Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

In this study, 16S rRNA gene sequencing was used to characterize the changes in taxonomic composition and environmental factors significantly influencing bacterial community structure across an annual cycle in the Estuary of Bilbao as well as its tributaries. In spite of this estuary being small and characterized by a short residence time, the environmental factors most highly correlated with the bacterial community mirrored those reported to govern larger estuaries, specifically salinity and temperature. Additionally, bacterial community changes in the estuary appeared to vary with precipitation. For example, an increase in freshwater bacteria (Comamonadaceae and Sphingobacteriaceae) was observed in high precipitation periods compared to the predominately marine-like bacteria (Rhodobacterales and Oceanospirillales) that were found in low precipitation periods. Notably, we observed a significantly higher relative abundance of Comamonadaceae than previously described in other estuaries. Furthermore, anthropic factors could have an impact on this particular estuary’s bacterial community structure. For example, ecosystem changes related to the channelization of the estuary likely induced a low dissolved oxygen (DO) concentration, high temperature, and high chlorophyll concentration period in the inner euhaline water in summer (samples with salinity >30 ppt). Those samples were characterized by a high abundance of facultative anaerobes. For instance, OTUs classified as Cryomorphaceae and Candidatus Aquiluna rubra were negatively associated with DO concentration, while Oleiphilaceae was positively associated with DO concentration. Additionally, microorganisms related to biological treatment of wastewater (e.g Bdellovibrio and Zoogloea) were detected in the samples immediately downstream of the Bilbao Wastewater Treatment Plant (WWTP). There are several human activities planned in the region surrounding the Estuary of Bilbao (e.g. sediment draining, architectural changes, etc.) which will likely affect this ecosystem. Therefore, the addition of bacterial community profiling and diversity analysis into the estuary’s ongoing monitoring program would provide a more comprehensive view of the ecological status of the Estuary of Bilbao

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

In this study, 16S rRNA gene sequencing was used to characterize the changes in taxonomic composition and environmental factors significantly influencing bacterial community structure across an annual cycle in the Estuary of Bilbao as well as its tributaries. In spite of this estuary being small and characterized by a short residence time, the environmental factors most highly correlated with the bacterial community mirrored those reported to govern larger estuaries, specifically salinity and temperature. Additionally, bacterial community changes in the estuary appeared to vary with precipitation. For example, an increase in freshwater bacteria (Comamonadaceae and Sphingobacteriaceae) was observed in high precipitation periods compared to the predominately marine-like bacteria (Rhodobacterales and Oceanospirillales) that were found in low precipitation periods. Notably, we observed a significantly higher relative abundance of Comamonadaceae than previously described in other estuaries. Furthermore, anthropic factors could have an impact on this particular estuary's bacterial community structure. For example, ecosystem changes related to the channelization of the estuary likely induced a low dissolved oxygen (DO) concentration, high temperature, and high chlorophyll concentration period in the inner euhaline water in summer (samples with salinity >30 ppt). Those samples were characterized by a high abundance of facultative anaerobes. For instance, OTUs classified as Cryomorphaceae and Candidatus Aquiluna rubra were negatively associated with DO concentration, while Oleiphilaceae was positively associated with DO concentration. Additionally, microorganisms related to biological treatment of wastewater (e.g Bdellovibrio and Zoogloea) were detected in the samples immediately downstream of the Bilbao Wastewater Treatment Plant (WWTP). There are several human activities planned in the region surrounding the Estuary of Bilbao (e.g. sediment draining, architectural changes, etc.) which will likely affect this ecosystem. Therefore, the addition of bacterial community profiling and diversity analysis into the estuary's ongoing monitoring program would provide a more comprehensive view of the ecological status of the Estuary of Bilbao.The authors received funding from Geonomic resources group (Grant IT558-10) to AE, and supported by SIEBM XVIII congress (Gijon). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Effects of Heavy Fuel Oil on the Bacterial Community Structure of a Pristine Microbial Mat▿

The effects of petroleum contamination on the bacterial community of a pristine microbial mat from Salins-de-Giraud (Camargue, France) have been investigated. Mats were maintained as microcosms and contaminated with no. 2 fuel oil from the wreck of the Erika. The evolution of the complex bacterial community was monitored by combining analyses based on 16S rRNA genes and their transcripts. 16S rRNA gene-based terminal restriction fragment length polymorphism (T-RFLP) analyses clearly showed the effects of the heavy fuel oil after 60 days of incubation. At the end of the experiment, the initial community structure was recovered, illustrating the resilience of this microbial ecosystem. In addition, the responses of the metabolically active bacterial community were evaluated by T-RFLP and clone library analyses based on 16S rRNA. Immediately after the heavy fuel oil was added to the microcosms, the structure of the active bacterial community was modified, indicating a rapid microbial mat response. Members of the Gammaproteobacteria were initially dominant in the contaminated microcosms. Pseudomonas and Acinetobacter were the main genera representative of this class. After 90 days of incubation, the Gammaproteobacteria were superseded by “Bacilli” and Alphaproteobacteria. This study shows the major changes that occur in the microbial mat community at different time periods following contamination. At the conclusion of the experiment, the RNA approach also demonstrated the resilience of the microbial mat community in resisting environmental stress resulting from oil pollution

