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Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care?

  • Gary M. King
Chapter

Abstract

A large percentage (~50 %) of the global human population lives in urban systems. The transition from largely rural to urban lifestyles began gradually, but has accelerated. Given the magnitude of anthropogenic changes in the Earth system as a whole and concerns about resource availability and continued population growth, questions about the sustainability of urban systems have become a focal point for a variety of research and civic efforts, including programs promoting urban agriculture as a means to provide local food sources and to better manage critical nutrients such as nitrogen and phosphorus. The last decade or so has also witnessed a remarkable transformation in our understanding of the centrality of microbes for virtually all aspects of human life and wellbeing. However, this transformation has not yet been incorporated into a fuller understanding of the biology and ecology of urban life. Research on microbial assemblages (or microbiomes) in the built environment, particularly building interiors, has provided compelling examples of the importance of microbes, but these results provide at most an incomplete picture of microbial distribution and activity in urban systems. For example, though very little is known about microbial interactions with urban agriculture, the success of urban agriculture and its potential to contribute to urban sustainability will depend in part of incorporating new knowledge about soil and plant microbiomes to optimize production and to minimize some of the adverse effects of agriculture in traditional settings (e.g., greenhouse gas emission, nitrogen and phosphorus eutrophication). To that end, this review defines and provides examples of the microbiome concept and the significance of microbiomes in urban systems; it also identifies large knowledge gaps and unanswered questions that must be addressed to develop a robust and predictive understanding of urban biology and ecology.

Keywords

Urban Soil Urban System Urban Agriculture Urban Atmosphere Urban Sustainability 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Arango CP, Tank JL, Johnson LT, Hamilton SK (2008) Assimilatory uptake rather than nitrification and denitrification determines nitrogen removal patterns in streams of varying land use. Limnol Oceanogr 53:2558–2572CrossRefGoogle Scholar
  2. Armougom F, Henry M, Vialettes B, Raccah D, Raoult D (2009) Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS One 4(9):e7125. doi: 10.1371/journal.pone.0007125 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Balvanera P et al (2006) Quantifying the evidence for biodiversity effects on ecosystem functioning and services. Ecol Lett 9:1146–1156CrossRefPubMedGoogle Scholar
  4. Belimov AA et al (2009) Rhizosphere bacteria containing 1-aminocyclopropane-1-carboxylate deaminase increase yield of plants grown in drying soil via both local and systemic hormone signalling. New Phytol 181:413–423CrossRefPubMedGoogle Scholar
  5. Bell T, Newman JA, Silverman BW, Turner SL, Lilley AK (2005) The contribution of species richness and composition to bacterial services. Nature 436:1157–1160CrossRefPubMedGoogle Scholar
  6. Berg G, Mahnert A, Moissl-Eichinger C (2014) Beneficial effects of plant-associated microbes on indoor microbiomes and human health? Front Microbiol 5:15. doi: 10.3389/fmicb.2014.00015 PubMedPubMedCentralGoogle Scholar
  7. Bettez ND, Groffman PM (2012) Denitrification potential in stormwater control structures and natural riparian zones in an urban landscape. Environ Sci Technol 46:10909–10917CrossRefPubMedGoogle Scholar
  8. Bowers RM, McLetchie S, Knight R, Fierer N (2011) Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments. ISME J 5:601–612CrossRefPubMedPubMedCentralGoogle Scholar
  9. Braun B, Böckelmann U, Grohmann E, Szewzyk U (2006) Polyphasic characterization of the bacterial community in an urban soil profile with in situ and culture-dependent methods. Appl Soil Ecol 31:267–279CrossRefGoogle Scholar
