Molecular phylogeny of Archaea in boreal forest soil, freshwater and temperate estuarine sediment

Suurin osa luonnossa havaitsemistamme mikrobeista on sellaisia, joita emme edelleenkään osaa kasvattaa laboratorio-oloissa, vaikka tietomme mikrobien monimuotoisuudesta paranevat koko ajan. Luonnontilaisen mikrobieliöstön kokoonpano eri ympäristöissä on paljolti epäselvä ja ymmärrämme vielä hyvin puutteellisesti mikrobien ekologiaa ja niiden rooleja eliöyhteisöissä. Nykyaikaiset molekulaariset tutkimusmenetelmät auttavat selvittämään mikrobien monimuotoisuutta kokonaisvaltaisesti ja nopeasti. Ympäristöstä kemiallisesti puhdistetut ribosomaalista RNA:ta koodaavat geenit edustavat periaatteessa kaikkia eliöyhteisön geneettisesti toisistaan poikkeavia eliöitä. Niistä voidaan valikoida halutut genomit jatkotutkimuksia varten. Uusien menetelmien käyttö on tuonut esiin sen merkittävän seikan, että "tavanomaisten" elinympäristöjen eliöyhteisöihin kuuluu suuri joukko entuudestaan tuntemattomia arkkieliöitä. Aiemmin kuviteltiin, että arkkieliöt asuttavat vain sellaisia "epätavallisia" tai "äärimmäisiä" elinympäristöjä, joita luonnehtii joku seuraavista ominaisuuksista: hyvin korkea lämpötila, korkea suolapitoisuus, korkea happamuus tai emäksisyys, hapettomuus. Tutkijat ovat viimeisen noin kymmenen vuoden aikana osoittaneet, että arkkieliöt asuttavat hyvin monenlaisia kylmän ja lauhkean vyöhykkeen ympäristöjä, yhtä hyvin maaperää kuin suolaisen ja makean veden pohjaa tai pintakerroksia. Nämä löydöt ovat avanneet uuden alun arkkieliöiden tutkimukselle, erityisesti sen selvittämiselle, mitkä ovat niiden fysiologiset ja ekologiset roolit monimuotoisissa mikrobiyhteisöissä. Tämä väitöskirja kuvaa entuudestaan tuntemattomien arkkieliöiden löytymistä havumetsävyöhykkeen metsämaasta. Arkkieliöitä löytyi myös lauhkean vyöhykkeen vuorovesialueelta, murtoveden huuhtelemasta pohjasta. Nämä löydöt ovat perustavalaatuisia vuorovesialueen eliöyhteisöjen ymmärtämiseksi. Suomalaisen metsäjärven vedestä määritettiin molempien arkkieliöiden pääryhmien - tieteellisiltä nimiltään Crenarchaeota ja Euryarchaeota - edustajia. Euryarchaeota-ryhmän edustajia voitiin havainnoida myös fluoresenssi-mikroskopoinnilla. Löydöt viittaavat siihen, että arkkieliöillä on oma biogeokemiallinen roolinsa makeanveden ravintoketjujen hiilen käytössä. Tässä työssä määritetyt uudet arkkieliöiden genomien nukleotidisekvenssit on toimitettu ARB-tietokantaan, jonka kasvava vertailuaineisto edelleen parantaa uusien arkkieliösekvenssien analyysiä ja auttaa hybridisaatiokoetinten ja polymeraasiketjureaktioalukkeiden suunnittelussa ja arvioinnissa. Tässä väitöskirjassa esitellyt tulokset yhdessä lukuisien vesi-, maaperä- ja muiden ympäristöjen arkkieliöitä käsittelevien julkaisujen kanssa osoittavat, että arkkieliöt asuttavat monia erilaisia elinympäristöjä ja että ne ovat ekologisesti paljon menestyneempiä, kuin tieteenalalla on kuviteltu. Voimme olettaa, että heti kun joitain näistä eliöistä onnistutaan kasvattamaan ja ylläpitämään laboratorio-oloissa, niiden joukosta löydetään aivan uusia, entuudestaan tuntemattomia fysiologisia fenotyyppejä, jotka avaavat mielenkiintoisia näkymiä aineenvaihdunnan ja perinnöllisten ominaisuuksien tutkimukselle.

