Exploring Actinobacteria assemblages in coastal marine sediments under contrasted Human influences in the West Istria Sea, Croatia

Abstract

The exploration of marine Actinobacteria has as major challenge to answer basic questions of microbial ecology that, in turn, will provide useful information to exploit Actinobacteria metabolisms in biotechnological processes. The ecological functions performed by Actinobacteria in marine sediments are still unclear and belongs to the most burning basic questions. The comparison of Actinobacteria communities inhabiting marine sediments that are under the influence of different contamination types will provide valuable information in the adaptation capacities of Actinobacteria to colonize specific ecological niche. In the present study, the characterization of different Actinobacteria assemblages according to contamination type revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a "core" Actinobacteria community and specific roles associated with the presence of contaminants. Indeed, the results allowed to distinguish Actinobacteria genera and species operational taxonomic units (OTUs) able to cope with the presence of either (i) As, (ii) metals Ni, Fe, V, Cr, and Mn, or (iii) polycyclic aromatic hydrocarbons (PAHs) and toxic metals (Hg, Cd, Cu, Pb, and Zn). Such observations highlighted the metabolic capacities of Actinobacteria and their potential that should be taken into consideration and advantage during the implementation of bioremediation processes in marine ecosystems.

Temperature affects microbial abundance, activity and interactions in anaerobic digestion

“…Analysis based on network will shed light on the mechanisms regulating the interactions among microorganisms that improve AD performance. Recently, there have been several studies in which the potential organization of the microbial community in networks was investigated, such as the microbial community in the soil (Navarrete et al, 2015), marine water (Duran et al, 2015) and human intestine (Zhang et al, 2014). However, little is known about the interactions among microorganisms in AD systems under a temperature gradient, and how these interactions are regulated by temperature.…”

Integron diversity in marine environments

“…intI1 to 8 sequences were included (except intI5). IntI libraries were constructed from coastal sediment metagenomes described in Duran et al (2015) and Stauffert et al (2013). Amplification of an 800-bp intI fragment was performed using as primers the inverted complementary sequence of AJH72 (Gillings et al 2005) and intI948R (Elsaied et al 2007).…”

“…4. For more details on samples from Croatia, see Duran et al (2015); on microcosms from French sediments, see Stauffert et al (2013). IntI libraries were obtained as described in Fig.…”

“…To evaluate the impact of contamination on integrase diversity, we performed analyses of intI libraries from sediments of West Istrian coast (Croatia) at sites contaminated by toxic metals, PAH and PCB (description of samples in Duran et al 2015 andDurmiši et al 2013) and from mesocosms of oil-contaminated mudflat sediments (Brittany, France; description of samples in Stauffert et al 2013). MDS analysis showed more similarities between IntI pools from geographically close samples than to their pollution level (Fig.…”

Microbial ecology of hydrocarbon-polluted coastal sediments

“…The powerful resolution of high-throughput sequencing approaches allows the characterization of structural and metabolic changes of microbial communities in contaminated marine ecosystems. The comparison of microbial communities from marine sites with contrasted contamination levels described in Duran et al (2015a) showed specific bacterial assemblages according to the type of contaminant. The study, focusing on Actinobacteria assemblage, revealed the ecological importance of Actinobacteria for maintaining both general biogeochemical functions through a Bcore^Actinobacteria community and specific roles associated with the presence of contaminants.…”