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Christian Sommer

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Christian Sommer
Doctoral Student
Alfred Nobels allé 7
Södertörns Högskola
Flemingsberg
Phone: +46 8 608 4011
MD 476 Moas Båge

My research project aims to study the effects of environmental change and disturbance on microbial communities and ecosystem functions in the Baltic Sea. As drivers of biogeochemical cycles and nutrient recycling, such as carbon turnover, the microbial functions are essential in sustaining a functioning ecosystem. Environmental heterogeneity in biotic and abiotic factors may have a sorting, or driving, effect on microbial processes. Environmental heterogeneity and environmental change in e.g. inorganic nutrient and oxygen concentration, organic content, salinity, temperature and pollution, could also be disturbances that directly or in-directly affect both microbial community structure/composition and microbial ecosystem functions. To what extent, how and in what way microbial community structure and functions respond to environmental change is, however, not well studied in eutrophied, brackish water environments, and especially not in the deep waters and sediments of the Baltic Proper. Furthermore, links and interactions between microbial communities and other trophic levels (meiofauna, fish) exposed to environmental heterogeneity are underexplored.

Key objectives of my doctoral research project are:

- To study how environmental heterogeneity and disturbance affect microbial communities and ecosystem functions in sediments in the Baltic Proper

- To study if and how microbial communities and other trophic levels co-vary at different environmental conditions

In order to meet these objectives, both field studies and experimental set ups with mesocosms will be included in the research design. Environmental genomics will be the main approach, which includes total community genomic analyses with high-throughput sequencing and bioinformatics. With the advent of modern high-throughput sequencing methods, the development of environmental genomics in the last decade is unparalleled. This approach makes it possible to access the total microbial community genetic content, even though more than 90 % of the organisms are not culturable. The environmental genomics methods I will use are extraction of nucleic acids (DNA and RNA) from sediment samples collected both from field surveys and from experimental setups using mesocosms, and analyses by high-trough put sequencing, bioinformatics and statistics, which will mainly consist of multivariate analysis (e.g. different kinds of ordination analyses).

Project 1 Microbial sediment community structure and environmental heterogeneity in the Baltic Proper

How aquatic microbial communities in sediments vary with environmental parameters remains largely unknown, especially when focusing on Baltic Sea sediments. The aim is to investigate if and how microbial community structure is linked to heterogeneity in environmental parameters, such as oxygen content, depth, salinity, organic carbon content and temperature. To investigate the microbial community taxonomic composition (structure) I will analyse a biomarker, a hyper-variable region of the 16S rRNA gene in total community DNA extracted from sediment samples from sites in the southern parts of the Baltic Proper up to the Stockholm archipelago. The sediment samples and environmental parameter data were collected in 2010 during the Swedish monitoring programme.

Project 2 Response and resilience of microbial community structure and functions to environmental change and disturbance

In December 2014 the largest salt-water inflow into the Baltic Sea in 20 years occurred. Such an inflow event likely provides more oxygen-saturated waters to the often hypoxic or anoxic bottoms of the Baltic Sea and a major change to the benthic environment. Having access to samples pre- (2010) and with new sampling post-inflow (spring 2015) will allow for comparative studies of community composition before and after the environmental change (predominantly a change in oxygen concentration and salinity). In order to investigate the response of the microbial community structure and function and for an improved understanding of the environmental drivers I will collect sediment samples during the monitoring programme in May 2015 and analyse these using similar methods as in project 1. To understand which ecosystem functions the microbial communities are active in, the samples from 2015 will be analysed by metatranscriptomic (community RNA) approaches, if feasible, to reach the first project objective. Selected functions will have particular focus and be quantitatively analysed, for example the relative abundance of the functional gene involved in sulphate reduction (dsrAB). In addition to what has been described above in project 2, plans together with researchers from Stockholm University are to investigate microbial community structure and co-variation with the structure of meiofauna and macrofauna communities in the Baltic Proper sediment using samples of May 2015. An aim is to test the hypothesis that microbial diversity gives meiofaunal diversity. Analyses of co-variation in community structure between trophic levels and response to environmental change may help the understanding of the tangled web of interactions between trophic levels.

Project 3 Changes in microbial ecosystem functions along a coastal pollution-gradient

One of the environmental disturbances in the Baltic Sea is pollution. Particularly, pollution by pharmaceutical contaminants is an increasing problem. How these contaminants affect microbial ecosystem functions are poorly understood and under studied. This project aims to investigate if pharmaceuticals, primarily focusing on selective serotonin reuptake inhibitors (SSRI), impact microbial ecosystem functions. Psychoactive drugs, such as different SSRI, have been identified in effluents of Swedish sewage treatment plants and have been shown to cause anxiolytic effects in fish. Controlled experiments using mesocosms will be supplemented by in situ collected sediment samples from effluent gradients in the vicinity of treatment plants.