Description of Freshwater Bacterial Assemblages from the Upper Paraná River Floodpulse System, Brazil

Lemke, Michael; Lienau, E. Kurt; Rothe, Jean; Pagioro, Thomaz Aurélio; Rosenfeld, Jeff; DeSalle, Rob

doi:10.1007/s00248-008-9398-3

Cited by 45 publications

(43 citation statements)

References 42 publications

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“…In addition, the TGGE fingerprints revealed greater genetic diversity than the morphological observations by microscopy, as has been noted in other studies (33,40). However, according to the databases, we found many bands that corresponded to uncultured bacteria, as has been observed in other studies using TGGE/DGGE techniques (41,42). The explanation could be that the organisms isolated and cultivated to date represent only a small fraction of the true microbial diversity (43).…”

Section: Discussionsupporting

confidence: 80%

Molecular Fingerprinting of Cyanobacteria from River Biofilms as a Water Quality Monitoring Tool

Loza

Perona

Mateo

2013

Appl Environ Microbiol

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Benthic cyanobacterial communities from Guadarrama River (Spain) biofilms were examined using temperature gradient gel electrophoresis (TGGE), comparing the results with microscopic analyses of field-fixed samples and the genetic characterization of cultured isolates from the river. Changes in the structure and composition of cyanobacterial communities and their possible association with eutrophication in the river downstream were studied by examining complex TGGE patterns, band extraction, and subsequent sequencing of 16S rRNA gene fragments. Band profiles differed among sampling sites depending on differences in water quality. The results showed that TGGE band richness decreased in a downstream direction, and there was a clear clustering of phylotypes on the basis of their origins from different locations according to their ecological requirements. Multivariate analyses (cluster analysis and canonical correspondence analysis) corroborated these differences. Results were consistent with those obtained from microscopic observations of field-fixed samples. According to the phylogenetic analysis, morphotypes observed in natural samples were the most common phylotypes in the TGGE sequences. These phylotypes were closely related to Chamaesiphon, Aphanocapsa, Pleurocapsa, Cyanobium, Pseudanabaena, Phormidium, and Leptolyngbya. Differences in the populations in response to environmental variables, principally nutrient concentrations (dissolved inorganic nitrogen and soluble reactive phosphorus), were found. Some phylotypes were associated with low nutrient concentrations and high levels of dissolved oxygen, while other phylotypes were associated with eutrophic-hypertrophic conditions. These results support the view that once a community has been characterized and its genetic fingerprint obtained, this technique could be used for the purpose of monitoring rivers.

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Section: Discussionsupporting

confidence: 80%

Molecular Fingerprinting of Cyanobacteria from River Biofilms as a Water Quality Monitoring Tool

Loza

Perona

Mateo

2013

Appl Environ Microbiol

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“…Such a strong effluent "signature" provides both a caution for the interpretation of molecular survey data from wastewater-impacted freshwater environments and the potential for source tracking with molecular "signatures" as a powerful approach for watershed management. Several previous studies used molecular (DNA/RNA-based) analyses to examine bacterial communities associated with river environments, including the Danube River, Europe (39), Changjiang River, China (40), Seine River, France (41), Cértima River, Portugal (42), Santa Ana River, United States (43), Paraná River, Brazil (44), and Anacostia River, United States (45). To our knowledge, no study has yet used these techniques to directly address the impact of wastewater treatment systems on perceived riverine bacterial communities as we have done here.…”

Section: Resultsmentioning

confidence: 99%

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

Sonthiphand

Cejudo

Schiff

et al. 2013

Appl Environ Microbiol

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The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH 3 and NH 4 ؉ ) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO 3 ؊ or N 2 ), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities.T he Grand River is the largest watershed in Southwestern Ontario, draining into Lake Erie, and is impacted by ammonia (NH 3 and NH 4 ϩ ) sources that directly affect water quality. The oxidation of anthropogenic ammonia to less toxic forms (e.g., NO 3 Ϫ or N 2 ) by ammonia-oxidizing prokaryotes (AOP) helps prevent ammonia from exceeding toxicity thresholds for aquatic organisms and limits for downstream drinking water intake. AOP include aerobic ammonia-oxidizing bacteria (AOB) and archaea (AOA) and anaerobic ammonia-oxidizing (anammox) bacteria.Nitrification is composed of two biological processes: ammonia and nitrite oxidation. Ammonia oxidation is considered the rate-limiting step in nitrification (1) and was believed for many decades to be mediated solely by a group of chemolithoautotrophic AOB (2). In 2005, AOA were also discovered (3). Although studies have confirmed the presence and abundance of AOA in both natural (e.g., references 4-6) and engineered (e.g., references 7-9) environments, relative contributions to ammonia oxidation in these environments are difficult to assess. Although AOA, rather than AOB, were active in soil microcosms and acid soils due to low ammonia availability and their kinetic constant (K m ) for ammonia (10), AOB showed e...

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“…Alphaproteobacteria, Betaproteobacteria, Gamma proteobacteria and Actinobacteria are ubiquitous groups in freshwater habitats (Gich et al, 2005;Anderson-Glenna et al, 2008) and are numerically important in river systems (Beier et al, 2008;Lemke et al, 2009). Members of Betaproteobacteria respond rapidly to organic and inorganic nutrient enrichment (Hahn, 2003;Simek et al, 2005) and have been isolated from various polluted and unpolluted freshwater bodies (De Figueiredo et al, 2011;Haller et al, 2011).…”

Section: Phylogenetic Diversity Of Bacterial Communitiesmentioning

confidence: 99%

The impact of physico-chemical water quality parameters on bacterial diversity in the Vaal River, South Africa

Jordaan¹,

Bezuidenhout²

2013

WSA

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This study aimed to identify bacterial community structures in the Vaal River using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) and high-throughput sequencing. The impact of physico-chemical characteristics on bacterial structures was investigated through multivariate analysis. Samples were collected from 4 sampling stations along the Upper Vaal River during winter (June 2009) and summer (December 2010). Physico-chemical analysis was conducted on-site. Additional physico-chemical data were obtained from statutory bodies. DNA was directly isolated from water samples and PCR amplified using universal bacterial primer pairs. PCR products were subjected to DGGE fingerprinting and high-throughput sequencing, followed by Shannon-Weaver diversity calculations, cluster analysis and multivariate analysis. Physico-chemical parameters did not exceed the prescribed South African water quality standards for domestic use, aquatic ecosystems, livestock watering and irrigation. DGGE banding patterns revealed similar bacterial community structures for 3 of the 4 sampling stations. PCA and RDA indicated that pH, water temperature and inorganic nutrient concentrations could be used to explain changes in bacterial community structures. High-throughput sequencing data showed that bacterial assemblages were dominated by common freshwater groups: Cyanobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Other freshwater phyla such as Deltaproteobacteria, Epsilonbacteria, Acidobacteria, Verrucomicrobia, Firmicutes, Fusobacteria, Flavobacteria and Fibrobacteres were found in low proportions. This study provides an overview of the dominant bacterial groups in the Upper Vaal River and the impact of environmental changes on bacterial diversity.

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Description of Freshwater Bacterial Assemblages from the Upper Paraná River Floodpulse System, Brazil

Cited by 45 publications

References 42 publications

Molecular Fingerprinting of Cyanobacteria from River Biofilms as a Water Quality Monitoring Tool

Molecular Fingerprinting of Cyanobacteria from River Biofilms as a Water Quality Monitoring Tool

Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

The impact of physico-chemical water quality parameters on bacterial diversity in the Vaal River, South Africa

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