Browsing by Subject "RIBOSOMAL-RNA"

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  • Sobenin, Igor A.; Sazonova, Margarita A.; Postnov, Anton Y.; Salonen, Jukka; Bobryshev, Yuri V.; Orekhov, Alexander N. (2013)
  • Pershina, Elizaveta; Valkonen, Jari Pekka Tapani; Kurki, Paivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny (2015)
    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.
  • Zamora, Juan Carlos; Svensson, Mans; Kirschner, Roland; Olariaga, Ibai; Ryman, Svengunnar; Alberto Parra, Luis; Geml, Jozsef; Rosling, Anna; Adamcik, Slavomir; Ahti, Teuvo; Aime, M. Catherine; Ainsworth, A. Martyn; Albert, Laszlo; Alberto, Edgardo; Garcia, Alberto Altes; Ageev, Dmitry; Agerer, Reinhard; Aguirre-Hudson, Begona; Ammirati, Joe; Andersson, Harry; Angelini, Claudio; Antonin, Vladimir; Aoki, Takayuki; Aptroot, Andre; Argaud, Didier; Sosa, Blanca Imelda Arguello; Aronsen, Arne; Arup, Ulf; Asgari, Bita; Assyov, Boris; Atienza, Violeta; Bandini, Ditte; Baptista-Ferreira, Joao Luis; Baral, Hans-Otto; Baroni, Tim; Barreto, Robert Weingart; Baker, Henry; Bell, Ann; Bellanger, Jean-Michel; Bellu, Francesco; Bemmann, Martin; Bendiksby, Mika; Bendiksen, Egil; Bendiksen, Katriina; Benedek, Lajos; Beresova-Guttova, Anna; Berger, Franz; Berndt, Reinhard; Bernicchia, Annarosa; Biketova, Alona Yu; Bizio, Enrico; Bjork, Curtis; Boekhout, Teun; Boertmann, David; Bohning, Tanja; Boittin, Florent; Boluda, Carlos G.; Boomsluiter, Menno W.; Borovicka, Jan; Brandrud, Tor Erik; Braun, Uwe; Brodo, Irwin; Bulyonkova, Tatiana; Burdsall, Harold H.; Buyck, Bart; Burgaz, Ana Rosa; Calatayud, Vicent; Callac, Philippe; Campo, Emanuele; Candusso, Massimo; Capoen, Brigitte; Carbo, Joaquim; Carbone, Matteo; Castaneda-Ruiz, Rafael F.; Castellano, Michael A.; Chen, Jie; Clerc, Philippe; Consiglio, Giovanni; Corriol, Gilles; Courtecuisse, Regis; Crespo, Ana; Cripps, Cathy; Crous, Pedro W.; da Silva, Gladstone Alves; da Silva, Meiriele; Dam, Marjo; Dam, Nico; Dammrich, Frank; Das, Kanad; Davies, Linda; De Crop, Eske; De Kesel, Andre; De Lange, Ruben; Bonzi, Barbara De Madrignac; dela Cruz, Thomas Edison E.; Delgat, Lynn; Demoulin, Vincent; Desjardin, Dennis E.; Diederich, Paul; Dima, Balint; Dios, Maria Martha; Divakar, Pradeep Kumar; Douanla-Meli, Clovis; Douglas, Brian; Drechsler-Santos, Elisandro Ricardo; Dyer, Paul S.; Eberhardt, Ursula; Ertz, Damien; Esteve-Raventos, Fernando; Salazar, Javier Angel Etayo; Evenson, Vera; Eyssartier, Guillaume; Farkas, Edit; Favre, Alain; Fedosova, Anna G.; Filippa, Mario; Finy, Peter; Flakus, Adam; Fos, Simon; Fournier, Jacques; Fraiture, Andre; Franchi, Paolo; Molano, Ana Esperanza Franco; Friebes, Gernot; Frisch, Andreas; Fryday, Alan; Furci, Giuliana; Marquez, Ricardo Galan; Garbelotto, Matteo; Garcia-Martin, Joaquina Maria; Otalora, Monica A. Garcia; Sanchez, Dania Garcia; Gardiennet, Alain; Garnica, Sigisfredo; Benavent, Isaac Garrido; Gates, Genevieve; Gerlach, Alice da Cruz Lima; Ghobad-Nejhad, Masoomeh; Gibertoni, Tatiana B.; Grebenc, Tine; Greilhuber, Irmgard; Grishkan, Bella; Groenewald, Johannes Z.; Grube, Martin; Gruhn, Gerald; Gueidan, Cecile; Gulden, Gro; Gusmao, Luis