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Raw Datasets for PhD thesis entitled Coastal-Estuarine Microbiology Explored: Community Dynamics, Biogeochemical Processes and Cell Specific Targeting of Nitrogen Cyclers
No full textThese datasets contain raw data for the PhD thesis entitled "Coastal-Estuarine Microbiology Explored: Community Dynamics, Biogeochemical Processes and Cell Specific Targeting of Nitrogen Cyclers", authored by Spencer Long.
Datasets are as follows:
- tamar_nutrients_master.csv contains raw nutrient data from the Tamar estuary, UK, for dates sampled in September 2019, March 2020, September 2021 and May 2022.
- L4_nutrients_master.csv contains raw nutrient data from Western Channel Observatory station L4, for dates sampled in September 2019, March 2020 and May 2022.
- nitrifier_CARD_stats.csv contains catalysed deposition fluorescence in situ hybridisation (CARD-FISH) obtained raw data for ammonia oxidising microbial communities within thew Tamar estuary. Data relates to samples taken in September 2019, March 2020, September 2021 and May 2022.
- nitrification_rate.csv contains calculated ammonia oxidation rate raw data for the Tamar estaury, relating to samples taken in September 2021 and May 2022.
- plate_reader_master.csv contains raw data obtained from all plate reader experiments relating to the chapter "Assessing the Applicability of DAF-FM Diacetate for the Specific Detection of Nitric Oxide Cycling Microorganisms"
- fluor_spreadsheet_final.csv contains raw data obtained from all epifluorescence microscopy experiments relating to the chapter "Assessing the Applicability of DAF-FM Diacetate for the Specific Detection of Nitric Oxide Cycling Microorganisms"
- readme.txt contains further data information
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Processing deep-sea particle-rich water samples for fluorescence in situ hybridization: consideration of storage effects, preservation, and sonication
Full text linkParticles are often regarded as microniches of enhanced microbial production and activities in the pelagic ocean and are vehicles of vertical material transport from the euphotic zone to the deep sea. Fluorescence in situ hybridization (FISH) can be a useful tool to study the microbial community structures associated with these particles, and thus their ecological significance, yet an appropriate protocol for processing deep-sea particle-rich water samples is lacking. Some sample processing considerations are discussed in the present study, and different combinations of existing procedures for preservation, size fractionation sequential filtration, and sonication were tested in conjunction with FISH. Results from this study show that water samples should be filtered and processed within no more than 10 to 12 h after collection, or else preservation is necessary. The commonly used prefiltration formaldehyde fixation was shown to be inadequate for the rRNA targeted by FISH. However, prefiltration formaldehyde fixation followed by immediate freezing and postfiltration paraformaldehyde fixation yielded highly consistent cell abundance estimates even after 96 days or potentially longer storage. Size fractionation sequential filtration and sonication together enhanced cell abundance estimates by severalfold. Size fractionation sequential filtration effectively separated particle-associated microbial communities from their free-living counterparts, while sonication detached cells from particles or aggregates for more-accurate cell counting using epifluorescence microscopy. Optimization in sonication time is recommended for different specific types of samples. These tested and optimized procedures can be incorporated into a FISH protocol for sampling in deep-sea particle-rich waters
Omic approaches to microbial geochemistry
No full textThe past two decades have witnessed an explosion of DNA sequencing technologies that provide unprecedented insights into genome sequences—the blueprints of life on Earth. Although initially driven by biomedical research, this revolution offers exciting opportunities in Earth sciences. Analyzing genomes and other biomolecules (“omic” methods) within environmental samples provides new vistas of microbial geochemistry. However, the massive amount of data produced can be hard to decipher, and the resources and infrastructure to train and support geoscientists in omics approaches are lacking. This article summarizes some of the opportunities and challenges in the applications of omic approaches to geochemical problems
Der Stickstoffkreislauf im ozean
No full textEin neu entdeckter bakterieller Prozess, die anaerobe Oxidation von Ammonium zu gasförmigem Stickstoff (Anammox), ist verantwortlich für das Entweichen von biologisch verfügbarem Stickstoff aus dem Ozean und verändert unser herkömmliches Bild vom Stickstoffkreislauf im Meer.A new microbial pathway, the anaerobic ammonium oxidation (Anammox) is widespread in the ocean and changes our view on the marine nitrogen cycle
Microbial nitrogen cycling processes in oxygen minimum zones
Full text linkOxygen minimum zones (OMZs) harbor unique microbial communities that rely on alternative electron acceptors for respiration. Conditions therein enable an almost complete nitrogen (N) cycle and substantial N-loss. N-loss in OMZs is attributable to anammox and heterotrophic denitrification, whereas nitrate reduction to nitrite along with dissimilatory nitrate reduction to ammonium are major remineralization pathways. Despite virtually anoxic conditions, nitrification also occurs in OMZs, converting remineralized ammonium to N-oxides. The concurrence of all these processes provides a direct channel from organic N to the ultimate N-loss, whereas most individual processes are likely controlled by organic matter. Many microorganisms inhabiting the OMZs are capable of multiple functions in the N- and other elemental cycles. Their versatile metabolic potentials versus actual activities present a challenge to ecophysiological and biogeochemical measurements. These challenges need to be tackled before we can realistically predict how N-cycling in OMZs, and thus oceanic N-balance, will respond to future global perturbations
Autotrophic ammonia oxidation in a deep-sea hydrothermal plume
