Urban energy fluxes in Helsinki and their high frequency spectral corrections

Inadvertent climate modification has led to an increase in urban temperatures compared to the surrounding rural area. The main reason for the temperature rise is the altered energy portioning of input net radiation to heat storage and sensible and latent heat fluxes in addition to the anthropogenic heat flux. The heat storage flux and anthropogenic heat flux have not yet been determined for Helsinki and they are not directly measurable. To the contrary, turbulent fluxes of sensible and latent heat in addition to net radiation can be measured, and the anthropogenic heat flux together with the heat storage flux can be solved as a residual. As a result, all inaccuracies in the determination of the energy balance components propagate to the residual term and special attention must be paid to the accurate determination of the components. One cause of error in the turbulent fluxes is the fluctuation attenuation at high frequencies which can be accounted for by high frequency spectral corrections. The aim of this study is twofold: to assess the relevance of high frequency corrections to water vapor fluxes and to assess the temporal variation of the energy fluxes. Turbulent fluxes of sensible and latent heat have been measured at SMEAR III station, Helsinki, since December 2005 using the eddy covariance technique. In addition, net radiation measurements have been ongoing since July 2007. The used calculation methods in this study consist of widely accepted eddy covariance data post processing methods in addition to Fourier and wavelet analysis. The high frequency spectral correction using the traditional transfer function method is highly dependent on relative humidity and has an 11% effect on the latent heat flux. This method is based on an assumption of spectral similarity which is shown not to be valid. A new correction method using wavelet analysis is thus initialized and it seems to account for the high frequency variation deficit. Anyhow, the resulting wavelet correction remains minimal in contrast to the traditional transfer function correction. The energy fluxes exhibit a behavior characteristic for urban environments: the energy input is channeled to sensible heat as latent heat flux is restricted by water availability. The monthly mean residual of the energy balance ranges from 30 Wm-2 in summer to -35 Wm-2 in winter meaning a heat storage to the ground during summer. Furthermore, the anthropogenic heat flux is approximated to be 50 Wm-2 during winter when residential heating is important.

Archaea, Bacteria, and methane production along environmental gradients in fens and bogs

