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Virgin TL, Sonthiphand P, Coyotzi S, Hall MW, Venkiteswaran JJ, Elgood RJ, Schiff SL, Neufeld JD. Microbial communities change along the 300 km length of the Grand River for extreme high- and low-flow regimes. Can J Microbiol 2024; 70:289-302. [PMID: 38747604 DOI: 10.1139/cjm-2023-0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Grand River watershed is the largest catchment in southern Ontario. The river's northern and southern sections are influenced by agriculture, whereas central regions receive wastewater effluent and urban runoff. To characterize in-river microbial communities, as they relate to spatial and environmental factors, we conducted two same-day sampling events along the entire 300 km length of the river, representing contrasting flow seasons (high flow spring melt and low flow end of summer). Through high-throughput sequencing of 16S rRNA genes, we assessed the relationship between river microbiota and spatial and physicochemical variables. Flow season had a greater impact on communities than spatial or diel effects and profiles diverged with distance between sites under both flow conditions, but low-flow profiles exhibited higher beta diversity. High-flow profiles showed greater species richness and increased presence of soil and sediment taxa, which may relate to increased input from terrestrial sources. Total suspended solids, dissolved inorganic carbon, and distance from headwaters significantly explained microbial community variation during the low-flow event, whereas conductivity, sulfate, and nitrite were significant explanatory factors for spring melt. This study establishes a baseline for the Grand River's microbial community, serving as a foundation for modeling the microbiology of anthropogenically impacted freshwater systems affected by lotic processes.
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Affiliation(s)
- Taylor L Virgin
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Prinpida Sonthiphand
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Department of Biology, Faculty of Science, Mahidol University, 272 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Sara Coyotzi
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Michael W Hall
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Faculty of Computer Science, Dalhousie University, 6050 University Ave, Halifax, NS B3H 1W5, Canada
| | - Jason J Venkiteswaran
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
- Department of Geography and Environmental Studies, Wilfrid Laurier University, 75 University Ave West, Waterloo, ON N2L 3C5, Canada
| | - Richard J Elgood
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Sherry L Schiff
- Department of Earth and Environmental Sciences, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, 200 University Ave West, Waterloo, ON N2L 3G1, Canada
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Suffridge CP, Shannon KC, Matthews H, Johnson RC, Jeffres C, Mantua N, Ward AE, Holmes E, Kindopp J, Aidoo M, Colwell FS. Connecting thiamine availability to the microbial community composition in Chinook salmon spawning habitats of the Sacramento River basin. Appl Environ Microbiol 2024; 90:e0176023. [PMID: 38084986 PMCID: PMC10807462 DOI: 10.1128/aem.01760-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 01/25/2024] Open
Abstract
Thiamine deficiency complex (TDC) is a major emerging threat to global populations of culturally and economically important populations of salmonids. Salmonid eggs and embryos can assimilate exogenous thiamine, and evidence suggests that microbial communities in benthic environments can produce substantial amounts of thiamine. We therefore hypothesize that natural dissolved pools of thiamine exist in the surface water and hyporheic zones of riverine habitats where salmonids with TDC migrate, spawn, and begin their lives. To examine the relationship between dissolved thiamine-related compounds (dTRCs) and their microbial source, we determined the concentrations of these metabolites and the compositions of microbial communities in surface and hyporheic waters of the Sacramento River, California and its tributaries. Here we determine that all dTRCs are present in femto-picomolar concentrations in a range of critically important salmon spawning habitats. We observed that thiamine concentrations in the Sacramento River system are orders of magnitude lower than those of marine waters, indicating substantial differences in thiamine cycling between these two environments. Our data suggest that the hyporheic zone is likely the source of thiamine to the overlying surface water. Temporal variations in dTRC concentrations were observed where the highest concentrations existed when Chinook salmon were actively spawning. Significant correlations were seen between the richness of microbial taxa and dTRC concentrations, particularly in the hyporheic zone, which would influence the conditions where embryonic salmon incubate. Together, these results indicate a connection between microbial communities in freshwater habitats and the availability of thiamine to spawning TDC-impacted California Central Valley Chinook salmon.IMPORTANCEPacific salmon are keystone species with considerable economic importance and immeasurable cultural significance to Pacific Northwest indigenous peoples. Thiamine deficiency complex has recently been diagnosed as an emerging threat to the health and stability of multiple populations of salmonids ranging from California to Alaska. Microbial biosynthesis is the major source of thiamine in marine and aquatic environments. Despite this importance, the concentrations of thiamine and the identities of the microbial communities that cycle it are largely unknown. Here we investigate microbial communities and their relationship to thiamine in Chinook salmon spawning habitats in California's Sacramento River system to gain an understanding of how thiamine availability impacts salmonids suffering from thiamine deficiency complex.