No full textDirect evidence for autotrophic ammonia oxidation is documented for the first time in a deep-sea hydrothermal plume. Elevated NH(4) (+) concentrations of up to 341+/-136 nM were recorded in the plume core at Main Endeavour Field, Juan de Fuca Ridge. This fueled autotrophic ammonia oxidation rates as high as 91 nM day(-1), or 92% of the total net NH(4) (+) removal. High abundance of ammonia-oxidizing bacteria was detected using fluorescence in situ hybridization. Ammonia-oxidizing bacteria within the plume core (1.0-1.4x10(4) cells ml(-1)) accounted for 7.0-7.5% of the total microbial community, and were at least as abundant as methanotrophs. Ammonia-oxidizing bacteria were a substantial component of the particle-associated communities (up to 51%), with a predominance of the r-strategist Nitrosomonas-like cells. In situ chemolithoautotrophic organic carbon production via ammonia oxidation may yield 3.9-18 mg C m(-2) day(-1) within the plume directly over Main Endeavour Field. This rate was comparable to that determined for methane oxidation in a previous study, or at least four-fold greater than the flux of photosynthetic carbon reaching plume depths measured in another study. Hence, autotrophic ammonia oxidation in the neutrally buoyant hydrothermal plume is significant to both carbon and nitrogen cycling in the deep-sea water column at Endeavour, and represents another important link between seafloor hydrothermal systems and deep-sea biogeochemistry
Prokaryotic niche partitioning between suspended and sinking marine particles
Full text linkSuspended particles are major organic carbon substrates for heterotrophic microorganisms in the mesopelagic ocean (100–1000 m). Nonetheless, communities associated with these particles have been overlooked compared with sinking particles, the latter generally considered as main carbon transporters to the deep ocean. This study is the first to differentiate prokaryotic communities associated with suspended and sinking particles, collected with a marine snow catcher at four environmentally distinct stations in the Scotia Sea. Amplicon sequencing of 16S rRNA gene revealed distinct prokaryotic communities associated with the two particle‐types in the mixed‐layer (0–100 m) and upper‐mesopelagic zone (mean dissimilarity 42.5% ± 15.2%). Although common remineralising taxa were present within both particle‐types, gammaproteobacterial Pseudomonadales and Vibrionales, and alphaproteobacterial Rhodobacterales were found enriched in sinking particles up to 32‐fold, while Flavobacteriales (Bacteroidetes) favoured suspended particles. We propose that this niche‐partitioning may be driven by organic matter properties found within both particle‐types: K‐strategists, specialised in the degradation of complex organic compounds, thrived on semi‐labile suspended particles, while generalists r‐strategists were adapted to the transient labile organic contents of sinking particles. Differences between the two particle‐associated communities were more pronounced in the mesopelagic than in the surface ocean, likely resulting from exchanges between particle‐pools enabled by the stronger turbulence
16S rRNA gene-based molecular analysis of mat-forming and accompanying bacteria covering organically-enriched marine sediments underlying a salmon farm in Southern Chile (Calbuco Island)
No full textThe mat forming bacteria covering organic matter-enriched and anoxic marine sediments underlying a salmon farm in Southern Chile, were examined using 16S rRNA gene phylogenies. This mat was absent in the sea bed outside the direct influence of the farm (360 m outside fish cages). Based on nearly complete 16S rRNA gene sequences (~1500 bp), matforming filamentous cells were settled as the sulphur-oxidizing and putatively dissimilative nitrate reducing Beggiatoa spp., being closely related (up to 97% sequence identity) to Beggiatoa spp. identified in eutrophic shallow sediments in northern Europe (Danish Limfjorden and German Dangast inlets). Their phylogenetic affiliation was consistent with their morphology as vacuolated and sulphur-containing cells arranged on tandem along trichomes (18 to 28 ?m diameter). Additionally, deltaproteobacterial sulphate reducers, Sulfurospirillum, Sulfurovum and Fusibacter were detected according to partial 16S rRNA gene sequences (~500 bp). Their concurrence with Beggiatoa suggested an intense and complex sulphur cycle within the surface of these aquaculture affected sediments, which may have important implications for the necessity of more efficient benthic bioremediation of finfish aquaculture in Chile and worldwide
Eukaryotic influence on the oceanic biological carbon pump in the Scotia Sea as revealed by 18S rRNA gene sequencing of suspended and sinking particles
Full text linkSuspended marine particles constitute most of the particulate organic matter pool in the oceans, thereby providing substantial substrates for heterotrophs, especially in the mesopelagic. Conversely, sinking particles are major contributors to carbon fluxes defining the strength of the biological carbon pump (BCP). This study is the first to investigate the differential influence of eukaryotic communities to suspended and sinking particles, using 18S rRNA gene sequencing on particles collected with a marine snow catcher in the mixed layer and upper mesopelagic of the Scotia Sea, Southern Ocean. In the upper mesopelagic, most eukaryotic phytoplankton sequences belonged to chain-forming diatoms in sinking particles and to prymnesiophytes in suspended particles. This suggests that diatom-enriched particles are more efficient in carbon transfer to the upper mesopelagic than those enriched in prymnesiophytes in the Scotia Sea, the latter more easily disintegrating into suspended particles. In the upper mesopelagic, copepods appeared most influential on sinking particles whereas soft-tissue metazoan sequences contributed more to suspended particles. Heterotrophic protists and fungi communities were distinct between mixed layer and upper mesopelagic, implying that few protists ride along sinking particles. Furthermore, differences between predatory flagellates and radiolarians between suspended and sinking particles implied different ecological conditions between the two particles pools, and roles in the BCP. Molecular analyses of sinking and suspended particles constitute powerful diagnostic tools to study the eukaryotic influence on the BCP in a more holistic manner compared to classic carbon export studies focusing on sinking particles.</p
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