  10. Brodie EL et al (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci U S A 104:299–304CrossRefPubMedPubMedCentralGoogle Scholar
  11. Brown KH, Jameton AL (2000) Public health implications of urban agriculture. J Public Health Policy 21:20–39CrossRefPubMedGoogle Scholar
  12. Cadenasso ML et al (2008) Exchanges across land-water-scape boundaries in urban systems: strategies for reducing nitrate pollution. Ann N Y Acad Sci 1134:213–232CrossRefPubMedGoogle Scholar
  13. Carvalhais LC et al (2013) Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS One 8:e56457. doi: 10.1371/journal.pone.0056457 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Corsi RL, Kinney KA, Levin H (2012) Microbiomes of built environments: 2011 symposium highlights and workgroup recommendations. Indoor Air 22:171–172CrossRefPubMedPubMedCentralGoogle Scholar
  15. Di Gregorio S et al (2006) Combined application of Triton X-100 and Sinorhizobium sp. Pb002 inoculum for the improvement of lead phytoextraction by Brassica juncea in EDTA amended soil. Chemosphere 63:293–299CrossRefPubMedGoogle Scholar
  16. Diaz PI et al (2012) Using high throughput sequencing to explore the biodiversity in oral bacterial communities. Mol Oral Microbiol. doi: 10.1111/j.2041-1014.2012.00642.x
  17. Dobrowsky PH, De Kwaadsteniet M, Cloete TE, Khan W (2014) Distribution of indigenous bacterial pathogens and potential pathogens associated with roof-harvested rainwater. Appl Environ Microbiol 80:2307–2316CrossRefPubMedPubMedCentralGoogle Scholar
  18. Doornbos RF, Loon LC, Bakker PAHM (2011) Impact of root exudates and plant defense signaling on bacterial communities in the rhizosphere. A review. Agron Sustain Dev 32:227–243CrossRefGoogle Scholar
  19. Ege MJ et al (2011) Exposure to environmental microorganisms and childhood asthma. New Engl J Med 364:701–709CrossRefPubMedGoogle Scholar
  20. Faith JJ et al (2013) The long-term stability of the human gut microbiota. Science 341:1237439. doi: 10.1126/science.1237439 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Faure D, Vereecke D, Leveau JHJ (2008) Molecular communication in the rhizosphere. Plant Soil 321:279–303CrossRefGoogle Scholar
  22. Feazel LM et al (2009) Opportunistic pathogens enriched in showerhead biofilms. Proc Natl Acad Sci U S A 106:16393–16399CrossRefPubMedPubMedCentralGoogle Scholar
  23. Fenchel T, King GM, Blackburn TH (2012) Bacterial biogeochemistry, the ecophysiology of mineral cycling, 3rd edn. Academic Press, LondonGoogle Scholar
  24. Fierer N et al (2012) From animalcules to an ecosystem: application of ecological concepts to the human microbiome. Annu Rev Ecol Evol Syst 43:137–155CrossRefGoogle Scholar
  25. Fujii Y, Fujiwara Y, Kigawa R, Suda T, Suzuki Y (2010) Characteristics and diagnosing technology of biodegradation in wooden historical buildings: a case study on Amida-do in Higashi Hongan-ji Temple in Kyoto. In: World conference on timber engineering, Riva del Garda, Italy, 19–24 June 2010Google Scholar
  26. Fujimura KE et al (2014) House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proc Natl Acad Sci U S A 111:805–810CrossRefPubMedPubMedCentralGoogle Scholar
  27. Gerhardt KE, Huang X-D, Glick BR, Greenberg BM (2009) Phytoremediation and rhizoremediation of organic soil contaminants: potential and challenges. Plant Sci 176:20–30CrossRefGoogle Scholar
  28. Gill SR et al (2006) Metagenomic analysis of the human gut distal microbiome. Science 312:1355–1359CrossRefPubMedPubMedCentralGoogle Scholar
  29. Groffman PM, Pouyat RV (2009) Methane uptake in urban forests and lawns. Environ Sci Technol 43:5229–5235CrossRefPubMedGoogle Scholar
  30. Groffman PM et al (2002) Soil nitrogen cycle processes in urban riparian zones. Environ Sci Technol 36:4547–4552CrossRefPubMedGoogle Scholar
  31. Harrison MD, Groffman PM, Mayer PM, Kaushal SS, Newcomer TA (2011) Denitrification in alluvial wetlands in an urban landscape. J Environ Qual 40:634. doi: 10.2134/jeq2010.0335 CrossRefPubMedGoogle Scholar
