<p>In Ethiopia industrial effluents containing high contents of organic matter, nitrogen and heavy metals are discharged into inland surface waters with little or no pre-treatment. Significant pollution concerns related to these effluents include dissolved oxygen depletion, toxicity and eutrophication of the receiving waters. This has not only forced the government to formulate regulations and standards for discharge limits but also resulted in an increasing interest and development of methods and systems by which wastewater can be recycled and used sustainably. The need for technologies for environmentally friendly treatment of industrial wastes such as tannery wastewaters is therefore obvious. Biological processes are not only cost effective but also environmentally sound alternatives to the chemical treatment of tannery wastewaters.</p><p>The aim of the research presented in this thesis was to develop and optimize processes for biological nitrogen removal from tannery wastewaters and to identify the most efficient denitrifying organisms in tannery wastewaters laden with toxic substances. A pilot plant consisting of a predenitrification anoxic system, aerated nitrification compartment and a sedimentation tank (clarifier) all arranged in series was developed and installed on the premises of Addis Ababa University, Ethiopia. In spite of high influent chromium and sulphide perturbations over the successive feeding phases, the performance of the pilot plant was encouraging. The overall removal efficiency of the pilot plant over the experimental feeding phases varied between 82-98% for total nitrogen, 95-98% for COD, 96-98% for BOD5, 46-95% for ammonia nitrogen, 95-99% for sulphide and 93-99% for trivalent Chromium. Six isolates from over 1000 pure cultures were identified as the most efficient denitrifying bacteria. From both cellular fatty acid profiles and 16S rRNA gene sequencing, the six selected strains were phylogenetically identified as Brachymonas denitrificans in the β-subdivision of the Proteobacteria. All the six strains contain cd1-type nitrite reductase. The efficient isolates characterized in this study are of great value because of their excellent denitrifying properties and high tolerance to the concentrations of toxic compounds prevailing in tannery wastewaters. Bio-augmentation of the pilot plant with this bacterium showed a clear correlation between in situ denitrifying activities measured by nitrate uptake rate, population dynamics of the introduced B.denitrificans monitored by fluorescent in situ hybridization and the pilot plant performance, suggesting that the strategy of introducing this species for enhancing process performance has potential applications.</p><p>Moreover, the nitrate-reducing, sulphur-oxidizing bacteria (NR-SOB) were also found in the pilot plant in abundance with steady sulphide removal efficiency during the study period. This could provide opportunities for the application of biologically mediated simultaneous removal of sulphide and nitrogen from tannery effluents. In addition to enriching high consortia of denitrifiers in the anoxic system to attain high denitrification efficiency and also improving the overall nitrification efficiency of the system, the predenitrification-nitrification pilot process plant stimulated the activity of indigenous NR-SOB to simultaneously remove sulphide from the system. Thus, the pilot plant was found to be operationally efficient for the removal of nitrogen, organic matter and other pollutants from tannery wastewaters.</p><p><b>Keywords:</b> Biological nitrogen and sulphide removal, denitrifying bacteria, nitrate-reducing, sulphur-oxidizing bacteria, nitrate uptake rate, fluorescent in situ hybridization, pollution, tannery effluents.</p>

published_or_final_version / Architecture / Master / Master of Architecture

Heterotrophic microorganisms are important for the flow of carbon and nutrients in the sea. Bacteria, nanoflagellates and ciliates are relevant components of the pelagic food web. In order to be able to predict the outcome of e.g. eutrophication or climate change we need to know how the different components of the pelagic food web are regulated. With the focus on the northern Baltic Sea food web, this thesis deals with limitation and control of heterotrophic protists, the effect of resource heterogeneity on food web efficiency and diversity of nanoflagellates. In-situ microcosm experiments showed that the net growth of heterotrophic flagellates were resource limited throughout the year. Field data confirmed that the abundance of flagellates was bottom-up controlled. Furthermore, field data also showed that the annual average biomass of protists, flagellates and ciliates increased with primary productivity. On a smaller seasonal scale temperature and bacterial biomass were able to explain most of the variation in flagellate biovolume. The temporal variation in ciliate biovolume could not be explained by any bottom-up factors like bacterial biomass, flagellate biomass or chlorophyll a. This and an in-situ microcosm experiment implied that the seasonal dynamics of ciliates were more regulated by predators like mesozooplankton. The food web efficiency i.e. how much of production at the resource level is converted to production at the top trophic level, may be affected by specific size or type of resource. Indoor mesocosms revealed that the food web efficiency was 11 times lower when heterotrophic bacteria dominated basal production instead of nano- and micro-sized phytoplankton. This was due to a lengthening of the food web when pico-sized bacteria constituted the main resource. The PCR-DGGE molecular biological method was used to study the diversity of heterotrophic or mixotrophic chrysomonads. The focus was set on chrysomonads due to their relatively large contribution to the nanoflagellate community. Group-specific PCR primers were optimized for the target group. A field survey in the northern Baltic Sea showed that a handful of chrysomonad sequences were present throughout the year. Significantly more chrysomonads were recorded in the basin with higher primary productive and salinity. In total 15-16 different chrysomonad sequences were recorded. Most of them matched uncultured chrysomonad clones.

