Table of contents I Processes and community structure in microbial biofilms of the River Elbe: relation to nutrient dynamics and particulate organic matter D I S S E R T A T I O N zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt der Fakultät Mathematik / Naturwissenschaft der Technischen Universität Dresden von Dipl. Biol. F r a n k K l o e p geboren am 11.06.1972 in Gerolstein Dresden, 2002 Table of contents II Dissertation der Technischen Universität Dresden Datum der mündlichen Prüfungen: 16.08.2001 Referenten: Prof. Dr. Isolde Röske Prof. Dr. Dietrich Uhlmann PD Dr. Werner Manz Table of contents III Table of contents 1 Introduction ........................................................................................................................... 1 1.1 EFFECTS OF DIURNAL CHANGES IN DISSOLVED OXYGEN ON DAILY AND SEASONAL NUTRIENT CONCENTRATIONS IN THE OPEN WATER AND THE HYPORHEIC ZONE OF THE RIVER ELBE......................................3 1.2 TRANSPORT BEHAVIOUR OF ALGAL CELLS IN HYPORHEIC SEDIMENTS ............................................................3 1.3 HYPORHEIC BIOFILMS AT TWO CONTRASTING RIVER ELBE SITES....................................................................5 1.4 ANALYSIS OF MICROBIAL COMMUNITIES OF THE RIVER ELBE.........................................................................6 2 Materials and Methods .........................................................................................................8 2.1 DIURNAL CHANGES IN DISSOLVED OXYGEN AND NUTRIENTS .........................................................................9 2.1.1 Field sampling.......................................................................................................................................9 2.1.1.1 Study site and sampling strategy .....................................................................................................................9 2.1.1.2 Sample treatment and analysis ......................................................................................................................10 2.1.2 Model description................................................................................................................................11 2.2 TRANSPORT OF ALGAL CELLS IN HYPORHEIC SEDIMENTS .............................................................................15 2.2.1 Field sampling strategy .......................................................................................................................15 2.2.2 Algae and microspheres used for column experiments .......................................................................15 2.2.3 Column experiments ............................................................................................................................15 2.2.4 Particle enumeration...........................................................................................................................18 2.3 HYPORHEIC BIOFILMS AT TWO CONTRASTING RIVER ELBE SITES..................................................................19 2.3.1 Study site and sampling procedure......................................................................................................19 2.3.2 Characteristics of the sediment biofilms .............................................................................................20 2.3.2.1 Detrital parameters - sedimentary particulate organic matter........................................................................20 2.3.2.2 Respiration rate..............................................................................................................................................20 2.3.2.3 Denitrification rates.......................................................................................................................................21 2.3.2.4 Nitrification rates...........................................................................................................................................22 2.3.2.5 Extracellular enzyme activities......................................................................................................................22 2.3.2.6 Bacterial cell counts ......................................................................................................................................22 2.3.2.7 Sediment total phosphorus.............................................................................................................................23 2.3.3 Chlorophyll a and pheophytin.............................................................................................................23 2.3.4 Chemical analyses...............................................................................................................................23 2.3.5 Grain size distribution.........................................................................................................................24 2.3.6 Statistical analysis...............................................................................................................................24 2.4 ANALYSIS OF MICROBIAL COMMUNITIES OF THE RIVER ELBE.......................................................................25 2.4.1 Sampling sites......................................................................................................................................25 2.4.2 Preparation of samples .......................................................................................................................25 2.4.3 Fluorescence in situ hybridization ......................................................................................................26 2.4.4 Microscopy ..........................................................................................................................................26 2.4.5 Statistical analysis...............................................................................................................................29 3 Results .................................................................................................................................. 31 3.1 DIURNAL CHANGES IN DISSOLVED OXYGEN AND NUTRIENTS .......................................................................31 3.1.1 Temporal variations in discharge and temperature............................................................................31 3.1.2 Temporal variations in water biochemistry.........................................................................................32 3.1.3 Modeling the effects of oxygen on diurnal inorganic nitrogen dynamics in the hyporheic zone .......40 3.2 TRANSPORT OF ALGAL CELLS IN HYPORHEIC SEDIMENTS .............................................................................42 3.2.1 Seasonal variations in algal cell abundance.......................................................................................42 3.2.2 Column experiments ............................................................................................................................43 3.2.2.1 Retention of algal cells ..................................................................................................................................45 3.2.2.2 Retardation of algal cells...............................................................................................................................45 3.3 HYPORHEIC BIOFILMS AT TWO CONTRASTING RIVER ELBE SITES..................................................................47 3.3.1 Sediment characteristics......................................................................................................................47 3.3.2 Water chemistry...................................................................................................................................47 3.3.3 Microbial activity and biofilm analysis...............................................................................................48 Table of contents IV 3.3.4 Microbial and other sediment variables per streambed surface area.................................................53 3.3.5 Relationship between bacterial biomass and activity, sediment composition and structure...............54 3.4 ANALYSIS OF MICROBIAL COMMUNITIES OF THE RIVER ELBE.......................................................................58 3.4.1 Community composition at the domain-specific level .........................................................................58 3.4.2 Community composition at the group-specific level............................................................................60 3.4.3 Community composition at the genus- and species-specific level.......................................................64 4 Discussion............................................................................................................................. 67 4.1 EFFECT OF DIURNAL CHANGES IN DISSOLVED OXYGEN ON DAILY AND SEASONAL NUTRIENT CONCENTRATIONS IN THE OPEN WATER AND THE HYPORHEIC ZONE ...................................................................67 4.1.1 Effect of oxygen concentration in the open water on hyporheic oxygen dynamics .............................67 4.1.2 Effect of oxygen on hyporheic nitrate dynamics..................................................................................68 4.1.3 Effect of oxygen on hyporheic ammonium dynamics...........................................................................69 4.1.4 Effect of oxygen on hyporheic nitrite dynamics...................................................................................70