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Green Infrastructure Design Influences Communities of Urban Soil Bacteria

Joyner, Jessica Lee, Kerwin, Jordan, Deeb, Maha, Lozefski, George, Prithiviraj, Bharath, Paltseva, Anna, McLaughlin, John, Groffman, Peter, Cheng, Zhongqi, Muth, Theodore R.·2019·Frontiers in Microbiology
DOI 10.3389/fmicb.2019.00982PMC PMC6531853
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  1. Adeniji A. O. Okoh O. O. Okoh A. I. (2017). Petroleum Hydrocarbon Fingerprints of Water and Sediment Samples of Buffalo River Estuary in the Eastern Cape Province, South Africa. J Anal Methods Chem 2017 2629365– 2629313. 10.1155/2017/2629365 28638675 PMC5468778 · DOI
  2. Allison S. D. Martiny J. (2008). Resistance, resilience, and redundancy in microbial communities. Proceedings of the National Academy of Sciences 105 11512– 11519. 10.1073/pnas.0801925105 18695234 PMC2556421 · DOI
  3. Ball B. C. (2013). Soil structure and greenhouse gas emissions: a synthesis of 20 years of experimentation. European Journal of Soil Science 64 357– 373. 10.1111/ejss.12013 · DOI
  4. Barathi S. Vasudevan N. (2001). Utilization of petroleum hydrocarbons by Pseudomonas fluorescens isolated from a petroleum-contaminated soil. Environment International 26 413– 416. 10.1016/S0160-4120(01)00021-6 11392760 · DOI
  5. Benedict M. A. McMahon E. T. (2006). Green infrastructure: linking landscapes and communities. Washington, DC: Island press.
  6. Caporaso J. G. Kuczynski J. Stombaugh J. Bittinger K. Bushman F. D. Costello E. K. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Meth 7 335– 336. 10.1038/nmeth.f.303 20383131 PMC3156573 · DOI · Paper page
  7. Capps K. A. Bentsen C. N. Ramírez A. (2016). Poverty, urbanization, and environmental degradation: urban streams in the developing world. Freshwater Science 35 429– 435. 10.1086/684945 12346811 · DOI · Paper page
  8. Cardenas E. Wu W.-M. Leigh M. B. Carley J. Carroll S. Gentry T. (2010). Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach. Applied and Environmental Microbiology 76 6778– 6786. 10.1128/AEM.01097-10 20729318 PMC2953039 · DOI
  9. Connop S. Vandergert P. Eisenberg B. Collier M. J. Nash C. Clough J. (2016). Renaturing cities using a regionally-focused biodiversity-led multifunctional benefits approach to urban green infrastructure. Environmental Science and Policy 62 99– 111. 10.1016/j.envsci.2016.01.013 · DOI
  10. Cosandey A. C. Maître V. Guenat C. (2003). Temporal denitrification patterns in different horizons of two riparian soils. Eur. J. Soil Sci. 54 2538 10.1111/j.1475-6765.2007.00705.x · DOI
  11. de Souza M. P. Amini A. Dojka M. A. Pickering I. J. Dawson S. C. Pace N. R. (2001). Identification and characterization of bacteria in a selenium-contaminated hypersaline evaporation pond. Appl. Environ. Microbiol. 67 3785– 3794. 10.1128/AEM.67.9.3785-3794.2001 11525968 PMC93092 · DOI
