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Phytoplankton and bacterial production, 14C-transfer and optical characteristics of dissolved organic matter (DOM) from a microcosm experiment, Gulf of Finland, Baltic Sea
No full textThe data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. Measured variables include phytoplankton and bacterial abundance, primary production, bacterial production and respiration, 14C-transfer from phytoplankton to DOM and bacteria, concentrations of particulate and dissolved organic carbon, nitrate, phosphate and chlorophyll a, and optical characteristics of dissolved organic matter. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication
Ice formation, growth and associated substrate supply determine sea-ice bacterial community dynamics
No full textSea ice, at its maximum extent, is one of the largest biomes on Earth. In addition to the polar oceans, it covers extensive sea areas at lower latitudes such as the Baltic Sea and the Sea of Okhotsk. During ice formation, organic and inorganic components in the parent seawater are concentrated into saline brines within the ice, which serve as a habitat for diverse auto- and heterotrophic organisms, including bacteria. Sea-ice bacteria are responsible for many biogeochemical processes, such as decomposition of particulate organic matter, recycling of dissolved organic matter and remineralization of nutrients, analogously to bacterially driven biogeochemical processes in the water column. Since bacterial groups vary by their metabolic traits and participation in biogeochemical processes, knowledge of the bacterial community structure and its seasonal variation is essential for an understanding of ice biogeochemistry.
This thesis characterises sea-ice bacterial communities during ice formation and during the winter/spring transition phase when the community composition is poorly known. Bacterial communities in Arctic and Baltic sea ice during the winter/spring transition were studied and compared. In addition, the effect of the dissolved organic matter regime on bacterial community formation was investigated in an experimental sea-ice system with North Sea water. The main methods applied were terminal-restriction fragment length polymorphism and/or Illumina Miseq sequencing together with bacterial production and abundance measurements.
During the early stages of sea-ice formation, the bacterial communities were similar to the parent water communities, suggesting that the parent water determines the initial sea-ice bacterial community composition. After congealment of the sea ice, the bacterial communities changed towards communities typical of sea ice in spring. During the winter/spring transition, members of the classes Flavobacteriia (formerly Flavobacteria), Gammaproteobacteria and Alphaproteobacteria were predominant both in Baltic and Arctic sea ice. The Baltic and Arctic sea-ice bacterial communities were significantly different; however, a few members of common sea-ice bacterial genera, such as Polaribacter and Shewanella, were closely related, pointing to similar selection in ice, regardless of differences in the prevailing environmental conditions.
In the experimental system, the bacterial communities were able to respond to altered substrate availability immediately after ice formation. This indicates successful adaptation of sea-ice bacteria to major shifts in temperature and salinity during ice formation. The results of this thesis suggest that sea-ice bacterial community formation and dynamics is defined by a combination of changes in environmental conditions during sea-ice maturation and its associated substrate availability, as well as resource competition. The sea-ice habitat provides an example of the enormous capacity of bacteria to adapt to changing environments and how minor members of the bacterial community can become predominant when environmental conditions change.Merijää peittää vuosittain jopa 7% maapallon pinta-alasta muodostaen yhden maapallon suurimmista eloyhteisöistä eli biomeista. Napa-alueiden lisäksi merijäätä muodostuu vuotuisesti myös alempien leveysasteiden merialueilla, kuten Itämerellä ja Ohotanmerellä. Merijään muodostuessa, meriveteen liuenneet orgaaniset ja epäorgaaniset ainesosat väkevöityvät toisiinsa takertuneiden jääkiteiden väliin muodostaen jään sisälle pieniä suolavesikanavia ja taskuja. Suolavesikanavissa ja taskuissa elää mikroskooppisia pieneliöitä, kuten bakteereita. Merijään bakteerit osallistuvat moniin biogeokemiallisiin prosesseihin kuten partikkelimaisen orgaanisen aineksen hajotukseen sekä liuenneen orgaanisen aineksen että ravinteiden kierrätykseen samaan tapaan kuin jään alla olevassa vesipatsaassa. Bakteeriyhteisöt koostuvat erilaisten bakteerilajien populaatioista joilla kullakin on oma tehtävänsä biogeokemiallisissa kierroissa. Jotta voisimme ymmärtää eri bakteeritaksonien tehtävät merijään biogeokemiallisissa kierroissa, on selvitettävä kuinka bakteeriyhteisöt muodostuvat ja kuinka ne muuttuvat vuodenaikojen mukaan.