F. P.; Hafellner, Josef; Hairaud, Michel; Halama, Marek; Hallenberg, Nils; Halling, Roy E.; Hansen, Karen; Harder, Christoffer Bugge; Heilmann-Clausen, Jacob; Helleman, Stip; Henriot, Alain; Hernandez-Restrepo, Margarita; Herve, Raphael; Hobart, Caroline; Hoffmeister, Mascha; Hoiland, Klaus; Holec, Jan; Holien, Hakon; Hughes, Karen; Hubka, Vit; Huhtinen, Seppo; Ivancevic, Boris; Jagers, Marian; Jaklitsch, Walter; Jansen, AnnaElise; Jayawardena, Ruvishika S.; Jeppesen, Thomas Stjernegaard; Jeppson, Mikael; Johnston, Peter; Jorgensen, Per Magnus; Karnefelt, Ingvar; Kalinina, Liudmila B.; Kantvilas, Gintaras; Karadelev, Mitko; Kasuya, Taiga; Kautmanova, Ivona; Kerrigan, Richard W.; Kirchmair, Martin; Kiyashko, Anna; Knapp, Daniel G.; Knudsen, Henning; Knudsen, Kerry; Knutsson, Tommy; Kolarik, Miroslav; Koljalg, Urmas; Kosuthova, Alica; Koszka, Attila; Kotiranta, Heikki; Kotkova, Vera; Koukol, Ondrej; Kout, Jiri; Kovacs, Gabor M.; Kriz, Martin; Kruys, Asa; Kudera, Viktor; Kudzma, Linas; Kuhar, Francisco; Kukwa, Martin; Kumar, T. K. Arun; Kunca, Vladimir; Kusan, Ivana; Kuyper, Thomas W.; Lado, Carlos; Laessoe, Thomas; Laine, Patrice; Langer, Ewald; Larsson, Ellen; Larsson, Karl-Henrik; Laursen, Gary; Lechat, Christian; Lee, Serena; Lendemer, James C.; Levin, Laura; Lindemann, Uwe; Lindstrom, Hakan; Liu, Xingzhong; Hernandez, Regulo Carlos Llarena; Llop, Esteve; Locsmandi, Csaba; Lodge, Deborah Jean; Loizides, Michael; Lokos, Laszlo; Luangsa-ard, Jennifer; Luderitz, Matthias; Lumbsch, Thorsten; Lutz, Matthias; Mahoney, Dan; Malysheva, Ekaterina; Malysheva, Vera; Manimohan, Patinjareveettil; Mann-Felix, Yasmina; Marques, Guilhermina; Martinez-Gil, Ruben; Marson, Guy; Mata, Gerardo; Matheny, P. Brandon; Mathiassen, Geir Harald; Matocec, Neven; Mayrhofer, Helmut; Mehrabi, Mehdi; Melo, Ireneia; Mesic, Armin; Methven, Andrew S.; Miettinen, Otto; Romero, Ana M. Millanes; Miller, Andrew N.; Mitchell, James K.; Moberg, Roland; Moreau, Pierre-Arthur; Moreno, Gabriel; Morozova, Olga; Morte, Asuncion; Muggia, Lucia; Gonzalez, Guillermo Munoz; Myllys, Leena; Nagy, Istvan; Nagy, Laszlo G.; Neves, Maria Alice; Niemela, Tuomo; Nimis, Pier Luigi; Niveiro, Nicolas; Noordeloos, Machiel E.; Nordin, Anders; Noumeur, Sara Raouia; Novozhilov, Yuri; Nuytinck, Jorinde; Ohenoja, Esteri; Fiuza, Patricia Oliveira; Orange, Alan; Ordynets, Alexander; Ortiz-Santana, Beatriz; Pacheco, Leticia; Pal-Fam, Ferenc; Palacio, Melissa; Palice, Zdenek; Papp, Viktor; Partel, Kadri; Pawlowska, Julia; Paz, Aurelia; Peintner, Ursula; Pennycook, Shaun; Pereira, Olinto Liparini; Daniels, Pablo Perez; Capella, Miguel A. Perez-De-Gregorio; del Amo, Carlos Manuel Perez; Gorjon, Sergio Perez; Perez-Ortega, Sergio; Perez-Vargas, Israel; Perry, Brian A.; Petersen, Jens H.; Petersen, Ronald H.; Pfister, Donald H.; Phukhamsakda, Chayanard; Piatek, Marcin; Piepenbring, Meike; Pino-Bodas, Raquel; Esquivel, Juan Pablo Pinzon; Pirot, Paul; Popov, Eugene S.; Popoff, Orlando; Alvaro, Maria Prieto; Printzen, Christian; Psurtseva, Nadezhda; Purahong, Witoon; Quijada, Luis; Rambold, Gerhard; Ramirez, Natalia A.; Raja, Huzefa; Raspe, Olivier; Raymundo, Tania; Reblova, Martina; Rebriev, Yury A.; Garcia, Juan de Dios Reyes; Ripoll, Miguel Angel