Description: Biological soil crusts (biocrusts) occur within drylands throughout the world, covering ~12% of the global terrestrial soil surface. Their occurrence in the deserts of the Arabian Peninsula has rarely been reported and their spatial distribution, diversity, and microbial composition remained largely unexplored. We investigated biocrusts at six different locations in the coastal and central deserts of Oman. The biocrust types were characterized, and the bacterial and fungal community compositions of biocrusts and uncrusted soils were analysed by amplicon sequencing. For each sample two different libraries were prepared: one for the V3V4 hypervariable region of the 16S rRNA gene (bacteria), and the other for the internal transcribed spacer 1 (ITS1; fungi). Sequences were processed in R using dada2. The code for sequence processing as well as statistical analysis, final OTU and taxonomy tables were archived on PANGAEA alongside the environmental information.

Description: In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from 2,500 m water depth at the Long-Term Ecological Research Observatory HAUSGARTEN (stationPS93/050-5 and 6), were retrieved using a TV-guided multiple corer. Surface sediments (0 - 2 cm) of 16 cores were mixed with sterile filtered deep-sea water to a final sediment dilution of 3.5 fold. The slurries were split and supplemented with five different types of habitat-related detritus: chitin, as the most abundant biopolymer in the oceans, and four different naturally occurring Arctic algae species, i.e. Thalassiosira weissflogii, Emiliania huxleyi, Bacillaria sp. and Melosira arctica. Incubations were performed in five replicates, at in situ temperature and at atmospheric pressure, as well as at in situ pressure of 250 atm. At the start of the incubation and after 23 days, changes in key community functions, i.e. extracellular enzymatic activity, oxygen respiration and secondary production of biomass (bacterial cell numbers and biomass), were assessed along with changes in the bacterial community composition based on 16S rRNA gene and 16S rRNA Illumina sequencing. In summary, differences in community structure and in the uptake and remineralization of carbon in the different treatments suggest an effect of organic matter quality on bacterial diversity as well as on carbon turnover at the seafloor.

Description: Physicochemical parameters and relative abundance of selected nutrient cycling genes were measured in sediment and pore water samples taken from a fish farming area (Site S3 16◦23.097 N, 119◦55.551 E, depth 12.6m) and a control site (Site S1 16◦22.960 N, 119◦54.723 E, depth 15m) not influenced by fish farming. From each site, five pairs of cores representing five biological replicates were collected. One core from each pair was used for physicochemical analysis while the other cores were used for microbial community analysis. Samples from S1 were collected on 2017-06-10 and samples from S3 were collected the following day. This dataset presents % Carbon (%C), % Nitrogen (%N), % total organic carbon (%Corg), and stable isotope (d13C and d15N) content. The following were measured in the pore water: dissolved organic carbon (DOC), total dissolved nitrogen (TDN), ammonium, phosphate, and silicate.

Description: Bacterial biofilms provide cues for the settlement of marine invertebrates such as coral larvae, and are therefore important for the resilience and recovery of coral reefs. This study aimed to better understand how ocean acidification may affect the community composition and diversity of bacterial biofilms on surfaces under naturally reduced pH conditions. Settlement tiles were deployed at coral reefs in Papua New Guinea along pH gradients created by two CO2 seeps, and upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis were used to characterize more than 200 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. The bacterial biofilm consisted predominantly of Alpha-, Gamma- and Deltaproteobacteria, as well as Cyanobacteria, Flavobacteriia and Cytophaga, whereas putative settlement-inducing taxa only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous with approximately 25% shared operational taxonomic units between samples. Among the observed environmental parameters, pH only had a weak effect on community composition (R² ~ 1%) and did not affect community richness and evenness. In contrast, there were strong differences between upper and lower surfaces (contrasting in light exposure and grazing intensity). There also appeared to be a strong interaction between bacterial biofilm composition and the macroscopic components of the tile community. Our results suggest that on mature settlement surfaces in situ, pH does not have a strong impact on the composition of bacterial biofilms. Other abiotic and biotic factors such as light exposure and interactions with other organisms may be more important in shaping bacterial biofilms than changes in seawater pH.

Description: To understand how ocean acidification (OA) influences sediment microbial communities, naturally CO2-rich sites are increasingly being used as OA analogues. However, the characterization of these naturally CO2-rich sites is often limited to OA-related variables, neglecting additional environmental variables that may confound OA effects. Here, we used an extensive array of sediment and bottom water parameters to evaluate pH effects on sediment microbial communities at hydrothermal CO2 seeps in Papua New Guinea. The geochemical composition of the sediment pore water showed variations in the hydrothermal signature at seep sites with comparable pH, allowing the identification of sites that may better represent future OA scenarios. At these sites, we detected a 60% shift in the microbial community composition compared with reference sites, mostly related to increases in Chloroflexi sequences. pH was among the factors significantly, yet not mainly, explaining changes in microbial community composition. pH variation may therefore often not be the primary cause of microbial changes when sampling is done along complex environmental gradients. Thus, we recommend an ecosystem approach when assessing OA effects on sediment microbial communities under natural conditions. This will enable a more reliable quantification of OA effects via a reduction of potential confounding effects. This pangaea entry contains the data on the microbial community structure and bottom water parameters.