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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.


Archaeal and bacterial diversities.(A) Proportion of reads classified as Euryarchaeota from Domain Archaea. In summer, this phylum increased its representation with increasing eutrophication, and in winter, there is a gradual longitudinal decrease in the abundance of this phylum. (B) Alpha-diversity results using Chao1 for summer and winter. The results show a tendency of greater homogeneity and Chao1 values in the winter than in the summer. (C) Beta-diversity results, using unweighted Unifrac. The analyses were performed independently for the sample groups representing seasons, course and PhyChem classification.
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pone.0120608.g003: Archaeal and bacterial diversities.(A) Proportion of reads classified as Euryarchaeota from Domain Archaea. In summer, this phylum increased its representation with increasing eutrophication, and in winter, there is a gradual longitudinal decrease in the abundance of this phylum. (B) Alpha-diversity results using Chao1 for summer and winter. The results show a tendency of greater homogeneity and Chao1 values in the winter than in the summer. (C) Beta-diversity results, using unweighted Unifrac. The analyses were performed independently for the sample groups representing seasons, course and PhyChem classification.

Mentions: We found a total of 4 bacteria phyla, with Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia and Firmicutes as the most representative groups found in all samples (Fig. 2B, 2C and S2 Table), representing a total of 85.6% and 91.1% of all classified reads for the summer and winter samples, respectively. At the family taxonomic level, we found Comamonadaceae, ACK-M1, Rhodobacteraceae, Chitinophagaceae and Flavobacteriaceae as the five most representative taxa for both, summer and winter samples (S2 Fig.). The Pseudomonadaceae is the family that presented the higher discrepancy between summer and winter, representing 0.5% and 2.7%, respectively. For Domain Archaea, we found 85 OTUs classified as Parvarchaeota, Crenarchaeota and Euryarchaeota, represented by 1,777 reads in all samples combined. Interestingly, the phylum Euryarchaeota showed an inverted trend between summer and winter (Fig. 3A). We found an increasing number of reads moving downstream, with a peak of read abundance in the S14 summer samples. In contrast, we found a decreasing abundance moving downstream of Euryarchaeota in winter, with the W02 sample having higher numbers of reads and the abundance gradually decreasing to W14.


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

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

Archaeal and bacterial diversities.(A) Proportion of reads classified as Euryarchaeota from Domain Archaea. In summer, this phylum increased its representation with increasing eutrophication, and in winter, there is a gradual longitudinal decrease in the abundance of this phylum. (B) Alpha-diversity results using Chao1 for summer and winter. The results show a tendency of greater homogeneity and Chao1 values in the winter than in the summer. (C) Beta-diversity results, using unweighted Unifrac. The analyses were performed independently for the sample groups representing seasons, course and PhyChem classification.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0120608.g003: Archaeal and bacterial diversities.(A) Proportion of reads classified as Euryarchaeota from Domain Archaea. In summer, this phylum increased its representation with increasing eutrophication, and in winter, there is a gradual longitudinal decrease in the abundance of this phylum. (B) Alpha-diversity results using Chao1 for summer and winter. The results show a tendency of greater homogeneity and Chao1 values in the winter than in the summer. (C) Beta-diversity results, using unweighted Unifrac. The analyses were performed independently for the sample groups representing seasons, course and PhyChem classification.
Mentions: We found a total of 4 bacteria phyla, with Proteobacteria, Bacteroidetes, Actinobacteria, Cyanobacteria, Verrucomicrobia and Firmicutes as the most representative groups found in all samples (Fig. 2B, 2C and S2 Table), representing a total of 85.6% and 91.1% of all classified reads for the summer and winter samples, respectively. At the family taxonomic level, we found Comamonadaceae, ACK-M1, Rhodobacteraceae, Chitinophagaceae and Flavobacteriaceae as the five most representative taxa for both, summer and winter samples (S2 Fig.). The Pseudomonadaceae is the family that presented the higher discrepancy between summer and winter, representing 0.5% and 2.7%, respectively. For Domain Archaea, we found 85 OTUs classified as Parvarchaeota, Crenarchaeota and Euryarchaeota, represented by 1,777 reads in all samples combined. Interestingly, the phylum Euryarchaeota showed an inverted trend between summer and winter (Fig. 3A). We found an increasing number of reads moving downstream, with a peak of read abundance in the S14 summer samples. In contrast, we found a decreasing abundance moving downstream of Euryarchaeota in winter, with the W02 sample having higher numbers of reads and the abundance gradually decreasing to W14.

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.