Biodiversity and Phylogeny of Planktic Cyanobacteria in Temperate Freshwater Lakes

Currently, the classification used for cyanobacteria is based mainly on morphology. In many cases the classification is known to be incongruent with the phylogeny of cyanobacteria. The evaluation of this classification is complicated by the fact that numerous strains are only described morphologically and have not been isolated. Moreover, the phenotype of many cyanobacterial strains alters during prolonged laboratory cultivation. In this thesis, cyanobacterial strains were isolated from lakes (mainly Lake Tuusulanjärvi) and both morphology and phylogeny of the isolates were investigated. The cyanobacterial community composition in Lake Tuusulanjärvi was followed for two years in order to relate the success of cyanobacterial phenotypes and genotypes to environmental conditions. In addition, molecular biological methods were compared with traditional microscopic enumeration and their ability and usefulness in describing the cyanobacterial diversity was evaluated. The Anabaena, Aphanizomenon, and Trichormus strains were genetically heterogeneous and polyphyletic. The phylogenetic relationships of the heterocytous cyanobacteria were not congruent with their classification. In contrast to heterocytous cyanobacteria, the phylogenetic relationships of the Snowella and Woronichinia strains, which had not been studied before this thesis, reflected the morphology of strains and followed their current classification. The Snowella strains formed a monophyletic cluster, which was most closely related to the Woronichinia strain. In addition, a new cluster of thin, filamentous cyanobacterial strains identified as Limnothrix redekei was revealed. This cluster was not closely related to any other known cyanobacteria. The cyanobacterial community composition in Lake Tuusulanjärvi was studied with molecular methods [denaturant gradient gel electrophoresis (DGGE) and cloning of the 16S rRNA gene], through enumerations of cyanobacteria under microscope, and by strain isolations. Microcystis, Anabaena/Aphanizomenon, and Synechococcus were the major groups in the cyanobacterial community in Lake Tuusulanjärvi during the two-year monitoring period. These groups showed seasonal succession, and their success was related to different environmental conditions. The major groups of the cyanobacterial community were detected by all used methods. However, cloning gave higher estimates than microscopy for the proportions of heterocytous cyanobacteria and Synechococcus. The differences were probably caused by the high 16S rRNA gene copy numbers in heterotrophic cyanobacteria and by problems in the identification and detection of unicellular cyanobacteria.

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.

Hydrographic observations and model simulation of the Bay of Bengal freshwater plume

Hydrographic observations were taken along two coastal sections and one open ocean section in the Bay of Bengal during the 1999 southwest monsoon, as a part of the Bay of Bengal Monsoon Experiment (BOBMEX). The coastal section in the northwestern Bay of Bengal, which was occupied twice, captured a freshwater plume in its two stages: first when the plume was restricted to the coastal region although separated from the coast, and then when the plume spread offshore. Below the freshwater layer there were indications of an undercurrent. The coastal section in the southern Bay of Bengal was marked by intense coastal upwelling in a 50 km wide band. In regions under the influence of the freshwater plume, the mixed layer was considerably thinner and occasionally led to the formation of a temperature inversion. The mixed layer and isothermal layer were of similar depth for most of the profiles within and outside the freshwater plume and temperature below the mixed layer decreased rapidly till the top of seasonal thermocline. There was no barrier layer even in regions well under the influence of the freshwater plume. The freshwater plume in the open Bay of Bengal does not advect to the south of 16 degrees N during the southwest monsoon. A model of the Indian Ocean, forced by heat, momentum and freshwater fluxes for the year 1999, reproduces the freshwater plume in the Bay of Bengal reasonably well. Model currents as well as the surface circulation calculated as the sum of geostrophic and Ekman drift show a southeastward North Bay Monsoon Current (NBMC) across the Bay, which forms the southern arm of a cyclonic gyre. The NBMC separates the very low salinity waters of the northern Bay from the higher salinities in the south and thus plays an important role in the regulation of near surface stratification. (c) 2007 Elsevier Ltd. All rights reserved.