Väitöskirjatyöni tarkoituksena oli kartoittaa bakteeriyhteisöjen rakennetta ja dynamiikkaa sekä merijään muodostuessa että kevättalvella, jolloin bakteeriyhteisön rakenne on puutteellisesti tunnettu. Näytteitä kerättiin sekä Itämereltä että Pohjoiselta jäämereltä. Bakteeriyhteisöjä tutkittiin myös kokeellisessa tutkimuksessa, jossa selvitettiin liuenneen orgaanisen aineksen laadun ja määrän vaikutusta muodostuviin bakteeriyhteisöihin. Bakteeriyhteisöjen rakennetta tutkittiin 16S rRNA geenin päätekatkokirjoanalyysillä ja DNA-jaksotuksella sekä vakiintunutta Sangerin jaksotusmenetelmää että syväjaksotusta käyttäen. Lisäksi bakteeriyhteisöjen runsautta ja aktiivisuutta tutkittiin bakteeribiomassa- ja bakteerituotantomittauksilla.
Jään muodostuessa bakteeriyhteisöt olivat hyvin samankaltaisia kuin vedessä mikä viittaa lähtöveden bakteeriyhteisön määräävän jään bakteeriyhteisön koostumuksen jäätymisen alkaessa. Jääpeitteen vahvistuessa yhteisöt erilaistuivat vesiyhteisöistä ja alkoivat muistuttaa rakenteeltaan kevätjäälle tyypillisiä yhteisöjä. Sekä Itämerellä että Pohjoisella jäämerellä yhteisöissä esiintyi runsaimmin Flavobacteriia (aikaisemmin Flavobacteria), Gammaproteobacteria and Alphaproteobacteria luokkien bakteereita. Kokonaisuudessaan Itämeren ja Pohjoisen jäämeren yhteisöt olivat erilaisia, mutta yhteisöistä havaittiin myös muutamia bakteerisukuja kuten Polaribacter ja Shewanella, joiden 16S rRNA geeniä koodaavat DNA-jaksot olivat keskenään hyvin samankaltaisia (>97%). Geenien samankaltaisuus viittaa samankaltaisiin valintapaineisiin huolimatta Itämeren ja Pohjoisen jäämeren erilaisista ympäristöolosuhteista.
Bakteeriyhteisöt muuttuivat kokeellisissa olosuhteissa hyvin nopeasti jäätymisen alettua kun veteen lisättiin liuennutta orgaanista ainesta. Tulos viittaa bakteerien kykyyn sopeutua nopeasti muuttuvaan suolaisuuteen ja lämpötilaan. Väitöskirjani tulosten perusteella merijään bakteeriyhteisöjen muodostumiseen ja dynamiikkaan vaikuttavat ympäristöolosuhteiden muutos jään muodostuessa ja kasvaessa, tarjolla olevan substraatin saatavuus sekä bakteerien välinen kilpailu. Merijään bakteeriyhteisöjen muodostuminen on esimerkki bakteerien huomattavasta kyvystä sopeutua muuttuviin ympäristöolosuhteisiin sekä ympäristöolosuhteiden muutoksen nopeasta heijastumisesta bakteeriyhteisöjen rakenteeseen.ei saavutettav
Monitoring of the growth phase of phytoplankton cultures in part 2 (dissolved organic matter consumption) of the microcosm experiment, Gulf of Finland, Baltic Sea
No full textThe data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. Measured variables include phytoplankton and bacterial abundance, primary production, bacterial production and respiration, 14C-transfer from phytoplankton to DOM and bacteria, concentrations of particulate and dissolved organic carbon, nitrate, phosphate and chlorophyll a, and optical characteristics of dissolved organic matter. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication.
This data table contains measurements collected during monitoring of the growth of phytoplankton batch cultures in part 2 of the experiment (DOM consumption experiment), i.e., before the initiation of the incubation. These phytoplankton cultures were used in the incubation of the DOM consumption experiment. The measured variables are phytoplankton abundance and abundance of A. malmogiense cells with lower chlorophyll a fluorescence
Monitoring of the growth of phytoplankton batch cultures in part 1 (dissolved organic matter release) of the microcosm experiment, Gulf of Finland, Baltic Sea
No full textThe data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant.
