and phytane confirm the contamination by petroleum residues at urban sites, at the MAT site, biological activity and long range transport of pollutants might influence the levels of pristane (C) 2010 Elsevier B V All rights reserved

Simultaneous analysis of free amino acids and biogenic amines in honey and wine samples using in loop orthophthalaldeyde derivatization procedure

This work presents a RP-HPLC method for the simultaneous quantification of free amino acids and biogenic amines in liquid food matrices and the results of the application to honey and wine samples obtained from different production processes and geographic origins. The developed methodology is based on a pre-column derivatization with o-phthaldialdehyde carried out in the sample injection loop. The compounds were separated in a Nova-Pack RP-C18 column (150 mm × 3.9 mm, 4 μm) at 35 °C. The mobile phase used was a mixture of phase A: 10 mM sodium phosphate buffer (pH 7.3), methanol and tetrahydrofuran (91:8:1); and phase B: methanol and phosphate buffer (80:20), with a flow rate of 1.0 ml/min. Fluorescence detection was used at an excitation wavelength of 335 nm and an emission wavelength of 440 nm. The separation and quantification of 19 amino acids and 6 amines was carried out in a single run as their OPA/MCE derivatives elute within 80 min, ensuring a reproducible quantification. The method showed to be adequate for the purpose, with an average RSD of 2% for the different amino acids; detection limits varying between 0.71 mg/l (Asn) and 8.26 mg/l (Lys) and recovery rates between 63.0% (Cad) and 98.0% (Asp). The amino acids present at the highest concentration in honey and wine samples were phenylalanine and arginine, respectively. Only residual levels of biogenic amines were detected in the analysed samples.

Caracterização do nicho alimentar do polvo octopus insularis (cephalopoda: octopodidae): da população ao indivíduo

Octopus insularis, target species in this study, is the dominant benthic octopus of the North and Northeast Brazil. Studies on behavior and ecology of the species have been conducted primarily on oceanic islands, with little information on the continental populations. In this study, two regions of the coast of RN, Rio do Fogo and Pirangi, were chosen for the characterization of the niche by O. insularis populations. The dietary niche, habitat and distribution of O. insularis of oceanic islands and the mainland, were compared. In addition, individual characteristics of feeding behavior in a population at Atol das Rocas was studied, taking into account the size of individuals, the proximity of the dens and characteristics of their "personality". The diet of the Rio do Fogo population was composed mainly of bivalve molluscs (82%), unlike Pirangi population that has a diet consisting mainly of crustaceans Decapoda (68%), similar to that described for the populations of the islands. Consequently, the feeding niches of the island populations were more similar, with greater overlap, but the niche breadth of the continent was larger. The habitats of occurrence on the coast includes reefs, rocks, gravel and an environment called Restinga, a plateau composed of biogenic gravel, sand, sponges and algae, showed a high density of animals. Similarly to that found in the islands, O. insularis in the continent, had a clumped distribution, and a bathymetric segregation between small and large individuals. The differences in diet composition among populations were explained by differences in habitat and coverage of the substrate, which may be directly influencing the diversity and prey availability in these environments. The individual analyzes of the population at Atol das Rocas, showed no relationship between the degree of individual specialization and the different personalities, or the distance between dens. The results suggest that the foraging strategy with greater availability of prey in the environment has an influence on diet octopuses over preferences or personalities

Caracterização Morfodinâmica e Sedimentologia da Plataforma Continental Rasa na APA Estadual dos Recifes de Corais - RN