Hydrographic observations and model simulation of the Bay of Bengal freshwater plume

Hydrographic observations were taken along two coastal sections and one open ocean section in the Bay of Bengal during the 1999 southwest monsoon, as a part of the Bay of Bengal Monsoon Experiment (BOBMEX). The coastal section in the northwestern Bay of Bengal, which was occupied twice, captured a freshwater plume in its two stages: first when the plume was restricted to the coastal region although separated from the coast, and then when the plume spread offshore. Below the freshwater layer there were indications of an undercurrent. The coastal section in the southern Bay of Bengal was marked by intense coastal upwelling in a 50 km wide band. In regions under the influence of the freshwater plume, the mixed layer was considerably thinner and occasionally led to the formation of a temperature inversion. The mixed layer and isothermal layer were of similar depth for most of the profiles within and outside the freshwater plume and temperature below the mixed layer decreased rapidly till the top of seasonal thermocline. There was no barrier layer even in regions well under the influence of the freshwater plume. The freshwater plume in the open Bay of Bengal does not advect to the south of 16 degrees N during the southwest monsoon. A model of the Indian Ocean, forced by heat, momentum and freshwater fluxes for the year 1999, reproduces the freshwater plume in the Bay of Bengal reasonably well. Model currents as well as the surface circulation calculated as the sum of geostrophic and Ekman drift show a southeastward North Bay Monsoon Current (NBMC) across the Bay, which forms the southern arm of a cyclonic gyre. The NBMC separates the very low salinity waters of the northern Bay from the higher salinities in the south and thus plays an important role in the regulation of near surface stratification. (c) 2007 Elsevier Ltd. All rights reserved.

Characterization of the carbonic anhydrase gene family and other key osmoregulatory genes in Australian freshwater crayfish (genus Cherax)

Cherax quadricarinatus (Redclaw), C. destructor (Yabby) and C. cainii (Marron) are a group of economically important freshwater crayfish and have been developed for aquaculture production in many countries. As crayfish are farmed in a wide range of culture conditions, optimisation of water quality parameters, are crucial for their maximum growth performance. Previous reports have shown that fluctuations in water quality can negatively impact on growth of crayfish. Therefore, this project aims to identify and characterize the major genes that enable freshwater crayfish to persist in different water chemistries and evaluate their patterns of expression under different water parameters. Overall, this project found a number of candidate genes in all three species and determined that water chemistry had a strong influence on the expression of candidate genes. This information is important in the optimization of water quality parameters in freshwater crayfish aquaculture production.

Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus

The pH and salinity balance mechanisms of crayfish are controlled by a set of transport-related genes. We identified a set of the genes from the gill transcriptome from a freshwater crayfish Cherax quadricarinatus using the Illumina NGS-sequencing technology. We identified and characterized carbonic anhydrase (CA) genes and some other key genes involved in systematic acid-base balance and osmotic/ionic regulation. We also examined expression patterns of some of these genes across different sublethal pH levels [1]. A total of 72,382,710 paired-end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. About 37% of the contigs received significant BLAST hits and 22% were assigned gene ontology terms. These data will assist in further physiological-genomic studies in crayfish.

Intraseasonal response of mixed layer temperature and salinity in the Bay of Bengal to heat and freshwater flux

Buoy and satellite data show pronounced subseasonal oscillations of sea surface temperature (SST) in the summertime Bay of Bengal. The SST oscillations are forced mainly by surface heat flux associated with the active break cycle of the south Asian summer monsoon. The input of freshwater (FW) from summer rain and rivers to the bay is large, but not much is known about subseasonal salinity variability. We use 2002-2007 observations from three Argo floats with 5 day repeat cycle to study the subseasonal response of temperature and salinity to surface heat and freshwater flux in the central Bay of Bengal. About 95% of Argo profiles show a shallow halocline, with substantial variability of mixed layer salinity. Estimates of surface heat and freshwater flux are based on daily satellite data sampled along the float trajectory. We find that intraseasonal variability of mixed layer temperature is mainly a response to net surface heat flux minus penetrative radiation during the summer monsoon season. In winter and spring, however, temperature variability appears to be mainly due to lateral advection rather than local heat flux. Variability of mixed layer freshwater content is generally independent of local surface flux (precipitation minus evaporation) in all seasons. There are occasions when intense monsoon rainfall leads to local freshening, but these are rare. Large fluctuations in FW appear to be due to advection, suggesting that freshwater from rivers and rain moves in eddies or filaments.

