Seasonality and depth distribution of the abundance and activity of ammonia oxidizing microorganisms in marine coastal sediments (North Sea)

Microbial processes such as nitrification and anaerobic ammonium oxidation (anammox) are important for nitrogen cycling in marine sediments. Seasonal variations of archaeal and bacterial ammonia oxidizers (AOA and AOB) and anammox bacteria, as well as the environmental factors affecting these groups, are not well studied. We have examined the seasonal and depth distribution of the abundance and potential activity of these microbial groups in coastal marine sediments of the southern North Sea. This was achieved by quantifying specific intact polar lipids as well as the abundance and gene expression of their 16S rRNA gene, the ammonia monooxygenase subunit A (amoA) gene of AOA and AOB, and the hydrazine synthase (hzsA) gene of anammox bacteria. AOA, AOB, and anammox bacteria were detected and transcriptionally active down to 12 cm sediment depth. In all seasons, the abundance of AOA was higher compared to the AOB abundance suggesting that AOA play a more dominant role in aerobic ammonia oxidation in these sediments. Anammox bacteria were abundant and active even in oxygenated and bioturbated parts of the sediment. The abundance of AOA and AOB was relatively stable with depth and over the seasonal cycle, while anammox bacteria abundance and transcriptional activity were highest in August. North Sea sediments thus seem to provide a common, stable, ecological niche for AOA, AOB, and anammox bacteria

Role of chemolithoautotrophic microorganisms involved in nitrogen and sulfur cycling in coastal marine sediments

The role of chemolithoautotrophic microorganisms has been considered to be of minor importance in coastal marine sediments and the impact of seasonal hypoxic/anoxic conditions on microbial chemolithoautotrophy in coastal marine sediments has not been investigated. Therefore, in this thesis the temporal and spatial changes of the diversity, abundance and activity of specific groups of chemolithoautotrophic microorganisms involved in the nitrogen and sulfur cycling, as well as the total microbial community, has been determined in coastal sediments by using DNA/RNA- and lipid-based biomarker approaches, i.e. the analysis and quantification of 16S rRNA and functional genes involved in carbon fixation and reoxidation pathways, intact polar and core lipids of Archaea, i.e. glycerol dibiphytanyl glycerol tetraethers (GDGTs), and ladderane lipids specific for anammox bacteria, as well as bacterial phospholipid-derived fatty acids (PLFAs). We focused on coastal marine sediments; (1) the Oyster Grounds in the central North Sea, exposed to decreasing bottom water oxygen concentrations (0−12 cm sediment depth), (2) different sediment types (sand, clay, and mud) of the Iceland Shelf (0−10 cm sediment depth), and (3) seasonally hypoxic and sulfidic sediments of saline Lake Grevelingen (The Netherlands) (0−5 cm sediment depth). Results show the presence and potential importance of chemolithoautotrophs in the biogeochemical cycling of carbon, nitrogen and sulfur. The research presented in this thesis has provided new insights on the temporal and spatial distribution of the diversity, abundance and activity of chemolithoautotrophic microorganisms such as ammonia oxidizing archaea (AOA, i.e. Thaumarchaeota) and ammonia oxidizing bacteria (AOB), anammox and denitrifying bacteria, as well as sulfate reducing and sulfur oxidizing microorganisms, including sulfide-dependent denitrifiers, and chemolithoautotrophic microorganisms involved in the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycle, in coastal marine sediments. Hypoxia and increasing sulfide concentration have proven to be key factors restricting the presence and activity of these groups. In addition, the interactions with other microbial groups and bioturbation seem to favor the presence of specific chemolithoautotrophs in unexpected sediment depths, for example the presence of Thaumarchaeota in depths where the oxygen concentration was expected to be undetectable, or the presence of anammox bacteria in bioturbated sediments where nitrate reducers could thrive and provide nitrite to fuel the anammox process

Role of chemolithoautotrophic microorganisms involved in nitrogen and sulfur cycling in coastal marine sediments

