Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes

Sadeghi, Javad; Chaganti, Subba Rao; Shahraki, Abdolrazagh Hashemi; Heath, Daniel D.

doi:10.1016/j.scitotenv.2021.146771

Cited by 30 publications

(28 citation statements)

References 64 publications

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“…We collected 2 samples per location and time and found that replicates had no significant differences in the BCC ( p > 0.05). We also observed no significant replicate effect with 3–9 samples/location in our recently published study of aquatic bacterial community dynamics in north temperate lakes [ 17 ], thus we combined sequence read data of the two replicates for each week at each location to increase the read depth for all further statistical analyses.…”

Section: Resultsmentioning

confidence: 99%

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems

2021

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Background Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. Results We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. Conclusions As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health.

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Section: Resultsmentioning

confidence: 99%

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems

2021

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“…It has been postulated that local environmental processes and geographic distances (dispersal related) factors are potential mechanisms in structuring microbial biogeography ( Liu et al, 2019 ; Sadeghi et al, 2021 ). Environmental processes include abiotic (e.g., nutrients) and biotic (e.g., predation and competition) factors that regulate the community structure ( Zhou and Ning, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes

et al. 2022

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Bacteria are vital components of lake systems, driving a variety of biogeochemical cycles and ecosystem services. Bacterial communities have been shown to have a skewed distribution with a few abundant species and a large number of rare species. The contribution of environmental processes or geographic distance in structuring these components is uncertain. The discrete nature of lakes provides an ideal test case to investigate microbial biogeographical patterns. In the present study, we used 16S rRNA gene metabarcoding to examine the distribution patterns on local and regional scales of abundant and rare planktonic bacteria across 167 New Zealand lakes covering broad environmental gradients. Only a few amplicon sequence variants (ASVs) were abundant with a higher proportion of rare ASVs. The proportion of locally abundant ASVs was negatively correlated with the percentage of high productivity grassland in the catchment and positively with altitude. Regionally rare ASVs had a restricted distribution and were only found in one or a few lakes. In general, regionally abundant ASVs had higher occupancy rates, although there were some with restricted occupancy. Environmental processes made a higher contribution to structuring the regionally abundant community, while geographic distances were more important for regionally rare ASVs. A better understanding of the processes structuring the abundance and distribution of bacterial communities within lakes will assist in understand microbial biogeography and in predicting how these communities might shift with environmental change.

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“…Bacterial DNA extraction and 16S rRNA gene library preparation DNA was extracted from fish hindgut content using a sucrose lysis buffer solution method previously described (Shahraki et al, 2019) and extracted DNA was subsequently stored at -20 degC, until further analysis. Additionally, the PCR conditions and 16S rRNA primer sets (1st and second PCR) were the same as those used in previously described methods (Sadeghi et al, 2021). Briefly, 16S rRNA variable regions of V5-V6 were amplified with a PCR cycle program of 95 degC for 3 min followed by 28 cycles of 95 degC for 30 s, 55 degC for 30 s, and 72 degC for 1 m, and a final step at 72 degC for 7 m. A second short-cycle PCR (7 cycles) using purified first PCR products ligated the adaptor and barcode (10 -12 bp) sequences to the amplicons as required for sample identification and sequencing.…”

Section: Lab Analysesmentioning

confidence: 99%

Regulation of Host Gene Expression by Gastrointestinal Tract Microbiota in Chinook Salmon (Oncorhynchus tshawytscha)

Sadeghi

Chaganti

Heath

2022

Preprint

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Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome bacterial communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Aeromonadaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signaling pathways, specifically targeting immune, developmental, and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.

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Microbial community and abiotic effects on aquatic bacterial communities in north temperate lakes

Cited by 30 publications

References 64 publications

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair’s large freshwater ecosystems

The Role of Environmental Processes and Geographic Distance in Regulating Local and Regionally Abundant and Rare Bacterioplankton in Lakes

Regulation of Host Gene Expression by Gastrointestinal Tract Microbiota in Chinook Salmon (Oncorhynchus tshawytscha)

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