Sediment Bacterial Communities in Nutrient Cycling and in the History of the Baltic Sea

The Baltic Sea has experienced fresh-, brackish, oxic and hypoxic water phases and its deepest bottom areas are naturally hypoxic. Recently, eutrophication has caused spreading of hypoxic areas and internal feedback mechanisms, such as the release of phosphorus (P) and nitrogen (N) nutrients from sediment to water, which sustains hypoxia. Bacteria participate in release of nutrients by mineralizing organic matter or by altering the sediment s ability to retain nutrients. In deeper sediment layers, most microbes are inactive, dead or only their DNA is preserved, representing the remains of the preceding sedimentary communities. This work investigated variation in bacterial communities in the northeastern Baltic Sea sediments along the gradients of chemical forms of P and elements related to its cycling, as well as organic matter and some properties of the upperlying water column such as oxygen concentrations. The results were discussed from the standpoint of nutrient recycling, which sustains the eutrophic conditions of the Baltic Sea. In addition, a sediment core covering the last 8000 years were investigated to determine whether historical phases of the Baltic Sea can be inferred from bacterial community data and this kind of data could be used as a palaeomicrobiological tool. Current and historical bacterial communities were studied using terminal restriction fragments length polymorphism and sequencing of the 16S rRNA genes. The data obtained were examined with sediment properties, using statistics and phylogenetics. Bacterial communities changed mainly along the gradients of chemical forms of P and organic matter. Most importantly, sulphate-reducing bacteria correlated with organic and Fe-bound P as well as redox-sensitive iron (Fe). The correlations indicated that sulphate reducers participated in the release of Fe-bound P, indirectly by producing sulphide, which captures Fe, or directly by reducing Fe oxyhydroxides. The predominance of sulphate reducers in most areas suggests that hypoxia has progressed in the phase where bacteria process most of the benthic energy. The phylum Chloroflexi, typical for organic-rich environments, increased downwards and was common throughout the sediment core spanning the 8000-year history of the Baltic Sea. This indicates that these bacteria were important in terminal mineralization and that the Baltic has been relatively organic-rich throughout its history, which makes it sensitive to external nutrient loading. The bacterial communities of the Early and Late Litorina Sea phase were distinguished from the communities of the Litorina Sea phase, which correlated positively with uranium and strontium, used as palaeooxygen and palaeosalinity proxies. Salinity changes also explained a sudden increase in the heterogeneity of the bacterial communities of Litorina Sea layers, which indicates that a salinity maximum occurred in the central Gulf of Finland 6200 6600 years ago. This study showed that bacterial community data may be used as an additional tool e.g. in ocean-drilling projects, which aim to detect historical environmental events from the sedimentary record.Historiansa aikana Itämeri on ollut vuoroin makea- tai murtovetinen ja pohja-alueiden happipitoisuus on vaihdellut. Luonnostaan hapettomat pohja-alueet ovat rehevöitymisen seurauksena laajentuneet ja hapettomuudesta johtuva ravinteiden kuten fosforin ja typen vapautuminen sedimentistä vesipatsaaseen on lisääntynyt, mikä ylläpitää rehevöitymistä. Bakteerit aiheuttavat ravinteiden vapautumista sedimentistä pohjaveteen esimerkiksi hajottaessaan eloperäistä ainetta. Tässä prosessissa aerobit bakteerit kuluttavat happea, mikä lisää esimerkiksi rautaan sitoutuneen fosforin vapautumista. Syvemmällä hapettomissa sedimenteissä eloperäinen aine on pidemmälle hajotettua ja suurin osa bakteereista on horrostilassa tai kuolleena. Syvemmällä menneet bakteeriyhteisöt heijastavat vesipatsaan aiempaa tilaa. Väitöskirjassani tutkin sedimenttien bakteeriyhteisöjen muutosta sedimentin kemiallisten ominaisuuksien ja ympäröivien olosuhteiden kuten pohjaveden happipitoisuuden muuttuessa Suomenlahdella ja Saaristomerellä. Käsittelin tuloksia ravinteiden vapautumisen näkökulmasta, koska vapautuvat ravinteet ylläpitävät Itämeren rehevöitynyttä tilaa. Lisäksi selvitin voiko sedimentin bakteeriyhteisöjä käyttää työkaluna tutkittaessa merien historiaa ja heijastivatko bakteeriyhteisön syvyyssuuntaiset muutokset Itämeren historiallisia vaiheita viimeisten 8000 vuoden ajalta. Määritin bakteeriyhteisön 16S rRNA geenien päätekatkokirjoanalyysillä (T-RFLP) ja sekvensoinnilla. Vertasin yhteisön muutosta sedimentin kemiallisiin, geokemiallisiin ynnä muihin muutoksiin tilastollisilla monimuuttujamenetelmillä. Fosforin käyttökelpoisuus vaikutti eniten sedimentin bakteeriyhteisöihin siirryttäessä maatalouden kuormittamalta Saaristomereltä Suomenlahdelle. Suomenlahdella bakteeriyhteisö muuttui eniten eloperäisen kuormituksen vaikutuksesta. Laajoilla ja erityisesti vähähappisilla pohjilla hallitsivat sulfaattia pelkistävät bakteerit, joiden määrä lisääntyi orgaanisen fosforin ja typen sekä hapetus-pelkistys-olosuhteisiin reagoivan raudan ja tähän rautaan sitoutuneen fosforin lisääntyessä. Sulfaatin pelkistäjät vapauttavat välillisesti rautaan sitoutunutta fosforia, sillä ne tuottavat sulfidia, joka saostuu raudan kanssa ferrosulfideina hapettomissa sedimenteissä. Tästä syystä rautaa ei ole saatavilla sitomaan fosforia hapellisiin sedimenttikerroksiin, jolloin fosfori vapautuu meriveteen. Syvyyssuunnassa lisääntyivät Chloroflexi-pääjaksoon kuuluvat bakteerit, jotka olivat yleisiä keskisen Suomenlahden sedimentissä viimeisten 8000 vuoden aikana. Nämä bakteerit ovat todennäköisesti tärkeitä eloperäisen aineen loppuvaiheen hajotuksessa rehevöityneessä Itämeressä. Ilmeisesti Itämeressä eloperäisen aineen määrä on ollut suuri koko sen noin 8000 vuotisen historian aikana, mikä tekee Itämeren herkästi rehevöityväksi. Suolaisuuden ja hapettomuuden mittareina käytettävät uranium ja strontium selittivät bakteeriyhteisön muutoksen Litorina-merivaiheessa, joka oli Itämeren vaiheista suolaisin. Litorina-vaiheen yhteisöt erottuivat varhaisen ja myöhäisen Litorina-vaiheen yhteisöistä. Suolaisuuden aiheuttamat muutokset pohjan happipitoisuudessa selittivät myös sen, miksi bakteeriyhteisö, joka yksinkertaistui säännöllisesti syvyyssuunnassa, yhtäkkiä monipuolistui noin 6200−6600 vuotta vanhoissa Litorina-sedimenteissä. Keskisellä Suomenlahdella vesi on ollut tuolloin ilmeisesti suolaisimmillaan

