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The source of the river as a nursery for microbial diversity.

de Oliveira LF, Margis R - PLoS ONE (2015)

Bottom Line: The application of NGS (next-generation sequencing technologies) for 16S analysis has been broadly used for understanding bacterioplankton composition and structure.Seasonal shifts reinforce the importance of the source of the river in maintaining the bacterial seed-bank that spreads throughout the river.Therefore, the preservation of the source of the river is important not only for hydrologic reasons but also to maintain the microbial composition and the ecological integrity of the river.

View Article: PubMed Central - PubMed

Affiliation: Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.

ABSTRACT
Bacteria are highly diverse and ubiquitous organisms that play a key role as drivers for ecosystem processes. The application of NGS (next-generation sequencing technologies) for 16S analysis has been broadly used for understanding bacterioplankton composition and structure. Most of studies conducted on aquatic ecosystems with 16S NGS have been in seawater and lakes. A few studies using NGS have been conducted in river environments and have suggested the presence of a bacterial seed-bank. We performed 16S highly variable V4 region high-throughput analysis in the Sinos River, which is located in one of most important Brazilian industrial centers. This region has several contrasts in its environmental characteristics, presenting a longitudinal gradient of eutrophication and making it a remarkable study site for observing the dynamics of bacterioplankton. We demonstrated consistent evidence for the existence of a bacterial seed-bank and its longitudinal persistence. Seasonal shifts reinforce the importance of the source of the river in maintaining the bacterial seed-bank that spreads throughout the river. Therefore, the preservation of the source of the river is important not only for hydrologic reasons but also to maintain the microbial composition and the ecological integrity of the river.

No MeSH data available.


Sinos River OTUs analysis and classification.(A) The Venn diagram shows the number of OTUs present in both seasons combined and each season. Blue circles indicate winter, and red indicates summer. In addition, the total number of reads belonging to the OTUs and their correspondent percentage in the total are shown. (B) Table of the most abundant phyla found in the analysis, with their respective proportions in the summer and winter samples. (C) Profile showing the proportion of phyla for each sample in summer (S01-S14) and winter (W01-W14). The profile also represents the proportion grouped along the course of the Sinos River (upper, middle and lower) and PhyChem analysis (Set1–4). Colored profiles correspond to the most abundant phyla presented in (B).
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pone.0120608.g002: Sinos River OTUs analysis and classification.(A) The Venn diagram shows the number of OTUs present in both seasons combined and each season. Blue circles indicate winter, and red indicates summer. In addition, the total number of reads belonging to the OTUs and their correspondent percentage in the total are shown. (B) Table of the most abundant phyla found in the analysis, with their respective proportions in the summer and winter samples. (C) Profile showing the proportion of phyla for each sample in summer (S01-S14) and winter (W01-W14). The profile also represents the proportion grouped along the course of the Sinos River (upper, middle and lower) and PhyChem analysis (Set1–4). Colored profiles correspond to the most abundant phyla presented in (B).

Mentions: Through sequencing barcoded amplicons from the 16S V4 region in the MiSeq Illumina platform, we generated a total of 5,790,065 pair-end reads for the 28 samples, which passed through rigorous quality control, classification through the OTU open reference picking process and OTU represented by less than 5 reads was discarded (S1 Table). This analysis resulted in 53,624 OTUs, which 35,850 OTUs (66.9%) were found in at least one sample from each season, representing 94.6% of all classified reads (Fig. 2A). These results strongly suggest that the bacterioplankton of the Sinos River are highly homogeneous in composition, exhibiting a seed-bank of bacteria in the river source (S01 and W01). Additionally, we found 6,334 OTUs (11.8%) restricted to winter and 11,440 (21.3%) OTUs restricted to summer samples. These OTUs found exclusively in summer and winter represent 4% and 1.4%, respectively, of all classified reads. Additionally, about of 93.8% of the reads classified in all samples refer to 28,260 OTU present at samples S01 and W01, from the river’s source.