The role of chemolithoautotrophic microorganisms has been considered to be of minor importance in coastal marine sediments and the impact of seasonal hypoxic/anoxic conditions on microbial chemolithoautotrophy in coastal marine sediments has not been investigated. Therefore, in this thesis the temporal and spatial changes of the diversity, abundance and activity of specific groups of chemolithoautotrophic microorganisms involved in the nitrogen and sulfur cycling, as well as the total microbial community, has been determined in coastal sediments by using DNA/RNA- and lipid-based biomarker approaches, i.e. the analysis and quantification of 16S rRNA and functional genes involved in carbon fixation and reoxidation pathways, intact polar and core lipids of Archaea, i.e. glycerol dibiphytanyl glycerol tetraethers (GDGTs), and ladderane lipids specific for anammox bacteria, as well as bacterial phospholipid-derived fatty acids (PLFAs). We focused on coastal marine sediments; (1) the Oyster Grounds in the central North Sea, exposed to decreasing bottom water oxygen concentrations (0−12 cm sediment depth), (2) different sediment types (sand, clay, and mud) of the Iceland Shelf (0−10 cm sediment depth), and (3) seasonally hypoxic and sulfidic sediments of saline Lake Grevelingen (The Netherlands) (0−5 cm sediment depth). Results show the presence and potential importance of chemolithoautotrophs in the biogeochemical cycling of carbon, nitrogen and sulfur. The research presented in this thesis has provided new insights on the temporal and spatial distribution of the diversity, abundance and activity of chemolithoautotrophic microorganisms such as ammonia oxidizing archaea (AOA, i.e. Thaumarchaeota) and ammonia oxidizing bacteria (AOB), anammox and denitrifying bacteria, as well as sulfate reducing and sulfur oxidizing microorganisms, including sulfide-dependent denitrifiers, and chemolithoautotrophic microorganisms involved in the Calvin-Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycle, in coastal marine sediments. Hypoxia and increasing sulfide concentration have proven to be key factors restricting the presence and activity of these groups. In addition, the interactions with other microbial groups and bioturbation seem to favor the presence of specific chemolithoautotrophs in unexpected sediment depths, for example the presence of Thaumarchaeota in depths where the oxygen concentration was expected to be undetectable, or the presence of anammox bacteria in bioturbated sediments where nitrate reducers could thrive and provide nitrite to fuel the anammox process

Impact of seasonal hypoxia on activity and community structure of chemolithoautotrophic bacteria in a coastal sediment

Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae. The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H2S, S0, and S2O32−) and electron acceptors (O2 and NO3−) regulated by seasonal hypoxia

The Core Seafloor Microbiome in the Gulf of Mexico is Remarkably Consistent and Shows Evidence of Recovery from Disturbance Caused by Major Oil Spills

The microbial ecology of oligotrophic deep ocean sediments is understudied relative to their shallow counterparts, and this lack of understanding hampers our ability to predict responses to current and future perturbations. The Gulf of Mexico has experienced two of the largest accidental marine oil spills, the 1979 Ixtoc-1 blowout and the 2010 Deepwater Horizon (DWH) discharge. Here, microbial communities were characterized for 29 sites across multiple years in \u3e 700 samples. The composition of the seafloor microbiome was broadly consistent across the region and was well approximated by the overlying water depth and depth within the sediment column, while geographic distance played a limited role. Biogeographical distributions were employed to generate predictive models for over 4000 OTU that leverage easy-to-obtain geospatial variables which are linked to measured sedimentary oxygen profiles. Depth stratification and putative niche diversification are evidenced by the distribution of taxa that mediate the microbial nitrogen cycle. Furthermore, these results demonstrate that sediments impacted by the DWH spill had returned to near baseline conditions after 2 years. The distributions of benthic microorganisms in the Gulf can be constrained, and moreover, deviations from these predictions may pinpoint impacted sites and aid in future response efforts or long-term stability studies