Työikäisten niskakipupotilaiden fysioterapia Suomessa : osa 3 : hoitokäytännöt fysiatrian poliklinikoilla

Tämän opinnäytetyön tarkoituksena oli selvittää epäspesifin niskakivun fysioterapian hoitokäytäntöjä työikäisillä potilailla Suomessa. Niskakivun hoidosta on olemassa tutkittua tietoa, ja tässä työssä pohdimme kuinka hyvin näyttöön perustuva fysioterapia toteutuu fysiatrian poliklinikoilla. Työ on osa laajempaa tutkimusta, joka kattaa yhteensä neljä eri sektoria, joista muut osat keskittyivät terveyskeskuksiin (osa 1), yksityiseen sektoriin (osa 2) sekä kuntoutuslaitoksiin (osa 4). Opinnäytetyössä käytettiin internetissä täytettävää kyselylomaketta, jonka avulla fysioterapeutit vastasivat hoitokäytännöistä viimeisimmän niskakipupotilaansa kohdalla. Kysely toteutettiin 19 sairaanhoitopiirin alueella sijaitsevissa fysiatrian poliklinikoissa, joista vastauksia saatiin viidestä eri sairaanhoitopiiristä. Pienen vastausprosentin vuoksi tulosten analyysissä keskityttiin nostamaan esille vastauksien keskuudessa toisistaan eriäviä ja keskenään samanlaisia fysioterapiakäytäntöjä. Näitä käytäntöjä arvioidaan tutkittuun tietoon perustaen. Vastausten perusteella fysioterapeutit ovat käyttäneet monipuolisesti eri harjoitusvälineitä, joista vastuskuminauha oli eniten hyödynnetty väline. Myös ohjauksessa on käytetty monia eri menetelmiä, kuten verbaalista ohjausta, demonstrointia ja fasilitointia. Suuri osa fysioterapeuteista ohjeisti harjoitteita jokaisella käyntikerralla. Työssä ilmeni kehitystarpeita, joita olivat erityisesti korkean intensiteetin harjoitteiden ohjauksen vähäisyys, hoidon seurantakäyntien vähyys sekä liian lyhyet hoitojaksot. Johtopäätöksenä todetaan, että ainoastaan pieni osa vastaajista ohjasi potilailleen korkean intensiteetin niskalihasharjoitteita, vaikka niiden vaikuttavuus on tutkitusti tehokkaampaa kuin matalan intensiteetin harjoitteet. Hoidon seurantaa hyödynnettiin melko vähän sekä hoitojakson pituus jäi yleisesti liian lyhyeksi.The purpose of this Bachelor’s thesis was to examine clinical practices of non-specific neck pain in working age patients in Finland. There are several studies about treatment for neck pain and in this thesis we reflect on how well physiotherapy treatments base on different studies in physiatrics clinics. This study is part of a larger survey which includes a total of four different sectors, focusing on health care centres (1), the private sector (2) and rehabilitation centres (4), number three being physiatrics clinics reported in this paper. We interviewed physiotherapists by using an internet questionnaire in which they answered questions concerning their most recent neck pain patient. The survey was implemented in a total of 19 different health care districts, out of which five districts participated. Due to the small number of responses instead of using quantitative methods to analyze the data we decided to reflect on themes that appeared to be the most significant in the questionnaire. In conclusion, we aimed to speculate different physiotherapy conventions used in the treatment of neck pain patients based on previous studies. Based on the answers in the questionnaires, all of the physiotherapists used a wide variety of training equipment, mainly elastic bands, in the treatment of their most recent neck pain patients. Several methods such as verbal guidance, demonstration and facilitation were applied during treatment periods and the majority of the physiotherapists instructed their patients on every visit. However, we discovered that there were deficiencies in high intensity training, the amount of follow-ups and the length of the treatment period. High intensity training was only applied in a minority of the physiotherapists exercise therapies although it has been proven to be more efficient than low intensity training. In addition, the number of follow-ups after the treatment period was generally low and the treatment periods themselves were often short

