Bacterial community structure and petroleum hydrocarbon degradation in the Baltic Sea

The Baltic Sea is unique by its biological, geochemical and physical features. The number of species of larger organisms is small and the species composition is distinctive. On the contrary microbial communities are diverse. Because of the low salinity levels, bacterial communities differ from the ones in the oceans. Knowing the structure of these communities better and how they response to different environmental conditions helps us to estimate how different factors affect the balance and function of the Baltic Sea ecosystem. Bacteria are the key players when it comes to natural biogeochemical processes and human-induced phenomena like eutrophication, oil spills or disposal of other harmful substances to the sea ecosystem. In this thesis, bacterial community structure in the sea surface microlayer and subsurface water of the Archipelago Sea were compared. In addition, the effect of diatom derived polyunsaturated aldehydes on bacterial community structure was studied by a mesocosm experiment. Diesel, crude oil and polycyclic aromatic hydrocarbon degradation capacity of the Baltic Sea bacteria was studied in smaller scale microcosm experiments. In diesel oil experiments bacteria from water phase of the Archipelago Sea was studied. Sediment and iron manganese concretions collected from the Gulf of Finland were used in the crude oil and polycyclic aromatic hydrocarbon experiments. The amount of polycyclic aromatic hydrocarbon degradation genes was measured in all of the oil degradation experiments. The results show how differences in bacterial community structure can be seen in the sea surface when compared to the subsurface waters. The mesocosm experiment demonstrated how diatom-bacteria interactions depend on other factors than diatom derived polyunsaturated aldehydes, which do not seem to have an effect on the bacterial community structure as has been suggested in earlier studies. The dominant bacterial groups in the diesel microcosms differed in samples taken from a pristine site when compared to a site with previous oil exposure in the Archipelago Sea area. Results of the study with sediment and iron-manganese concretions indicate that there are diverse bacterial communities, typical to each bottom type, inhabiting the bottoms of the Gulf of Finland capable to degrade oil and polycyclic aromatic hydrocarbon compounds.  Itämeri on ainutlaatuinen biologisilta, geokemiallisilta ja fysikaalisilta ominaisuuksiltaan. Suurempien eliöiden suhteen lajisto on Itämerelle tunnusomainen ja harvalukuinen, mutta mikrobilajisto on monimuotoinen. Alhaisemman suolapitoisuuden vuoksi bakteeriyhteisöt poikkeavat valtamerten yhteisöistä. Tutkimustieto Itämeren bakteeriyhteisöistä ja niiden vasteista erilaisille ympäristötekijöille auttaa arvioimaan myös laajemmin erilaisten tekijöiden vaikutusta Itämeren ekosysteemin tasapainoon ja toimintaan. Bakteerit ovat keskeisessä roolissa luonnon biogeokemiallisissa prosesseissa ja ihmisen aiheuttamissa ilmiöissä kuten rehevöityminen, öljyonnettomuudet tai haitallisten aineiden päätyminen mereen. Tässä väitöskirjatyössä verrattiin Saaristomeren pinnan mikrokerroksen bakteeriyhteisöjä niiden alapuolisen veden bakteeriyhteisöihin. Lisäksi tutkittiin piilevien tuottamien monityydyttymättömien aldehydiyhdisteiden vaikutusta Itämeren veden bakteeriyhteisöihin mesokosmoskokeen avulla. Diesel- ja raakaöljyn sekä polysyklisten aromaattisten hiilivetyjen hajottamispotentiaalia seurattiin pienempien mikrokosmoskokeiden avulla. Dieselöljykokeissa tutkittiin Saaristomeren vesifaasin bakteerien kykyä hajottaa dieselöljyä. Suomenlahden sedimentin ja rautamangaanisaostumien bakteerien kykyä hajottaa raakaöljyä ja polysyklisiä aromaattisia hiilivetyjä tutkittiin niitä sisältävissä kokeissa. Polysyklisten aromaattisten hiilivetyjen hajoamisprosessiin liittyvien geenien määrää mitattiin kaikissa öljykokeissa. Tulokset osoittavat kuinka Saaristomeren pinnan mikrokerroksen bakteeriyhteisöt poikkeavat alusveden bakteeriyhteisöistä. Mesokosmoskokeiden perusteella selvisi, että piilevien tuottamat monityydyttymättömät aldehydiyhdisteet eivät ole piileväbakteeri- vuorovaikutukseen vaikuttava tekijä, toisin kuin aiemmissa laboratoriotutkimuksissa on esitetty. Dieselöljykokeissa hallitsevat bakteeriryhmät riippuivat aiemmasta öljyaltistuksesta; bakteeriryhmät poikkesivat aiemmin öljylle altistuneessa vesinäytteessä puhtaan alueen näytteen yhteisöistä. Raakaöljyn- ja polysyklisten aromaattisten hiilivetyjen hajotusta tutkittaessa kokeiden tulokset osoittivat, että Suomenlahden sedimentissä ja rauta-mangaanisaostumissa on niille tyypilliset monimuotoiset bakteeriyhteisöt, joilla on kyky hajottaa näitä yhdisteitä.Siirretty Doriast