Metanogeenit ovat hapettomissa oloissa eläviä arkkien pääryhmään kuuluvia mikrobeja, joiden ainutlaatuisen aineenvaihdunnan seurauksena syntyy metaania. Ilmakehässä metaani on voimakas kasvihuonekaasu. Yksi suurimmista luonnon metaanilähteistä ovat kosteikot. Pohjoisten soiden metaanipäästöt vaihtelevat voimakkaasti eri soiden välillä ja yhden suon sisälläkin, riippuen muun muassa vuodenajasta, suotyypistä ja kasvillisuudesta. Väitöskirjatyössä tutkittiin metaanipäästöjen vaihtelun mikrobiologista taustaa. Tutkimuksessa selvitettiin suotyypin, vuodenajan, tuhkalannoituksen ja turvesyvyyden vaikutusta metanogeeniyhteisöihin sekä metaanintuottoon kolmella suomalaisella suolla. Lisäksi tutkittiin ei-metanogeenisia arkkeja ja bakteereita, koska ne muodostavat metaanin tuoton lähtöaineet osana hapetonta hajotusta. Mikrobiyhteisöt analysoitiin DNA- ja RNA-lähtöisillä, polymeraasiketjureaktioon (PCR) perustuvilla menetelmillä. Merkkigeeneinä käytettiin metaanin tuottoon liittyvää mcrA-geeniä sekä arkkien ja bakteerien ribosomaalista 16S RNA-geeniä. Metanogeeniyhteisöt ja metaanintuotto erosivat huomattavasti happaman ja vähäravinteisen rahkasuon sekä ravinteikkaampien sarasoiden välillä. Rahkasuolta löytyi lähes yksinomaan Methanomicrobiales-lahkon metanogeeneja, jotka tuottavat metaania vedystä ja hiilidioksidista. Sarasoiden metanogeeniyhteisöt olivat monimuotoisempia, ja niillä esiintyi myös asetaattia käyttäviä metanogeeneja. Vuodenaika vaikutti merkittävästi metaanintuottoon. Talvella havaittiin odottamattoman suuri metaanintuottopotentiaali sekä viitteitä aktiivisista metanogeeneista. Arkkiyhteisön koostumus sen sijaan vaihteli vain vähän. Tuhkalannoitus, jonka tarkoituksena on edistää puiden kasvua ojitetuilla soilla, ei merkittävästi vaikuttanut metaanintuottoon tai -tuottajiin. Ojitetun suon yhteisöt kuitenkin muuttuivat turvesyvyyden mukaan. Vertailtaessa erilaisia PCR-menetelmiä todettiin, että kolmella mcrA-geeniin kohdistuvalla alukeparilla havaittiin pääosin samat ojitetun suon metanogeenit, mutta lajien runsaussuhteet riippuvat käytetyistä alukkeista. Soilla havaitut bakteerit kuuluivat pääjaksoihin Deltaproteobacteria, Acidobacteria ja Verrucomicrobia. Lisäksi löydettiin Crenarchaeota-pääjakson ryhmiin 1.1c ja 1.3 kuuluvia ei-metanogeenisia arkkeja. Tulokset ryhmien esiintymisestä hapettomassa turpeessa antavat lähtökohdan selvittää niiden mahdollisia vuorovaikutuksia metanogeenien kanssa. Tutkimuksen tulokset osoittivat, että metanogeeniyhteisön koostumus heijastaa metaanintuottoon vaikuttavia kemiallisia tai kasvillisuuden vaihteluita kuten suotyyppiä. Soiden metanogeenien ja niiden fysiologian parempi tuntemus voi auttaa ennustamaan ympäristömuutosten vaikutusta soiden metaanipäästöihin.

Coastal environmental gradients – Key to reproduction habitat mapping of freshwater fish in the Baltic Sea

Habitat requirements of fish are most strict during the early life stages, and the quality and quantity of reproduction habitats lays the basis for fish production. A considerable number of fish species in the northern Baltic Sea reproduce in the shallow coastal areas, which are also the most heavily exploited parts of the brackish marine area. However, the coastal fish reproduction habitats in the northern Baltic Sea are poorly known. The studies presented in this thesis focused on the influence of environmental conditions on the distribution of coastal reproduction habitats of freshwater fish. They were conducted in vegetated littoral zone along an exposure and salinity gradient extending from the innermost bays to the outer archipelago on the south-western and southern coasts of Finland, in the northern Baltic Sea. Special emphasis was placed on reed-covered Phragmites australis shores, which form a dominant vegetation type in several coastal archipelago areas. The main aims of this research were to (1) develop and test new survey and mapping methods, (2) investigate the environmental requirements that govern the reproduction of freshwater fish in the coastal area and (3) survey, map and model the distribution of the reproduction habitats of pike (Esox lucius) and roach (Rutilus rutilus). The white plate and scoop method with a standardized sampling time and effort was demonstrated to be a functional method for sampling the early life stages of fish in dense vegetation and shallow water. Reed-covered shores were shown to form especially important reproduction habitats for several freshwater fish species, such as pike, roach, other cyprinids and burbot, in the northern Baltic Sea. The reproduction habitats of pike were limited to sheltered reed- and moss-covered shores of the inner and middle archipelago, where suitable zooplankton prey were available and the influence of the open sea was low. The reproduction habitats of roach were even more limited and roach reproduction was successful only in the very sheltered reed-covered shores of the innermost bay areas, where salinity remained low (< 4‰) during the spawning season due to freshwater inflow. After identifying the critical factors restricting the reproduction of pike and roach, the spatial distribution of their reproduction habitats was successfully mapped and modelled along the environmental gradients using only a few environmental predictor variables. Reproduction habitat maps are a valuable tool promoting the sustainable use and management of exploited coastal areas and helping to maintain the sustainability of fish populations. However, the large environmental gradients and the extensiveness of the archipelago zone in the northern Baltic Sea demand an especially high spatial resolution of the coastal predictor variables. Therefore, the current lack of accurate large-scale, high-resolution spatial data gathered at exactly the right time is a considerable limitation for predictive modelling of shallow coastal waters.

