Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator

Garrido, Laura; Sánchez, Olga; Ferrera, Isabel; Tomàs, N.; Mas, Jordi

doi:10.1016/j.scitotenv.2013.08.065

Cited by 27 publications

(12 citation statements)

References 45 publications

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“…We determined common alphadiversity indices as possible descriptors of the environmental status since pressures can lead to changes in microbial composition (Torsvik et al, 2002;Smith and Schindler, 2009) (Connell, 1978), which suggests that intermediate intensity of disturbance maximizes diversity, and therefore systems with low and high disturbance, such Stations 5 and 1 in terms of nutrient load, can harbor similar levels of diversity. In any case, as previously observed in other systems (Garrido et al, 2014) these indices do not seem promising as indicators to asses environmental status. Contrarily, a clear decrease in richness was observed from coast to offshore.…”

Section: Does Plankton Diversity Have Informative Potential For Envirsupporting

confidence: 45%

“…These indices may also offer ecological information (i.e., species relative composition). In fact, this approach has been explored in other ecosystems; for example in reclaimed waters, the ratio between the Bacteroidetes, Gammaproteobacteria, and Nitrospira/Betaproteobacteria (BGN:β) seems a possible alternative indicator of water quality (Garrido et al, 2014). We tested the correlation of different taxa and the degree of eutrophication (i.e., nutrient concentration) and found significant correlations between certain picoeukaryotic taxa e.g., Ciliophora, and nutrient load; this taxa has been found previously in high abundances in eutrophic waters (Romari and Vaulot, 2004).…”

Section: Does Plankton Diversity Have Informative Potential For Envirmentioning

confidence: 99%

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Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons

et al. 2016

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Sequencing of rRNA gene polymerase chain reaction amplicons (rRNA tags) is the most common approach for investigating microbial diversity. The recent development of high-throughput sequencing (HTS) technologies has enabled the exploration of microbial biodiversity at an unprecedented scale, greatly expanding our knowledge on the microbiomes of marine ecosystems. These approaches provide accurate, fast, and cost efficient observations of the marine communities, and thus, may be suitable tools in biodiversity monitoring programs. To reach this goal, consistent and comparable methodologies must be used over time and within sites. Here, we have performed a cross-platform study of the two most common HTS methodologies, i.e., 454-pyrosequencing and Illumina tags to evaluate their usefulness in biodiversity monitoring and assessment of environmental status. Picoplankton biodiversity has been compared through both methodologies by sequencing the 16 and 18 S rRNA genes of a set of samples collected in the coast of Barcelona (NW Mediterranean). The results show that, despite differences observed in the rare OTUs retrieved, both platforms provide a comparable view of the marine picoplankton communities. On a taxonomic level, there was an accurate overlap in the detected phyla between the two methods and the overall estimates of alpha-and betadiversity were comparable. In addition, we explored the concept of "indicator species" and found that certain taxa (i.e., members of the Gammaproteobacteria among others) as well as the ratio between some phylogenetic groups (i.e., the ratio of Alphaproteobacteria/Gammaproteobacteria, Alteromonas/SAR11, and Alteromonas + Oceanospirillales/SAR11) have potential for being useful indicators of environmental status. The data show that implementing new protocols and identifying indicators of environmental status based on rRNA amplicon sequencing is feasible, and that is worth exploring whether the identified indices are universally applicable.

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Section: Does Plankton Diversity Have Informative Potential For Envirsupporting

confidence: 45%

Section: Does Plankton Diversity Have Informative Potential For Envirmentioning

confidence: 99%

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons

et al. 2016

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“…Traditionally, culture-dependent techniques were used to study bacterial diversities (Alegría et al 2012;Ferrando et al 2012;Vandecandelaere et al 2012), but these methods could not provide accurate representations of the bacterial populations, as most bacteria in the environment are viable, but currently unculturable. Molecular approaches, such as 16S ribosomal RNA (rRNA) clone libraries (Eichler et al 2006;Gihring et al 2012;Zhang et al 2013a) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) (Garrido et al 2014;González-Arenzana et al 2013;Sun et al 2013;Zhang et al 2013b), have greatly increased our comprehension of microbial communities, although these methods poorly represent the rare bacterial groups. In recent years, 454 pyrosequencing has been introduced as a next-generation sequencing method for revealing relatively detailed profiles of microbial communities (Beloshapka et al 2013;Jackson et al 2012).…”