Environmental factors influence species and habitats on multiple scales creating a mosaic of distribution patterns. Studying factors shaping these patterns are central to our understanding of population dynamics and ultimately ecosystem functioning. Information on the distribution of resources and conservation values are also highly needed in marine management as coastal areas are increasingly influenced by human activities. In this thesis, large-scale field data is used to explore how strong environmental gradients found on multiple scales in the coastal areas of the Baltic Sea influence fish habitats. The underlying concepts are based in the field of species distribution modelling, whereby habitat maps can be produced using environmental layers in a geographic information system. Distribution modelling is further used to address both ecological and applied questions by examining effects of habitat limitation on fish population sizes and to evaluate management actions aimed at habitat conservation. I show that specific habitat requirements for fish species of both freshwater and marine origin can be described using environmental variables and that species-environment relationships can be used to predict the distribution of early life-stages of fish in the Baltic Sea archipelagos. Further, predicted habitat availability of a specific life-stage was directly related to adult population size of Eurasian perch Perca fluviatilis, signifying that the abundance of large predatory fish can be limited by specific recruitment habitats. Lastly, by predicting the distribution of an assemblage of coastal fish species and their associated habitats, an assessment of a network of marine protected areas was performed. Results revealed large gaps in the current network and identified areas suitable for future protection. By demonstrating how current habitat protection can be improved by including critical habitats for coastal fish population sizes this thesis points to the benefits of integrating nature conservation and fisheries management. Based on these findings I conclude that species distribution modelling provides a suitable analytical framework for assessing the habitat requirements of organisms. An increased understanding of habitat-population relationships and an ability to accurately map ecologically important features will be of great value for an ecosystem-based marine management. ­ / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 709

This doctoral dissertation was produced in a cooperation between Halmstad University (Wetland Research Centre, School of Business and Engineering) and Lund University (Limnology &amp; Marine Biology, Department of Ecology). Abstract . Wetland creation at large, regional scales is implemented as a measure to abate the biodiversity loss in agricultural landscapes and the eutrophication of watersheds and coastal areas by non-point source nutrient pollution (mainly nitrogen). The consequences of creating many new wetlands for biodiversity conservation and nutrient reten- tion (ecosystem functioning) in agricultural landscapes are still relatively unknown, both on local (per wetland) and regional (per landscape) scales. In Sweden, wetland creation has progressed already since the 1990s, and by now larger numbers of created wetlands are present, mainly in the intensively farmed landscapes of southwestern Sweden. This thesis aimed to investigate the following aspects in these systems: (i) their large-scale effects on biodiversity, (ii) their functional diversity of bacterial denitrifiers, (iii) the abiotic and biotic influences on wetland ecosystem functioning, (iv) the potential for biodiversity-function links, and (v) the potential for functional links and joint functioning.(i) Created wetlands hosted diverse assemblages of macroinvertebrates and plants. They maintained a similar com- position and diversity as natural ponds in agricultural landscapes. The environmental conditions per wetland did hardly affect macroinvertebrate and plant assemblages, and the prerequisites for nutrient retention did neither. In landscapes were wetland creation efforts had increased the total density of small water bodies by more than 30%, macroinver- tebrate diversity of created wetlands was facilitated on both local and regional scales. (ii) Diverse communities of denitrifying bacteria with the capacity for conducting different denitrification steps (functional types) were present in all investigated wetlands. The richness of denitrifying bacteria communities was affected by nitrate concentration and hydraulic loading rate, which may potentially be relevant for the nitrogen retention function of created wetlands. The diversity across different functional types of bacterial denitrifiers increased with nitrate concentration. (iii) Both abiotic and biotic factors influenced ecosystem functions of created wetlands. Variation in nitrogen retention was associated to nitrate load, but even to vegetation parameters. In wetlands with constant nitrate load, planted emergent vegetation facilitated nitrogen retention compared to other vegetation types. In wetlands with variable loads, nitrogen retention was facilitated if nitrate load was high and many different vegetation types were present; nitrogen load could explain the majority of the variation in nitrogen retention compared to vegetation parameters. Phosporus retention of created wetlands was best explained by vegetation parameters. Litter decomposition was inhibited at high nitrate to phosphorus ratios. Methane production increased with age and decreased with plant cover. (iv) Biodiversity may facilitate wetland ecosystem functions, particularly in dynamic wetland ecosystems. Nitrogen retention increased with vegetation type diversity, phosphorus retention capacity with plant richness, and litter decomposition with macroinvertebrate diversity. (v) Created wetlands have the capacity of sustaining several parallel ecosystem services. Some wetland functions were coupled; nitrogen retention increased with fast litter decomposition. On the other hand, methane emission and nitro- gen retention were independent of each other, as were nitrogen and phosphorus retention.In conclusion, created wetlands have the potential to at least partly abate the lost biodiversity and multifunctionality caused by the past extensive destruction of natural wetlands in agricultural landscapes. / <p>[Paper II] Milenkovski S., Thiere G., Weisner S.E.B., Berglund O. &amp; Lindgren P.-E. Variation of eubacterial and denitrifying bacterial biofilm communities among constructed wetlands. Submitted manuscript. [Paper V] Thiere G. &amp; Weisner S.E.B. Influence of biotic and abiotic parameters on ecosystem functioning of created wetlands. Manuscript.</p>