The source of the river as a nursery for microbial diversity.

de Oliveira LF, Margis R - PLoS ONE (2015)

Sinos River OTUs analysis and classification.(A) The Venn diagram shows the number of OTUs present in both seasons combined and each season. Blue circles indicate winter, and red indicates summer. In addition, the total number of reads belonging to the OTUs and their correspondent percentage in the total are shown. (B) Table of the most abundant phyla found in the analysis, with their respective proportions in the summer and winter samples. (C) Profile showing the proportion of phyla for each sample in summer (S01-S14) and winter (W01-W14). The profile also represents the proportion grouped along the course of the Sinos River (upper, middle and lower) and PhyChem analysis (Set1–4). Colored profiles correspond to the most abundant phyla presented in (B).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4372583&req=5

pone.0120608.g002: Sinos River OTUs analysis and classification.(A) The Venn diagram shows the number of OTUs present in both seasons combined and each season. Blue circles indicate winter, and red indicates summer. In addition, the total number of reads belonging to the OTUs and their correspondent percentage in the total are shown. (B) Table of the most abundant phyla found in the analysis, with their respective proportions in the summer and winter samples. (C) Profile showing the proportion of phyla for each sample in summer (S01-S14) and winter (W01-W14). The profile also represents the proportion grouped along the course of the Sinos River (upper, middle and lower) and PhyChem analysis (Set1–4). Colored profiles correspond to the most abundant phyla presented in (B).
Mentions: Through sequencing barcoded amplicons from the 16S V4 region in the MiSeq Illumina platform, we generated a total of 5,790,065 pair-end reads for the 28 samples, which passed through rigorous quality control, classification through the OTU open reference picking process and OTU represented by less than 5 reads was discarded (S1 Table). This analysis resulted in 53,624 OTUs, which 35,850 OTUs (66.9%) were found in at least one sample from each season, representing 94.6% of all classified reads (Fig. 2A). These results strongly suggest that the bacterioplankton of the Sinos River are highly homogeneous in composition, exhibiting a seed-bank of bacteria in the river source (S01 and W01). Additionally, we found 6,334 OTUs (11.8%) restricted to winter and 11,440 (21.3%) OTUs restricted to summer samples. These OTUs found exclusively in summer and winter represent 4% and 1.4%, respectively, of all classified reads. Additionally, about of 93.8% of the reads classified in all samples refer to 28,260 OTU present at samples S01 and W01, from the river’s source.

Bottom Line: The application of NGS (next-generation sequencing technologies) for 16S analysis has been broadly used for understanding bacterioplankton composition and structure.Seasonal shifts reinforce the importance of the source of the river in maintaining the bacterial seed-bank that spreads throughout the river.Therefore, the preservation of the source of the river is important not only for hydrologic reasons but also to maintain the microbial composition and the ecological integrity of the river.

View Article: PubMed Central - PubMed

Affiliation: Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.

ABSTRACT
Bacteria are highly diverse and ubiquitous organisms that play a key role as drivers for ecosystem processes. The application of NGS (next-generation sequencing technologies) for 16S analysis has been broadly used for understanding bacterioplankton composition and structure. Most of studies conducted on aquatic ecosystems with 16S NGS have been in seawater and lakes. A few studies using NGS have been conducted in river environments and have suggested the presence of a bacterial seed-bank. We performed 16S highly variable V4 region high-throughput analysis in the Sinos River, which is located in one of most important Brazilian industrial centers. This region has several contrasts in its environmental characteristics, presenting a longitudinal gradient of eutrophication and making it a remarkable study site for observing the dynamics of bacterioplankton. We demonstrated consistent evidence for the existence of a bacterial seed-bank and its longitudinal persistence. Seasonal shifts reinforce the importance of the source of the river in maintaining the bacterial seed-bank that spreads throughout the river. Therefore, the preservation of the source of the river is important not only for hydrologic reasons but also to maintain the microbial composition and the ecological integrity of the river.

No MeSH data available.