Profiling the microbial community structure and functional diversity of a dam‐regulated river undergoing gravel bar restoration

Serrana, Joeselle M.; Li, Bin; Takemon, Yasuhiro; Watanabe, Kozo

doi:10.1111/fwb.13824

Cited by 7 publications

(6 citation statements)

References 102 publications

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“…This finding implies that the taxonomic structure divergence observed between points or gravel bars reflects different putative metabolic functions that emerged among the heterogeneous environments. This result is in good agreement with previous studies on stream microbial communities (Serrana et al, 2022;Galand et al, 2018;Fasching et al,2020). However, it should be noted that the use of 16S rRNA gene sequences to predict metabolic function is constrained by the limited information content of the amplicon and limited databases.…”

Section: Discussionsupporting

confidence: 93%

“…Recent studies on freshwater microbial communities also estimated functional traits based on taxonomic annotation using databases (e.g. SILVA rRNA, Greengenes, National Center for Biotechnology, and Ribosomal Database Project) and 16S rRNA metabarcoding (Serrana et al, 2022;Galand et al, 2018;Fasching et al, 2020) Several studies have demonstrated the validity and utility of this approach, although the estimated functional traits were putative as 16S rRNA metabarcoding could not identify functional genes in the genome, and database limitations allowed annotating only a proportion of the taxa. However, applied cases are still scarce and further verifications would be required.…”

Section: Introductionmentioning

confidence: 99%

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The influence of river discharge on gravel bar hyporheic microbial community structure and putative metabolic functions

Watanabe

Serrana

Takahashi

et al. 2022

Preprint

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1) Microbial communities in the hyporheic zone (HZ) are important in self-purification as the riverbed is metabolically active and responsible for the retention, storage and mineralisation of organic matter transported to the surface water. However, studies exploring HZ microbial community responses to disturbances (e.g. floods) remain scarce. 2) Here, we characterised the microbial community structure among the three (downwelling, upwelling and intermediate) HZ points within and among gravel bars at high and low discharge levels in a dam-regulated river using 16S rRNA metabarcoding. 3) We observed significant dissimilarity in the microbial community at low discharge exhibiting local adaptation due to gravel bar spatial environmental heterogeneity. Moreover, the homogenisation effect resulted in similar microbial community structures among the three points within the gravel bars at high discharge. Microbial communities across adjacent gravel bars were dissimilar, potentially attributing to different bar morphologies. 4) Our study highlights the role of spatial environmental heterogeneity in the biological processes that govern microbial community structure at three hyporheic points in gravel bars at two discharge levels. 5) Our results are essential to understand the HZ microbial communities response to the river discharge levels.

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Section: Discussionsupporting

confidence: 93%

Section: Introductionmentioning

confidence: 99%

The influence of river discharge on gravel bar hyporheic microbial community structure and putative metabolic functions

Watanabe

Serrana

Takahashi

et al. 2022

Preprint

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“…The sediment samples assessed in this study were collected from three sites (i.e., sites A and C are from up-welling zones; site B from a down-welling zone) on selected gravel bars in the Trinity River assessed in the study of Serrana et al [ 38 ]. The experimental procedure of the sediment-associated microbial community profiling employed in this study is illustrated in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Sediment samples from three sites (i.e., sites A and C are from up-welling zones; site B from a down-welling zone) were collected approximately 10 cm below the submerged surface of selected gravel bars in the Trinity River assessed in the study of Serrana et al [ 38 ]. The Trinity River is a large gravel-bed river impounded by the Trinity Dam (164 m a.b.l.…”

