Cyanobacterial taxonomy, metabolism, and cyanophage association in dark and anoxic sediment

The authors have requested that this preprint be withdrawn due to author disagreement.

Cyanobacterial taxonomy, metabolism, and cyanophage association in dark and anoxic sediment

The authors have requested that this preprint be withdrawn due to author disagreement.

Cyanobacterial taxonomy, metabolism, and cyanophage association in dark and anoxic sediment

BackgroundCyanobacteria are photosynthetic ancient bacteria ubiquitous in terrestrial and aquatic environments. Even though they carry a photosynthesis apparatus they are known to survive in dark environments. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Here we present the first study that investigate the metabolic spectrum of cyanobacteria in dark and anoxic environments, as well as their associated cyanophages. We sampled surface sediments during April 2018 located along a water depth gradient of 60–210 m—representing oxic, hypoxic and anoxic conditions—in the largest dead zone in the world (Baltic Sea). We combined metagenomic and RNA-seq to investigate cyanobacterial taxonomy, activity and their associated cyanophages.ResultsCyanobacteria were detected at all four stations (n = 3 per station) along the sampled gradient, including the anoxic sediment. Top genera in the anoxic sediment included Anabaena (19% RNA data), Synechococcus (16%), and Cyanobium (5%). The mRNA data showed that cyanobacteria were surviving through i) anaerobic carbon metabolism indicated by glycolysis plus fatty acid biosynthesis, and ii) nitrogen (N2) fixation (likely by heterocystous Anabaena). Interestingly, in the mRNA data cyanobacteria were also transcribing photosynthesis, phytochromes, and gas vesicle genes. Cyanophages were detected at all stations, and compared to the oxic sediment had a different beta diversity in the hypoxic-anoxic sediment. Moreover, our results show that these cyanophages can infect cyanobacteria affecting the photosystem and phosphate regulation.ConclusionsCyanobacteria were found to transcribe genes for photosynthesis, phytochromes, and gas vesicles and this suggests that cyanobacteria try to ascend to the surface waters. The difference in cyanophage beta diversity between oxic and hypoxic-anoxic sediment suggests that anaerobic cyanobacteria select for specific cyanophages. Cyanobacteria are known to fuel oxygen depleted benthic ecosystems with phosphorous (so called internal loading), and our study suggests that cyanophage-controlled lysis of cyanobacteria likely provides a source of nitrogen. Our results suggest that cyanobacteria might also provide nutrients via N2 fixation and viral lysis in dark and anoxic environments.

Authigenic formation of Ca–Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

Despite advances regarding the microbial and organic-molecular impact on nucleation, the formation of dolomite in sedimentary environments is still incompletely understood. Since 1960, apparent dolomite formation has been reported from mud sediments of the shallow, oligohaline and alkaline Lake Neusiedl, Austria. To trace potential dolomite formation or diagenetic alteration processes in its deposits, lake water samples and sediment cores were analyzed with respect to sediment composition, hydrochemistry and bacterial community composition. Sediments comprise 20 cm of homogenous mud with 60 wt % carbonate, which overlies dark-laminated consolidated mud containing 50 wt % carbonate and plant debris. Hydrochemical measurements reveal a shift from oxic lake water with pH 9.0 to anoxic sediment pore water with pH 7.5. A decrease in SO42- with a concomitant increase in ΣH2S and NH4+ from 0 to 15 cm core depth indicates anaerobic heterotrophic decomposition, including sulfate reduction. The bacterial community composition reflects the zonation indicated by the pore water chemistry, with a distinct increase in fermentative taxa below 15 cm core depth. The water column is highly supersaturated with respect to (disordered) dolomite and calcite, whereas saturation indices of both minerals rapidly approach zero in the sediment. Notably, the relative proportions of different authigenic carbonate phases and their stoichiometric compositions remain constant with increasing core depth. Hence, evidence for Ca–Mg carbonate formation or ripening to dolomite is lacking within the sediment of Lake Neusiedl. As a consequence, precipitation of high-magnesium calcite (HMC) and protodolomite does not occur in association with anoxic sediment and sulfate-reducing conditions. Instead, analytical data for Lake Neusiedl suggest that authigenic HMC and protodolomite precipitate from the supersaturated, well-mixed aerobic water column. This observation supports an alternative concept to dolomite formation in anoxic sediments, comprising Ca–Mg carbonate precipitation in the water column under aerobic and alkaline conditions.

