FEMS Microbiology Ecology

Geochemical and NanoSIMS data for "NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction"

Melting snow and glacier surfaces host microalgal blooms in polar and mountainous regions. The aim of this study was to determine the dominant taxa at the species level in the European Arctic and the Alps. A standardized protocol for amplicon metabarcoding using 18S rRNA gene and ITS2 markers was developed. This is important because previous biodiversity studies have been hampered by the dominance of closely related algal taxa in snow and ice. Due to the limited resolution of partial 18S rRNA Illumina sequences, the hypervariable ITS2 region was used to further discriminate between the genotypes. Our results show that red snow was caused by the cosmopolitan Sanguina nivaloides (Chlamydomonadales, Chlorophyta) and two as of yet undescribed Sanguina species. Arctic orange snow was dominated by S. aurantia, which was not found in the Alps. On glaciers, at least three Ancylonema species (Zygnematales, Streptophyta) dominated. Golden-brown blooms consisted of Hydrurus spp. (Hydrurales, Stramenophiles) and these were mainly an Arctic phenomenon. For chrysophytes, only 18S rRNA gene but not ITS2 sequences were amplified, showcasing how delicate the selection of eukaryotic “universal” primers for community studies is, and that primer specificity will affect diversity results dramatically. We propose our approach as a “best practice”. The repository files contain the original (raw and annotated) marker sequences files used in the following study: https://doi.org/10.1093/femsec/fiad134 They were accidently not linked with the original supplmental material, which is also included here.

This data is part of the submitted manuscript “Dissolved Organic Phosphorus Bond-Class Utilization by Synechococcus” by Emily M Waggoner, Kahina Djaoudi, Julia M Diaz, and Solange Duhamel. This dataset aims to identify the enzymes expressed when picophytoplankton Synechococcus is phosphorus stressed. Synechococcus strains WH8102 (open-ocean strain isolated from the Atlantic Ocean) and WH5701 (coastal strain isolated from Maine, US) were grown in the Duhamel Lab at the University of Arizona. Axenic culture was grown in triplicate 500 mL culture flasks in SN media amended with 1 µmol L-1 KH2PO4; a concentration previously determined as being low enough to induce phosphorus stress while still maintaining biomass (Cox and Saito, 2013). Peptide samples were analyzed at the Proteomics and Mass Spectrometry (PAMS) facility at the University of Georgia on a Thermo-Fisher LTQ Orbitrap Elite mass spectrometer coupled with a Proxeon Easy NanoLC system (Waltham, MA, United States) following Adams et al. (2022). Peptides were mapped to the Synechococcus genome (NCBI BioProject PRJNA230) (Palenik et al. 2003; McCarren et al. 2005). The protein set was searched in BLASTP against NCBI non-redundant databases, and accession numbers were cross-referenced on UniProt to confirm putative function and identify alkaline phosphatases. For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu

This data is part of the submitted manuscript “Dissolved Organic Phosphorus Bond-Class Utilization by Synechococcus” by Emily M Waggoner, Kahina Djaoudi, Julia M Diaz, and Solange Duhamel. This dataset aims to identify the enzymes expressed when picophytoplankton Synechococcus is phosphorus stressed. Synechococcus strains WH8102 (open-ocean strain isolated from the Atlantic Ocean) and WH5701 (coastal strain isolated from Maine, US) were grown in the Duhamel Lab at the University of Arizona. Axenic culture was grown in triplicate 500 mL culture flasks in SN media amended with 1 µmol L-1 KH2PO4; a concentration previously determined as being low enough to induce phosphorus stress while still maintaining biomass (Cox and Saito, 2013). Peptide samples were analyzed at the Proteomics and Mass Spectrometry (PAMS) facility at the University of Georgia on a Thermo-Fisher LTQ Orbitrap Elite mass spectrometer coupled with a Proxeon Easy NanoLC system (Waltham, MA, United States) following Adams et al. (2022). Peptides were mapped to the Synechococcus genome (NCBI BioProject PRJNA230) (Palenik et al. 2003; McCarren et al. 2005). The protein set was searched in BLASTP against NCBI non-redundant databases, and accession numbers were cross-referenced on UniProt to confirm putative function and identify alkaline phosphatases. For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to data-management@arizona.edu