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Affiliation(s)
| | - Kelly C. Shannon
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - H. Matthews
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
| | - R. C. Johnson
- Fisheries Ecology Division, NOAA Fisheries, Southwest Fisheries Science Center, Santa Cruz, California, USA
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - C. Jeffres
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - N. Mantua
- Fisheries Ecology Division, NOAA Fisheries, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - A. E. Ward
- University of California, Center for Watershed Sciences, Davis, California, USA
| | - E. Holmes
- University of California, Center for Watershed Sciences, Davis, California, USA
- California Department of Water Resources, West Sacramento, California, USA
| | - J. Kindopp
- California Department of Water Resources, Division of Integrated Science and Engineering, Oroville, California, USA
| | - M. Aidoo
- Bronx Community College, Bronx, New York, USA
| | - F. S. Colwell
- Department of Microbiology, Oregon State University, Corvallis, Oregon, USA
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, Oregon, USA
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Power JF, Lowe CL, Carere CR, McDonald IR, Cary SC, Stott MB. Temporal dynamics of geothermal microbial communities in Aotearoa-New Zealand. Front Microbiol 2023; 14:1094311. [PMID: 37020721 PMCID: PMC10068964 DOI: 10.3389/fmicb.2023.1094311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023] Open
Abstract
Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60–70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.
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Affiliation(s)
- Jean F. Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Caitlin L. Lowe
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
| | - Ian R. McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
- S. Craig Cary,
| | - Matthew B. Stott
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- *Correspondence: Matthew B. Stott,
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Spencer-Williams I, Balangoda A, Dabundo R, Elliott E, Haig SJ. Exploring the Impacts of Full-Scale Distribution System Orthophosphate Corrosion Control Implementation on the Microbial Ecology of Hydrologically Connected Urban Streams. Microbiol Spectr 2022; 10:e0215822. [PMID: 36321898 PMCID: PMC9769763 DOI: 10.1128/spectrum.02158-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/04/2022] [Indexed: 12/24/2022] Open
Abstract
Many cities across the nation are plagued by lead contamination in drinking water. As such, many drinking water utilities have undertaken lead service line (LSL) replacement to prevent further lead contamination. However, given the urgency of lead mitigation, and the socioeconomic challenges associated with LSL replacement, cities have used phosphate-based corrosion inhibitors (i.e., orthophosphate) alongside LSL replacement. While necessary to ensure public health protection from lead contamination, the addition of orthophosphate into an aging and leaking drinking water system may increase the concentration of phosphate leaching into urban streams characterized by century-old failing water infrastructure. Such increases in phosphate availability may cascade into nutrient and microbial community composition shifts. The purpose of this study was to determine how this occurs and to understand whether full-scale distribution system orthophosphate addition impacts the microbial ecology of urban streams. Through monthly collection of water samples from five urban streams before and after orthophosphate addition, significant changes in microbial community composition (16S rRNA amplicon sequencing) and in the relative abundance of typical freshwater taxa were observed. In addition, key microbial phosphorus and nitrogen metabolism genes (e.g., two component regulatory systems) were predicted to change via BugBase. No significant differences in the absolute abundances of total bacteria, Cyanobacteria, and "Candidatus Accumulibacter" were observed. Overall, the findings from this study provide further evidence that urban streams are compromised by unintentional hydrologic connections with drinking water infrastructure. Moreover, our results suggest that infiltration of phosphate-based corrosion inhibitors can impact urban streams and have important, as-yet-overlooked impacts on urban stream microbial communities. IMPORTANCE Elevated lead levels in drinking water supplies are a public health risk. As such, it is imperative for cities to urgently address lead contamination from aging drinking water supplies by way of lead service line replacements and corrosion control methods. However, when applying corrosion control methods, it is also important to consider the chemical and microbiological effects that can occur in natural settings, given that our water infrastructure is aging and more prone to leaks and breaks. Here, we examine the impacts on the microbial ecology of five urban stream systems before and after full-scale distribution system orthophosphate addition. Overall, the results suggest that infiltration of corrosion inhibitors may impact microbial communities; however, future work should be done to ascertain the true impact to protect both public and environmental health.
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Affiliation(s)
- Isaiah Spencer-Williams
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Anusha Balangoda
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Richard Dabundo
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily Elliott
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sarah-Jane Haig
- Department of Civil and Environmental Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Environmental and Occupational Health, School of Public Health, University of Pittsburgh, Pennsylvania, USA
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Teng T, Liang J, Wu Z. Identification of pyrene degraders via DNA-SIP in oilfield soil during natural attenuation, bioaugmentation and biostimulation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149485. [PMID: 34392205 DOI: 10.1016/j.scitotenv.2021.149485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 06/13/2023]
Abstract
Pyrene is a model contaminant of high molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs), which are compounds that have potential carcinogenic effects and pose a serious threat to human health. Finding effective pyrene-degrading bacteria is crucial for removing PAHs from soil. In this study, DNA-based stable isotope probing (DNA-SIP) technology was used to investigate pyrene degraders in PAH-contaminated oilfield soil during natural attenuation (NA), bioaugmentation (BA) and biostimulation (BS). The results show that BA played an important role in pyrene degradation with the highest pyrene removal rate (~95%) after 12 days incubation, followed by removal rates of ~90% for NA and ~30% for BS. In addition, 6 novel pyrene degraders were identified, while 12 well-known PAH degraders were demonstrated to participate in the biodegradation of pyrene. Additionally, the external homologous strains introduced during BA promoted the degradation of pyrene, but not by directly participating in the metabolism of the target compound. Rhamnolipid supplementation during BS promoted the involvement of more microorganisms in the degradation of pyrene, which was beneficial to identifying more pyrene degraders via DNA-SIP. These findings provide new insight into the effects of external homologous strains and supplementary rhamnolipids on pyrene degradation.
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Affiliation(s)
- Tingting Teng
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Jidong Liang
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China.
| | - Zijun Wu
- Department of Environmental Engineering, Xi'an Jiaotong University, Xi'an 710049, China
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