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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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Hu E, Hu L, Zheng Y, Wu Y, Wang X, Sun C, Su Y. Bacterial abundance and community structure in response to nutrients and photodegraded terrestrial humic acids in a eutrophic lake. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:8218-8231. [PMID: 34482461 DOI: 10.1007/s11356-021-16288-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/28/2021] [Indexed: 06/13/2023]
Abstract
The exposure of humic substances to solar radiation can alter their concentration and composition and subsequently influences their bioavailability in aquatic food webs. With eutrophication increasingly prominent in lakes, nutrients, such as inorganic N and P, are a prerequisite for heterotrophic bacteria that use organic matter. Here photodegradation of terrestrial humic acids and nutrient addition were performed to investigate the response of bacterial abundance and community structure to photodegraded humic acids and increased nutrient concentrations in a eutrophic lake. Results showed that the decreasing level of absorption coefficient at 460 nm in the treatment irradiated with 40 W UV lamps was more remarkable than that of the treatment irradiated with 20 W UV lamps and the control. This reduced coefficient corresponds to the greatest decrease in humic acid concentration in the 40 W group. Bacteria showed high abundance after incubation with humic acids which underwent strong irradiation intensity. An increased nutrient concentration significantly affected bacterial abundance. The dominant bacteria were Aquabacterium for the irradiated group, Aquabacterium and Limnobacter for the 20 W group and Flavobacterium and Limnobacter for the 40 W group. Armatimonadetes-gp4 and Sediminibacterium showed evident response to high nutrient concentration. Our results showed that the exposure of terrestrial humic acids to UV light and the increasing concentration of nutrients have obviously changed bacterial community.
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Affiliation(s)
- En Hu
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Longgang Hu
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Yu Zheng
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Yuxin Wu
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Xifeng Wang
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Changshun Sun
- Shaanxi Provincial Academy of Environmental Science, Xi'an, 710061, China
| | - Yaling Su
- Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
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Patterns of Structural and Functional Bacterioplankton Metacommunity along a River under Anthropogenic Pressure. SUSTAINABILITY 2021. [DOI: 10.3390/su132011518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bacteria, an integral part of aquatic ecosystems, are responsible for the circulation of matter and flow of energy. Since bacterioplankton rapidly responds to any natural and human-induced disturbances in the environment, it can serve as a bioindicator of these changes. Knowing factors that shape the microbial community structure may help the sustainable management of the water environment. However, the identification of environmental signals affecting the structure and function of bacterioplankton is still a challenge. The study analyses the impact of environmental variables on basic microbial parameters, which determines the effectiveness of ecological processes in rivers. Measurements of bacterioplankton abundance (BA) and extracellular enzyme activity (EEA) were based on fluorescent markers. The bacterial community structure was determined by 16S rRNA gene amplicon sequencing (Illumina). The results indicate spatial variation in bacterioplankton abundance. Temporal variation was not significant. Lipase and aminopeptidase had the highest level of activity. EEA was not correlated with bacterial abundance but was significantly correlated with temperature. Moreover, differences in lipase, α-glucosidase and β-glucosidase activity levels between spring and summer were noted. At the same time, the location of sampling site had a significant influence on aminopeptidase activity. The taxonomic analysis of bacterioplankton communities in the Brda River indicated that, although different numbers of OTUs were recorded in the studied river sections, bacterioplankton biodiversity did not change significantly along the river with distance downstream. Anthropogenically modified river sections were characterized by the dominance of Flavobacterium (Bacterioidetes) and hgcl clade (Actinobacteria) taxa, known for their ability to produce extracellular enzymes. PCoA analysis revealed that the sites located in the lower river course (urban area) had the most similar bacterial community structure (β-diversity). The study provides new insight into the changes in microbial communities along the river and emphasizes the potential impact of anthropogenization on these processes.
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Baker SS, Alhassan MS, Asenov KZ, Choi JJ, Craig GE, Dastidar ZA, Karim SJ, Sheardy EE, Sloulin SZ, Aggarwal N, Al-Habib ZM, Camaj V, Cleminte DD, Hamady MH, Jaafar M, Jones ML, Khan ZM, Khoshaba ES, Khoshaba R, Ko SS, Mashrah AT, Patel PA, Rajab R, Tandon S. Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples. Front Microbiol 2021; 12:579325. [PMID: 33679627 PMCID: PMC7929996 DOI: 10.3389/fmicb.2021.579325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Course-based undergraduate research experience (CURE) courses incorporate high-impact pedagogies that have been shown to increase undergraduate retention among underrepresented minorities and women. As part of the Building Infrastructure Leading to Diversity program at the University of Detroit Mercy, a CURE metagenomics course was established in the winter of 2019. Students investigated the bacterial community composition in a eutrophic cove in Lake Saint Clair (Harrison Township, MI, United States) from water samples taken in the summer and winter. The students created 16S rRNA libraries that were sequenced using next-generation sequencing technology. They used a public web-based supercomputing resource to process their raw sequencing data and web-based tools to perform advanced statistical analysis. The students discovered that the most common operational taxonomic unit, representing 31% of the prokaryotic sequences in both summer and winter samples, corresponded to an organism that belongs to a previously unidentified phylum. This result showed the students the power of metagenomics because the approach was able to detect unclassified organisms. Principal Coordinates Analysis of Bray-Curtis dissimilarity index data showed that the winter community was distinct from the summer community [Analysis of Similarities (ANOSIM) r = 0.59829, n = 18, and p < 0.001]. Dendrograms based on hierarchically clustered Pearson correlation coefficients of phyla were divided into a winter clade and a summer clade. The conclusion is that the winter bacterial population was fundamentally different from the summer population, even though the samples were taken from the same locations in a protected cove. Because of the small class sizes, qualitative as well as statistical methods were used to evaluate the course's impact on student attitudes. Results from the Laboratory Course Assessment Survey showed that most of the respondents felt they were contributing to scientific knowledge and the course fostered student collaboration. The majority of respondents agreed or strongly agreed that the course incorporated iteration aspects of scientific investigations, such as repeating procedures to fix problems. In summary, the metagenomics CURE course was able to add to scientific knowledge and allowed students to participate in authentic research.
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Affiliation(s)
- Stokes S Baker
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mohamed S Alhassan
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Kristian Z Asenov
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Joyce J Choi
- Biology Department, University of Detroit Mercy, Detroit, MI, United States.,School of Environment and Sustainability, University of Michigan, Ann Arbor, MI, United States
| | - Griffin E Craig
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zayn A Dastidar
- Biology Department, University of Detroit Mercy, Detroit, MI, United States.,Mike Ilitch School of Business, Wayne State University, Detroit, MI, United States
| | - Saleh J Karim
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Erin E Sheardy
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Salameh Z Sloulin
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Nitish Aggarwal
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zahraa M Al-Habib
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Valentina Camaj
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Dennis D Cleminte
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mira H Hamady
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Mike Jaafar
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Marcel L Jones
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Zayan M Khan
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Evileen S Khoshaba
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Rita Khoshaba
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Sarah S Ko
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | | | - Pujan A Patel
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Rabeeh Rajab
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
| | - Sahil Tandon
- Biology Department, University of Detroit Mercy, Detroit, MI, United States
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