Physical Activity and Learning Environment Qualities in Finnish Day Care

AbstractWhen evaluating children's physical activity in day care, both the direct education and the children's activities in their personal contexts must be studied. In this study children's physical activity level was systematically observed in 2010 in 47 day care centre groups. Other children increased children‘s physical activity (p < .05). If the educators had spent more time planning activities or concentrated more on children's social relations, children were more physically active (p < .05). The planning of educational activities and interaction planned between children in the group may activate them more effectively than traditional planning for the group

Increasing Immigrant Children’s Participation in the Finnish Early Childhood Education Context

Creative Commons Attribution License (CC BY-NC-ND)Peer reviewe

Lasten ajankäyttö ja vähintään kohtuukuormitteinen fyysinen aktiivisuus varhaiskasvatuksessa

Background: The role of early childhood education and care (ECEC) is crucial in the implementation of the physical activity recommendations during long ECEC days. Young children should engage in 180 minutes of physical activity spread throughout the day, including 60 minutes of moderate-to-vigorous physical activity (MVPA). To attain the goal more information is needed on children’s time use and PA in children’s activities. Aim: The purposes of this quantitative observational study were twofold: (a) to examine children’s time use and (b) to describe which children’s activities best generate physical activity, specifically MVPA, in ECEC. Setting: Altogether, 2,879 Finnish children, aged 1- to 6-years, participated in this study. Methods: The data of 57,881 observations were analysed using cross-tabulation and a z-test. Results: Daily routines (e.g. eating, dressing, napping and transition), task or seatwork and material play accounted for almost 70% of children’s sedentary behaviour and less than 10% of MVPA. The best MVPA generators were physical activities (that generated 57.4% of all MVPA in boys vs. 62.8% in girls, respectively), rule play (11% in boys vs. 6.7% in girls), and role play (10.1% in boys vs. 9.9% in girls), as well as action not allowed (3.3% in boys vs 1.2% in girls). Conclusions: Educators should integrate physical activities, rule play and role play more in ECEC day to support the realization of the recommendations.Peer reviewe

