Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Karayanni, Hera; Macingo, Sofia C.; Tolis, Vasilis; Alivertis, Dimitrios

doi:10.3390/w11030467

Cited by 8 publications

(4 citation statements)

References 72 publications

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“…Though the collection vessels were filled to the lip, closed with an air-tight cap, and kept on wet-ice for less than 2 h, some organisms, such as obligate anaerobes, may have been lost. Many other metagenomic investigations of environmental water samples have stored samples on wet-ice before microbe isolation ( Yannarell et al, 2003 ; Shade et al, 2007 ; Van Rossum et al, 2015 ; Uyaguari-Diaz et al, 2016 ; Linz et al, 2017 ; Karayanni et al, 2019 ; Mohiuddin et al, 2019 ). Thus, the collection procedure that were used by the students is within the norms of basic research.…”

Section: Discussionmentioning

confidence: 99%

“…A similar pattern was observed in a separate study of the Great Lakes, canals, and streams of the Niagara Peninsula ( Mohiuddin et al, 2019 ). In contrast, a study of oligotrophic versus eutrophic lakes in Greece showed greater species diversity in the eutrophic samples ( Karayanni et al, 2019 ). These results suggest that trophic status can alter the freshwater prokaryote diversity, but a general rule on the relationship between nutrient level and prokaryote community diversity has not been established.…”

Section: Introductionmentioning

confidence: 94%

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Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

et al. 2021

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

et al. 2021

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“…6C ). Hgcl clade taxa have previously been associated with eutrophic aquatic settings, which could correspond to diatom overabundances that could indicate algal bloom states ( 83 ). These ASVs also displayed heightened relative abundances in sample sites binned into low HMP and HET, yet no change in relative abundance in B 1 bins, indicating evidence for precursor auxotrophy, drawdown, and limited thiamine biosynthesis.…”

Section: Discussionmentioning

confidence: 99%

Connecting thiamine availability to the microbial community composition in Chinook salmon spawning habitats of the Sacramento River basin

Suffridge,

Shannon,

Matthews

et al. 2024

Appl Environ Microbiol

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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. IMPORTANCE Pacific 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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“…Sporichthyaceae ASVs captured the above trend and the hgcl clade (genus annotation of Sporichthyaceae) was the most abundant genus across all samples sites yet were exceedingly low in relative abundances in Battle and Butte Creeks (Figure 6C). Hgcl clade taxa have previously been associated with eutrophic aquatic settings, which could correspond to diatom overabundances that could indicate algal bloom states (83). These ASVs also displayed heightened relative abundances in sample sites binned into low HMP and HET, yet no change in relative abundance in B1 bins, indicating evidence for precursor auxotrophy and drawdown.…”

Section: Relationship Between Microbial Taxa and Dtrcsmentioning

confidence: 91%

Connecting Thiamine Availability to the Microbial Community Composition in Chinook Salmon Spawning Habitats of the Sacramento River Basin

Suffridge,

Shannon,

Matthews

et al. 2023

Preprint

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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 microbially produced thiamine in both riverine surface water and hyporheic zones could serve to rescue early life stages of salmonids suffering from TDC. The distributions of thiamine and its metabolically related compounds (dTRCs) have never been determined in freshwater systems. Similarly, the microbial cycling of these compounds has never been investigated. Here we determine that all dTRCs are present in femto-picomolar concentrations across diverse salmon spawning habitats in California's Sacramento River system. We observed that thiamine concentrations in the Sacramento River are orders of magnitude lower than marine environments, 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 concentration were observed where highest concentrations were seen when Chinook salmon were actively spawning. Significant correlations were identified between the richness of differentially abundant ASVs and dTRC concentrations. The influence of these ASVs on dTRC concentrations provide evidence of dTRC cycling by microbes 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.

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Diversity of Bacteria in Lakes with Different Chlorophyll Content and Investigation of Their Respiratory Activity through a Long-Term Microcosm Experiment

Cited by 8 publications

References 72 publications

Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

Students in a Course-Based Undergraduate Research Experience Course Discovered Dramatic Changes in the Bacterial Community Composition Between Summer and Winter Lake Samples

Connecting thiamine availability to the microbial community composition in Chinook salmon spawning habitats of the Sacramento River basin

Connecting Thiamine Availability to the Microbial Community Composition in Chinook Salmon Spawning Habitats of the Sacramento River Basin

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