  12. Deeb M. Grimaldi M. Lerch T. Z. Pando A. Gigon A. Blouin M. (2016). Interactions between organisms and parent materials of a constructed Technosol shape its hydrostructural properties. Soil 2 163– 174. 10.5194/soil-2-163-2016 · DOI
  13. Deeb M. Groffman P. M. Joyner J. L. Lozefski G. Paltseva A. Lin B. (2018). Soil and microbial properties of green infrastructure stormwater management systems. Ecological Engineering 125 68– 75. 10.1016/j.ecoleng.2018.10.017 · DOI · Paper page
  14. Delgado-Balbuena L. Bello-López J. M. Navarro-Noya Y. E. Rodríguez-Valentín A. Luna-Guido M. L. Dendooven L. (2016). Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils. PLoS ONE 11: e160991– e160928. 10.1371/journal.pone.0160991 27727277 PMC5058544 · DOI
  15. Delgado-Baquerizo M. Oliverio A. M. Brewer T. E. Benavent-Gonzalez A. Eldridge D. J. Bardgett R. D. (2018). A global atlas of the dominant bacteria found in soil. Science 359 320– 325. 10.1126/science.aap9516 29348236 · DOI
  16. Delmont T. O. Robe P. Cecillon S. Clark I. M. Constancias F. Simonet P. (2011). Accessing the soil metagenome for studies of microbial diversity. Applied and Environmental Microbiology 77 1315– 1324. 10.1128/AEM.01526-10 21183646 PMC3067229 · DOI
  17. Edgar R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26 2460– 2461. 10.1093/bioinformatics/btq461 20709691 · DOI
  18. Ellis D. E. Lutz E. J. Odom J. M. Buchanan R. J. Bartlett C. L. Lee M. D. (2000). Bioaugmentation for Accelerated In Situ Anaerobic Bioremediation. Environ. Sci. Technol. 34 2254– 2260. 10.1021/es990638e 29906723 · DOI
  19. Fierer N. (2017). Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Publishing Group 15 1– 12. 10.1038/nrmicro.2017.87 28824177 · DOI
  20. Fierer N. Jackson R. B. (2006). The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences 103 626– 631. 10.1073/pnas.0507535103 16407148 PMC1334650 · DOI · Paper page
  21. Flynn K. M. Traver R. G. (2013). Green infrastructure life cycle assessment: A bio-infiltration case study. Ecological Engineering 55 9– 22. 10.1016/j.ecoleng.2013.01.004 · DOI
  22. Gadd G. M. (2007). Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bioweathering and bioremediation. Mycological Research 111 3– 49. 10.1016/j.mycres.2006.12.001 17307120 · DOI
  23. Gill A. S. Lee A. McGuire K. L. (2017). Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils. Appl. Environ. Microbiol. 83 1– 35. 10.1128/AEM.00287-17 28576763 PMC5541207 · DOI · Paper page
  24. Gkorezis P. Daghio M. Franzetti A. Van Hamme J. D. Sillen W. Vangronsveld J. (2016). The Interaction between Plants and Bacteria in the Remediation of Petroleum Hydrocarbons: An Environmental Perspective. Front. Microbiol. 7: 653– 627. 10.3389/fmicb.2016.01836 27917161 PMC5116465 · DOI
  25. Glick B. R. (2010). Using soil bacteria to facilitate phytoremediation. Biotechnology Advances 28 367– 374. 10.1016/j.biotechadv.2010.02.001 20149857 · DOI
  26. Handl S. Dowd S. E. Garcia-Mazcorro J. F. Steiner J. M. Suchodolski J. S. (2011). Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiology Ecology 76 301– 310. 10.1111/j.1574-6941.2011.01058.x 21261668 · DOI