Surface freshwater from Bay of Bengal runoff and Indonesian Throughflow in the Tropical Indian Ocean

According to recent estimates, the annual total continental runoff into the Bay of Bengal (BoB) is about 2950 km 3, which is more than half that into the entire tropical Indian Ocean (IO). Here we use climatological observations to trace the seasonal pathways of near surface freshwater from BoB runoff and Indonesian Throughflow (ITF) by removing the net contribution from precipitation minus evaporation. North of 20 degrees S, the amount of freshwater from BoB runoff and ITF changes with season in a manner consistent with surface currents from drifters. BoB runoff reaches remote regions of the Arabian Sea; it also crosses the equator in the east to join the ITF. This freshwater subsequently flows west across the southern tropical IO in the South Equatorial Current.

Ganga-Brahmaputra river discharge from Jason-2 radar altimetry: An update to the long-term satellite-derived estimates of continental freshwater forcing flux into the Bay of Bengal

This paper discusses the use of Jason-2 radar altimeter measurements to estimate the Ganga-Brahmaputra surface freshwater flux into the Bay of Bengal for the period mid-2008 to December 2011. A previous estimate was generated for 1993-2008 using TOPEX-Poseidon, ERS-2 and ENVISAT, and is now extended using Jason-2. To take full advantages of the new availability of in situ rating curves, the processing scheme is adapted and the adjustments of the methodology are discussed here. First, using a large sample of in situ river height measurements, we estimate the standard error of Jason-2-derived water levels over the Ganga and the Brahmaputra to be respectively of 0.28 m and 0.19 m, or less than similar to 4% of the annual peak-to-peak variations of these two rivers. Using the in situ rating curves between water levels and river discharges, we show that Jason-2 accurately infers Ganga and Brahmaputra instantaneous discharges for 2008-2011 with mean errors ranging from similar to 2180 m(3)/s (6.5%) over the Brahmaputra to similar to 1458 m(3)/s (13%) over the Ganga. The combined Ganga-Brahmaputra monthly discharges meet the requirements of acceptable accuracy (15-20%) with a mean error of similar to 16% for 2009-2011 and similar to 17% for 1993-2011. The Ganga-Brahmaputra monthly discharge at the river mouths is then presented, showing a marked interannual variability with a standard deviation of similar to 12500 m(3)/s, much larger than the data set uncertainty. Finally, using in situ sea surface salinity observations, we illustrate the possible impact of extreme continental freshwater discharge event on the northern Bay of Bengal as observed in 2008.

Surface freshwater storage and variability in the Amazon basin from multi-satellite observations, 1993-2007

The amount of water stored and moving through the surface water bodies of large river basins (river, floodplains, wetlands) plays a major role in the global water and biochemical cycles and is a critical parameter for water resources management. However, the spatiotemporal variations of these freshwater reservoirs are still widely unknown at the global scale. Here, we propose a hypsographic curve approach to estimate surface freshwater storage variations over the Amazon basin combining surface water extent from a multi-satellite-technique with topographic data from the Global Digital Elevation Model (GDEM) from Advance Spaceborne Thermal Emission and Reflection Radiometer (ASTER). Monthly surface water storage variations for 1993-2007 are presented, showing a strong seasonal and interannual variability, and are evaluated against in situ river discharge and precipitation. The basin-scale mean annual amplitude of similar to 1200 km(3) is in the range of previous estimates and contributes to about half of the Gravity Recovery And Climate Experiment (GRACE) total water storage variations. For the first time, we map the surface water volume anomaly during the extreme droughts of 1997 (October-November) and 2005 (September-October) and found that during these dry events the water stored in the river and floodplains of the Amazon basin was, respectively, similar to 230 (similar to 40%) and 210 (similar to 50%) km(3) below the 1993-2007 average. This new 15 year data set of surface water volume represents an unprecedented source of information for future hydrological or climate modeling of the Amazon. It is also a first step toward the development of such database at the global scale.