Implications of ocean acidification for microbial life and for microbial interactions

Ocean acidification (OA) is a major threat to marine systems. Very little is known about OA effects on microbial communities and the services they provide to the ecosystem. Here, shallow-water hydrothermal CO2 vents in a tropical coral reef were investigated as model system to provide an ecosystem perspective on OA effects on the diversity and function of microbial communities, as well as interactions with other reef organisms. In conclusion, microbial communities, functions and interactions were fundamentally altered at the CO2 vents. However, the strength of the influence of the CO2 vents seemed to depend on the investigated reef environment. The changes in microbial communities and processes may contribute to a general decline of the reef ecosystem at hydrothermal CO2 vents. This thesis offers new insights into microbial life at shallow-water hydrothermal CO2 vents, as well as predictions about potential OA impacts. Yet, it also emphasizes the challenge of estimating future OA effects based on observation at OA analogues that exhibit a high environmental complexity such as shallow-water hydrothermal CO2 vents

Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2 seeps in Papua New Guinea

Hassenrück C, Tegetmeyer H, Ramette A, Fabricius KE. Minor impacts of reduced pH on bacterial biofilms on settlement tiles along natural pH gradients at two CO2 seeps in Papua New Guinea. ICES Journal of Marine Science. 2017;74(4):978-987.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. Biofilms on upper and lower tiles surfaces were sampled 5 and 13 months after deployment. Automated Ribosomal Intergenic Spacer Analysis was used to characterize 240 separate bacterial communities, complemented by amplicon sequencing of the bacterial 16S rRNA gene of 16 samples. Bacterial biofilms consisted predominantly of Alpha-, Gamma-, and Delta-proteobacteria, as well as Cyanobacteria, Flavobacteriia, and Cytophagia, whereas taxa that induce settlement of invertebrate larvae only accounted for a small fraction of the community. Bacterial biofilm composition was heterogeneous, with on average only similar to 25% of operational taxonomic units shared between samples. Among the observed environmental parameters, pH was only weakly related to community composition (R-2 similar to 1%), and was unrelated to community richness and evenness. In contrast, biofilms strongly differed between upper and lower tile 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 on mature surfaces than changes in seawater pH

Seagrass biofilm communities at a naturally CO2-rich vent

Seagrass meadows are a crucial component of tropical marine reef ecosystems. Seagrass plants are colonized by a multitude of epiphytic organisms that contribute to broadening the ecological role of seagrasses. To better understand how environmental changes like ocean acidification might affect epiphytic assemblages, the microbial community composition of the epiphytic biofilm of Enhalus acroides was investigated at a natural CO2 vent in Papua New Guinea using molecular fingerprinting and next generation sequencing of 16S and 18S rRNA genes. Both bacterial and eukaryotic epiphytes formed distinct communities at the CO2-impacted site compared to the control site. This site-related CO2 effect was also visible in the succession pattern of microbial epiphytes. We further found an increased abundance of bacterial types associated with coral diseases at the CO2-impacted site (Fusobacteria, Thalassomonas) whereas eukaryotes such as certain crustose coralline algae commonly related to healthy reefs were less diverse. These trends in the epiphytic community of E. acroides suggest a potential role of seagrasses as vectors of coral pathogens and may support previous predictions of a decrease in reef health and prevalence of diseases under future ocean acidification scenarios

