Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment

Abstract

a b s t r a c tThe dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip 4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.

Functional diversity and redundancy across fish gut, sediment and water bacterial communities

“…That being said, Bayer et al . () reported 392 functional genes associated with sponge and seawater microbiomes, while organic remediation and metal resistance genes have been detected in high proportion in Elbe river sediments (Störmer et al ., ), in aerobic bioreactor (Zhao et al ., ) and in mangrove sediments (Bai et al ., ). Here, we bring further evidence that bacterial communities associated with macro‐organisms exhibit a highly diversified functional potential (Dinsdale et al ., ; Lavery et al ., ; Xing et al ., ; Bayer et al ., ; Polónia et al ., ; Cleary et al ., ; de Voogd et al ., ), which is equivalent to the one observed in water and sediment communities and thus should be accounted for when assessing microbial functional diversity within aquatic ecosystems.…”

“…The richness of gene variants estimated at the ecosystem scale (43% of the potential, i.e., 29 028 out of 67 628 variants) was comparable to those estimated with the same tool in bacterial communities from marine (18 7987; Störmer et al ., ) and mangrove (35 000; Bai et al ., ) sediments, anaerobic reactors (28 575; Zhao et al ., ), sponge‐associated communities (20 273; Bayer et al ., ) and in grassland soils (49 520; Yang et al ., ). The variants richness was around two orders of magnitude higher than the richness of functional genes and many variants were detected for each gene.…”

“…Direct comparison of our functional gene richness estimates with other Geochip-based studies are difficult because most of these studies only reported the number of gene variants but also as the Geochip design evolves constantly (we used Geochip v4.0 but v4.2, v4.4 and v4.6 also existed). That being said, Bayer et al (2014) reported 392 functional genes associated with sponge and seawater microbiomes, while organic remediation and metal resistance genes have been detected in high proportion in Elbe river sediments (St€ ormer et al, 2013), in aerobic bioreactor (Zhao et al, 2014a) and in mangrove sediments (Bai et al, 2013).…”

Negligible microbial heterotrophic quantitative contribution onto trace metals remobilization during marine sediment resuspension - insights from a Mediterranean urbanized bay

“…When mixing occur, physical-chemical conditions such as redox potential, pH or solid/liquid ratio may change drastically compare to those in the sediment (Caille et al, 2003;Dang et al, 2020;Shipley et al, 2011). Microbial responses also vary significantly within hours to months, as demonstrated by studies focusing on the phytoplankton dynamics (Coclet et al, 2018;Lafabrie et al, 2013) or on the structure and functional properties of the prokaryotic community (Galand et al, 2016;Störmer et al, 2013;Won et al, 2017;Zouch et al, 2018). Planktonic active microbes can react very quickly to the large input of organic matter and nutrients in oxic water (Coclet et al, 2018;Lafabrie et al, 2013;Schäfer et al, 2001).…”