Spectral Tuning and Adaptation to Different Light Environments of Mysid Visual Pigments

In the present thesis, questions of spectral tuning, the relation of spectral and thermal properties of visual pigments, and evolutionary adaptation to different light environments were addressed using a group of small crustaceans of the genus Mysis as a model. The study was based on microspectrophotometric measurements of visual pigment absorbance spectra, electrophysiological measurements of spectral sensitivities of dark-adapted eyes, and sequencing of the opsin gene retrieved through PCR. The spectral properties were related to the spectral transmission of the respective light environments, as well as to the phylogentic histories of the species. The photoactivation energy (Ea) was estimated from temperature effects on spectral sensitivity in the long-wavelength range, and calculations were made for optimal quantum catch and optimal signal-to-noise ratio in the different light environments. The opsin amino acid sequences of spectrally characterized individuals were compared to find candidate residues for spectral tuning. The general purpose was to clarify to what extent and on what time scale adaptive evolution has driven the functional properties of (mysid) visual pigments towards optimal performance in different light environments. An ultimate goal was to find the molecular mechanisms underlying the spectral tuning and to understand the balance between evolutionary adaptation and molecular constraints. The totally consistent segregation of absorption maxima (λmax) into (shorter-wavelength) marine and (longer-wavelength) freshwater populations suggests that truly adaptive evolution is involved in tuning the visual pigment for optimal performance, driven by selection for high absolute visual sensitivity. On the other hand, the similarity in λmax and opsin sequence between several populations of freshwater M. relicta in spectrally different lakes highlights the limits to adaptation set by evolutionary history and time. A strong inverse correlation between Ea and λmax was found among all visual pigments studied in these respects, including those of M. relicta and 10 species of vertebrate pigments, and this was used to infer thermal noise. The conceptual signal-to-noise ratios thus calculated for pigments with different λmax in the Baltic Sea and Lake Pääjärvi light environments supported the notion that spectral adaptation works towards maximizing the signal-to-noise ratio rather than quantum catch as such. Judged by the shape of absorbance spectra, the visual pigments of all populations of M. relicta and M. salemaai used exclusively the A2 chromophore (3, 4-dehydroretinal). A comparison of amino acid substitutions between M. relicta and M. salemaai indicated that mysid shrimps have a small number of readily available tuning sites to shift between a shorter - and a longer -wavelength opsin. However, phylogenetic history seems to have prevented marine M. relicta from converting back to the (presumably) ancestral opsin form, and thus the more recent reinvention of marine spectral sensitivity has been accomplished by some other novel mechanism, yet to be found

Spectral states and accretion geometries in Galactic black hole binaries

Black hole X-ray binaries, binary systems where matter from a companion star is accreted by a stellar mass black hole, thereby releasing enormous amounts of gravitational energy converted into radiation, are seen as strong X-ray sources in the sky. As a black hole can only be detected via its interaction with its surroundings, these binary systems provide important evidence for the existence of black holes. There are now at least twenty cases where the measured mass of the X-ray emitting compact object in a binary exceeds the upper limit for a neutron star, thus inferring the presence of a black hole. These binary systems serve as excellent laboratories not only to study the physics of accretion but also to test predictions of general relativity in strongly curved space time. An understanding of the accretion flow onto these, the most compact objects in our Universe, is therefore of great importance to physics. We are only now slowly beginning to understand the spectra and variability observed in these X-ray sources. During the last decade, a framework has developed that provides an interpretation of the spectral evolution as a function of changes in the physics and geometry of the accretion flow driven by a variable accretion rate. This doctoral thesis presents studies of two black hole binary systems, Cygnus~X-1 and GRS~1915+105, plus the possible black hole candidate Cygnus~X-3, and the results from an attempt to interpret their observed properties within this emerging framework. The main result presented in this thesis is an interpretation of the spectral variability in the enigmatic source Cygnus~X-3, including the nature and accretion geometry of its so-called hard spectral state. The results suggest that the compact object in this source, which has not been uniquely identified as a black hole on the basis of standard mass measurements, is most probably a massive, ~30 Msun, black hole, and thus the most massive black hole observed in a binary in our Galaxy so far. In addition, results concerning a possible observation of limit-cycle variability in the microquasar GRS~1915+105 are presented as well as evidence of `mini-hysteresis' in the extreme hard state of Cygnus X-1.