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei aquaculture

Bacterial diseases cause production failures in shrimp aquacultures.to understand environmental conditions and bacterial community dynamics contributing to white faeces disease (WFD) events, we analysed water quality and compared bacterial communities in water as well as in intestines and faeces of healthy and diseased shrimps, respectively, via 16S rRNA gene sequencing and qPCR of transmembrane regulatory protein (toxR), thermolabile haemolysin (tlh), and thermostable direct haemolysin genes of pathogenic Vibrio parahaemolyticus as a proxy for virulence. WfD occurred when pH decreased to 7.71–7.84, and Alteromonas, Pseudoalteromonas and Vibrio dominated the aquatic bacterial communities. the disease severity further correlated with increased proportions of Alteromonas, Photobacterium, Pseudoalteromonas and Vibrio in shrimp faeces. these opportunistic pathogenic bacteria constituted up to 60% and 80% of the sequences in samples from the early and advances stages of the disease outbreak, respectively, and exhibited a high degree of co-occurrence. Furthermore, toxR and tlh were detected in water at the disease event only. Notably, bacterial community resilience in water occurred when pH was adjusted to 8. Then WFD ceased without a mortality event. In conclusion, pH was a reliable indicator of the WFD outbreak risk. Dissolved oxygen and compositions of water and intestinal bacteria may also serve as indicators for better prevention of WFD event

Response of Bacterial Communities to Different Detritus Compositions in Arctic Deep-Sea Sediments

Benthic deep-sea communities are largely dependent on particle flux from surface waters. In the Arctic Ocean, environmental changes occur more rapidly than in other ocean regions, and have major effects on the export of organic matter to the deep sea. Because bacteria constitute the majority of deep-sea benthic biomass and influence global element cycles, it is important to better understand how changes in organic matter input will affect bacterial communities at the Arctic seafloor. In a multidisciplinary ex situ experiment, benthic bacterial deep-sea communities from the Long-Term Ecological Research Observatory HAUSGARTEN were supplemented with different types of habitat-related detritus (chitin, Arctic algae) and incubated for 23 days under in situ conditions. Chitin addition caused strong changes in community activity, while community structure remained similar to unfed control incubations. In contrast, the addition of phytodetritus resulted in strong changes in community composition, accompanied by increased community activity, indicating the need for adaptation in these treatments. High-throughput sequencing of the 16S rRNA gene and 16S rRNA revealed distinct taxonomic groups of potentially fast-growing, opportunistic bacteria in the different detritus treatments. Compared to the unfed control, Colwelliaceae, Psychromonadaceae, and Oceanospirillaceae increased in relative abundance in the chitin treatment, whereas Flavobacteriaceae, Marinilabiaceae, and Pseudoalteromonadaceae increased in the phytodetritus treatments. Hence, these groups may constitute indicator taxa for the different organic matter sources at this study site. 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, an important feedback mechanism to be considered in future climate change scenarios

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches

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

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North-West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2-3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions.Fil: Bachmann, Jennifer. Universitat Bremen; Alemania. Leibniz Centre for Tropical Marine Research; AlemaniaFil: Heimbach, Tabea. Leibniz Centre for Tropical Marine Research; Alemania. Universitat Bremen; Alemania. Max Plank Institute for Marine Microbiology; AlemaniaFil: Hassenrück, Christiane. Leibniz Centre for Tropical Marine Research; AlemaniaFil: Kopprio, Germán Adolfo. Leibniz Centre for Tropical Marine Research; Alemania. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; ArgentinaFil: Iversen, Morten Hvitfeldt. Universitat Bremen; Alemania. Alfred Wegener Institute for Polar and Marine Research; AlemaniaFil: Grossart, Hans Peter. Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Alemania. University of Potsdam; AlemaniaFil: Gärdes, Astrid. Leibniz Centre for Tropical Marine Research; Alemani

Environmental Drivers of Free-Living vs. Particle-Attached Bacterial Community Composition in the Mauritania Upwelling System

