Prokaryotic community composition and distribution in coastal sediments following a Po river flood event (northern Adriatic Sea, Italy)

Fazi, Stefano; Baldassarre, Laura; Cassin, Daniele; Quero, Grazia Marina; Pizzetti, Ilaria; Cibic, Tamara; Luna, Gian Marco; Zonta, Roberto; Negro, Paola Del

doi:10.1016/j.ecss.2019.106547

Cited by 11 publications

(11 citation statements)

References 82 publications

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“…Indeed, a strong difference in the prokaryote assemblage's composition was observed along the salinity gradient across the river-lagoon-sea transect and was accompanied by an increasing dominance of exclusive taxa in each of the investigated systems. This result corroborates previous investigations showing either an increasing presence of freshwater taxa at stations more influenced by the river discharge or a core microbiome present across all study areas [81]. Unfortunately, as our results do not allow us to provide information on the prokaryotic taxonomic identity (due to the limitations of the ARISA molecular technique, which does not allow DNA sequencing), we cannot make inferences about the specific ecological role of the different prokaryotic groups in each investigated system.…”

Section: Discussionsupporting

confidence: 87%

Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient

et al. 2020

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In benthic ecosystems, organic matter (OM), prokaryotes, and meiofauna represent a functional bottleneck in the energy transfer towards higher trophic levels and all respond to a variety of natural and anthropogenic disturbances. The relationships between OM and the different components of benthic communities are influenced by multiple environmental variables, which can vary across different habitats. However, analyses of these relationships have mostly been conducted by considering the different habitats separately, even though freshwater, transitional, and marine ecosystems, physically linked to each other, are not worlds apart. Here, we investigated the quantity and nutritional quality of sedimentary OM, along with the prokaryotic and meiofauna abundance, biomass, and biodiversity, in two sampling periods, corresponding to high vs. low freshwater inputs to the sea, along a river-to-sea transect. The highest values of sedimentary organic loads and their nutritional quality, prokaryotic and meiofaunal abundance, and biomass were consistently observed in lagoon systems. Differences in the prokaryotic Operational Taxonomic Units (OTUs) and meiofaunal taxonomic composition, rather than changes in the richness of taxa, were observed among the three habitats and, in each habitat, between sampling periods. Such differences were driven by either physical or trophic variables, though with differences between seasons. Overall, our results indicate that the apparent positive relationship between sedimentary OM, prokaryote and meiofaunal abundance, and biomass across the river-lagoon-sea transect under scrutiny is more the result of a pattern of specifically adapted prokaryotic and meiofaunal communities to different habitats, rather than an actually positive ‘response’ to OM enrichment. We conclude that the synoptic analysis of prokaryotes and meiofauna can provide useful information on the relative effect of organic enrichment and environmental settings across gradients of environmental continuums, including rivers, lagoons, and marine coastal ecosystems.

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Section: Discussionsupporting

confidence: 87%

Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient

et al. 2020

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“…According to our findings, the microbial community structure is profoundly dependent on the physicochemical features of the region, confirming previous results on microbial communities from sediments in coastal areas, estuaries and rivers (Freixa et al, 2016; Aylagas et al, 2017; Borja, 2018; Fazi et al, 2020). While several environmental characteristics were associated with the epilithic community dynamics, the driving environmental parameter appears to be the acidity of water (as confirmed by the pH results of the envfit analysis, r 2 = 0.9, p <.001), which is considerably lower in the southwestern region of Norway.…”

Section: Discussionsupporting

confidence: 92%

“…The combination of two techniques, 16S rRNA sequencing and CARD‐FISH, allowed us to gain insight into the community composition of epilithic prokaryotes, which are still poorly understood in the context of riverine ecosystems. Quantitative results such as those obtained by CARD‐FISH allow us to detect variations in actual cells numbers and activity of specific taxa, which would be otherwise lost by analysing only the number of gene copies provided by sequencing (Fazi et al, 2020). The CARD‐FISH results obtained in our study revealed a great variation at small spatial scales, such as in biofilms belonging to the same river, and thus seems to detect in‐system variability in the microbial community composition to a greater extent than metabarcoding.…”

