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.

Terrestrial organic matter input drives sedimentary trace metal sequestration in a human-impacted boreal estuary.

Coastal sediments play a fundamental role in processing anthropogenic trace metal inputs. Previous studies have shown that terrestrial organic matter (OM) is a significant vector for trace metal transport across the land-to-sea continuum, but little is known about the fate of land-derived metal-OM complexes in coastal sediments. Here, we use a comprehensive set of sediment pore water and solid-phase analyses to investigate how variations in terrestrial OM delivery since the 1950s have influenced trace metal accumulation and diagenesis in a human-impacted boreal estuary in the northern Baltic Sea. A key feature of our dataset is a strong correlation between terrestrial OM deposition and accumulation of metal-OM complexes in the sediments. Based on this strong coupling, we infer that the riverine input of terrestrial metal-OM complexes from the hinterland, followed by flocculation-induced settling in the estuary, effectively modulates sedimentary trace metal sequestration. While part of the trace metal pool associated with these complexes is efficiently recycled in the surface sediments during diagenesis, a substantial fraction is permanently buried as refractory metal-OM complexes or through incorporation into insoluble sulfides, thereby escaping further biological processing. These findings suggest that terrestrial OM input could play a more pivotal role in trace metal processing in coastal environments than hitherto acknowledged.

Metabarcoding Insights Into the Trophic Behavior and Identity of Intertidal Benthic Foraminifera.

Foraminifera are ubiquitous marine protists with an important role in the benthic carbon cycle. However, morphological observations often fail to resolve their exact taxonomic placement and there is a lack of field studies on their particular trophic preferences. Here, we propose the application of metabarcoding as a tool for the elucidation of the in situ feeding behavior of benthic foraminifera, while also allowing the correct taxonomic assignment of the feeder, using the V9 region of the 18S (small subunit; SSU) rRNA gene. Living foraminiferal specimens were collected from two intertidal mudflats of the Wadden Sea and DNA was extracted from foraminiferal individuals and from the surrounding sediments. Molecular analysis allowed us to confirm that our foraminiferal specimens belong to three genetic types: Ammonia sp. T6, Elphidium sp. S5 and Haynesina sp. S16. Foraminiferal intracellular eukaryote communities reflected to an extent those of the surrounding sediments but at different relative abundances. Unlike sediment eukaryote communities, which were largely determined by the sampling site, foraminiferal intracellular eukaryote communities were driven by foraminiferal species, followed by sediment depth. Our data suggests that Ammonia sp. T6 can predate on metazoan classes, whereas Elphidium sp. S5 and Haynesina sp. S16 are more likely to ingest diatoms. These observations, alongside the use of metabarcoding in similar ecological studies, significantly contribute to our overall understanding of the ecological roles of these protists in intertidal benthic environments and their position and function in the benthic food webs.

Unexpected biotic resilience on the Japanese seafloor caused by the 2011 Tohoku-Oki tsunami.

On March 11(th), 2011 the Mw 9.0 2011 Tohoku-Oki earthquake resulted in a tsunami which caused major devastation in coastal areas. Along the Japanese NE coast, tsunami waves reached maximum run-ups of 40 m, and travelled kilometers inland. Whereas devastation was clearly visible on land, underwater impact is much more difficult to assess. Here, we report unexpected results obtained during a research cruise targeting the seafloor off Shimokita (NE Japan), shortly (five months) after the disaster. The geography of the studied area is characterized by smooth coastline and a gradually descending shelf slope. Although high-energy tsunami waves caused major sediment reworking in shallow-water environments, investigated shelf ecosystems were characterized by surprisingly high benthic diversity and showed no evidence of mass mortality. Conversely, just beyond the shelf break, the benthic ecosystem was dominated by a low-diversity, opportunistic fauna indicating ongoing colonization of massive sand-bed deposits.

Vertical migration, nitrate uptake and denitrification: survival mechanisms of foraminifers (Globobulimina turgida) under low oxygen conditions.

(15)NO(3)(-) isotope labelling experiments were performed to investigate foraminiferal nitrate uptake strategies and the role of pseudopodial networks in nitrate uptake. Globobulimina turgida were placed below the nitrate penetration depth in homogenized sediment cores incubated in artificial seawater containing (15)NO(3)(-) . A nylon net prevented the vertical migration of foraminifera to strata containing nitrate and oxygen, but allowed potential access to such strata by extension of pseudopods. No (15)NO(3)(-) was found in G. turgida in these cores, suggesting that foraminifera cannot extend their pseudopods for nitrate uptake through several millimetres of sediment, but must physically migrate upwards closer to nitrate-containing strata. However, foraminiferal migration patterns in control cores with no nylon net were erratic, suggesting that individuals move in random orientations until they find favourable conditions (i.e. free nitrate or oxygen). A second experiment showed that foraminifera actively collect nitrate both in the presence and in the absence of oxygen, although uptake was initiated faster if oxygen was absent from the environment. However, no systematic influence of the size of the intracellular nitrate pool on nitrate uptake was observed, as specimens containing a large range of intracellular nitrate (636-19 992 pmol per cell) were measured to take up (15)NO(3)(-) at comparable rates.