Saharan dust input and seasonal upwelling along North–West Africa provide a model system for studying microbial processes related to the export and recycling of nutrients. This study offers the first molecular characterization of prokaryotic particle-attached (PA; >3.0 μm) and free-living (FL; 0.2–3.0 μm) players in this important ecosystem during August 2016. Environmental drivers for alpha-diversity, bacterial community composition, and differences between FL and PA fractions were identified. The ultra-oligotrophic waters off Senegal were dominated by Cyanobacteria while higher relative abundances of Alphaproteobacteria, Bacteroidetes, Verrucomicrobia, and Planctomycetes (known particle-degraders) occurred in the upwelling area. Temperature, proxy for different water masses, was the best predictor for changes in FL communities. PA community variation was best explained by temperature and ammonium. Bray Curtis dissimilarities between FL and PA were generally very high and correlated with temperature and salinity in surface waters. Greatest similarities between FL and PA occurred at the deep chlorophyll maximum, where bacterial substrate availability was likely highest. This indicates that environmental drivers do not only influence changes among FL and PA communities but also differences between them. This could provide an explanation for contradicting results obtained by different studies regarding the dissimilarity/similarity between FL and PA communities and their biogeochemical functions

Growth rates of Desmophyllum dianthus - Effect of association with endolithic algae

It has long been suggested that endolithic algae inside the skeleton of living corals might have a symbiotic relationship with the coral host and would positively affect coral calcification. However, so far this hypothesis has not yet been further explored. This study investigated the effect of endolithic algae on the growth performance of the cold-water coral Desmophyllum dianthus that is frequently associated with the endolithic chlorophyte Ostreobium queckettii and the cyanobacterium Plectonema terebrans. The fluorescent staining agent calcein was used to document the upward and inward linear growth of septa of specimens of D. dianthus at Fjord Comau, southern Chile. Further qualitative observations concerned skeletal microstructure and density using light field and fluorescence microscopy and x-ray computed tomography, respectively. Since the D. dianthus was sampled in a region displaying strong annual fluctuations of environmental parameters that might influence calcification, growth rates were also tested for a seasonal pattern. The results of this study show a severe reduction of growth rates associated with endolithic algae. Infested individuals grew about half as fast as non-infested polyps referring to both directions of septal growth with median values of 1.18μm/day for upward and 0.49μm/day for inward growth compared to 2.76μm/day and 0.82μm/day, respectively. These results point towards a parasitic relationship between D. dianthus and its endolithic algae refuting the hypothesis of a mutually beneficial association. This theory is further supported by observations on skeletal density and microstructure which suggest a reduction in skeletal density probably caused by extensive tunnelings of both endolithic species. Unlike expected the seasonal variation of upward septal growth rates of D. dianthus was inconsistent with the annual temperature pattern at Fjord Comau. Minimum growth rates were reported in periods of maximum temperatures – a phenomenon that might be explained by the trade-off between growth and reproduction which is suspected to take place in summer. Inward growth rates displayed a continuous decrease with time that is most likely attributed to the increasing influence of morphological constraints towards the center of the polyp. Although this study appears to conclusively indicate a negative effect of the association of D. dianthus with endolithic algae, controversial evidence has been discovered regarding metabolic links between the coral host and the endoliths and further research is necessary to fully resolve the issue

Effects of Thermal Stress on the Gut Microbiome of Juvenile Milkfish (Chanos chanos)

Milkfish, an important aquaculture species in Asian countries, are traditionally cultured in outdoor-based systems. There, they experience potentially stressful fluctuations in environmental conditions, such as temperature, eliciting changes in fish physiology. While the importance of the gut microbiome for the welfare and performance of fish has been recognized, little is known about the effects of thermal stress on the gut microbiome of milkfish and its interactions with the host’s metabolism. We investigated the gut microbiome of juvenile milkfish in a thermal stress experiment, comparing control (26 °C) and elevated temperature (33 °C) treatments over three weeks, analyzing physiological biomarkers, gut microbiome composition, and tank water microbial communities using 16S amplicon sequencing. The gut microbiome was distinct from the tank water and dominated by Cetobacterium, Enterovibrio, and Vibrio. We observed a parallel succession in both temperature treatments, with microbial communities at 33 °C differing more strongly from the control after the initial temperature increase and becoming more similar towards the end of the experiment. As proxy for the fish’s energy status, HSI (hepatosomatic index) was correlated with gut microbiome composition. Our study showed that thermal stress induced changes in the milkfish gut microbiome, which may contribute to the host’s habituation to elevated temperatures over time