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 L.; 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.
  • Parnanen, Katariina M. M.; Hultman, Jenni; Markkanen, Melina; Satokari, Reetta; Rautava, Samuli; Lamendella, Regina; Wright, Justin; McLimans, Christopher J.; Kelleher, Shannon L.; Virta, Marko P. (2022)
    Background Infants are at a high risk of acquiring fatal infections, and their treatment relies on functioning antibiotics. Antibiotic resistance genes (ARGs) are present in high numbers in antibiotic-naive infants' gut microbiomes, and infant mortality caused by resistant infections is high. The role of antibiotics in shaping the infant resistome has been studied, but there is limited knowledge on other factors that affect the antibiotic resistance burden of the infant gut. Objectives Our objectives were to determine the impact of early exposure to formula on the ARG load in neonates and infants born either preterm or full term. Our hypotheses were that diet causes a selective pressure that influences the microbial community of the infant gut, and formula exposure would increase the abundance of taxa that carry ARGs. Methods Cross-sectionally sampled gut metagenomes of 46 neonates were used to build a generalized linear model to determine the impact of diet on ARG loads in neonates. The model was cross-validated using neonate metagenomes gathered from public databases using our custom statistical pipeline for cross-validation. Results Formula-fed neonates had higher relative abundances of opportunistic pathogens such as Staphylococcus aureus, Staphylococcus epidermidis, Klebsiella pneumoniae, Klebsiella oxytoca, and Clostridioides difficile. The relative abundance of ARGs carried by gut bacteria was 69% higher in the formula-receiving group (fold change, 1.69; 95% CI: 1.12-2.55; P = 0.013; n = 180) compared to exclusively human milk-fed infants. The formula-fed infants also had significantly less typical infant bacteria, such as Bifidobacteria, that have potential health benefits. Conclusions The novel finding that formula exposure is correlated with a higher neonatal ARG burden lays the foundation that clinicians should consider feeding mode in addition to antibiotic use during the first months of life to minimize the proliferation of antibiotic-resistant gut bacteria in infants.
  • 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.
  • Geerlings, Sharon Y.; Ouwerkerk, Janneke P.; Koehorst, Jasper J.; Ritari, Jarmo; Aalvink, Steven; Stecher, Bärbel; Schaap, Peter J.; Paulin, Lars; de Vos, Willem M.; Belzer, Clara (2021)
    Background Akkermansia muciniphila is a member of the human gut microbiota where it resides in the mucus layer and uses mucin as the sole carbon, nitrogen and energy source. A. muciniphila is the only representative of the Verrucomicrobia phylum in the human gut. However, A. muciniphila 16S rRNA gene sequences have also been found in the intestines of many vertebrates. Results We detected A. muciniphila-like bacteria in the intestines of animals belonging to 15 out of 16 mammalian orders. In addition, other species belonging to the Verrucomicrobia phylum were detected in fecal samples. We isolated 10 new A. muciniphila strains from the feces of chimpanzee, siamang, mouse, pig, reindeer, horse and elephant. The physiology and genome of these strains were highly similar in comparison to the type strain A. muciniphila Muc(T). Overall, the genomes of the new strains showed high average nucleotide identity (93.9 to 99.7%). In these genomes, we detected considerable conservation of at least 75 of the 78 mucin degradation genes that were previously detected in the genome of the type strain Muc(T). Conclusions The low genomic divergence observed in the new strains may indicate that A. muciniphila favors mucosal colonization independent of the differences in hosts. In addition, the conserved mucus degradation capability points towards a similar beneficial role of the new strains in regulating host metabolic health.
  • 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.
  • Pessi, Igor S.; Viitamäki, Sirja; Virkkala, Anna-Maria; Eronen-Rasimus, Eeva; Delmont, Tom O.; Marushchak, Maija E.; Luoto, Miska; Hultman, Jenni (2022)
    Background In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra. Results We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23. Conclusions By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.
  • 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)
  • Mönttinen, Heli; Löytynoja, Ari (2022)
    The evolutionary origin of RNA stem structures and the preservation of their base pairing under a spontaneous and random mutation process have puzzled theoretical evolutionary biologists. DNA replication-related template switching is a mutation mechanism that creates reverse-complement copies of sequence regions within a genome by replicating briefly along either the complementary or nascent DNA strand. Depending on the relative positions and context of the four switch points, this process may produce a reverse-complement repeat capable of forming the stem of a perfect DNA hairpin or fix the base pairing of an existing stem. Template switching is typically thought to trigger large structural changes, and its possible role in the origin and evolution of RNA genes has not been studied. Here, we show that the reconstructed ancestral histories of RNA genes contain mutation patterns consistent with the DNA replication-related template switching. In addition to multibase compensatory mutations, the mechanism can explain complex sequence changes, although mutations breaking the structure rarely get fixed in evolution. Our results suggest a solution for the long-standing dilemma of RNA gene evolution and demonstrate how template switching can both create perfect stems with a single mutation event and help maintaining the stem structure over time. Interestingly, template switching also provides an elegant explanation for the asymmetric base pair frequencies within RNA stems.