Ribes; Richard, Franck; Richardson, Mike J.; Rico, Victor J.; Robledo, Gerardo Lucio; Barbosa, Flavia Rodrigues; Rodriguez-Caycedo, Cristina; Rodriguez-Flakus, Pamela; Ronikier, Anna; Casas, Luis Rubio; Rusevska, Katerina; Saar, Gunter; Saar, Irja; Salcedo, Isabel; Martinez, Sergio M. Salcedo; Montoya, Carlos A. Salvador; Sanchez-Ramirez, Santiago; Sandoval-Sierra, J. Vladimir; Santamaria, Sergi; Monteiro, Josiane Santana; Schroers, Hans Josef; Schulz, Barbara; Schmidt-Stohn, Geert; Schumacher, Trond; Senn-Irlet, Beatrice; Sevcikova, Hana; Shchepin, Oleg; Shirouzu, Takashi; Shiryaev, Anton; Siepe, Klaus; Sir, Esteban B.; Sohrabi, Mohammad; Soop, Karl; Spirin, Viacheslav; Spribille, Toby; Stadler, Marc; Stalpers, Joost; Stenroos, Soili; Suija, Ave; Sunhede, Stellan; Svantesson, Sten; Svensson, Sigvard; Svetasheva, Tatyana Yu; Swierkosz, Krzysztof; Tamm, Heidi; Taskin, Hatira; Taudiere, Adrien; Tedebrand, Jan-Olof; Lahoz, Raul Tena; Temina, Marina; Thell, Arne; Thines, Marco; Thor, Goren; Thus, Holger; Tibell, Leif; Tibell, Sanja; Timdal, Einar; Tkalcec, Zdenko; Tonsberg, Tor; Trichies, Gerard; Triebel, Dagmar; Tsurykau, Andrei; Tulloss, Rodham E.; Tuovinen, Veera; Sosa, Miguel Ulloa; Urcelay, Carlos; Valade, Francois; Garza, Ricardo Valenzuela; van den Boom, Pieter; Van Vooren, Nicolas; Vasco-Palacios, Aida M.; Vauras, Jukka; Santos, Juan Manuel Velasco; Vellinga, Else; Verbeken, Annemieke; Vetlesen, Per; Vizzini, Alfredo; Voglmayr, Hermann; Volobuev, Sergey; von Brackel, Wolfgang; Voronina, Elena; Walther, Grit; Watling, Roy; Weber, Evi; Wedin, Mats; Weholt, Oyvind; Westberg, Martin; Yurchenko, Eugene; Zehnalek, Petr; Zhang, Huang; Zhurbenko, Mikhail P.; Ekmani, Stefan (2018)
    Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
  • Liu, Liwei; Herfindal, Lars; Jokela, Jouni; Shishido, Tania Keiko; Wahlsten, Matti; Doskeland, Stein Ove; Sivonen, Kaarina (2014)
  • Aalto, Sanni; Saarenheimo, Jatta; Arvola, Lauri; Tiirola, Marja; Huotari, Jussi; Rissanen, Antti (2019)
    Streams have an important role in regulating nitrogen (N) transportation from terrestrial ecosystems to downstream waters. Here, we examined how catchment land-use affects potential denitrification rates and the function and composition of denitrifier communities in boreal stream sediments, using stable isotope incubations and qPCR and 454-pyrosequencing targeted on nirS, nirK and nosZ genes. Although land-use influenced the water chemistry as higher nitrite+nitrate (NOx)-concentration at the agriculture-affected sampling point, sediment organic matter content was found to be the key factor in regulating potential denitrification rates. However, the abundance as well as the diversity and community composition of denitrifying microbes, and genetic N2O production potential (the ratio between nirS+nirK and nosZ gene abundances) were connected to both NOx- and sediment quality. Overall, our results suggest that catchment land-use-driven changes in N and carbon availability affect the denitrification rates, and possibly N-2:N2O production ratio, in boreal streams, through altering denitrifier abundance and community composition.
  • Nummi, Maaret; Mannonen, Laura; Puolakkainen, Mirja (2015)
