Molecular fingerprinting and amplicon sequencing of the bacterial biofilm on settlement tiles deployed along natural pH gradients in Papua New Guinea

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.

Seawater carbonate chemistry and particulate organic particles during a semicontinuous batch culture experiment with Trichodesmium IMS101, 2007

Diazotrophic (N2-fixing) cyanobacteria provide the biological source of new nitrogen for large parts of the ocean. However, little is known about their sensitivity to global change. Here we show that the single most important nitrogen fixer in today's ocean, Trichodesmium, is strongly affected by changes in CO2 concentrations. Cell division rate doubled with rising CO2 (glacial to projected year 2100 levels) prompting lower carbon, nitrogen and phosphorus cellular contents, and reduced cell dimensions. N2 fixation rates per unit of phosphorus utilization as well as C:P and N:P ratios more than doubled at high CO2, with no change in C:N ratios. This could enhance the productivity of N-limited oligotrophic oceans, drive some of these areas into P limitation, and increase biological carbon sequestration in the ocean. The observed CO2 sensitivity of Trichodesmium could thereby provide a strong negative feedback to atmospheric CO2 increase.

Response of spring diatoms to CO2 availability in the Western North Pacific as determined by next-generation sequencing

Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 µatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 µatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350µatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.

Experimental data from column and batch samples

The presented thesis was written in the frame of a project called 'seepage water prognosis'. It was funded by the Federal Ministry for Education and Science (BMBF). 41 German institutions among them research institutes of universities, public authorities and engineering companies were financed for three years respectively. The aim was to work out the scientific basis that is needed to carry out a seepage water prognosis (Oberacker und Eberle, 2002). According to the Federal German Soil Protection Act (Federal Bulletin, 1998) a seepage water prognosis is required in order to avoid future soil impacts from the application of recycling products. The participants focused on the development of either methods to determine the source strength of the materials investigated, which is defined as the total mass flow caused by natural leaching or on models to predict the contaminants transport through the underlying soil. Annual meetings of all participants as well as separate meetings of the two subprojects were held. The department of Geosciences in Bremen participated with two subprojects. The aim of the subproject that resulted in this thesis was the development of easily applicable, valid, and generally accepted laboratory methods for the determination of the source strength. In the scope of the second subproject my colleague Veith Becker developed a computer model for the transport prognosis with the source strength as the main input parameter.