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Benthic foraminifera are known to play an important role in marine carbon and nitrogen cycles. Here, we report an enrichment of sulphur cycle -associated bacteria inside intertidal benthic foraminifera (Ammonia sp. (T6), Haynesina sp. (S16) and Elphidium sp. (S5)), using a metabarcoding approach targeting the 16S rRNA and aprA -genes. The most abundant intracellular bacterial groups included the genus Sulfurovum and the order Desulfobacterales. The bacterial 16S OTUs are likely to originate from the sediment bacterial communities, as the taxa found inside the foraminifera were also present in the sediment. The fact that 16S rRNA and aprA –gene derived intracellular bacterial OTUs were species-specific and significantly different from the ambient sediment community implies that bacterivory is an unlikely scenario, as benthic foraminifera are known to digest bacteria only randomly. Furthermore, these foraminiferal species are known to prefer other food sources than bacteria. The detection of sulphur-cycle related bacterial genes in this study suggests a putative role for these bacteria in the metabolism of the foraminiferal host. Future investigation into environmental conditions under which transcription of S-cycle genes are activated would enable assessment of their role and the potential foraminiferal/endobiont contribution to the sulphur-cycle.

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.

The Mn / Ca of calcium carbonate tests of living (rose-Bengal-stained) benthic foraminifera (Elphidium batialis, Uvigerina spp., Bolivina spissa, Nonionellina labradorica and Chilostomellina fimbriata) were determined in relation to pore water manganese (Mn) concentrations for the first time along a bottom water oxygen gradient across the continental slope along the NE Japan margin (western Pacific). The local bottom water oxygen (BWO) gradient differs from previous field study sites focusing on foraminiferal Mn / Ca and redox chemistry, therefore allowing further resolution of previously observed trends. The Mn / Ca ratios were analysed using laser ablation inductively coupled plasma-mass spectrometer (ICP-MS), allowing single-chamber determination of Mn / Ca. The incorporation of Mn into the carbonate tests reflects environmental conditions and is not influenced by ontogeny. The inter-species variability in Mn / Ca reflected foraminiferal in-sediment habitat preferences and associated pore water chemistry but also showed large interspecific differences in Mn partitioning. At each station, Mn / Ca ratios were always lower in the shallow infaunal E. batialis, occupying relatively oxygenated sediments, compared to intermediate infaunal species, Uvigerina spp. and B. spissa, which were typically found at greater depth, under more reducing conditions. The highest Mn / Ca was always recorded by the deep infaunal species N. labradorica and C. fimbriata. Our results suggest that although partitioning differs, Mn / Ca ratios in the intermediate infaunal taxa are promising tools for palaeoceanographic reconstructions as their microhabitat exposes them to higher variability in pore water Mn, thereby making them relatively sensitive recorders of redox conditions and/or bottom water oxygenation.

The Mn/Ca of carbonate tests of living deep-sea foraminifera (Hoeglundina elegans, Bulimina aculeata, Uvigerina peregrina and Melonis barleeanus) were determined together with pore water manganese along a bottom water oxygen gradient across the lower boundary of the Arabian Sea oxygen minimum zone. Although Mn has long been considered an indicator for contamination, new cleaning protocols and high-resolution laser ablation ICP-MS now allow the reliable analyses of test-associated Mn. Within locations, Mn incorporation between species varies as a function of their in-sediment depth preferences and associated pore water chemistry. Under well-oxygenated bottom water conditions, shallow infaunal species incorporate little Mn in their test, whereas the species collected from deeper habitats show elevated Mn concentrations. With decreasing oxygen contents pore water Mn concentrations and benthic foraminiferal in-sediment distribution change. Whereas Mn/Ca in shallow infaunal species responds moderately to bottom water oxygenation, Mn/Ca of the infaunal species M. barleeanus correlates well to oxygenation. Although high productivity results in a shallower redox cline within the sediment, pore water Mn is retained as long as the bottom water remains oxygenated. Under reduced bottom water oxygen conditions, Mn escapes to the overlying water column and test-associated Mn/Ca decreases also in the infaunal species. By combining pore water chemistry of Mn, calcitic Mn/Ca and foraminiferal ecology, a new conceptual model is presented (TROXCHEM3) that provides a framework for deconvolving past organic matter input and bottom water oxygenation.

Live (Rose-Bengal stained) deep-sea foraminiferal faunashave been studied at five stations between 500–2000-m depthalong the NE Japanese margin (western Pacific) tounderstand how complex environmental conditions (e.g.,oxygen depletion, organic matter) control their structure(i.e., diversity, standing stocks, and microhabitats). Allstations are characterized by silty sediments with no evidenceof recent physical disturbances. The three stations locatedbetween 760–1250 m are bathed by dysoxic bottom waters(,45 mmol/L). Although high organic-carbon contents arerecorded at all stations (.2.2% DW), only the oxygendepletedsites are characterized by higher concentrations ofsugars, lipids, and enzymatically hydrolysable amino acids(EHAA). Sedimentary contents in chlorophyllic pigmentsdecrease with water depth without any major change in theirfreshness (i.e., [Chl a/(Chl a + Pheo a)] ratios) . BothUvigerina akitaensis and Bolivina spissa are restricted to thestations bathed by dysoxic waters, proving their oxygendepletiontolerance. In such conditions, both phytophagoustaxa are obviously able to take advantage of labile organiccompounds (e.g., lipids and EHAA) contained in phytodetritus.Nonionella stella and Rutherfordoides cornuta survivein oxygen-depleted environments probably via alternativemetabolic pathways (e.g., denitrification ability) and a largeflexibility in trophic requirements. At stations where oxygenavailability is higher (i.e., .70 mmol/L in bottom water) andwhere bioavailable organic compounds are slightly lessabundant, diversity indices remain low, and more competitivespecies (e.g., Uvigerina curticosta, U. cf. U. graciliformis,Nonionella globosa, Nonionellina labradorica, and Elphidiumbatialis) are dominant.

On March 11th, 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.

Burial of organic matter (OM) plays an important role in marine sediments, linking the short-term, biological carbon cycle with the long-term, geological subsurface cycle. It is well established that low-oxygen conditions promote organic carbon burial in marine sediments. However, the mechanism remains enigmatic. Here we report biochemical quality, microbial degradability, OM preservation and accumulation along an oxygen gradient in the Indian Ocean. Our results show that more OM, with biochemically higher quality, accumulates under low oxygen conditions. Nevertheless, microbial degradability does not correlate with the biochemical quality of OM. This decoupling of OM biochemical quality and microbial degradability, or bioavailability, violates the ruling paradigm that higher quality implies higher microbial processing. The inhibition of bacterial OM remineralisation may play an important role in the burial of organic matter in marine sediments and formation of oil source rocks.