This data table contains measurements collected during monitoring of the growth of phytoplankton batch cultures in part 1 of the experiment (DOM release experiment), i.e., before and in between of the KPIs. These phytoplankton cultures were used in the three key point incubations of the DOM release experiment. The variables measured during the monitoring, and included in this data file, are phytoplankton abundance, abundance of A. malmogiense cells with lower chlorophyll a fluorescence, percentage of phytoplankton cells with intact membranes, and optical properties of DOM. The experimental design is explained in figure 1 of the associated publication
Production line part of the key point incubations in part 1 (dissolved organic matter release) of the microcosm experiment, Gulf of Finland, Baltic Sea
No full textThe data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication.
This data table contains measurements taken during the production line, i.e. all the measurements involving radioisotopes. It is structured based on two light and one dark measurements of primary production. Primary production measurements themselves are given in https://doi.pangaea.de/10.1594/PANGAEA.937723. From each of these subsamples (2 light and 1 dark) the following variables were measured: 14C-DOM production from 14C-NaHCO3, bacterial incorporation of 14C originating from 14C-NaHCO3, 3H-thymidine incorporation rate, and 3H-thymidine based bacterial production (calculated from thymidine incorporation rate). Raw reads from the scintillation counting are not given, only the calculated production rates calculated as explained in the methods of the associated publication. This data table is explained in figure 2 of the associated publication
Phytoplankton and bacteria incubations in part 2 (dissolved organic matter consumption) of the microcosm experiment, Gulf of Finland, Baltic Sea
No full textThe data were collected from an experiment using phytoplankton cultures (Apocalathium malmogiense and Rhodomonas marina). The aim of the experiment was to study carbon cycling among phytoplankton and bacteria, and the effects on the dissolved organic matter (DOM) pool. Measured variables include phytoplankton and bacterial abundance, primary production, bacterial production and respiration, 14C-transfer from phytoplankton to DOM and bacteria, concentrations of particulate and dissolved organic carbon, nitrate, phosphate and chlorophyll a, and optical characteristics of dissolved organic matter. The experiment was conducted at Tvärminne Zoological Station, Hanko, Finland with non-axenic unialgal phytoplankton cultures and bacteria originating from the Baltic Sea. The experiment was conducted between Dec. 2017 and Apr. 2018. The experiment consisted of two parts, the DOM release experiment (part 1) and the DOM consumption experiment (part 2). Separate triplicate batch cultures of both phytoplankton species were grown for each experiment. In the DOM release experiment the cultures were grown for over 4 months and three day-long incubations (key point incubations, KPI's) were initiated on three occasions; the first KPI at early exponential growth phase and the second and third KPI's when the phytoplankton had grown more abundant. During each KPI and aliquot of the culture was inoculated with freshly collected sea water bacteria, and bacterial community composition was measured. This aliquot was then divided into two further aliquots; one was incubated with radioisotopes for productivity (primary and bacterial production) and 14C-flow analyses (production line) and one filtered through 0.8 µm for analysis of DOM optical properties. During the KPI's measurements were taken at 0, 4, 8 and 12 h. Nutrient concentrations (measured from non-filtered and 0.8 µm filtered samples) and concentration of dissolved organic carbon were measured only at 0 and 12 h. Concentrations of particulate organic carbon and nitrogen and chlorophyll a were measured only once for each KPI at the beginning of the incubation. In the DOM consumption experiments the cultures were grown to high abundance, after which the phytoplankton and most of the bacteria were filtered out. The filtrate was then inoculated with freshly collected sea water bacteria, after which it was incubated for 7 days. Bacterial abundance, production, respiration, and community composition, and concentration and optical properties of DOM were measured daily. The experimental design is explained in figure 1 of the associated publication.
This data table contains measurements collected during the 7-day incubation of part 2 of the experiment (DOM consumption experiment). The measured variables are concentrations of nitrate, phosphate and dissolved organic carbon, incorporation rates of 3H-thymidine and 14C-leucine and bacterial production calculated based on these, abundance of high and low nucleic acid and total bacteria, flow cytometric side scatter of high and low nucleic acid bacteria, optical properties of DOM, and bacterial respiration rate. Daily respiration rate is calculated from continues oxygen measurement using optodes as explained in the associated publication
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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