  27. Hostetler M. Allen W. Meurk C. (2011). Conserving urban biodiversity? Creating green infrastructure is only the first step. Landscape and Urban Planning 100 369– 371. 10.1016/j.landurbplan.2011.01.011 · DOI
  28. Huang P. M. Bollag J. M. Senesi N. (2002). Interactions between soil particles and microorganisms: impact on the terrestrial ecosystem. Chem. Inter. Newsmagazine IUPAC 24: 26 10.1515/ci.2002.24.4.26a · DOI · Paper page
  29. Huot H. Joyner J. Córdoba A. Shaw R. K. Wilson M. A. Walker R. (2017). Characterizing urban soils in New York City: profile properties and bacterial communities. J Soils Sediments 17 393– 407. 10.1007/s11368-016-1552-9 · DOI
  30. Ji X. Ripp S. A. Layton A. C. Sayler G. S. DeBruyn J. M. (2013). Assessing Long Term Effects of Bioremediation: Soil Bacterial Communities 14 Years after Polycyclic Aromatic Hydrocarbon Contamination and Introduction of a Genetically Engineered Microorganism. J Bioremed Biodeg 04 1– 8. 10.4172/2155-6199.1000209 · DOI
  31. Jia Z. Conrad R. (2009). Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol 11 1658– 1671. 10.1111/j.1462-2920.2009.01891.x 19236445 · DOI
  32. Jiao S. Chen W. Wang E. Wang J. Liu Z. Li Y. (2016). Microbial succession in response to pollutants in batch-enrichment culture. Sci. Rep. 6 21791– 21711. 10.1038/srep21791 26905741 PMC4764846 · DOI
  33. Kaye J. Groffman P. Grimm N. Baker L. Pouyat R. (2006). A distinct urban biogeochemistry? Trends in Ecology & Evolution 21 192– 199. 10.1016/j.tree.2005.12.006 16701085 · DOI
  34. Kumar K. Hundal L. S. (2016). Soil in the City: Sustainably Improving Urban Soils. Journal of Environment Quality 45 2– 7. 10.2134/jeq2015.11.0589 26828154 · DOI
  35. Legendre P. De Cáceres M. (2013). Beta diversity as the variance of community data: dissimilarity coefficients and partitioning. Ecology Letters 16 951– 963. 10.1111/ele.12141 23809147 · DOI
  36. Li J. Li Y. Zhang J. Li H. Li Y. (2016). Bio-Swale Column Experiments and Simulation of Hydrologic Impacts on Urban Road Stormwater Runoff. Pol. J. Environ. Stud. 25 173– 184. 10.15244/pjoes/60280 · DOI
  37. Macías F. Camps Arbestain M. (2010). Soil carbon sequestration in a changing global environment. Mitigation and Adaptation Strategies for Global Change 15 511– 529. 10.1007/s11027-010-9231-4 · DOI
  38. MacNaughton S. J. Stephen J. R. Venosa A. D. Davis G. A. Chang Y. J. White D. C. (1999). Microbial population changes during bioremediation of an experimental oil spill. Appl. Environ. Microbiol. 65 3566– 3574. 10427050 PMC91535
  39. Marcin C. Marcin G. Justyna M.-P. Katarzyna K. Maria N. (2013). Diversity of microorganisms from forest soils differently polluted with heavy metals. Applied Soil Ecology 64 7– 14. 10.1016/j.apsoil.2012.11.004 · DOI
  40. McGranahan G. Marcotullio P. Bai X. Balk D. Braga T. Douglas I. (2005). “ Urban Systems,” in Ecosystems and Human Well-being Current State and Trends Vol. 1 eds Hassan R. Scholes R. Ash N. (Washington, DC: Island Press), 795– 825.
