Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater
| Autor: | Thaddeus D. Seher, Joseph I. Kliegman, Olin Applegate, Edward R. Atwill, Joseph L. DeRisi, William B. Ludington, Thomas Harter, Xunde Li, Charles Langelier |
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| Přispěvatelé: | Yang, Shihui |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genomics Statistics Thaumarchaeota Microbial metabolism lcsh:Medicine Marine and Aquatic Sciences Plant Science Database and Informatics Methods chemistry.chemical_compound Nitrate Crenarchaeota lcsh:Science Groundwater Data Management 2. Zero hunger Multidisciplinary Bacterial Genomics biology Plant Bacterial Pathogens Ecology Microbial Genetics Agriculture Genomics Genomic Databases 6. Clean water Chemistry Physical Sciences Water Microbiology Research Article Lagoons Computer and Information Sciences Environmental remediation General Science & Technology 030106 microbiology Plant Pathogens Microbial Genomics Research and Analysis Methods Microbiology 03 medical and health sciences Genetics Bacterial Genetics Taxonomy Nitrates lcsh:R Chemical Compounds Biology and Life Sciences Computational Biology Bacteriology Plant Pathology Bodies of Water Comparative Genomics 15. Life on land Genome Analysis biology.organism_classification Biological Databases 030104 developmental biology chemistry 13. Climate action Metagenomics Earth Sciences lcsh:Q Surface water |
| Zdroj: | PloS one, vol 12, iss 4 PLoS ONE Ludington, WB; Seher, TD; Applegate, O; Li, X; Kliegman, JI; Langelier, C; et al.(2017). Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PLoS ONE, 12(4). doi: 10.1371/journal.pone.0174930. UC Davis: Retrieved from: http://www.escholarship.org/uc/item/2h11b468 PLoS ONE, Vol 12, Iss 4, p e0174930 (2017) |
| Popis: | © 2017 Ludington et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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. |
| Databáze: | OpenAIRE |
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