Authigenic formation of Ca-Mg carbonates in the shallow alkaline Lake Neusiedl, Austria

Despite advances regarding the microbial and organic-molecular impact on nucleation, the formation of dolomite in sedimentary environments is still incompletely understood. Since 1960, apparent dolomite formation has been reported from mud sediments of the shallow, oligohaline and alkaline Lake Neusiedl, Austria. To trace potential dolomite formation or diagenetic alteration processes in its deposits, lake water samples and sediment cores were analyzed with respect to sediment composition, hydrochemistry and bacterial community composition. Sediments comprise 20 cm of homogenous mud with 60 wt % carbonate, which overlie dark-laminated consolidated mud containing 50 wt % carbonate and plant debris. Hydrochemical measurements reveal a shift from oxic lake water with pH 9.0 to anoxic sediment pore water with pH 7.5. A decrease in SO42− with a concomitant increase of ΣH2S and NH4+ from 0–15 cm core depth, indicates anaerobic heterotrophic decomposition, including sulfate reduction. The bacterial community composition reflects the zonation indicated by the pore water chemistry, with a distinct increase of fermentative taxa below 15 cm core depth. The water column is highly supersaturated with respect to (disordered) dolomite and calcite, whereas saturation indices of both minerals rapidly approach zero in the sediment. Notably, the relative proportions of different authigenic carbonate phases and their stoichiometric compositions remain constant with increasing core depth. Hence, evidence for Ca-Mg carbonate formation or ripening to dolomite is lacking within the sediment of Lake Neusiedl. As a consequence, precipitation of high-magnesium-calcite (HMC) and very-high-magnesium-calcite (VHMC) does not occur in association with anoxic sediment and sulfate reducing conditions. Instead, analytical data for Lake Neusiedl suggest that authigenic HMC and VHMC precipitate from the supersaturated, well-mixed aerobic water column. This observation supports an alternative concept to dolomite formation in anoxic sediments, comprising Ca-Mg carbonate precipitation in the water column under aerobic and alkaline conditions.

Cyanobacterial taxonomy, metabolism, and cyanophage association in dark and anoxic sediment

Background Cyanobacteria are photosynthetic ancient bacteria ubiquitous in terrestrial and aquatic environments. Even though they carry a photosynthesis apparatus they are known to survive in dark environments. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Here we present the first study that investigate the metabolic spectrum of cyanobacteria in dark and anoxic environments, as well as their associated cyanophages. We sampled surface sediments during April 2018 located along a water depth gradient of 60–210 m—representing oxic, hypoxic and anoxic conditions—in the largest dead zone in the world. We combined metagenomic and total RNA sequencing to investigate cyanobacterial taxonomy, activity and their associated cyanophages. Results Cyanobacteria were detected at all four stations (n = 3 per station) along the sampled gradient, including the anoxic sediment. Top active genera in the anoxic sediment included Anabaena (19% RNA data), Synechococcus (16%), and Cyanobium (5%). The mRNA data showed that cyanobacteria were surviving through i) anaerobic carbon metabolism indicated by glycolysis plus fatty acid biosynthesis, and ii) nitrogen (N2) fixation (likely by heterocystous Anabaena). Interestingly, cyanobacteria were also actively transcribing photosynthesis, phytochromes, and gas vesicle genes. Cyanophages were also detected at all stations, and compared to the oxic sediment had a different beta diversity in the hypoxic-anoxic sediment. Moreover, our results show that these cyanophages infect cyanobacteria affecting the photosystem and phosphate regulation of cyanobacteria. Conclusions Cyanobacteria were found to transcribe genes for photosynthesis, phytochromes, and gas vesicles and this suggests that cyanobacteria are trying to ascend to the surface waters. The difference in cyanophage beta diversity between oxic and hypoxic-anoxic sediment suggests that anaerobic cyanobacteria select for specific cyanophages. Cyanobacteria are known to fuel oxygen depleted benthic ecosystems with phosphorous (so called internal loading), and our study suggests that cyanophage-controlled lysis of cyanobacteria likely provides a source of nitrogen. Photosynthetic cyanobacteria are commonly thought to have been essential in the great oxygenation event on Earth ca. 2.4 billion years ago. Our results suggest that active cyanobacteria might also provide nutrients (via N2 fixation and viral lysis) in dark and anoxic environments.