    The aim of this study was to improve detection of Mycoplasma pneumoniae and Chlamydia pneumoniae in clinical specimens by developing a multiplex real-time PCR assay that includes identification of macrolide-resistant M. pneumoniae. Novel assays targeting a M. pneumoniae conserved hypothetical protein gene, M. pneumoniae 23S rRNA gene mutations associated with macrolide resistance and human beta-globin gene (an endogenous internal control) were designed and combined with a previously published C. pneumoniae PCR targeting ompA gene. The resulting quadraplex PCR was validated with a panel of clinical specimens supplemented with external quality assessment specimens, simulated specimens and various bacterial and viral strains. The obtained results were compared to those obtained by reference PCRs or confirmed by sequencing (typing of macrolide resistance). The novel multiplex PCR assay was in 100 % agreement with reference PCRs. Four M. pneumoniae strains with macrolide resistance-associated mutations were identified among 42 strains, which comprises 9.5 % of the study material. Amplification of an internal control excluded sample-derived inhibition possibly leading to false-negative reporting. In conclusion, we have developed a resources conserving multiplex real-time PCR assay for simultaneous detection of M. pneumoniae, C. pneumoniae and the most common mutations leading to macrolide resistance in M. pneumoniae. The assay is a widely useful tool for detection of these respiratory pathogens and will also shed light on the occurrence of macrolide resistance in M. pneumoniae.
  • Saarenheimo, Jatta; Rissanen, Antti J.; Arvola, Lauri; Nykänen, Hannu; Lehmann, Moritz F.; Tiirola, Marja (2015)
    We studied potential links between environmental factors, nitrous oxide (N2O) accumulation, and genetic indicators of nitrite and N2O reducing bacteria in 12 boreal lakes. Denitrifying bacteria were investigated by quantifying genes encoding nitrite and N2O reductases (nirS/nirK and nosZ, respectively, including the two phylogenetically distinct clades nosZ(I) and nosZ(II)) in lake sediments. Summertime N2O accumulation and hypolimnetic nitrate concentrations were positively correlated both at the inter-lake scale and within a depth transect of an individual lake (Lake Vanajavesi). The variability in the individual nirS, nirK, nosZ(I), and nosZ(II) gene abundances was high (up to tenfold) among the lakes, which allowed us to study the expected links between the ecosystem's nir-vs-nos gene inventories and N2O accumulation. Inter-lake variation in N2O accumulation was indeed connected to the relative abundance of nitrite versus N2O reductase genes, i.e. the (nirS+nirK)/nosZ(I) gene ratio. In addition, the ratios of (nirS+ nirK)/nosZ(I) at the inter-lake scale and (nirS+ nirK)/nosZ(I+II) within Lake Vanajavesi correlated positively with nitrate availability. The results suggest that ambient nitrate concentration can be an important modulator of the N2O accumulation in lake ecosystems, either directly by increasing the overall rate of denitrification or indirectly by controlling the balance of nitrite versus N2O reductase carrying organisms.