  41. McGuire K. L. Payne S. G. Palmer M. I. Gillikin C. M. Keefe D. Kim S. J. (2013). Digging the New York City Skyline: Soil Fungal Communities in Green Roofs and City Parks. PLoS ONE 8: e58020– e58013. 10.1371/journal.pone.0058020 23469260 PMC3585938 · DOI
  42. McMurdie P. J. Holmes S. (2012). Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data. Pac Symp Biocomput 235– 246∗. 22174279 PMC3357092
  43. Mishra S. Jyot J. Kuhad R. C. Lal B. (2001). In Situ Bioremediation Potential of an Oily Sludge-Degrading Bacterial Consortium. Current Microbiology 43 328– 335. 10.1007/s002840010311 11688796 · DOI
  44. Morel J. L. Chenu C. Lorenz K. (2014). Ecosystem services provided by soils of urban, industrial, traffic, mining, and military areas (SUITMAs). J Soils Sediments 15 1659– 1666. 10.1007/s11368-014-0926-0 · DOI
  45. Morse N. R. McPhillips L. E. Shapleigh J. P. Walter M. T. (2017). The Role of Denitrification in Stormwater Detention Basin Treatment of Nitrogen. Environ. Sci. Technol. 51 7928– 7935. 10.1021/acs.est.7b01813 28640610 · DOI
  46. Mukherjee A. Chettri B. Langpoklakpam J. S. Basak P. Prasad A. Mukherjee A. K. (2017). Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments. Sci. Rep. 7 1– 22. 10.1038/s41598-017-01126-3 28439121 PMC5430712 · DOI
  47. Neilson J. W. Califf K. Cardona C. Copeland A. Van Treuren W. Josephson K. L. (2017). Significant Impacts of Increasing Aridity on the Arid Soil Microbiome. mSystems 2 e195– e116. 10.1128/mSystems.00195-16 28593197 PMC5451488 · DOI
  48. Ng D. H. P. Kumar A. Cao B. (2016). Microorganisms meet solid minerals: interactions and biotechnological applications. Appl Microbiol Biotechnol 100 6935– 6946. 10.1007/s00253-016-7678-2 27338573 · DOI
  49. Nikhil T. Deepa V. Rohan G. Satish B. (2013). Isolation, Characterization and Identification of Diesel Engine Oil Degrading Bacteria from Garage Soil and Comparison of their Bioremediation Potential. International Research Journal of Environment Sciences 2 48– 52.
  50. Nowak D. J. Greenfield E. J. (2012). Tree and impervious cover in the United States. Landscape and Urban Planning 107 21– 30. 10.1016/j.landurbplan.2012.04.005 · DOI
  51. Ojuederie O. Babalola O. (2017). Microbial and Plant-Assisted Bioremediation of Heavy Metal Polluted Environments: A Review. IJERPH 14 1504– 1526. 10.3390/ijerph14121504 29207531 PMC5750922 · DOI
  52. Pataki D. E. Carreiro M. M. Cherrier J. Grulke N. E. Jennings V. Pincetl S. (2011). Coupling biogeochemical cycles in urban environments: ecosystem services, green solutions, and misconceptions. Front. Ecol. Environ 9: 27– 36. 10.1890/090220 · DOI · Paper page
  53. Paul D. Pandey G. Pandey J. Jain R. K. (2005). Accessing microbial diversity for bioremediation and environmental restoration. Trends in Biotechnology 23 135– 142. 10.1016/j.tibtech.2005.01.001 15734556 · DOI
  54. Pires M. (2004). Watershed protection for a world city: the case of New York. Land Use Policy 21 161– 175. 10.1016/j.landusepol.2003.08.001 · DOI
  55. Rahman K. S. M. Rahman T. Lakshmanaperumalsamy P. Banat I. M. (2002). Occurrence of crude oil degrading bacteria in gasoline and diesel station soils. J. Basic Microbiol. 42 284– 291. 12210553
  56. Rakhshandehroo M. Mohdyusof M. J. Tahir O. M. (2015). The social benefits of urban open green spaces: A literature review. Research and Practice 7 60– 71.