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confidence: 99%

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

Wei

Wang

Liu

et al. 2015

Environ Sci Pollut Res

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As a better understanding of Beijing surface water ecosystems can provide clues for environmental management and public health, here, we report a study of the bacterial communities of five Beijing surface waters conducted using 454 pyrosequencing of 16S ribosomal RNA (rRNA) genes. We expected to observe a core bacterial community among the surface waters and differences in bacterial community abundance over the different locations of sampling. In this study, we obtained a total of 60,810 trimmed reads from the five samples after the removal of unqualified reads. Bacterial sequences from the five samples were classified into taxonomic classes using the default settings of the mothur platform. Our results provided insight into the bacterial community composition of surface waters and revealed that there was a core microbial community in the microbial populations of surface samples at different geographic locations, with 13 phyla and 40 genera in common. Our findings also revealed the differences in bacterial communities among five surface water samples obtained at different locations.

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“…Considering the fact that H of control beds was significantly larger (P ≤ 0.05) than IBP-enriched beds, it could be inferred that the enriched OTU in the control community was distributed more evenly than those in the IBP-enriched beds. Many studies have calculated Shannon diversity index (H ) in aquatic systems and values typically range from 0.5 to 5, with values of 0.5-2.0 implying low diversity and values of 2.0-5.0 indicating high diversity (Garrido et al, 2014). In this study, the majority of H were higher than 2.0, with a range of 1.59-5.60, suggesting a relatively high H value and wide range of diversity for the present treatment wetlands compared to previous studies on CWs (2.0-3.8 in Arroyo et al (2013); 1.74-2.93 in Peralta et al (2013)).…”

Section: Diversity Of Microbial Communitiesmentioning

confidence: 99%

Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater

Zhang

Luo

Lee

et al. 2016

Ecological Engineering

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a b s t r a c tA 16S rRNA gene multiplex 454 pyrosequencing approach was used to characterize the structure of the bacterial community in subsurface flow constructed wetlands planted with Typha angustifolia and unplanted wetland mesocosms receiving ibuprofen-enriched wastewater at a concentration of 250 g L −1 . The removal efficiency of ibuprofen (IBP) in the planted beds (78.5%) was significantly higher than that in the unplanted beds (57.9%) (P ≤ 0.05). The presence of ibuprofen significantly (P ≤ 0.05) reduced the diversity of the bacterial community. In total, 20 phyla comprising 265 genera were identified. The most predominant phyla were Firmicutes (27.6%), Actinobacteria (26.0%) and Proteobacteria (24.9%), making up 57-95% of the 16S rDNA sequences. Other dominating phyla in wetland soils were Chloroflexi (7.3%), Bacteroidetes (2.7%), Synergistetes (2.1%), and Acidobacteria (2.0%). A distinct profile of bacterial community in the wetland mesocosms was observed after IBP enrichment. IBP-enrichment enhanced the relative abundance of Actinobacteria, Bacilli and ␥-Proteobacteria at class level. The efficient ibuprofen removal observed in this study suggested that the IBP-enriched wetland systems may have selected a restricted group of bacteria that was able to survive best in the disturbed condition and participate in the IBP biodegradation. Our findings also indicated that the presence of macrophytes may have a vital impact on the microbial community and planted wetlands may be more robust and buffered against significant shifts in microbial composition in response to IBP-disturbance.

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Dynamics of microbial diversity profiles in waters of different qualities. Approximation to an ecological quality indicator

Cited by 27 publications

References 45 publications

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons

Bacterial communities of Beijing surface waters as revealed by 454 pyrosequencing of the 16S rRNA gene

Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater

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