  • Broman, Elias; Bonaglia, Stefano; Norkko, Alf; Creer, Simon; Nascimento, Francisco J. A. (2021)
    Benthic macrofauna is regularly used in monitoring programmes, however the vast majority of benthic eukaryotic biodiversity lies mostly in microscopic organisms, such as meiofauna (invertebrates <1 mm) and protists, that rapidly responds to environmental change. These communities have traditionally been hard to sample and handle in the laboratory, but DNA sequencing has made such work less time consuming. While DNA sequencing captures both alive and dead organisms, environmental RNA (eRNA) better targets living organisms or organisms of recent origin in the environment. Here, we assessed the biodiversity of three known bioindicator microeukaryote groups (nematodes, foraminifera, and ciliates) in sediment samples collected at seven coastal sites along an organic carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing can be used to simultaneously detect differences in (i) biodiversity of multiple microeukaryotic communities; and (ii) functional feeding traits of nematodes. Results showed that biodiversity was lower for nematodes and foraminifera in high OC (6.2%-6.9%), when compared to low OC sediments (1.2%-2.8%). Dissimilarity in community composition increased for all three groups between Low OC and High OC, as well as the classified feeding type of nematode genera (with more nonselective deposit feeders in high OC sediment). High relative abundant genera included nematodeSabatieriaand foraminiferaElphidiumin high OC, andCryptocaryon-like ciliates in low OC sediments. Considering that future sequencing technologies are likely to decrease in cost, the use of eRNA shotgun sequencing to assess biodiversity of benthic microeukaryotes could be a powerful tool in recurring monitoring programmes.
  • Pärnänen, Katariina; Karkman, Antti; Hultman, Jenni; Lyra, Christina; Bengtsson-Palme, Johan; Larsson, D. G. Joakim; Rautava, Samuli; Isolauri, Erika; Salminen, Seppo; Kumar, Himanshu; Satokari, Reetta; Virta, Marko (2018)
    The infant gut microbiota has a high abundance of antibiotic resistance genes (ARGs) compared to adults, even in the absence of antibiotic exposure. Here we study potential sources of infant gut ARGs by performing metagenomic sequencing of breast milk, as well as infant and maternal gut microbiomes. We find that fecal ARG and mobile genetic element (MGE) profiles of infants are more similar to those of their own mothers than to those of unrelated mothers. MGEs in mothers' breast milk are also shared with their own infants. Termination of breastfeeding and intrapartum antibiotic prophylaxis of mothers, which have the potential to affect microbial community composition, are associated with higher abundances of specific ARGs, the composition of which is largely shaped by bacterial phylogeny in the infant gut. Our results suggest that infants inherit the legacy of past antibiotic consumption of their mothers via transmission of genes, but microbiota composition still strongly impacts the overall resistance load.
  • Shi, Yonghong; Posse, Viktor; Zhu, Xuefeng; Hyvärinen, Anne K.; Jacobs, Howard T.; Falkenberg, Maria; Gustafsson, Claes M. (2016)
    During replication of nuclear ribosomal DNA (rDNA), clashes with the transcription apparatus can cause replication fork collapse and genomic instability. To avoid this problem, a replication fork barrier protein is situated downstream of rDNA, there preventing replication in the direction opposite rDNA transcription. A potential candidate for a similar function in mitochondria is the mitochondrial transcription termination factor 1 (MTERF1, also denoted mTERF), which binds to a sequence just downstream of the ribosomal transcription unit. Previous studies have shown that MTERF1 prevents antisense transcription over the ribosomal RNA genes, a process which we here show to be independent of the transcription elongation factor TEFM. Importantly, we now demonstrate that MTERF1 arrests mitochondrial DNA (mtDNA) replication with distinct polarity. The effect is explained by the ability of MTERF1 to act as a directional contrahelicase, blocking mtDNA unwinding by the mitochondrial helicase TWINKLE. This conclusion is also supported by in vivo evidence that MTERF1 stimulates TWINKLE pausing. We conclude that MTERF1 can direct polar replication fork arrest in mammalian mitochondria.
