Divergent marine anaerobic ciliates harbor closely related Methanocorpusculum endosymbionts.

Ciliates are a diverse group of protists known for their ability to establish various partnerships and thrive in a wide variety of oxygen-depleted environments. Most anaerobic ciliates harbor methanogens, one of the few known archaea living intracellularly. These methanogens increase the metabolic efficiency of host fermentation via syntrophic use of host end-product in methanogenesis. Despite the ubiquity of these symbioses in anoxic habitats, patterns of symbiont specificity and fidelity are not well known. We surveyed two unrelated, commonly found groups of anaerobic ciliates, the Plagiopylea and Metopida, isolated from anoxic marine sediments. We sequenced host 18S rRNA and symbiont 16S rRNA marker genes as well as the symbiont internal transcribed spacer region from our cultured ciliates to identify hosts and their associated methanogenic symbionts. We found that marine ciliates from both of these co-occurring, divergent groups harbor closely related yet distinct intracellular archaea within the Methanocorpusculum genus. The symbionts appear to be stable at the host species level, but at higher taxonomic levels, there is evidence that symbiont replacements have occurred. Gaining insight into this unique association will deepen our understanding of the complex transmission modes of marine microbial symbionts, and the mutualistic microbial interactions occurring across domains of life.

The dataset for the chronology of the sedimentation in the Danube abyssal fan which records the major episodes of the late-Holocene Black Sea evolution.

Anoxic marine sediments at the confluence with large rivers are key archives for monitoring the anthropogenic impact in the environment and asses the carbon sink character of oxygen deprived waters. This data article describes the analysis methodology and the results of the deep-sea sediments sampled from the NW part of the Black Sea, using the 14C dating, stable carbon isotopes, C/N ratio, metallic traces and 210Pb and 137Cs radioactivity. For this purpose, 26 sediment samples were taken from the MN183-3 sampling point (43.925.917 N, 30.758.911 E, 658 m water depth) using a Mark II-400-type multicorer. The samples were collected during the two weeks Mare Nigrum (MN) #183 marine expedition, which took place at the beginning of September 2018, in the Romanian section of the Black Sea shelf and continental slope. These analyses were employed in the construction of a Bayesian high-resolution sedimentation model, reported in M.Ilie et al. (2022).

Bacterial community of sediments under the Eastern Boundary Current System shows high microdiversity and a latitudinal spatial pattern.

The sediments under the Oxygen Minimum Zone of the Eastern Boundary Current System (EBCS) along Central-South Peru and North-Central Chile, known as Humboldt Sulfuretum (HS), is an organic-matter-rich benthic habitat, where bacteria process a variety of sulfur compounds under low dissolved-oxygen concentrations, and high sulfide and nitrate levels. This study addressed the structure, diversity and spatial distribution patterns of the HS bacterial community along Northern and South-Central Chile using 16S rRNA gene amplicon sequencing. The results show that during the field study period, the community was dominated by sulfur-associated bacteria. Indeed, the most abundant phylum was Desulfobacterota, while Sva0081 sedimentary group, of the family Desulfosarcinaceae (the most abundant family), which includes sulfate-reducer and H2 scavenger bacteria, was the most abundant genus. Furthermore, a spatial pattern was unveiled along the study area to which the family Desulfobulbaceae contributed the most to the spatial variance, which encompasses 42 uncharacterized amplicon sequence variants (ASVs), three assigned to Ca. Electrothrix and two to Desulfobulbus. Moreover, a very high microdiversity was found, since only 3.7% of the ASVs were shared among localities, reflecting a highly diverse and mature community.

Iron reactivity in anoxic sediments in the Ría de Vigo (NW Spain).

The high sedimentation rates and high organic matter contents in the sediments of the Ría de Vigo (NW Spain) promote the development of anoxic conditions, determining the dynamics of elements like Fe and conditioning his speciation and reactivity. Four gravity cores were retrieved in anoxic sediments of the Ría de Vigo in November 2012. In order to understand the behavior of Fe in these complex environments different fractions of reactive iron were analyzed. The decrease in highly reactive iron and sulfide contents with depth showed the relationship between the iron and sulfur cycle in the middle and outer zones of the ría. In the inner zone, the apparition of shallow methane gas may cause the slower decrease of the highly reactive iron contents. In zones without methane, sediment layers enriched in iron -with a reactivity higher than in other sediment samples- were observed. An increase was observed in the dithionite and total reactive iron contents from the inner to the outer zone of the ría, according to the gas depth. Furthermore, a decrease in Fe (III)-bearing minerals contents with depth was observed in the outer and middle zones, but not in the innermost area where the gas is shallow. The high organic matter and sulfide contents, mainly in the inner zone of the ría, indicate that the most of the Fe (II) is FeS. Moreover, the high contents of total reactive iron and pH values (6.86-7.98) could contribute the formation of stable minerals like pyrite along the Ría de Vigo.