This study had to aimed to characterize the sediments of shallow continental shelf and realize the mapping of features visible for satellite images by using remote sensing techniques, digital image processing and analysis of bathymetry between Maxaranguape and Touros - RN. The study s area is located in the continental shallow shelf of Rio Grande do Norte, Brazil, and is part of the Environmental Protection Area (APA) of Coral Reefs. A total of 1186 sediment samples were collected using a dredge type van veen and positioning of the vessel was made out with the aid of a Garmin 520s. The samples were treated In the laboratory to analyze particle size of the sediment, concentration of calcium carbonate and biogenic composition. The digital images from the Landsat-5 TM were used to mapping of features. This stage was used the band 1 (0,45-1,52 μm) where the image were georeferenced, and then adjusting the histogram, giving a better view of feature bottom and contacts between different types of bottom. The results obtained from analysis of the sediment showed that the sediments of the continental shelf east of RN have a dominance of carbonate facies and a sand-gravelly bottom because the region is dominated by biogenic sediments, that are made mainly of calcareous algae. The bedform types identified and morphological features found were validated by bathymetric data and sediment samples examined. From the results obtained a division for the shelf under study is suggested, these regions being subdivided, in well characterized: (1) Turbid Zone, (2) Coral Patch Reefs Zone, (3) Mixed Sediments Carbonates Zone, ( 4) Algae Fouling Zone, (5) Alignment Rocky Zone, (6) Sand Waves Field (7) Deposit siliciclastic sands

Population structure and breeding period of Pachycheles monilifer (Dana) (Anomura, Porcellanidae) inhabiting sabellariid sand reefs from the littoral coast of São Paulo State, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Daily cleaning activity and diversity of clients of the barber goby, Elacatinus figaro, on rocky reefs in southeastern Brazil

Gobies of the genus Elacatinus are regarded as the most specialised cleaner fishes in the western tropical Atlantic, yet there are no studies on these cleaners in the southern portion of West Atlantic. We studied the diversity of clients and the daily cleaning activity of the barber goby, Elacatinus figaro, on rocky reefs in southeastern Brazil (23-24 degrees S). A total of 34 fish client species in 16 families were recorded over 484 cleaning events. The most frequent clients were damselfishes, Pomacentridae (37.9% of cleaning events) and grunts, Haemulidae (16.9%). Planktivores were the most frequently attended trophic category, and two species in that category accounted for about a half (44%) of the total cleaning events. Size of clients ranged 4.5-55 cm and most individuals were medium-sized (12-30 cm); as the barber goby ranged 2-4.5 cm, clients were 1.5 to 15 times larger than the cleaner was. Cleaning activity started at dawn and ended shortly before nightfall, the highest frequency of interactions occurring at early morning (nocturnal clients) and mid-afternoon (diurnal clients). By midday the frequency of cleaning events decreased and their duration increased. A total of 109 +/- 3 cleaning events and 30 +/- 1 min of cleaning activity were estimated per cleaning station per day, both figures low when compared to those recorded for cleaner fishes in tropical areas of the western Atlantic and Indo-Pacific.

Aerosol and precipitation chemistry measurements in a remote site in Central Amazonia: the role of biogenic contribution

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Influence of artificial reefs on fish assemblage of the Barra Bonita Reservoir (São Paulo, Brazil)

This paper deals with the effects of introduced artificial reefs on the diversity of freshwater fish communities in lentic and lotic zones of a very impacted river in southeastern Brazil. To accomplish this goal, artificial reefs were introduced, in December 1997, in the Barra Bonita reservoir and in the lotic zone immediately below the dam. Fish diversity was always higher in the lotic zone than in the reservoir. Accordingly, fish diversity near the artificial reefs was consistently higher than in the control areas. We propose that the higher environmental complexity in the lotic zone, as compared to the reservoir, is incremented in areas where artificial reefs were introduced; also, we present that, in both areas, diversity is mainly affected by the introduction of artificial reefs.

Artificial reefs and their effects on fish assemblages in a Brazilian reservoir and Tailrace

In this paper, we evaluate the effects of artificial reefs on fish assemblages in a hypereutrophic reservoir and in the lotic zone immediately below dam. Fish diversity was highest in the lotic zone relative to the reservoir. We also found an inverse relationship between diversity and distance from the river margin. Catches near the artificial reefs were more diverse than in control areas. A seasonal effect, possibly caused by variation in temperature, was significant in all comparisons. We argue that, in a scale of local effects, the ecological function of these structures would be similar to refuges.