Urea is a widely used nitrogen (N) fertilizer in agriculture, but considerable amounts of urea are lost through ammonia volatilization. Soil microbes are major urease producers; however, the impact of urea application on the soil ureolytic microbial community is poorly understood. In this study, the urease activity and the abundance and composition of the ureolytic bacterial community in soil (30 cm deep) under long-term urea application (four treatments: 0, 200, 400 and 600 kg N ha−1yr−1) were investigated by quantitative polymerase chain reaction and high-throughput sequencing of the ureC gene. Urease activity and ureC abundance decreased with the soil depth and increased with urea fertilization. The ureC/16S rRNA gene ratio slightly varied in the different treatments, and the ureC gene abundance was significantly and positively correlated with urease activity only in surface soil (0–10 cm), despite the greater impact of urea application on the ureolytic bacterial community structure observed in deeper soil layers (10–20 and 20–30 cm). The diversity of the ureolytic bacterial community was higher in upper soil layers than deeper ones and decreased with the urea application rate. These results suggest that long-term intensive urea fertilization may increase the risk of N loss through ammonia volatilization and increase the risk of soil degradation due to the collapse of soil microbial diversity.

Host-associated bacterial communities can play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S amplicon sequencing to compare gut- and body- bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.

We quantified the relative importance of substrate-associated and black soldier fly (BSF) egg-associated microorganisms on BSF larval performance, bacterial abundance, and bacterial community composition, when larvae were fed with chicken feed or chicken manure. We found that microbes from the feed substrate have a large impact on BSF larval microbiota and performance, whereas microbes from the insect eggs only play a minor role.

We quantified the relative importance of substrate-associated and black soldier fly (BSF) egg-associated microorganisms on BSF larval performance, bacterial abundance, and bacterial community composition, when larvae were fed with chicken feed or chicken manure. We found that microbes from the feed substrate have a large impact on BSF larval microbiota and performance, whereas microbes from the insect eggs only play a minor role.

Hydrothermal fluid samples were retrieved during dives made by the remotely operated vehicle (ROV) QUEST (MARUM, University of Bremen) during the HYDROMAR I (M60/3, 2004) and HYDROMAR II (M64/2, 2005) cruises to the Logatchev hyrothermal field. The samples were retrieved using a pumped flow-through system (Kiel Pumping System KIPS) specially designed for the ROV QUEST. Once on board the ship, the liquids intended for microbiological studies were concentrated on 0.2 µm pore size polycarbonate filters (Sartorius) and stored at -20°C. The pH and sulfide concentrations were determined immediately after sample recovery. The pH was measured (Mettler electrodes with Ag/AgCl reference electrode) at 25°C in unfiltered sample aliquots. Sulfide concentrations were determined photometrically following the methylene blue method or, for samples with low concentrations, by voltammetry (Metrohm Application Bulletin 199/3e). Methane was analyzed on board by applying a purge and trap technique. For on-board measurements of dissolved hydrogen the water sample was degassed into a high-grade vacuum. Aliquots of the released gas were analyzed by gas chromatography (Thermo Electron Corporation Trace GC Ultra with a pulsed discharge detector). The abundance of bacterial and archaeal taxa was investigated by sequencing of the 16S rRNA gene. The diversity of the cbbL, cbbM and aclb was investigated by sequencing of the genes.

Polar lipid-derived fatty acids (PLFAs) and their stable carbon isotopes are frequently combined to characterize microbial populations involved in the degradation of organic matter, offering a link to biogeochemical processes and carbon sources used. However, PLFA patterns derive from multiple species and may be influenced by substrate types. Here, we investigated such dependencies by monitoring the transformation of position-specifically 13C-labeled amino acids (AAs) in coastal marine sediments dominated by heterotrophic bacteria. Alanine was assimilated into straight-chain FAs, while valine and leucine incorporation led to the characteristic production of even- and odd-numbered iso-series FAs. This suggests that identical microbial communities adjust lipid biosynthesis according to substrate availability. Transformation into precursor molecules for FA biosynthesis was manifested in increased 13C recoveries of the corresponding volatiles acetate, isobutyrate and isovalerate of up to 39.1%, much higher than for PLFAs (<0.9%). A significant fraction of 13C was found in dissolved inorganic carbon (up to 37.9%), while less was recovered in total organic carbon (up to 17.3%). We observed a clear discrimination against the carboxyl C, whereby C2 and C3 positions were preferentially incorporated into PLFAs. Therefore, position-specific labeling is an appropriate tool for reconstructing the metabolic fate of protein-derived AAs in marine environments.