Redox processes in pore water of anoxic sediments with shallow gas.

The Ría de Vigo (NW Spain) has a high organic matter content and high rates of sedimentation. The microbial degradation of this organic matter has led to shallow gas accumulations of methane, currently distributed all along the ría. These peculiar characteristics favor the development of anoxic conditions that can determine the dynamics of iron and manganese. In order to study the role played by iron and manganese in the processes that take place in anoxic sediments with shallow gas, four gravity cores were retrieved in anoxic sediments of the Ría de Vigo in November 2012. Methane was present in two of them, below 90cm in the inner zone and below 200cm, in the outer zone. Pore water was collected and analyzed for vertical profiles of pH, sulfide, sulfate, iron and manganese concentrations. Sulfate concentrations decreased with depth but never reached the minimum detection limit. High sulfide concentrations were measured in all cores. The highest sulfide concentrations were found in the inner zone with methane and the lowest were in the outer zone without methane. Concentrations of iron and manganese reached maximum values in the upper layers of the sediment, decreasing with depth, except in the outer zone without gas, where iron and manganese concentration increased strongly toward the bottom of the sediment. In areas with shallow gas iron reduction, sulfate reduction and methane production processes coexist, showing that the traditional redox cascade is highly simplified and suggesting that iron may be involved in a cryptic sulfur cycle and in the oxidation of methane.

Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats.

The Miscellaneous Crenarchaeotic Group (MCG) is an archaeal lineage whose members are widespread and abundant in marine sediments. MCG archaea have also been consistently found in stratified euxinic lakes. In this work, we have studied archaeal communities in three karstic lakes to reveal potential habitat segregation of MCG subgroups between planktonic and sediment compartments. In the studied lakes, archaeal assemblages were strikingly similar to those of the marine subsurface with predominance of uncultured Halobacteria in the plankton and Thermoplasmata and MCG in anoxic, organic-rich sediments. Multivariate analyses identified sulphide and dissolved organic carbon as predictor variables of archaeal community composition. Quantification of MCG using a newly designed qPCR primer pair that improves coverage for MCG subgroups prevalent in the studied lakes revealed conspicuous populations in both the plankton and the sediment. Subgroups MCG-5a and -5b appear as planktonic specialists thriving in euxinic bottom waters, while subgroup MCG-6 emerges as a generalist group able to cope with varying reducing conditions. Besides, comparison of DNA- and cDNA-based pyrotag libraries revealed that rare subgroups in DNA libraries, i.e. MCG-15, were prevalent in cDNA-based datasets, suggesting that euxinic, organic-rich sediments of karstic lakes provide optimal niches for the activity of some specialized MCG subgroups.

Effective bioremediation strategy for rapid in situ cleanup of anoxic marine sediments in mesocosm oil spill simulation.

The purpose of present study was the simulation of an oil spill accompanied by burial of significant amount of petroleum hydrocarbons (PHs) in coastal sediments. Approximately 1000 kg of sediments collected in Messina harbor were spiked with Bunker C furnace fuel oil (6500 ppm). The rapid consumption of oxygen by aerobic heterotrophs created highly reduced conditions in the sediments with subsequent recession of biodegradation rates. As follows, after 3 months of ageing, the anaerobic sediments did not exhibit any significant levels of biodegradation and more than 80% of added Bunker C fuel oil remained buried. Anaerobic microbial community exhibited a strong enrichment in sulfate-reducing PHs-degrading and PHs-associated Deltaproteobacteria. As an effective bioremediation strategy to clean up these contaminated sediments, we applied a Modular Slurry System (MSS) allowing the containment of sediments and their physical-chemical treatment, e.g., aeration. Aeration for 3 months has increased the removal of main PHs contaminants up to 98%. As revealed by CARD-FISH, qPCR, and 16S rRNA gene clone library analyses, addition of Bunker C fuel oil initially affected the activity of autochthonous aerobic obligate marine hydrocarbonoclastic bacteria (OMHCB), and after 1 month more than the third of microbial population was represented by Alcanivorax-, Cycloclasticus-, and Marinobacter-related organisms. In the end of the experiment, the microbial community composition has returned to a status typically observed in pristine marine ecosystems with no detectable OMHCB present. Eco-toxicological bioassay revealed that the toxicity of sediments after treatment was substantially decreased. Thus, our studies demonstrated that petroleum-contaminated anaerobic marine sediments could efficiently be cleaned through an in situ oxygenation which stimulates their self-cleaning potential due to reawakening of allochtonous aerobic OMHCB.