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4. Global taxonomic and phylogenetic assembly of AM fungi

Author

Vasar, Martti, Davison, John, Sepp, Siim-Kaarel, Oja, Jane, Al-Quraishy, Saleh, Bueno, C. Guillermo, Cantero, Juan José, Fabiano, Ezequiel Chimbioputo, Decocq, Guillaume, Fraser, Lauchlan, Hiiesalu, Inga, Hozzein, Wael N., Koorem, Kadri, Moora, Mari, Mucina, Ladislav, Onipchenko, Vladimir, Öpik, Maarja, Pärtel, Meelis, Phosri, Cherdchai, Vahter, Tanel, Tedersoo, Leho, and Zobel, Martin

Published
2022
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6. Detecting macroecological patterns in bacterial communities across independent studies of global soils.

Author

Ramirez, Kelly S, Knight, Christopher G, de Hollander, Mattias, Brearley, Francis Q, Constantinides, Bede, Cotton, Anne, Creer, Si, Crowther, Thomas W, Davison, John, Delgado-Baquerizo, Manuel, Dorrepaal, Ellen, Elliott, David R, Fox, Graeme, Griffiths, Robert I, Hale, Chris, Hartman, Kyle, Houlden, Ashley, Jones, David L, Krab, Eveline J, Maestre, Fernando T, McGuire, Krista L, Monteux, Sylvain, Orr, Caroline H, van der Putten, Wim H, Roberts, Ian S, Robinson, David A, Rocca, Jennifer D, Rowntree, Jennifer, Schlaeppi, Klaus, Shepherd, Matthew, Singh, Brajesh K, Straathof, Angela L, Bhatnagar, Jennifer M, Thion, Cécile, van der Heijden, Marcel GA, and de Vries, Franciska T

Subjects
Bacteria, DNA, Bacterial, RNA, Ribosomal, 16S, Soil, Ecology, Soil Microbiology, Ecosystem, Biodiversity, Phylogeny, Bacterial Physiological Phenomena, Microbial Interactions, High-Throughput Nucleotide Sequencing, Microbiota, Machine Learning
Abstract

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Published
2018

12. GlobalAMFungi: a global database of arbuscular mycorrhizal fungal occurrences from high‐throughput sequencing metabarcoding studies

Author

Větrovský, Tomáš, primary, Kolaříková, Zuzana, additional, Lepinay, Clémentine, additional, Awokunle Hollá, Sandra, additional, Davison, John, additional, Fleyberková, Anna, additional, Gromyko, Anastasiia, additional, Jelínková, Barbora, additional, Kolařík, Miroslav, additional, Krüger, Manuela, additional, Lejsková, Renata, additional, Michalčíková, Lenka, additional, Michalová, Tereza, additional, Moora, Mari, additional, Moravcová, Andrea, additional, Moulíková, Štěpánka, additional, Odriozola, Iñaki, additional, Öpik, Maarja, additional, Pappová, Monika, additional, Piché‐Choquette, Sarah, additional, Skřivánek, Jakub, additional, Vlk, Lukáš, additional, Zobel, Martin, additional, Baldrian, Petr, additional, and Kohout, Petr, additional

Published
2023
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15. Work and Career Experiences of Men from Families without College Experience

Author

Woodside, Marianne, Gibbons, Melinda M., and Davison, John

Abstract

A dearth of research exists exploring the career and work development of adult men and the influence of family-of-origin on that development. In this qualitative study, the researchers used a phenomenological approach to examine the career and work experiences of men whose parents have no education beyond high school and the influences of family on these experiences. We describe five constituents: (a) what work is like; (b) preparation/education; (c) who or what influenced them; (d) how to act at work; and (e)challenges/opportunities/choices; and one essence: mottos from father, which articulate the meaning of the experience of work and career and the family influence on the experience. In conclusion, we provide implications for counselors working with adult men whose parents lack post-secondary education. (Contains 1 table.)

Published
2012

16. Comparison of alternative falls data collection methods in the Prevention of Falls Injury Trial (PreFIT)

Author

Lamb, Sarah E., Underwood, Martin, Martin, Finbarr, Yardley, Lucy, Skelton, Dawn, Willett, Keith, Eldridge, Sandra, Slowther, Anne-Marie, Duggan, Sarah, Bruce, Julie, Hennings, Susie, Withers, Emma, Mant, Rhys, Rai, Rishpal, Turner, Craig, Andrews, Agata, Fearn, Rachael, Finnegan, Susanne, Walker, Nicola, Potter, Rachel, Lall, Ranjit, Hulme, Claire, Bojke, Chris, Longo, Roberta, Westacott, Katherine, Ralhan, Shvaita, Sheridan, Ray, Treml, Jonathan, Riglin, Jackie, Gordjin, Harm, Dutta, Ruma, Burns, Jo, Shaw, Fiona, Davison, John, Willis, Ade, Muthiah, Chocks, Adjei, Henry, and Griffin, James

Published
2019
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17. Niche types and community assembly.