  57. Ramirez K. S. Leff J. W. Barberan A. Bates S. T. Betley J. Crowther T. W. (2014). Biogeographic patterns in below-ground diversity in New York City’s Central Park are similar to those observed globally. Proceedings of the Royal Society B: Biological Sciences 281 20141988– 20141988. 10.1098/rspb.2014.1988 25274366 PMC4213626 · DOI
  58. Reese A. T. Savage A. Youngsteadt E. McGuire K. L. Koling A. Watkins O. (2015). Urban stress is associated with variation in microbial species composition; but not richness; in Manhattan. The ISME Journal 10 1– 10. 10.1038/ismej.2015.152 26394011 PMC4817683 · DOI
  59. Robinson G. Caldwell G. S. Wade M. J. Free A. Jones C. L. W. Stead S. M. (2016). Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes. Sci. Rep. 6 1– 13. 10.1038/srep38850 27941918 PMC5150640 · DOI
  60. Roesch L. F. W. Fulthorpe R. R. Riva A. Casella G. Hadwin A. K. M. Kent A. D. (2007). Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1 283– 290. 10.1038/ismej.2007.53 18043639 PMC2970868 · DOI
  61. Santos Dos J. J. Maranho L. T. (2018). Rhizospheric microorganisms as a solution for the recovery of soils contaminated by petroleum: A review. Journal of Environmental Management 210 104– 113. 10.1016/j.jenvman.2018.01.015 29331851 · DOI
  62. Sauvé S. McBride M. B. Norvell W. A. Hendershot W. H. (1997). Copper Solubility and Speciation of In Situ Contaminated Soils: Effects of Copper Level, pH and Organic Matter. Water Air Soil Pollut 100 133– 149. 10.1023/A:1018312109677 · DOI
  63. Shuster W. D. Bonta J. Thurston H. Warnemuende E. Smith D. R. (2005). Impacts of impervious surface on watershed hydrology: A review. Urban Water Journal 2 263– 275. 10.1080/15730620500386529 · DOI
  64. Takaijudin H. Ghani A. A. Zakaria N. A. (2016). Challenges and developments of bioretention facilities in treating urban stormwater runoff; A review. Pollution 2 489– 508.
  65. Tzoulas K. Korpela K. Venn S. Yli-Pelkonen V. Kaźmierczak A. Niemela J. (2007). Promoting ecosystem and human health in urban areas using Green Infrastructure: A literature review. Landsc. Urban Plann. 81 167– 178. 10.1016/j.landurbplan.2007.02.001 30321733 · DOI
  66. Vasenev V. Kuzyakov Y. (2018). Urban soils as hot spots of anthropogenic carbon accumulation: Review of stocks, mechanisms and driving factors. Land Degradation & Development 29 1607– 1622. 10.1002/ldr.2944 · DOI
  67. Wall D. H. (2004). Sustaining Biodiversity and Ecosystem Services in Soils and Sediments. Washington, DC: Island Press.
  68. Wang H. Cheng M. Dsouza M. Weisenhorn P. Zheng T. Gilbert J. A. (2018). Soil Bacterial Diversity Is Associated with Human Population Density in Urban Greenspaces. Environ. Sci. Technol. 52 5115– 5124. 10.1021/acs.est.7b06417 29624051 · DOI
  69. Williams R. J. Howe A. Hofmockel K. S. (2014). Demonstrating microbial co-occurrence pattern analyses within and between ecosystems. 5 1– 10. 10.3389/fmicb.2014.00358/abstract PMC4102878 25101065 · DOI
  70. Wilson V. L. Tatford B. C. Yin X. Rajki S. C. Walsh M. M. LaRock P. (1999). Species-specific detection of hydrocarbon-utilizing bacteria. Journal of Microbiological Methods 39 59– 78. 10.1016/s0167-7012(99)00098-6 10579508 · DOI
  71. Yan B. Li J. Xiao N. Qi Y. Fu G. Liu G. (2016). Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing. Sci. Rep. 6 1– 9. 10.1038/srep38811 27934957 PMC5146926 · DOI
  72. Young I. M. Crawford J. W. (2004). Interactions and Self-Organization in the Soil-Microbe Complex. Sci. Ed. 304 1634– 1637. 10.1126/science.1097394 15192219 · DOI
  73. Yu J. Deem L. M. Crow S. E. Deenik J. L. Penton C. R. (2018). Biochar application influences microbial assemblage complexity and composition due to soil and bioenergy crop type interactions. Soil Biology and Biochemistry 117 97– 107. 10.1016/j.soilbio.2017.11.017 · DOI

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Authors
Joyner, J. L., Kerwin, J., Deeb, M., Lozefski, G., Prithiviraj, B., Paltseva, A., McLaughlin, J., Groffman, P., Cheng, Z., & Muth, T. R.
Venue
Frontiers in Microbiology
Publisher
Frontiers Media SA
Published
2019-05-16
Volume
10
ISSN
1664-302X
DOI
10.3389/fmicb.2019.00982
PMC
PMC6531853
Cited by
55
References
0
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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