16S and 18S rRNA Gene Metabarcoding Provide Congruent Information on the Responses of Sediment Communities to Eutrophication

Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.Peer reviewe

16S rRNA Gene Metabarcoding Indicates Species-Characteristic Microbiomes in Deep-Sea Benthic Foraminifera

Foraminifera are unicellular eukaryotes that are an integral part of benthic fauna in many marine ecosystems, including the deep sea, with direct impacts on benthic biogeochemical cycles. In these systems, different foraminiferal species are known to have a distinct vertical distribution, i.e., microhabitat preference, which is tightly linked to the physico-chemical zonation of the sediment. Hence, foraminifera are well-adapted to thrive in various conditions, even under anoxia. However, despite the ecological and biogeochemical significance of foraminifera, their ecology remains poorly understood. This is especially true in terms of the composition and diversity of their microbiome, although foraminifera are known to harbor diverse endobionts, which may have a significant meaning to each species' survival strategy. In this study, we used 16S rRNA gene metabarcoding to investigate the microbiomes of five different deep-sea benthic foraminiferal species representing differing microhabitat preferences. The microbiomes of these species were compared intra- and inter-specifically, as well as with the surrounding sediment bacterial community. Our analysis indicated that each species was characterized with a distinct, statistically different microbiome that also differed from the surrounding sediment community in terms of diversity and dominant bacterial groups. We were also able to distinguish specific bacterial groups that seemed to be strongly associated with particular foraminiferal species, such as the family Marinilabiliaceae for Chilostomella ovoidea and the family Hyphomicrobiaceae for Bulimina subornata and Bulimina striata. The presence of bacterial groups that are tightly associated to a certain foraminiferal species implies that there may exist unique, potentially symbiotic relationships between foraminifera and bacteria that have been previously overlooked. Furthermore, the foraminifera contained chloroplast reads originating from different sources, likely reflecting trophic preferences and ecological characteristics of the different species. This study demonstrates the potential of 16S rRNA gene metabarcoding in resolving the microbiome composition and diversity of eukaryotic unicellular organisms, providing unique in situ insights into enigmatic deep-sea ecosystems.Peer reviewe

Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone

This work was funded by the Natural Environment Research Council (grant NE/E01559X/1)

Impact of crude oil on bacterial communities in marine ecosystems

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Impact of crude oil on bacterial communities in marine ecosystems

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Temporal changes in the contribution of methane-oxidizing bacteria to the biomass of chironomid larvae determined using stable carbon isotopes and ancient DNA

International audienceFreshwater lakes are important sources of methane (CH4) emissions, by organic matter degradation under anaerobic conditions (methanogenesis). Previous studies suggest that lakes contribute up to 16 % of natural emissions. About 60 % of the CH4 produced is used as an energy source by methaneoxidizing bacteria (MOB--methanotrophs), which could support higher trophic levels, especially Chironomidae (Diptera). Because biogenic methane has a very low stable carbon isotope value, evidence of methane-derived organic-matter assimilation can be tracked by stable carbon isotope analysis in consumers such as chironomids. In some cases, however, chironomid d13C values are not low enough to unambiguously demonstrate methanotroph assimilation and an alternative line of evidence is required. Analysis of ancient DNA (aDNA) from the methanotroph community preserved in lake sediment provides reliable information about past methane oxidation in freshwater lakes. A combination of these two approaches was used to study a sediment core from the deepest zone of Lake Narlay (Jura, France), which covers the last 1,500 years of sediment accumulation. Results show a significant change ca.AD1600, with an increase in the proportion of MOB in the total bacteria community, and a decrease in chironomid headcapsule d13C. These trends suggest assimilation of MOB by chironomid larvae, and account for up to 36 %of the chironomid biomass. The data also provide information about the feeding behavior of chironomids, with evidence for preferential assimilation of methanotroph type I and the NC10 phylum. The combination of aDNA analysis and carbon stable isotopes strengthens the reliability of inferences about carbon sources incorporated into chironomid biomas