Fourth Graders’ Objectively Measured Week Long Physical Activity

We explored 10–11 year-old children’s moderate to vigorous physical activity (MVPA) to describe how it is distributed within weekdays, weekend days, the segments of a schoolday and how it meets the global recommendation of ≥ 60 min daily MVPA. Participants were from two fourth classes (N = 33, 20 boys, 13 girls) in the city of Vantaa, capitol area of Finland. PA was measured using a Polar Active® (PAC) wrist-worn accelerometer. A diary supported the accelerometer data. Raw metabolic equivalent (MET) data from accelerometers were transmitted to computer, organized and uploaded to SPSS. We used MET-thresholds moderate PA (MPA) ≥ 3 < 6, vigorous (VPA) ≥ 6 and consequently moderate to vigorous PA (MVPA) ≥ 3. Average daily MVPA was 92 min. Differences between weekdays and weekend days existed, but they were at least partly caused by the weather. Global recommendation was met by 21 %, more often by girls than boys. However, almost everyone met the recommendation ≥ 4 a week. Segments of the schoolday (lessons, long recesses, short recesses and lunch breaks) were physically quite active with 5, 12, 4 and 8 min, respectively. Hypothetically summed up schoolday accumulated 50 min MVPA. Boys accumulated quite systematically slightly more MVPA during schooldays and leisure time. Schooldays play an important role in children’s total MVPA and the current situation is decent. However, teacher educators, decision makers, school administration, principals, teachers and school staff should still aim at finding new ways of making the schooldays even more physically active.We explored 10–11 year-old children’s moderate to vigorous physical activity (MVPA) to describe how it is distributed within weekdays, weekend days, the segments of a schoolday and how it meets the global recommendation of ≥ 60 min daily MVPA. Participants were from two fourth classes (N = 33; 20 boys, 13 girls) in the city of Vantaa, capitol area of Finland. PA was measured using a Polar Active® (PAC) wrist-worn accelerometer. A diary supported the accelerometer data. Raw metabolic equivalent (MET) data from accelerometers were transmitted to computer, organized and uploaded to SPSS. We used MET-thresholds moderate PA (MPA) ≥ 3 < 6, vigorous (VPA) ≥ 6 and consequently moderate to vigorous PA (MVPA) ≥ 3. Average daily MVPA was 92 minutes. Differences between weekdays and weekend days existed, but they were at least partly caused by the weather. Global recommendation was met by 21%, more often by girls than boys. However, almost everyone met the recommendation ≥ 4 a week. In segments of the schoolday (lessons, long recesses, short recesses and lunch breaks) the children were physically quite active at 5, 12, 4 and 8 minutes, respectively. Hypothetically summed up, a schoolday accumulated 50 minutes MVPA. Boys accumulated quite systematically slightly more MVPA during schooldays and leisure time. Schooldays play an important role in children’s total MVPA and the current situation is decent. However, teacher educators, decision makers, school administration, principals, teachers and school staff should still aim at finding new ways of making schooldays even more physically active.Peer reviewe

Ajankäyttö ja vähintään kohtuukuormitteinen fyysinen aktiivisuus lasten toiminnoissa varhaiskasvatuksessa

The role of early childhood education (ECE) is significant in children’s physical activity. Young children should engage in moderate- to-vigorous physical activity (MVPA) for at least 60 minutes per day, which – according to the recommendations – should be spread throughout the day, including the ECE days. The purposes of this study were to explore children’s time use and MVPA in children’s activities and to see which activities are the most efficacious for MVPA in three different age groups (1–3-year-olds; 4–5-year-olds; 6–7-year-olds) during ECE days. Altogether, 2,879 children participated in this study in Southern Finland. The children were systematically observed for 6 mornings and for one afternoon. Children’s activities were classified to 11 different categories and the intensity level in each time interval was categorized into three levels. The data of 51,427 observations were analysed using cross-tabulation and a z-test. Significant differences in time-spent in the activities and in MVPA among the age groups were found. All age groups spent most of their time in daily routines (1–7-year-olds: 41%; 4–5-year-olds: 35%; 6–7-year-olds: 26%), which were ineffective in generating MVPA, as were tasks, reading and material play. Physically active play (e.g. running) and role play (the player has a role) accumulated the greatest amount of MVPA in all age groups, as did rule play (e.g. dodgeball), specifically in 6–7-yearolds. The variation was the highest in rule play. It is important that the educators include physically active play and role play in all common activity settings for all age groups, and rule play, especially for 6–7-year-olds. The contents and properties of the efficacious action not allowed would be worth examining both in preschools and in the future studies.Peer reviewe

Guidelines for using environmental DNA in Finnish marine phytoplankton monitoring – Improved biodiversity assessment through method complementation