  • Hess, Stefanie; Kneis, David; Osterlund, Tobias; Li, Bing; Kristiansson, Erik; Berendonk, Thomas U. (2019)
    Airplane sanitary facilities are shared by an international audience. We hypothesized the corresponding sewage to be an extraordinary source of antibiotic-resistant bacteria (ARB) and resistance genes (ARG) in terms of diversity and quantity. Accordingly, we analyzed ARG and ARB in airplane-borne sewage using complementary approaches: metagenomics, quantitative polymerase chain reaction (qPCR), and cultivation. For the purpose of comparison, we also quantified ARG and ARB in the inlets of municipal treatment plants with and without connection to airports. As expected, airplane sewage contained an extraordinarily rich set of mobile ARG, and the relative abundances of genes were mostly increased compared to typical raw sewage of municipal origin. Moreover, combined resistance against third-generation cephalosporins, fluorochinolones, and aminoglycosides was unusually common (28.9%) among Escherichia coli isolated from airplane sewage. This percentage exceeds the one reported for German clinical isolates by a factor of 8. Our findings suggest that airplane-borne sewage can effectively contribute to the fast and global spread of antibiotic resistance.
  • Grönroos, Mira; Parajuli, Anirudra; Laitinen, Olli H.; Roslund, Marja Irmeli; Vari, Heli Kristiina; Hyöty, Heikki; Puhakka, Riikka; Sinkkonen, Aki Tapio (2019)
    Immune-mediated diseases have increased during the last decades in urban environments. The hygiene hypothesis suggests that increased hygiene level and reduced contacts with natural biodiversity are related to the increase in immune-mediated diseases. We tested whether short-time contact with microbiologically diverse nature-based materials immediately change bacterial diversity on human skin. We tested direct skin contact, as two volunteers rubbed their hands with sixteen soil and plant based materials, and an exposure via fabric packets filled with moss material. Skin swabs were taken before and after both exposures. Next-generation sequencing showed that exposures increased, at least temporarily, the total diversity of skin microbiota and the diversity of Acidobacteria, Actinobacteria, Bacteroidetes, Proteobacteria and Alpha-, Beta- and Gammaproteobacteria suggesting that contact with nature-based materials modify skin microbiome and increase skin microbial diversity. Until now, approaches to cure or prevent immune system disorders using microbe-based treatments have been limited to use of a few microbial species. We propose that nature-based materials with high natural diversity, such as the materials tested here, might be more effective in modifying human skin microbiome, and eventually, in reducing immune system disorders. Future studies should investigate how long-term changes in skin microbiota are achieved and if the exposure induces beneficial changes in the immune system markers.
  • Hiltunen, Lea H.; Tarvainen, Oili; Kelloniemi, Jani; Tanskanen, Jaakko; Karhu, Jouni; Valkonen, Jari P. T. (2021)
    Disease suppressive soils are important for managing soil-borne diseases that cannot be controlled with chemicals. One such disease is the potato common scab caused by Streptomyces species. Suppressiveness against common scab can develop spontaneously in fields where potato is grown for years without interruption, and this has been attributed to non-pathogenic Streptomyces strains. Streptomyces spp. have been used as inoculants in biological control, but their long-term effects have gained less attention. In our previous studies, a nonpathogenic Streptomyces strain (Str272) isolated from a potato common scab lesion suppressed common scab in field trials lasting over 5 years. In this study, bacterial communities in the tuberosphere i.e. in the soil adjacent to potato tubers, were analysed by next generation sequencing (NGS). The aim was to compare bacterial communities in untreated control plots to those in which seed tubers were treated with Str272 in one or several growing seasons. Str272 applications increased soil bacterial diversity and affected the bacterial composition in the potato tuberosphere. The most pronounced differences were observed between the untreated control and the treatments in which the antagonist had been applied in three or four consecutive years. The differences remained similar until the following growing season. Bacterial composition after repeated antagonist applications was associated with lower common scab severity. The antagonist applications had no or only slight effect on the number or abundance of OTUs belonging to Actinobacteria or Streptomyces, and no differences in quantities of pathogenic Streptomyces populations were detected by qPCR. This indicates that suppression of common scab by Str272 may not be based on direct effect on the common scab pathogens but is more likely to be associated with the alterations of the soil bacterial community. The most abundant bacteria phyla in the potato tuberosphere were Actinobacteria, Proteobacteria and Acidobacteria. However, the OTUs responding greatest to the antagonist treatments belonged to Bacterioidetes and Gemmatimonadetes. Results indicate that repeated applications of Str272 can change the bacterial community in the potato tuberosphere and lead to development of soil that is suppressive against potato common scab for several growing seasons after the last application.