Analysis of 15N-NO3− Via Anoxic Slurries Coupled to MIMS Analysis: An Application to Estimate Nitrification by Burrowing Macrofauna

The increasing use of the stable isotope 15N-NO3− for the quantification of ecological processes requires analytical approaches able to distinguish between labelled and unlabeled N forms. We present a method coupling anoxic sediment slurries and membrane inlet mass spectrometry to quantify dissolved 15N-NO3− and 14N-NO3−. The approach is based on the microbial reduction of 14N-NO3− and 15N-NO3− mixed pool, the determination of the produced 29N2 and 30N2, and the calculation of the original 15N-NO3− and 14N-NO3− concentrations. The reduction is carried out in 12 mL exetainers containing 2 mL of sediment and 10 mL of water, under anoxia. To validate this approach, we prepared multiple standard solutions containing 15N-NO3− alone or in combinations with 14N-NO3−, with final concentrations varying from 0.5 to 3000 µM. We recovered nearly 90% of the initial 14N-NO3− or 15N-NO3−, over a wide range of concentrations and isotope ratios in the standards. We applied this method to a 15N-NO3− dilution experiment targeting the measurement of nitrification in sediments with and without the burrower Sparganophilus tamesis. The oligochaete did not stimulate nitrification, likely due to limited ventilation and unfavorable conditions for nitrifiers growth. The proposed method is reliable, fast, and could be applied to multiple ecological studies.

Sulfide oxidation in deep Baltic Sea sediments upon oxygenation and colonization by macrofauna

Coastal and shelf sediments affected by transient or long-term bottom water anoxia and sulfidic conditions undergo drastic changes in macrofauna communities and abundances. This study investigates how early colonization by two macrofaunal functional traits (epifauna vs. infauna) affects oxygen, sulfide, and pH dynamics in anoxic sediment upon recent bottom water oxygenation. Large mesocosms (area 900 cm2) with 150-m-deep Baltic Sea soft sediments were exposed to three treatments: (1) no animals; (2) addition of 170 polychaetes (Marenzelleria arctia); (3) addition of 181 amphipods (Monoporeia affinis). Porewater chemistry was investigated repeatedly by microsensor profiling over a period of 65 days. Colonization by macrofauna did not significantly deepen penetration of oxygen compared to the animal-free sediment. Bioturbation by M. affinis increased the volume of the oxidized, sulfide-free sediment by 66% compared to the animal-free control already after 13 days of incubation. By the end of the experiment M. affinis and M. arctia increased the oxidized sediment volume by 87 and 35%, respectively. Higher efficiency of epifaunal amphipods in removing hydrogen sulfide than deep-burrowing polychaetes is likely due to more substantial re-oxidation of manganese and/or nitrogen compounds associated with amphipod mixing activity. Our results thus indicate that early colonization of different functional groups might have important implications for the later colonization by benthic macrofauna, meiofauna and microbial communities that benefit from oxidized and sulfide-free sediments.