Section: Discussionmentioning

confidence: 99%

Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators

Eiler

Fazi

et al. 2021

Molecular Ecology Resources

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Microbial communities are major players in the biogeochemical processes and ecosystem functioning of river networks. Despite their importance in the ecosystem, biomonitoring tools relying on prokaryotes are still lacking. Only a few studies have employed both metabarcoding and quantitative techniques such as catalysed reported deposition fluorescence in situ hybridization (CARD‐FISH) to analyse prokaryotic communities of epilithic biofilms in river ecosystems. We intended to investigate the efficacy of both techniques in detecting changes in microbial community structure associated with environmental drivers. We report a significant correlation between the prokaryotic community composition and pH in rivers from two different geographical areas in Norway. Both CARD‐FISH and metabarcoding data were following the pattern of the environmental variables, but the main feature distinguishing the community composition was the regional difference itself. Beta‐dispersion analyses on both CARD‐FISH abundance and metabarcoding data revealed higher accuracy of metabarcoding to differentiate regions and river systems. The CARD‐FISH results showed high variability, even for samples within the same river, probably due to some unmeasured microscale ecological variability which we could not resolve. We also present a statistical method, which uses variation coefficient and overall prevalence of taxonomic groups, to detect possible biological indicators among prokaryotes using metabarcoding data. The development of new prokaryotic bioindicators would benefit from both techniques used in this study, but metabarcoding seems to be faster and more reliable than CARD‐FISH for large scale bio‐assessment.

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“…The prokaryotic communities in the Uranouchi Inlet (Fig. 1D) were similar to those reported for other coastal areas, where the communities are mainly composed of Proteobacteria, Bacteroidetes, and Cyanobacteria (10, 15, 16), but different from those in brackish water (40) or freshwater (12), which are dominated by the same phyla, but different classes. In the present study, the Mimiviridae communities were characterized using a previously developed highly sensitive metabarcoding method (33), which was used for the first time on a time-series sample set.…”

Section: Discussionsupporting

confidence: 83%

Year-round dynamics of amplicon sequence variant communities differ among eukaryotes,Mimiviridae, and prokaryotes in a coastal ecosystem

Prodinger

Endo

Takano

et al. 2021

Preprint

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Coastal seawater is the habitat of diverse microbial communities. These communities are affected by seasonal environmental changes and fluctuating nutrient availability, as well as competitive and cooperative interspecific interactions. The complex interplay of these factors affects elemental cycles and therefore, the environment, which in turn affects microbial communities. In this work, we investigated the seasonal dynamics of communities of eukaryotes, a major group of double-stranded DNA viruses infecting eukaryotes (i.e., Mimiviridae), as well as prokaryotes in the Uranouchi Inlet, Kochi, Japan. This inlet harbors several microalgae that recurrently form blooms throughout the year. We performed metabarcoding using ribosomal RNA genes and a Mimiviridae DNA polymerase gene as marker genes and counted cells of major algal species in 43 seawater samples collected during 20 months. Communities of eukaryotes, Mimiviridae, and prokaryotes characterized at the amplicon sequence variant (ASV) level showed similar seasonal cycles but differences in several aspects such as the recovery rate after a year. The ASV persistence level differed among eukaryote, Mimiviridae, and prokaryote communities. Mimiviridae ASVs were less persistent than were eukaryotic ASVs, and prokaryotic ASVs were the most persistent. These observations are discussed in the context of survival strategies of the major microbes in these three communities.

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Prokaryotic community composition and distribution in coastal sediments following a Po river flood event (northern Adriatic Sea, Italy)

Cited by 11 publications

References 82 publications

Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient

Sedimentary Organic Matter, Prokaryotes, and Meiofauna across a River-Lagoon-Sea Gradient

Two different approaches of microbial community structure characterization in riverine epilithic biofilms under multiple stressors conditions: Developing molecular indicators

Year-round dynamics of amplicon sequence variant communities differ among eukaryotes,Mimiviridae, and prokaryotes in a coastal ecosystem

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