  • Vetterli, Adrien; Hietanen, Susanna; Leskinen, Elina (2016)
    The diversity and dynamics of ammonia-oxidizing bacteria (AOB) and archaea (AOA) nitrifying communities in the sediments of the eutrophic Gulf of Finland (GoF) were investigated. Using clone libraries of ammonia monooxygenase (amoA) gene fragments and terminal restriction fragment length polymorphism (TRFLP), we found a low richness of both AOB and AOA. The AOB amoA phylogeny matched that of AOB 16S ribosomal genes from the same samples. AOA communities were characterized by strong spatial variation while AOB communities showed notable temporal patterns. At open sea sites, where transient anoxic conditions prevail, richness of both AOA and AOB was lowest and communities were dominated by organisms with gene signatures unique to the GoF. Given the importance of nitrification as a link between the fixation of nitrogen and its removal from aquatic environments, the low diversity of ammonia-oxidizing microbes across the GoF could be of relevance for ecosystem resilience in the face of rapid global environmental changes. (C) 2015 Elsevier Ltd. All rights reserved.
  • Dicksved, Johan; Ellstrom, Patrik; Engstrand, Lars; Rautelin, Hilpi (2014)
  • Thrall, Peter H.; Laine, Anna-Liisa; Broadhurst, Linda M.; Bagnall, David J.; Brockwell, John (2011)
  • Parajuli, Anirudra; Gronroos, Mira; Kauppi, Sari; Plociniczak, Tomasz; Roslund, Marja I.; Galitskaya, Polina; Laitinen, Olli H.; Hyöty, Heikki; Jumpponen, Ari; Strömmer, Rauni; Romantschuk, Martin; Hui, Nan; Sinkkonen, Aki (2017)
    Long-term exposure to polyaromatic hydrocarbons (PAHs) has been connected to chronic human health disorders. It is also well-known that i) PAH contamination alters soil bacterial communities, ii) human microbiome is associated with environmental microbiome, and iii) alteration in the abundance of members in several bacterial phyla is associated with adverse or beneficial human health effects. We hypothesized that soil pollution by PAHs altered soil bacterial communities that had known associations with human health. The rationale behind our study was to increase understanding and potentially facilitate reconsidering factors that lead to health disorders in areas characterized by PAH contamination. Large containers filled with either spruce forest soil, pine forest soil, peat, or glacial sand were left to incubate or contaminated with creosote. Biological degradation of PAHs was monitored using GC-MS, and the bacterial community composition was analyzed using 454 pyrosequencing. Proteobacteria had higher and Actinobacteria and Bacteroidetes had lower relative abundance in creosote contaminated soils than in non-contaminated soils. Earlier studies have demonstrated that an increase in the abundance of Proteobacteria and decreased abundance of the phyla Actinobacteria and Bacteroidetes are particularly associated with adverse health outcomes and immunological disorders. Therefore, we propose that pollution-induced shifts in natural soil bacterial community, like in PAH-polluted areas, can contribute to the prevalence of chronic diseases. We encourage studies that simultaneously address the classic "adverse toxin effect" paradigm and our novel "altered environmental microbiome" hypothesis.