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

<div><p>In this study, 16S rRNA gene sequencing was used to characterize the changes in taxonomic composition and environmental factors significantly influencing bacterial community structure across an annual cycle in the Estuary of Bilbao as well as its tributaries. In spite of this estuary being small and characterized by a short residence time, the environmental factors most highly correlated with the bacterial community mirrored those reported to govern larger estuaries, specifically salinity and temperature. Additionally, bacterial community changes in the estuary appeared to vary with precipitation. For example, an increase in freshwater bacteria (<i>Comamonadaceae</i> and <i>Sphingobacteriaceae</i>) was observed in high precipitation periods compared to the predominately marine-like bacteria (<i>Rhodobacterales</i> and <i>Oceanospirillales</i>) that were found in low precipitation periods. Notably, we observed a significantly higher relative abundance of <i>Comamonadaceae</i> than previously described in other estuaries. Furthermore, anthropic factors could have an impact on this particular estuary’s bacterial community structure. For example, ecosystem changes related to the channelization of the estuary likely induced a low dissolved oxygen (DO) concentration, high temperature, and high chlorophyll concentration period in the inner euhaline water in summer (samples with salinity >30 ppt). Those samples were characterized by a high abundance of facultative anaerobes. For instance, OTUs classified as <i>Cryomorphaceae</i> and <i>Candidatus Aquiluna rubra</i> were negatively associated with DO concentration, while <i>Oleiphilaceae</i> was positively associated with DO concentration. Additionally, microorganisms related to biological treatment of wastewater (e.g <i>Bdellovibrio</i> and <i>Zoogloea)</i> were detected in the samples immediately downstream of the Bilbao Wastewater Treatment Plant (WWTP). There are several human activities planned in the region surrounding the Estuary of Bilbao (e.g. sediment draining, architectural changes, etc.) which will likely affect this ecosystem. Therefore, the addition of bacterial community profiling and diversity analysis into the estuary’s ongoing monitoring program would provide a more comprehensive view of the ecological status of the Estuary of Bilbao.</p></div

The OTUs significantly related with DO concentration, temperature, and chlorophyll concentration in B30 water mass through time.

<p>eLSA analysis was conducted for the 14 time points (total sampling months in duplicate) of the B30 water mass samples. In analysis, the 85 most abundant OTUs and all the environmental features measured were included (salinity, temperature, precipitation, pH, turbidity, and chlorophyll and DO concentration). The matrix of the variables was normalized by ‘robustZ’ method. A network was created with Cytoscape software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178755#pone.0178755.ref045" target="_blank">45</a>] using the significant (q < 0.01) correlations obtained in the eLSA analysis. The directionality of the relationship is marked with arrows with its temporal delay (in months) in the edge label (green) and the relation type between them positive (red) or negative (blue).</p

Confusion matrix for the water masses of the Estuary of Bilbao.

<p>Confusion matrix for the water masses of the Estuary of Bilbao.</p

Bacterial community distribution for Estuary and tributary samples.

<p>A Bray-Curtis DCA plot showing the community dissimilarity among estuarine water samples (IS, MS, OS, B30, B33, B35) and the samples of the two tributary stations (GAL, NER) collected in April, August, and October 2014.</p

Microbial community composition in the water masses of the Estuary of Bilbao.

<p>OTUs relative abundances per water mass were plotted. Each column shows the mean relative abundance of the top 10 most abundant orders per water sample (B30, B33, B35, IS, MS, OS) along the annual cycle (14 months). These bacteria account for the 68% of the total community.</p

Main environmental features variations (temperature, salinity and precipitation) and community richness changes along the annual cycle.

<p>A) Monthly salinity and precipitation variation per surface water mass IS, MS, OS; B) Observed alpha diversity, temperature and precipitation fluctuation per surface water mass IS, MS, OS; C) Observed alpha diversity, temperature and precipitation changes per euhaline water mass B30, B33, B35.</p

Microbial taxonomic composition of the Estuary of Bilbao tributaries Nervion (NER) and Galindo (GAL).

<p>In the bar-plot, each column shows the mean relative abundances of the top 10 most abundant orders in each tributary in April, August, and October 2014. The taxonomic groups represented in the plot account for 63% of the total community.</p