Canopy processes, fluxes and microclimate in a pine forest

Interaction between forests and the atmosphere occurs by radiative and turbulent transport. The fluxes of energy and mass between surface and the atmosphere directly influence the properties of the lower atmosphere and in longer time scales the global climate. Boreal forest ecosystems are central in the global climate system, and its responses to human activities, because they are significant sources and sinks of greenhouse gases and of aerosol particles. The aim of the present work was to improve our understanding on the existing interplay between biologically active canopy, microenvironment and turbulent flow and quantify. In specific, the aim was to quantify the contribution of different canopy layers to whole forest fluxes. For this purpose, long-term micrometeorological and ecological measurements made in a Scots pine (Pinus sylvestris) forest at SMEAR II research station in Southern Finland were used. The properties of turbulent flow are strongly modified by the interaction between the canopy elements: momentum is efficiently absorbed in the upper layers of the canopy, mean wind speed and turbulence intensities decrease rapidly towards the forest floor and power spectra is modulated by spectral short-cut . In the relative open forest, diabatic stability above the canopy explained much of the changes in velocity statistics within the canopy except in strongly stable stratification. Large eddies, ranging from tens to hundred meters in size, were responsible for the major fraction of turbulent transport between a forest and the atmosphere. Because of this, the eddy-covariance (EC) method proved to be successful for measuring energy and mass exchange inside a forest canopy with exception of strongly stable conditions. Vertical variations of within canopy microclimate, light attenuation in particular, affect strongly the assimilation and transpiration rates. According to model simulations, assimilation rate decreases with height more rapidly than stomatal conductance (gs) and transpiration and, consequently, the vertical source-sink distributions for carbon dioxide (CO2) and water vapor (H2O) diverge. Upscaling from a shoot scale to canopy scale was found to be sensitive to chosen stomatal control description. The upscaled canopy level CO2 fluxes can vary as much as 15 % and H2O fluxes 30 % even if the gs models are calibrated against same leaf-level dataset. A pine forest has distinct overstory and understory layers, which both contribute significantly to canopy scale fluxes. The forest floor vegetation and soil accounted between 18 and 25 % of evapotranspiration and between 10 and 20 % of sensible heat exchange. Forest floor was also an important deposition surface for aerosol particles; between 10 and 35 % of dry deposition of particles within size range 10 30 nm occurred there. Because of the northern latitudes, seasonal cycle of climatic factors strongly influence the surface fluxes. Besides the seasonal constraints, partitioning of available energy to sensible and latent heat depends, through stomatal control, on the physiological state of the vegetation. In spring, available energy is consumed mainly as sensible heat and latent heat flux peaked about two months later, in July August. On the other hand, annual evapotranspiration remains rather stable over range of environmental conditions and thus any increase of accumulated radiation affects primarily the sensible heat exchange. Finally, autumn temperature had strong effect on ecosystem respiration but its influence on photosynthetic CO2 uptake was restricted by low radiation levels. Therefore, the projected autumn warming in the coming decades will presumably reduce the positive effects of earlier spring recovery in terms of carbon uptake potential of boreal forests.