This document is a methodological guide for using a genomic ecosystem survey technique (eDNA metabarcoding) to supplement conventional phytoplankton monitoring of the Finnish marine monitoring program. The guidelines describe the detection of eukaryotic and prokaryotic phytoplankton with 18S and 16S rDNA gene primers, using high-throughput sequencing. The document includes information on sampling, sample processing, molecular biological work, quality control, and bioinformatics so that the method can be applied in addition to standardized light microscopy. The guidelines are based on a first pilot project testing the integration of eDNA metabarcoding in Finnish marine phytoplankton monitoring and will be developed further, according to evolving genetic methods and international guidelines and standards. Suggestions on steps towards introducing eDNA methodology in phytoplankton monitoring are included in the guidelines. Using eDNA metabarcoding to complement standardized light microscopy advances conventional monitoring and research of phytoplankton communities to assess biodiversity and the status of the marine environment. Menetelmäohje DNA-viivakoodaustekniikan käyttöön meren kasviplanktonseurannassa Tässä julkaisussa kuvataan menetelmäohje DNA-viivakoodeihin perustuvan eDNA (ympäristö-DNA) -metaviivakoodaustekniikan käytöstä Suomen merenhoidon seurantaohjelmaan kuuluvan kasviplanktonseurannan tukena. Aitotumaisen kasviplanktonin (mikrolevät) tunnistamiseen soveltuvan 18S rDNA -menetelmän lisäksi ohjeessa kuvataan esitumaisten syanobakteerien (sinilevät) analysointi 16S rDNA -menetelmällä käyttäen korkean käsittelytehon sekvensointia (high-throughput sequencing). Ohje sisältää yksityiskohtaiset tiedot eDNA -näytteiden keräämisestä, näytteiden käsittelystä, molekyylibiologisista työvaiheista, bioinformatiikka-analyyseistä ja laadunvarmennuksesta. Ohje perustuu ympäristöministeriön rahoittaman hankkeen tuloksiin. Ohjeistusta tullaan kehittämään jatkossa sitä mukaa, kun uusia tutkimustuloksia, kansainvälisiä ohjeita ja standardeja julkaistaan. Ohjeistus sisältää ehdotuksen etenemisvaiheista, jotka kannattaa huomioida, kun eDNA-menetelmää ryhdytään ottamaan mukaan kasviplanktonseurantaan. eDNA-menetelmää voidaan käyttää valomikroskopointimenetelmän ohella tarkentamaan ja tehostamaan kasviplanktonyhteisöjen biodiversiteetin seurantaa ja tutkimusta meriympäristön tilan arvioita varten

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area

Two long-term potentially oil exposed Baltic Sea coastal sites near old oil refineries and harbours were compared to nearby less exposed sites in terms of bacterial, archaeal and fungal microbiomes and oil degradation potential. The bacterial, archaeal and fungal diversities were similar in oil exposed and less exposed sampling sites based on bacterial and archaeal 16S rRNA gene and fungal 5.8S rRNA gene amplicon sequencing from both DNA and RNA fractions. The number of genes participating in alkane degradation (alkB) or PAH-ring hydroxylation (PAH–RHDα) were detected by qPCR in all water and sediment samples. These numbers correlated with the number of bacterial 16S rRNA gene copies in sediment samples but not with the concentration of petroleum hydrocarbons or PAHs. This indicates that both the clean and the more polluted sites at the Baltic Sea coastal areas have a potential for petroleum hydrocarbon degradation. The active community (based on RNA) of the coastal Baltic Sea water differed largely from the total community (based on DNA). The most noticeable difference was seen in the bacterial community in the water samples were the active community was dominated by Cyanobacteria and Proteobacteria whereas in total bacterial community Actinobacteria was the most abundant phylum. The abundance, richness and diversity of Fungi present in water and sediment samples was in general lower than that of Bacteria and Archaea. Furthermore, the sampling location influenced the fungal community composition, whereas the bacterial and archaeal communities were not influenced. This may indicate that the fungal species that are adapted to the Baltic Sea environments are few and that Fungi are potentially more vulnerable to or affected by the Baltic Sea conditions than Bacteria and Archaea