Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater

• Published in: PloS one 2017-04, Vol.12 (4), p.e0174930
• Main Authors: Ludington, William B, Seher, Thaddeus D, Applegate, Olin, Li, Xunde, Kliegman, Joseph I, Langelier, Charles, Atwill, Edward R, Harter, Thomas, DeRisi, Joseph L
• Format: Article
• Language: English
• Subjects: Activated sludge; Agricultural pollution; Agricultural practices; Agricultural resources; Agriculture; Agrochemicals; Ammonia; Ammonium; Analysis; Animal wastes; Antimicrobial agents; Aquifers; Biochemistry; Bioinformatics; Biology and Life Sciences; Biomaterials; Bioremediation; Borers; Chemical analysis; Climate change; Climatic extremes; Computer and Information Sciences; Computer programs; Contaminants; Contamination; Corn; Data processing; Dissolved organic carbon; Drinking water; Drought; E coli; Earth Sciences; Effluents; Evaluation; Feces; Fertilizers; Firn; Food; Geochemistry; Groundwater; Groundwater - chemistry; Groundwater pollution; Groundwater resources; Heavy metals; Lagoons; Long-term potentiation; Manure; Manures; Metabolism; Metabolites; Metagenomics; Metal concentrations; Microorganisms; Nitrates; Nitrates - analysis; Nitrogen removal; Odor; Organic carbon; Oxidation; Physical Sciences; Radiation; Redox properties; Research and Analysis Methods; Sampling; Sewage treatment; Solutes; Surface water; Surfactants; Temperature effects; Wastewater treatment plants; Water analysis; Water chemistry; Water Microbiology; Water monitoring; Water resources; Water sampling; Water table
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0174930

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. 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. 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. 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.