Enrichment of novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria in an oxygen-limited, methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments

Microbial methane oxidation is a major biofilter preventing larger emissions of this powerful greenhouse gas from marine coastal areas into the atmosphere. In these zones, various electron acceptors such as sulfate, metal oxides, nitrate or oxygen can be utilized. However, the key microbial players and mechanisms of methane oxidation are poorly understood. In this study, we inoculated a bioreactor with methane- and iron-rich sediments from the Bothnian Sea in order to investigate microbial methane and iron cycling under low oxygen concentrations. Using metagenomics, we observed shifts in the microbial community over approximately 2.5 years of bioreactor operation. Marker genes for methane and iron cycling, as well as respiratory and fermentative metabolism, were investigated. Metagenome-assembled genomes representing novel Verrucomicrobia, Bacteroidetes and Krumholzibacteria were recovered and revealed potential for methane oxidation, organic matter degradation, and iron cycling, respectively. This work brings new insights into the identity and metabolic versatility of microorganisms that may be members of such functional guilds in coastal marine sediments and highlights that the methane biofilter in these sediments may be more diverse than previously appreciated.ImportanceDespite the essential role of microorganisms in preventing most methane in the ocean floor to reach the atmosphere, comprehensive knowledge on the identity and the mechanisms employed by these microorganisms is still lacking. This is problematic because such information is needed to understand how the ecosystem functions in the present and how microorganisms may respond to climate change in the future. Here, we enriched and identified novel taxa potentially involved in methane and iron cycling in an oxygen-limited bioreactor inoculated with methane- and iron-rich coastal sediments. Metagenomic analyses provided hypotheses about the mechanisms they may employ, such as the use of oxygen at very low concentrations. The implication of our results is that in more shallow sediments, where oxygen-limited conditions are present, the methane biofilter is potentially composed of novel, metabolically versatile Verrucomicrobia that could contribute to mitigating methane emissions from coastal marine zones.

Ventilation of the northern Baltic Sea

The Baltic Sea is a semi-enclosed, brackish water sea in northern Europe. The deep basins of the central Baltic Sea regularly show hypoxic conditions. In contrast, the northern parts of the Baltic Sea, the Bothnian Sea and Bothnian Bay, are well oxygenated. Lateral inflows or a ventilation due to convection are possible mechanisms for high oxygen concentrations in the deep water of the northern Baltic Sea. In March 2017, conductivity–temperature–depth (CTD) profiles and bottle samples, ice core samples, and brine were collected in the Bothnian Bay. In addition to hydrographic standard parameters, light absorption has been measured in all samples. A complementary numerical model simulation provides quantitative estimates of the spread of newly formed bottom water. The model uses passive and age tracers to identify and trace different water masses. Observations indicate a recent ventilation of the deep bottom water at one of the observed stations. The analysis of observations and model simulations shows that the Bothnian Bay is ventilated by dense water formed due to mixing of Bothnian Sea and Bothnian Bay surface water initializing lateral inflows. The observations show the beginning of the inflow and the model simulation demonstrates the further northward spreading of bottom water. These events occur during wintertime when the water temperature is low. Brine rejected during ice formation barely contributes to dense bottom water.

Nitrogen fixation estimates for the Baltic Sea indicate high rates for the previously overlooked Bothnian Sea

Dense blooms of diazotrophic filamentous cyanobacteria are formed every summer in the Baltic Sea. We estimated their contribution to nitrogen fixation by combining two decades of cyanobacterial biovolume monitoring data with recently measured genera-specific nitrogen fixation rates. In the Bothnian Sea, estimated nitrogen fixation rates were 80 kt N year−1, which has doubled during recent decades and now exceeds external loading from rivers and atmospheric deposition of 69 kt year−1. The estimated contribution to the Baltic Proper was 399 kt N year−1, which agrees well with previous estimates using other approaches and is greater than the external input of 374 kt N year−1. Our approach can potentially be applied to continuously estimate nitrogen loads via nitrogen fixation. Those estimates are crucial for ecosystem adaptive management since internal nitrogen loading may counteract the positive effects of decreased external nutrient loading.