Author

Davison, John, Gerz, Maret, Hiiesalu, Inga, Moora, Mari, Semchenko, Marina, and Zobel, Martin

Subjects
*VESICULAR-arbuscular mycorrhizas, *FUNGAL communities
Abstract

Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche‐based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche. [ABSTRACT FROM AUTHOR]

Published
2024
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32. Metabarcoding of soil environmental DNA to estimate plant diversity globally

Author

Vasar, Martti, primary, Davison, John, additional, Moora, Mari, additional, Sepp, Siim-Kaarel, additional, Anslan, Sten, additional, Al-Quraishy, Saleh, additional, Bahram, Mohammad, additional, Bueno, C. Guillermo, additional, Cantero, Juan José, additional, Fabiano, Ezequiel Chimbioputo, additional, Decocq, Guillaume, additional, Drenkhan, Rein, additional, Fraser, Lauchlan, additional, Oja, Jane, additional, Garibay-Orijel, Roberto, additional, Hiiesalu, Inga, additional, Koorem, Kadri, additional, Mucina, Ladislav, additional, Öpik, Maarja, additional, Põlme, Sergei, additional, Pärtel, Meelis, additional, Phosri, Cherdchai, additional, Semchenko, Marina, additional, Vahter, Tanel, additional, Doležal, Jiři, additional, Palacios, Aida M. Vasco, additional, Tedersoo, Leho, additional, and Zobel, Martin, additional

Published
2023
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40. Use of experience curves to estimate the future cost of power plants with CO2 capture

Author

Rubin, Edward S., Yeh, Sonia, Antes, Matt, Berkenpas, Michael, and Davison, John

Subjects
UCD-ITS-RP-07-27
Abstract

Given the dominance of power plant emissions of greenhouse gases, and the growing worldwide interest in CO2 capture and storage (CCS) as a potential climate change mitigation option, the expected future cost of power plants with CO2 capture is of significant interest. Reductions in the cost of technologies as a result of learning-by-doing, R&D investments and other factors have been observed over many decades. This study uses historical experience curves as the basis for estimating future cost trends for four types of electric power plants equipped with CO2 capture systems: pulverized coal (PC) and natural gas combined cycle (NGCC) plants with post-combustion CO2 capture; coal-based integrated gasification combined cycle (IGCC) plants with pre-combustion capture; and coal-fired oxyfuel combustion for new PC plants. We first assess the rates of cost reductions achieved by other energy and environmental process technologies in the past. Then, by analogy with leading capture plant designs, we estimate future cost reductions that might be achieved by power plants employing CO2 capture. Effects of uncertainties in key parameters on projected cost reductions also are evaluated via sensitivity analysis.

Published
2007

41. Abnormal Psychology

Author

Gordon L. Flett, Nancy L. Kocovski, Gerald C. Davison, John M. Neale and Gordon L. Flett, Nancy L. Kocovski, Gerald C. Davison, John M. Neale

Published
2018

45. Global diversity and distribution of nitrogen-fixing bacteria in the soil

Author

Sepp, Siim-Kaarel, primary, Vasar, Martti, additional, Davison, John, additional, Oja, Jane, additional, Anslan, Sten, additional, Al-Quraishy, Saleh, additional, Bahram, Mohammad, additional, Bueno, C. Guillermo, additional, Cantero, Juan José, additional, Fabiano, Ezequiel Chimbioputo, additional, Decocq, Guillaume, additional, Drenkhan, Rein, additional, Fraser, Lauchlan, additional, Garibay Oriel, Roberto, additional, Hiiesalu, Inga, additional, Koorem, Kadri, additional, Kõljalg, Urmas, additional, Moora, Mari, additional, Mucina, Ladislav, additional, Öpik, Maarja, additional, Põlme, Sergei, additional, Pärtel, Meelis, additional, Phosri, Cherdchai, additional, Semchenko, Marina, additional, Vahter, Tanel, additional, Vasco Palacios, Aida M., additional, Tedersoo, Leho, additional, and Zobel, Martin, additional

Published
2023
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49. Global diversity and distribution of nitrogen-fixing bacteria in the soil

Author

Sepp, Siim-Kaarel, Vasar, Martti, Davison, John, Oja, Jane, Anslan, Sten, Al-Quraishy, Saleh, Bahram, Mohammad, Bueno, C. Guillermo, Cantero, Juan Jose, Fabiano, Ezequiel Chimbioputo, Decocq, Guillaume, Drenkhan, Rein, Garibay Oriel, Roberto, Hiiesalu, Inga, Koorem, Kadri, Koljalg, Urmas, Moora, Mari, Mucina, Ladislav, opik, Maarja, Polme, Sergei, Partel, Meelis, Phosri, Cherdchai, Semchenko, Marina, Vahter, Tanel, Vasco Palacios, Aida M. M., Tedersoo, Leho, and Zobel, Martin

Subjects
Ecology
Abstract

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.

Published
2023

50. Metabarcoding of soil environmental DNA to estimate plant diversity globally

Author

Zobel, Martin, Tedersoo, Leho, Vasar, Martti, Davison, John, Moora, Mari, Sepp, Siim-Kaarel, Anslan, Sten, Al-Quraishy, Saleh, Bahram, Mohammad, Bueno, C. Guillermo, Cantero, Juan Jose, Fabiano, Ezequiel Chimbioputo, Decocq, Guillaume, Drenkhan, Rein, Fraser, Lauchlan, Oja, Jane, Garibay-Orijel, Roberto, Hiiesalu, Inga, Koorem, Kadri, Opik, Maarja, Semchenko, Marina, Vahter, Tanel, and Palacios, Aida M. Vasco

Subjects
Ecology
Abstract

IntroductionTraditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. MethodsWe sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. ResultsLarge-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. DiscussioneDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Published
2023

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