Digging the New York City Skyline: soil fungal communities in green roofs and city parks.
Krista L. McGuire,Sara G. Payne,Matthew I. Palmer,Caitlyn Marie Gillikin,Dominique Russenberger Keefe,Su Jin Kim,Seren Michelle Gedallovich,Julia Marie Discenza,Ramya Rangamannar,Jennifer Anne Koshner,Audrey L. Massmann,Giulia Orazi,Adam Lang Essene,Jonathan W. Leff,Noah Fierer,Noah Fierer +15 more
TLDR
Fungus living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services ofgreen roofs.Abstract:
In urban environments, green roofs provide a number of benefits, including decreased urban heat island effects and reduced energy costs for buildings. However, little research has been done on the non-plant biota associated with green roofs, which likely affect their functionality. For the current study, we evaluated whether or not green roofs planted with two native plant communities in New York City functioned as habitats for soil fungal communities, and compared fungal communities in green roof growing media to soil microbial composition in five city parks, including Central Park and the High Line. Ten replicate roofs were sampled one year after planting; three of these roofs were more intensively sampled and compared to nearby city parks. Using Illumina sequencing of the fungal ITS region we found that green roofs supported a diverse fungal community, with numerous taxa belonging to fungal groups capable of surviving in disturbed and polluted habitats. Across roofs, there was significant biogeographical clustering of fungal communities, indicating that community assembly of roof microbes across the greater New York City area is locally variable. Green roof fungal communities were compositionally distinct from city parks and only 54% of the green roof taxa were also found in the park soils. Phospholipid fatty acid analysis revealed that park soils had greater microbial biomass and higher bacterial to fungal ratios than green roof substrates. City park soils were also more enriched with heavy metals, had lower pH, and lower quantities of total bases (Ca, K, and Mg) compared to green roof substrates. While fungal communities were compositionally distinct across green roofs, they did not differentiate by plant community. Together, these results suggest that fungi living in the growing medium of green roofs may be an underestimated component of these biotic systems functioning to support some of the valued ecological services of green roofs.read more
Citations
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Book ChapterDOI
Nutrient Cycling in Green Roof Ecosystems
Ishi Buffam,Mark E. Mitchell +1 more
TL;DR: In this article, the authors consider the cycling of Carbon (C), Nitrogen (N) and Phosphorus (P) in green roof ecosystems and focus primarily on N and P because these are the nutrients most often limiting to plant growth in terrestrial ecosystems, and because leaching of these elements to downstream aquatic ecosystems is a concern due to their potential to contribute to eutrophication.
Patent
Seed-origin endophyte populations, compositions, and methods of use
Geoffrey von Maltzahn,Richard Bailey Flavell,Gerardo V. Toledo,Slavica Djonovic,Luis Miguel Marquez,David Morris Johnston,Yves Alain Millet,Jeffrey Lyford,Alexander Naydich,Craig Sadowski +9 more
TL;DR: In this article, the authors present methods and materials for providing a benefit to a seed or seedling of an agricultural plant (e.g., an agricultural grass plant), or the agricultural plant derived from the seed and seedling.
Journal ArticleDOI
Photobiomodulation of human dermal fibroblasts in vitro: decisive role of cell culture conditions and treatment protocols on experimental outcome
Charles Mignon,Natallia E. Uzunbajakava,Bianca Raafs,Natalia V. Botchkareva,Desmond J. Tobin +4 more
TL;DR: It is concluded that a significant source of problematic interpretations in photobiomodulation reports derives from poor optimization of study design, and further development of this field using in vitro/ex vivo models should embrace significant standardization ofStudy design, ideally within a design-of-experiment setting.
Journal ArticleDOI
Association of Shifting Populations in the Root Zone Microbiome of Millet with Enhanced Crop Productivity in the Sahel Region (Africa)
Spencer J. Debenport,Komi Assigbetse,Roger Bayala,Lydie Chapuis-Lardy,Richard P. Dick,Brian B. McSpadden Gardener +5 more
TL;DR: It is suggested that the intercropping system used here can influence the recruitment of potentially beneficial microorganisms to the root zone of millet and aid subsistence farmers in producing higher-yielding crops.
Journal ArticleDOI
Green Infrastructure Design Influences Communities of Urban Soil Bacteria.
Jessica Joyner,Jordan Kerwin,Maha Deeb,George Lozefski,Bharath Prithiviraj,Anna Paltseva,John McLaughlin,Peter M. Groffman,Zhongqi Cheng,Theodore R. Muth +9 more
TL;DR: The overall design and management of GI features with a channeled connection with street runoff, such as ROWB, have a comprehensive effect on soil parameters (particularly organic matter) and the bacterial community.
References
More filters
Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI
Search and clustering orders of magnitude faster than BLAST
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Journal ArticleDOI
ITS primers with enhanced specificity for basidiomycetes--application to the identification of mycorrhizae and rusts.
M. Gardes,Thomas D. Bruns +1 more
TL;DR: In this paper, two taxon-selective primers for the internal transcribed spacer (ITS) region in the nuclear ribosomal repeat unit were proposed, which were intended to be specific to fungi and basidiomycetes, respectively.
Journal ArticleDOI
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
J. Gregory Caporaso,Christian L. Lauber,William A. Walters,Donna Berg-Lyons,James Huntley,Noah Fierer,Noah Fierer,Sarah M. Owens,Jason Betley,Louise Fraser,Markus J. Bauer,Niall Anthony Gormley,Jack A. Gilbert,Jack A. Gilbert,Geoff Smith,Rob Knight +15 more
TL;DR: It is shown that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.
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QIIME allows analysis of high-throughput community sequencing data.
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