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate

The widespread use of motor oil makes it a notable risk factor to cause scattered contamination in soil. The monitoring of microbial community dynamics can serve as a comprehensive tool to assess the ecological impact of contaminants and their disappearance in the ecosystem. Hence, a field study was conducted to monitor the ecological impact of used motor oil under different perennial cropping systems (fodder galega, brome grass, galega-brome grass mixture and bare fallow) in a boreal climate zone. Length heterogeneity PCR characterized a successional pattern in bacterial community following oil contamination over a four-year bioremediation period. Soil pH and electrical conductivity were associated with the shifts in bacterial community composition. Crops had no detectable effect on bacterial community composition or complexity. However, the legume fodder galega increased soil microbial biomass, expressed as soil total DNA. Oil contamination induced an abrupt change in bacterial community composition at the early stage, yet the effect did not last as long as the oil in soil. The successional variation in bacterial community composition can serve as a sensitive ecological indicator of oil contamination and remediation in situ. (C) 2015 Elsevier B.V. All rights reserved.Peer reviewe

Owners perception of acquiring infections through raw pet food: a comprehensive internet-based survey

Peer reviewe

Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor

The gut microbiome produces metabolites that interact with the aryl hydrocarbon receptor (AhR), a key regulator of immune homoeostasis in the gut(1,2). Here we show that oral exposure to graphene oxide (GO) modulates the composition of the gut microbiome in adult zebrafish, with significant differences in wild-type versus ahr2-deficient animals. Furthermore, GO was found to elicit AhR-dependent induction of cyp1a and homing of lck(+) cells to the gut in germ-free zebrafish larvae when combined with the short-chain fatty acid butyrate. To obtain further insights into the immune responses to GO, we used single-cell RNA sequencing to profile cells from whole germ-free embryos as well as cells enriched for lck. These studies provided evidence for the existence of innate lymphoid cell (ILC)-like cells(3) in germ-free zebrafish. Moreover, GO endowed with a 'corona' of microbial butyrate triggered the induction of ILC2-like cells with attributes of regulatory cells. Taken together, this study shows that a nanomaterial can influence the crosstalk between the microbiome and immune system in an AhR-dependent manner.Peer reviewe

