title: Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater.
abstract: BACKGROUND
  Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood.
  
  
  METHODS
  On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4.3 m (two wells) and 100 m (one well) below ground surface (bgs) as well as an effluent surface water lagoon that fertilizes surrounding corn fields. We analyzed the samples for concentrations of solutes, heavy metals, and USDA pathogenic bacteria of the Escherichia coli and Enterococcus groups as part of a long term groundwater monitoring study. Whole metagenome shotgun sequencing and assembly revealed taxonomic composition and metabolic potential of the community.
  
  
  RESULTS
  Elevated nitrate and dissolved organic carbon occurred at 4.3m but not at 100m bgs. Metagenomics confirmed chemical observations and revealed several Planctomycete genomes, including a new Brocadiaceae lineage and a likely Planctomycetes OM190, as well novel diversity and high abundance of nano-prokaryotes from the Candidate Phyla Radiation (CPR), the Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea (DPANN) and the Thaumarchaeota, Aigarchaeota, Crenarchaeota, Korarchaeota (TACK) superphyla. Pathway analysis suggests community interactions based on complimentary primary metabolic pathways and abundant secondary metabolite operons encoding antimicrobials and quorum sensing systems.
  
  
  CONCLUSIONS
  The metagenomes show strong resemblance to activated sludge communities from a nitrogen removal reactor at a wastewater treatment plant, suggesting that natural bioremediation occurs through microbial metabolism. Elevated nitrate and rich secondary metabolite biosynthetic capacity suggest incomplete remediation and the potential for novel pharmacologically active compounds.
authors.affiliation: Molecular Cell Biology Department, University of California, Berkeley, United States of America.
authors.forename: William B
authors.identifier: http://orcid.org/0000-0001-9637-4493
authors.initials: WB
authors.lastname: Ludington
authors.affiliation: Molecular Cell Biology Department, University of California, Berkeley, United States of America.
authors.forename: Thaddeus D
authors.initials: TD
authors.lastname: Seher
authors.affiliation: Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America.
authors.forename: Olin
authors.initials: O
authors.lastname: Applegate
authors.affiliation: Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America.|Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America.
authors.forename: Xunde
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America.
authors.forename: Joseph I
authors.initials: JI
authors.lastname: Kliegman
authors.affiliation: Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America.
authors.forename: Charles
authors.initials: C
authors.lastname: Langelier
authors.affiliation: Department of Population Health and Reproduction, University of California, Davis, Davis, United States of America.|Western Institute for Food Safety and Security, University of California, Davis, Davis, United States of America.
authors.forename: Edward R
authors.initials: ER
authors.lastname: Atwill
authors.affiliation: Department of Land, Air and Water Resources, University of California, Davis, Davis, United States of America.
authors.forename: Thomas
authors.initials: T
authors.lastname: Harter
authors.affiliation: Department of Biophysics & Biochemistry, University of California, San Francisco, San Francisco, United States of America.|Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America.
authors.forename: Joseph L
authors.initials: JL
authors.lastname: DeRisi
mesh_terms: D000383:Agriculture; D060587:Groundwater / Q000737:chemistry; D056186:Metagenomics; D009566:Nitrates / Q000032:analysis*; D014871:Water Microbiology
chemical_list: D009566:Nitrates