  32. Hassan S, Mathesius U (2012) The role of flavonoids in root-rhizosphere signalling: opportunities and challenges for improving plant-microbe interactions. J Exp Bot 63:3429–3444CrossRefPubMedGoogle Scholar
  33. Herrera LK, Videla HA (2004) The importance of atmospheric effects on biodeterioration of cultural heritage constructional materials. Int Biodeterior Biodegrad 54:125–134CrossRefGoogle Scholar
  34. Herrera LK, Arroyave C, Guiamet P, de Saravia SG, Videla H (2004) Biodeterioration of peridotite and other constructional materials in a building of the Colombian cultural heritage. Int Biodeterior Biodegrad 54:135–141CrossRefGoogle Scholar
  35. Hospodsky D et al (2012) Human occupancy as a source of indoor airborne bacteria. PLoS One 7:e34867. doi: 10.1371/journal.pone.0034867 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Hou J, Cao X, Song C, Zhou Y (2013) Predominance of ammonia-oxidizing archaea and nirK-gene-bearing denitrifiers among ammonia-oxidizing and denitrifying populations in sediments of a large urban eutrophic lake (Lake Donghu). Can J Microbiol 59:456–464CrossRefPubMedGoogle Scholar
  37. Hu S, Dong TS, Dalal SR, Wu F, Bissonnette M (2011) The microbe-derived short chain fatty acid butyrate targets miRNA-dependent p21 gene expression in human colon cancer. PLoS One 6(1):e16221. doi: 10.1371/journal.pone.0016221 CrossRefPubMedPubMedCentralGoogle Scholar
  38. Illi S et al (2012) Protection from childhood asthma and allergy in Alpine farm environments-the GABRIEL advanced studies. J Allergy Clin Immunol 129:1470.e6–1477.e6. doi: 10.1016/j.jaci.2012.03.013 CrossRefGoogle Scholar
  39. Kaye JP, Burke IC, Mosier AR, Guerschman JP (2004) Methane and nitrous oxide fluxes from urban soils to the atmosphere. Ecol Appl 14:975–981CrossRefGoogle Scholar
  40. Kaye JP, Groffman PM, Grimm NB, Baker LA, Pouyat RV (2006) A distinct urban biogeochemistry? Trends Ecol Evol 21:192–199CrossRefPubMedGoogle Scholar
  41. Kelley ST, Dobler S (2011) Comparative analysis of microbial diversity in Longitarsus flea beetles (Coleoptera: Chrysomelidae). Genetica 139:541–550CrossRefPubMedGoogle Scholar
  42. Kelley ST, Gilbert JA (2013) Studying the microbiology of the indoor environment. Genome Biol 14:202. doi: 10.1186/gb-2013-14-2-202 CrossRefPubMedPubMedCentralGoogle Scholar
  43. Kembel SW et al (2014) Architectural design drives the biogeography of indoor bacterial communities. PLoS One 9:e87093. doi: 10.1371/journal.pone.0087093 CrossRefPubMedPubMedCentralGoogle Scholar
  44. King GM (2014) Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities? J Microbiol 9:721–728CrossRefGoogle Scholar
  45. King GM, Judd C, Kuske CR, Smith C (2012) Analysis of stomach and gut microbiomes of the Eastern Oyster (Crassostrea virginica) from Coastal Louisiana, USA. PLoS One 7(12):e51475. doi: 10.1371/journal.pone.0051475 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Klocker CA, Kaushal SS, Groffman PM, Mayer PM, Morgan RP (2009) Nitrogen uptake and denitrification in restored and unrestored streams in urban Maryland, USA. Aquat Sci 71:411–424CrossRefGoogle Scholar
  47. Knapp CW, Dodds WK, Wilson KC, O’Brien JM, Graham DW (2009) Spatial heterogeneity of denitrification genes in a highly homogenous urban stream. Environ Sci Technol 43:4273–4279CrossRefPubMedGoogle Scholar
  48. Kolvenbach BA, Helbling DE, Kohler H-PE, Corvini PF-X (2014) Emerging chemicals and the evolution of biodegradation pathways and capacities in bacteria. Curr Opin Biotechnol 27:8–14CrossRefPubMedGoogle Scholar
  49. Langenheder S, Bulling MT, Solan M, Prosser JI (2010) Bacterial biodiversity-ecosystem functioning relations are modified by environmental complexity. PLoS One 5:e10834. doi: 10.1371/journal.pone.0010834 CrossRefPubMedPubMedCentralGoogle Scholar
  50. Larsen N et al (2010) Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 5(2):e9085. doi: 10.1371/journal.pone.0009085 CrossRefPubMedPubMedCentralGoogle Scholar
