ALBERT

Description: 16S rRNA and metabolic gene abundances as well as gene reconstructions were generated using a novel, modified version of the phyloFlash pipeline (https://github.com/HRGV/phyloFlash) called funcFlash for metabolic genes. In brief, the generated reads were mapped with BBMap at minimal global nucleotide identity of 70% against curated nucleotide databases: The SILVA SSURef v119 database [75], a published dsrAB gene database (http://www.microbial-ecology.net/db_download/dsr_v3.zip, [83]) and two newly generated pmoA and mcrA gene databases that are publicly available at PANGAEA, see [61]. The mapped read pairs were counted when at least one read had a positive mapping. Full length (〉70% of the target length) genes were assembled with SPAdes [84] or reconstructed with EMIRGE [85]. The mapping of reconstructed metabolic genes to curated databases using funcFlash can be used to distinguish, whether a gene of interest is affiliated with organisms performing the reductive or oxidative pathway. In our case this new analysis allowed us to distinguish between dsrAB genes from sulfate reducers and from sulfur oxidizers, as well as between mcrA genes from methanogens and from methanotrophs.

Description: The Guaymas Basin hydrothermal vents in the Gulf of California have been visited during RV Atlantis mission AT37-06 in December 2016. Aim of this mission was to understand element fluxes and microbially driven reactions at the diffusive vent sites. The submarine ALVIN and push cores were used to sample undisturbed sediments at specific locations covering different temperature and geochemical regimes. From these cores porewater was sampled using Rhizons. Here we present concentrations of select anions in the porewater. We measured the concentrations of sulfate, sulfide, chloride, ammonia, phosphate and silicate.

Description: Vesicomyidae clams harbor sulfide-oxidizing endosymbionts and are typical members of cold seep communities associated with tectonic faults where active venting of fluids and gases takes place. We investigated the central biogeochemical processes that supported a vesicomyid clam colony as part of a locally restricted seep community in the Japan Trench at 5346 m water depth, one of the deepest seep settings studied to date. An integrated approach of biogeochemical and molecular ecological techniques was used combining in situ and ex situ measurements. During the cruise YK06-05 in 2006 with the RV Yokosuka to the Japan Trench, we investigated a clam colony inhabited by Abyssogena phaseoliformis (former known as Calyptogena phaseoliformis) and Isorropodon fossajaponicum (former known as Calyptogena fossajaponica). The targeted sampling and precise positioning of the in situ instruments were achieved with the manned research submersible Shinkai 6500 (JAMSTEC, Nankoku, Kochi, Japan). Sampling was first performed close to the rim of the JTC colony and then at the center. Immediately after sample recovery onboard, the sediment core was sub-sampled for ex situ rate measurements or preserved for later analyses. In sediment of the clam colony, low sulfate reduction (SR) rates (max. 128 nmol ml**-1 d**-1) were coupled to the anaerobic oxidation of methane (AOM). They were observed over a depth range of 15 cm, caused by active transport of sulfate due to bioturbation of the vesicomyid clams. A distinct separation between the seep and the surrounding seafloor was shown by steep horizontal geochemical gradients and pronounced microbial community shifts. The sediment below the clam colony was dominated by anaerobic methanotrophic archaea (ANME-2c) and sulfate-reducing Desulfobulbaceae (SEEP-SRB-3, SEEP-SRB-4). Aerobic methanotrophic bacteria were not detected in the sediment and the oxidation of sulfide seemed to be carried out chemolithoautotrophically by Sulfurovum species. Thus, major redox processes were mediated by distinct subgroups of seep-related microorganisms that might have been selected by this specific abyssal seep environment. Fluid flow and microbial activity was low but sufficient to support the clam community over decades and to build up high biomasses. Hence, the clams and their microbial communities adapted successfully to a low-energy regime and may represent widespread chemosynthetic communities in the Japan Trench.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of 〉100 groundwater samples from 90 monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This dataset contains the nucleotide sequences and taxonomy of archaeal 16S rRNA gene amplicons retrieved from groundwater samples of aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning DNA extraction, sequencing and sequence analyses can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of 〉100 groundwater samples from 90 monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This dataset contains the nucleotide sequences and taxonomy of bacterial 16S rRNA gene amplicons retrieved from groundwater samples of aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning DNA extraction, sequencing and sequence analyses can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of 〉100 groundwater samples from 90 monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This dataset contains relative abundances of archaeal lineages based on 16S rRNA gene amplicons retrieved from 52 groundwater samples of aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning DNA extraction, sequencing and sequence analyses can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We therefore investigated the total microbial cell counts of 78 groundwater samples from aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning microscopy and cell enumeration can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of groundwater samples from various monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This dataset contains archaeal community diversity indices based on 16S rRNA gene amplicons retrieved from 52 groundwater samples of aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning DNA extraction, sequencing and sequence analyses can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. This dataset contains values and calculations to estimate microbial oxygen consumption in groundwater samples from aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning microbial cell counts and oxygen consumption can be found in the associated publication by Ruff et al. 2023.

Description: Groundwater ecosystems are globally widespread yet still poorly understood. We investigated the microbiology of groundwater samples from various monitoring wells (〈250m depth) located in 14 aquifers in the Canadian Prairie. This dataset contains bacterial community diversity indices based on 16S rRNA gene amplicons retrieved from 119 groundwater samples of aquifers in the Canadian Prairie, collected between 2015 and 2020. The study area comprised 14 major aquifers and a geographic area of ~210.000 km2. The goal of the study was to understand the links between the biogeochemistry and microbial ecology of groundwater ecosystems in diverse geological settings on a broad spatial scale. Details concerning DNA extraction, sequencing and sequence analyses can be found in the associated publication by Ruff et al. 2023.