Skin microbiota of oxazolone-induced contact hypersensitivity mouse model

Funding Information: K.M. received personal funding from Instrumentarium Science Foundation. The study was supported by grants from the Academy of Finland (decisions 307768 and 333178) admitted to P.K. and H.S. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors wish to acknowledge Prof. Otso Ovaskainen for providing help with HMSC, and CSC–IT Center for Science, Finland, for computational resources. The DNA sequencing service was provided by the Institute of Molecular Medicine Finland (FIMM) at the Helsinki Institute of Life Science and Biocenter Finland at the University of Helsinki. Publisher Copyright: © 2022 Mäenpää et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Contact allergy is a common skin allergy, which can be studied utilising contact hypersensitivity (CHS) animal model. However, it is not clear, whether CHS is a suitable model to investigate skin microbiota interactions. We characterised the effect of contact dermatitis on the skin microbiota and studied the biological effects of oxazolone (OXA) -induced inflammation on skin thickness, immune cell numbers and changes of the microbiota in CHS mouse model (n = 72) for 28 days. Through 16S rRNA gene sequencing we defined the composition of bacterial communities and associations of bacteria with inflammation. We observed that the vehicle solution of acetone and olive oil induced bacterial community changes on day 1, and OXA-induced changes were observed mainly on day 7. Many of the notably enriched bacteria present in the OXA-challenged positive group represented the genus Faecalibaculum which were most likely derived from the cage environment. Additionally, skin inflammation correlated negatively with Streptococcus, which is considered a native skin bacterium, and positively with Muribacter muris, which is typical in oral environment. Skin inflammation favoured colonisation of cage-derived faecal bacteria, and additionally mouse grooming transferred oral bacteria on the skin. Due to the observed changes, we conclude that CHS model could be used for certain skin microbiome-related research set-ups. However, since vehicle exposure can alter the skin microbiome as such, future studies should include considerations such as careful control sampling and statistical tests to account for potential confounding factors.Peer reviewe

Sediment Bacterial Communities Reflect the History of a Sea Basin

Peer reviewe

Contrasting microbiotas between Finnish and Estonian infants : exposure to Acinetobacter may contribute to the allergy gap

Background Allergic diseases are more common in Finland than in Estonia, which-according to the biodiversity hypothesis-could relate to differences in early microbial exposures. Methods We aimed at defining possible microbial perturbations preceding early atopic sensitization. Stool, nasal and skin samples of 6-month-old DIABIMMUNE study participants with HLA susceptibility to type 1 diabetes were collected. We compared microbiotas of sensitized (determined by specific IgE results at 18 months of age) and unsensitized Estonian and Finnish children. Results Sensitization was differentially targeted between populations, as egg-specific and birch pollen-specific IgE was more common in Finland. Microbial diversity and community composition also differed; the genusAcinetobacterwas more abundant in Estonian skin and nasal samples. Particularly, the strain-level profile ofAcinetobacter lwoffiiwas more diverse in Estonian samples. Early microbiota was not generally associated with later sensitization. Microbial composition tended to differ between children with or without IgE-related sensitization, but only in Finland. While land-use pattern (ie green areas vs. urban landscapes around the children's homes) was not associated with microbiota as a whole, it associated with the composition of the genusAcinetobacter. Breastfeeding affected gut microbial composition and seemed to protect from sensitization. Conclusions In accordance with the biodiversity hypothesis, our results support disparate early exposure to environmental microbes between Finnish and Estonian children and suggest a significant role of the genusAcinetobacterin the allergy gap between the two populations. The significance of the observed differences for later allergic sensitization remains open.Peer reviewe

Increasing oxygen deficiency changes rare and moderately abundant bacterial communities in coastal soft sediments

Coastal hypoxia is a major environmental problem worldwide. Hypoxia-induced changes in sediment bacterial communities harm marine ecosystems and alter biogeochemical cycles. Nevertheless, the resistance of sediment bacterial communities to hypoxic stress is unknown. We investigated changes in bacterial communities during hypoxic-anoxic disturbance by artificially inducing oxygen deficiency to the seafloor for 0, 3, 7, and 48 days, with subsequent molecular biological analyses. We further investigated relationships between bacterial communities, benthic macrofauna and nutrient effluxes across the sediment-water-interface during hypoxic-anoxic stress, considering differentially abundant operational taxonomic units (OTUs). The composition of the moderately abundant OTUs changed significantly after seven days of oxygen deficiency, while the abundant and rare OTUs first changed after 48 days. High bacterial diversity maintained the resistance of the communities during oxygen deficiency until it dropped after 48 days, likely due to anoxia-induced loss of macrofaunal diversity and bioturbation. Nutrient fluxes, especially ammonium, correlated positively with the moderate and rare OTUs, including potential sulfate reducers. Correlations may reflect bacteria-mediated nutrient effluxes that accelerate eutrophication. The study suggests that even slightly higher bottom-water oxygen concentrations, which could sustain macrofaunal bioturbation, enable bacterial communities to resist large compositional changes and decrease the harmful consequences of hypoxia in marine ecosystems.Peer reviewe

Bacteria Contribute to Sediment Nutrient Release and Reflect Progressed Eutrophication-Driven Hypoxia in an Organic-Rich Continental Sea

Peer reviewe