Section: Methodsmentioning

confidence: 99%

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

Serrana

Watanabe

2022

BMC Microbiol

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Background Sequential membrane filtration as a pre-processing step for capturing sediment-associated microorganisms could provide good quality and integrity DNA that can be preserved and kept at ambient temperatures before community profiling through culture-independent molecular techniques. However, the effects of sample pre-processing via filtration on DNA-based profiling of sediment-associated microbial community diversity and composition are poorly understood. Specifically, the influences of pre-processing on the quality and quantity of extracted DNA, high-throughput DNA sequencing reads, and detected microbial taxa need further evaluation. Results We assessed the impact of pre-processing freshwater sediment samples by sequential membrane filtration (from 10, 5 to 0.22 μm pore size) for 16S rRNA-based community profiling of sediment-associated microorganisms. Specifically, we examined if there would be method-driven differences between non- and pre-processed sediment samples regarding the quality and quantity of extracted DNA, PCR amplicon, resulting high-throughput sequencing reads, microbial diversity, and community composition. We found no significant difference in the qualities and quantities of extracted DNA and PCR amplicons, and the read abundance after bioinformatics processing (i.e., denoising and chimeric-read filtering steps) between the two methods. Although the non- and pre-processed sediment samples had more unique than shared amplicon sequence variants (ASVs), we report that their shared ASVs accounted for 74% of both methods’ absolute read abundance. More so, at the genus level, the final collection filter identified most of the genera (95% of the reads) captured from the non-processed samples, with a total of 51 false-negative (2%) and 59 false-positive genera (3%). We demonstrate that while there were differences in shared and unique taxa, both methods revealed comparable microbial diversity and community composition. Conclusions Our observations highlight the feasibility of pre-processing sediment samples for community analysis and the need to further assess sampling strategies to help conceptualize appropriate study designs for sediment-associated microbial community profiling.

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“…Understanding the functional traits of each species could contribute to deepening our knowledge of the biological processes and ecological mechanisms that shape community structure variation along environmental gradients. Recent studies on freshwater microbial communities also estimated functional traits based on taxonomic annotation using databases (e.g., SILVA rRNA, Greengenes, National Center for Biotechnology, and Ribosomal Database Project) and 16S rRNA gene sequencing (Galand et al, 2018;Fasching et al, 2020;Serrana et al, 2022). Several studies have demonstrated the validity and utility of this approach, although the estimated functional traits were putative as 16S rRNA gene sequencing could not identify functional genes in the genome, and database limitations allowed annotating only a proportion of the taxa.…”

Section: Introductionmentioning

confidence: 99%

Short-term influences of flow alteration on microbial community structure and putative metabolic functions in gravel bar hyporheic zones

Doloiras-Laraño,

Serrana,

Takahashi

et al. 2023

Front. Environ. Sci.

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Microbial communities in the hyporheic zone are important for self-purification as the riverbed is metabolically active and responsible for the retention, storage, and mineralisation of organic matter transported in the surface water. Studies exploring the response of the hyporheic microbial community to flow regime alterations remain scarce. Here, we characterised the microbial community structure over downwelling, upwelling and intermediate hyporheic zone areas within and among gravel bars at high and low discharge levels to determine flow-induced changes in a dam-regulated river using 16S rRNA gene sequencing. At low discharge, microbial composition varied across the different areas of gravel bars, reflecting heterogeneity in local abiotic conditions. However, high discharge lead to microbial community homogenisation across the three areas of the gravel bars. Microbial communities across adjacent gravel bars remained dissimilar regardless of discharge levels, likely reflecting differences in bar morphology. Our results can help better understand how anthropogenic changes in hydrologic conditions can affect microbial diversity and function in the hyporheic zone. This knowledge will help us to understand better how changes in hydrological conditions affect ecosystem functions and services in rivers affected by human impacts.

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Profiling the microbial community structure and functional diversity of a dam‐regulated river undergoing gravel bar restoration

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 7 publications

References 102 publications

The influence of river discharge on gravel bar hyporheic microbial community structure and putative metabolic functions

The influence of river discharge on gravel bar hyporheic microbial community structure and putative metabolic functions

Sediment-associated microbial community profiling: sample pre-processing through sequential membrane filtration for 16S rRNA amplicon sequencing

Short-term influences of flow alteration on microbial community structure and putative metabolic functions in gravel bar hyporheic zones

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