  • Amiryousefi, Ali; Hyvönen, Jaakko Tapani; Poczai, Péter (2018)
    Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp). It consists of 112 unique genes from which 81 are protein-coding, 27 tRNA and four rRNA genes. All bittersweet plastid genes including non-functional ones and even intergenic spacer regions are transcribed in primary plastid transcripts covering 95.22% of the genome. These are later substantially edited in a post-transcriptional phase to activate gene functions. By comparing the bittersweet plastid genome with all available Solanaceae sequences we found that gene content and synteny are highly conserved across the family. During genome comparison we have identified several annotation errors, which we have corrected in a manual curation process then we have identified the major plastid genome structural changes in Solanaceae. Interpreted in a phylogenetic context they seem to provide additional support for larger clades. The plastid genome sequence of bittersweet could help to benchmark Solanaceae plastid genome annotations and could be used as a reference for further studies. Such reliable annotations are important for gene diversity calculations, synteny map constructions and assigning partitions for phylogenetic analysis with de novo sequenced plastomes of Solanaceae.
  • Stsepetova, Jelena; Baranova, Juliana; Simm, Jaak; Parm, Ulle; Rööp, Tiiu; Sokmann, Sandra; Korrovits, Paul; Jaagura, Madis; Rosenstein, Karin; Salumets, Andres; Mandar, Reet (2020)
    Background Only a few microbial studies have conducted in IVF (in vitro fertilization), showing the high-variety bacterial contamination of IVF culture media to cause damage to or even loss of cultured oocytes and embryos. We aimed to determine the prevalence and counts of bacteria in IVF samples, and to associate them with clinical outcome. Methods The studied samples from 50 infertile couples included: raw (n = 48), processed (n = 49) and incubated (n = 50) sperm samples, and IVF culture media (n = 50). The full microbiome was analyzed by 454 pyrosequencing and quantitative analysis by real-time quantitative PCR. Descriptive statistics, t-, Mann-Whitney tests and Spearman's correlation were used for comparison of studied groups. Results The study involved normozoospermic men. Normal vaginal microbiota was present in 72.0% of female partners, while intermediate microbiota and bacterial vaginosis were diagnosed in 12.0 and 16.0%, respectively. The decreasing bacterial loads were found in raw (35.5%), processed (12.0%) and sperm samples used for oocyte insemination (4.0%), and in 8.0% of IVF culture media. The most abundant genera of bacteria in native semen and IVF culture media were Lactobacillus, while in other samples Alphaproteobacteria prevailed. Staphylococcus sp. was found only in semen from patients with inflammation. Phylum Bacteroidetes was in negative correlation with sperm motility and Alphaproteobacteria with high-quality IVF embryos. Conclusion Our study demonstrates that IVF does not occur in a sterile environment. The prevalent bacteria include classes Bacilli in raw semen and IVF culture media, Clostridia in processed and Bacteroidia in sperm samples used for insemination. The presence of Staphylococcus sp. and Alphaproteobacteria associated with clinical outcomes, like sperm and embryo quality.
  • Somervuo, Panu; Koskela, Sonja; Pennanen, Juho; Nilsson, R. Henrik; Ovaskainen, Otso (2016)
    Motivation: When targeted to a barcoding region, high-throughput sequencing can be used to identify species or operational taxonomical units from environmental samples, and thus to study the diversity and structure of species communities. Although there are many methods which provide confidence scores for assigning taxonomic affiliations, it is not straightforward to translate these values to unbiased probabilities. We present a probabilistic method for taxonomical classification (PROTAX) of DNA sequences. Given a pre-defined taxonomical tree structure that is partially populated by reference sequences, PROTAX decomposes the probability of one to the set of all possible outcomes. PROTAX accounts for species that are present in the taxonomy but that do not have reference sequences, the possibility of unknown taxonomical units, as well as mislabeled reference sequences. PROTAX is based on a statistical multinomial regression model, and it can utilize any kind of sequence similarity measures or the outputs of other classifiers as predictors. Results: We demonstrate the performance of PROTAX by using as predictors the output from BLAST, the phylogenetic classification software TIPP, and the RDP classifier. We show that PROTAX improves the predictions of the baseline implementations of TIPP and RDP classifiers, and that it is able to combine complementary information provided by BLAST and TIPP, resulting in accurate and unbiased classifications even with very challenging cases such as 50% mislabeling of reference sequences.