  51. Li S, Deng H, Rensing C, Zhu YG (2014) Compaction stimulates denitrification in an urban park soil using (15)N tracing technique. Environ Sci Pollut Res Int 21:3783–3791CrossRefPubMedGoogle Scholar
  52. Livesley SJ et al (2010) Soil-atmosphere exchange of carbon dioxide, methane and nitrous oxide in urban garden systems: impact of irrigation, fertiliser and mulch. Urban Ecosyst 13:273–293CrossRefGoogle Scholar
  53. Meadow JF et al (2014) Bacterial communities on classroom surfaces vary with human contact. Microbiome 2:7:microbiomejournal.com/content/2/1/7Google Scholar
  54. Milesi C et al (2005) Mapping and modeling the biogeochemical cycling of turf grasses in the United States. Environ Manage 36:426–438CrossRefPubMedGoogle Scholar
  55. Papida S, Murphy W, May E (2000) Enhancement of physical weathering of building stones by microbial populations. Int Biodeterior Biodegrad 46:305–317CrossRefGoogle Scholar
  56. Pickett ST et al (2008) Beyond urban legends: an emerging framework of urban ecology, as illustrated by the Baltimore Ecosystem Study. Bioscience 58:139–150CrossRefGoogle Scholar
  57. Pouyat RV, Szlavecz K, Yesilonis ID, Groffman PM, Schwarz K (2010) Chemical, physical and biological characterization of urban soils. Agron Monogr 55. doi: 10.2134/agronmonogr55.c7:10.2134/agronmonogr55.c7
  58. Ramirez KE et al (2014) Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proc R Soc B 281:20141988. doi:http://dx.doi.org/10.1098/rspb.2014.1988
  59. Rawls JF, Samuel BS, Gordon JI (2004) Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota. Proc Natl Acad Sci U S A 101:4596–4601CrossRefPubMedPubMedCentralGoogle Scholar
  60. Relman DA, Hamburg MA, Choffnes ER, Mack A (2009) Microbial evolution and co-adaptation: a tribute to the life and scientific legacies of Joshua Lederberg. National Academies Press, Washington, DC, 339 pGoogle Scholar
  61. Riedler J et al (2001) Exposure to farming in early life and development of asthma and allergy: a cross-sectional survey. The Lancet 358:1129–1133CrossRefGoogle Scholar
  62. Saiz-Jimenez C (1997) Biodeterioration vs biodegradation: the role of microorganisms in the removal of pollutants deposited on historic buildings. Int Biodeterior Biodegrad 40:225–232CrossRefGoogle Scholar
  63. Sears CL (2005) A dynamic partnership: celebrating our gut flora. Anaerobe 11:247–251CrossRefPubMedGoogle Scholar
  64. Tate RL III (2000) Soil microbiology, 2nd edn. Wiley, New YorkGoogle Scholar
  65. Thompson CL, Hofer MJ, Campbell IL, Holmes AJ (2010) Community dynamics in the mouse gut microbiota: a possible role for IRF9-regulated genes in community homeostasis. PLoS One 5(4):e10335. doi: 10.1371/journal.pone.0010335 CrossRefPubMedPubMedCentralGoogle Scholar
  66. Townsend-Small A, Pataki DE, Czimczik CI, Tyler SC (2011) Nitrous oxide emissions and isotopic composition in urban and agricultural systems in southern California. J Geophys Res 116: 10.1029/2010jg001494
  67. Wang H, Edwards MA, Falkinham JO III, Pruden A (2013) Probiotic approach to pathogen control in premise plumbing systems? A review. Environ Sci Technol 47:10117–101128CrossRefPubMedGoogle Scholar
  68. Webster A, May E (2006) Bioremediation of weathered-building stone surfaces. Trends Biotechnol 24:255–260CrossRefPubMedGoogle Scholar
  69. Werner JJ et al (2011) Bacterial community structures are unique and resilient in full-scale bioenergy systems. Proc Natl Acad Sci USA. pnas.org/cgi/doi/10.1073/pnas.1015676108
  70. Wittebolle L et al (2009) Initial community evenness favours functionality under selective stress. Nature 458:623–626CrossRefPubMedGoogle Scholar
  71. Yashiro E, Spear RN, McManus PS (2011) Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere. J Appl Microbiol 110:1284–1296CrossRefPubMedGoogle Scholar
  72. Yeager CM, Northup DE, Grow CC, Barns SM, Kuske CR (2005) Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Appl Environ Microbiol 71:2713–2722CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  1. 1.Department of Biological SciencesLouisiana State UniversityBaton RougeUSA

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