Ventilation of the Northern Baltic Sea

The Baltic Sea is a semi-enclosed, brackish water sea in northern Europe. The deep basins of the central Baltic Sea regularly show hypoxic conditions. In contrast, the northern parts of the Baltic Sea, the Bothnian Sea and Bay, are well oxygenated. Lateral inflows or a ventilation due to convection are possible mechanisms for high oxygen concentrations in the deep water of the northern Baltic Sea. Owing to the high latitudes of the northern Baltic, this region is regularly covered by sea ice during the winter season. In March 2017, the RV Maria S. Merian was for two days in the Bothnian Bay collecting ice core samples, brine water, and CTD profiles. The bulk sea ice salinity was on average 0.6 g/kg and in brine samples, a salinity of 11.5 g/kg and 17.8 g/kg have been measured. At one station, the CTD profiles indicated a recent ventilation event of the deep water. A water mass analysis showed that the ventilation is most probably due to mixing of Bothnian Sea and Bothnian Bay surface water which results in sufficient dense water able to replace older bottom water. However, the high salinity of brine provides the potential for forming dense bottom water masses as well.

The first large-scale assessment of three-spined stickleback (Gasterosteus aculeatus) biomass and spatial distribution in the Baltic Sea

Declines in predatory fish in combination with the impact of climate change and eutrophication have caused planktivores, including three-spined stickleback (Gasterosteus aculeatus), to increase dramatically in parts of the Baltic Sea. Resulting impacts of stickleback on coastal and offshore foodwebs have been observed, highlighting the need for increased knowledge on its population characteristics. In this article, we quantify abundance, biomass, size structure, and spatial distribution of stickleback using data from the Swedish and Finnish parts of the Baltic International Acoustic Survey (BIAS) during 2001–2014. Two alternative methods for biomass estimation suggest an increase in biomass of stickleback in the Baltic Proper, stable or increasing mean size over time, and larger individuals toward the north. The highest abundance was found in the central parts of the Baltic Proper and Bothnian Sea. The proportion of stickleback biomass in the total planktivore biomass increased from 4 to 10% in the Baltic Proper and averaged 6% of the total planktivore biomass in the Bothnian Sea. In some years, however, stickleback biomass has ranged from half to almost twice that of sprat (Sprattus sprattus) in both basins. Given the recent population expansion of stickleback and its potential role in the ecosystem, we recommend that stickleback should be considered in future monitoring programmes and in fisheries and environmental management of the Baltic Sea.

Metagenomic analysis reveals large potential for carbon, nitrogen and sulfur cycling in coastal methanic sediments of the Bothnian Sea

The Bothnian Sea is an oligotrophic brackish basin characterized by low salinity and high concentrations of reactive iron, methane and ammonium in the sediments potentially enabling an intricate microbial network. Therefore, we analyzed and compared biogeochemical and microbial profiles at one offshore and two near coastal sites in the Bothnian Sea. 16S rRNA amplicon sequence analysis revealed stratification of both bacterial and archaeal taxa in accordance with the geochemical gradients of iron, sulfate and methane. The communities at the two near coastal sites were more similar to each other than that at the offshore site located at a greater water depth. To obtain insights into the metabolic networks within the iron-rich methanic sediment layer located below the sulfate-methane transition zone (SMTZ), we performed metagenomic sequencing of sediment-derived DNA. Genome bins retrieved from the most abundant bacterial and archaeal community members revealed a broad potential for respiratory sulfur metabolism via partially reduced sulfur species. Nitrogen cycling was dominated by reductive processes via a truncated denitrification pathway encoded exclusively by bacterial lineages. Gene-centric fermentative metabolism analysis indicated the central role of acetate, formate, alcohols and hydrogen in the analyzed anaerobic sediment. Methanogenic/-trophic pathways were dominated by Methanosaetaceae, Methanosarcinaceae, Methanomassiliicoccaceae, Methanoregulaceae and ANME-2 archaea. Thorarchaeota and Bathyarchaeota encoded pathways for acetogenesis. Our results indicate flexible metabolic capabilities of core community bacterial and archaeal taxa, which can adapt to changing redox conditions, and with a spatial distribution in Bothnian Sea sediments that is likely governed by the quality of available organic substrates.