Harmful algal blooms, commonly referred to as red tides, occur yearly with dramatic impacts on marine ecology, coastal economies, and human health. As a consequence, research into the zooplankton grazers that consume HABs is highly important. However, changes in ocean temperature may increase the range of many HABs, exposing historically naive copepods to new species and their associated chemicals. Little research into the impact of allopatric verses sympatric species, particularly on the immediate behavioral impact, has been performed, leaving the indirect fitness effects of HAB exposure and consumption relatively unknown. We measured alterations in the swimming behavior of the calanoid copepod Temora longicornis following exposure to sympatric Alexandrium fundyense and allopatric Karenia brevis treatments. After a 15-16 hours depuration period postA. fundyense exposure, T. longicornis exhibited increased average swimming speed and an elevated net to gross displacement ratio (NGDR). During exposure toK. brevis, copepods exhibited an immediate decrease in swimming speed and NGDR, as well as an increased frequency of jump behavior. However, these effects faded after an one-hour depuration period, and disappeared after a 15-16 hour depuration period. The alterations in swimming behavior demonstrated by the copepods treated A. fundyense may increase encounter rate with predators, while copepods treated with K. brevis remain in bloom conditions for longer periods of time, negatively affecting survivorship. Temora longicornis individuals also may be made more visible to predators due to the increase in jumps seen during treatment with K. brevis. These behavioral changes suggest how HABs escape from zooplankton grazer control by altering copepod swimming behavior, and the pattern of predator-prey evolution that occurs over time.

I investigated effects of environmental change on disease, and effects of disease on ecosystems, using a freshwater zooplankton host and its fungal parasite. This research involved lake surveys, manipulative experiments, and mathematical models. My results indicate that ecosystem characteristics such as habitat structure, nutrient availability, and quality of a host’s resources (here, phytoplankton) can affect the spread of disease. For example, a survey of epidemics in lakes revealed direct and indirect links between habitat structure and epidemic size, where indirect connections were mediated by non-host species. Then, in a mesocosm experiment in a lake, manipulations of habitat structure and nutrient availability interactively affected the spread of disease, and nutrient enrichment increased densities of infected hosts. In a separate laboratory experiment, poor quality resources were shown to decrease parasite transmission rate by altering host foraging behavior. My experimental results also suggest that disease can affect ecosystems through effects on host densities and host traits. In the mesocosm experiment, the parasite indirectly increased abundance of algal resources by decreasing densities of the zooplankton host. Disease in the experimental zooplankton populations also impacted nutrient stoichiometry of algae, which could entail a parasite-mediated shift in food quality for grazers such as the host. Additionally, I showed that infection dramatically reduces host feeding rate, and used a dynamic epidemiological model to illustrate how this parasite-mediated trait change could affect densities of resources and hosts, as well as the spread of disease. I discuss the implications of these ecosystem–disease interactions in light of ongoing changes to habitat and nutrient regimes in freshwater ecosystems.

Benthic diatoms are valuable tools for biological monitoring and paleo-ecological reconstruction of past environmental conditions. This thesis aims at describing size-related properties of benthic diatoms and suggests that data assessment for community analysis can be improved by considering the importance of scale. It investigates which environmental factors structure epilithic diatom communities on the coast of the Gulf of Bothnia and identifies environmental factors correlated with phytobenthic biomass. It also contributes to the floristic knowledge of the Baltic Sea. Diatom species show large variation in size. The responses of large species (≥1000 μm3) in diatom communities to environmental factors are underestimated if solely measured as relative abundance, as is the common practice. However, relative abundance gives the best gradient resolution, as compared to surface area and biovolume, if species are counted separately in two biovolume classes. Small and large species in the same community may respond differently to the same environmental factors. To assess the principal environmental factors structuring diatom communities in the Gulf of Bothnia, 270 quantitative samples were collected from submerged stones. Sampling was carried out in spring in four areas of the Bothnian Bay, characterized by a stable north-south salinity gradient (0.4-3.3 psu), and in three areas of the Bothnian Sea which has a rather uniform salinity of ca. 5 psu. Canonical correspondence analysis (CCA) identified salinity and exposure to wave action as the principal factors structuring the diatom communities of the Bothnian Bay, whereas exposure to wave action was the principal factor in the Bothnian Sea. Measurements of relative ignition loss suggested that the cover of macroalgae, and thereby the higher abundance of epiphytic diatoms in the epilithic samples, was positively correlated with salinity in the Bothnian Bay and with water movement in the Bothnian Sea. Two new brackish water species are described, Navicula sjoersii S. Busse &amp; Snoeijs and N. bossvikensis S. Busse &amp; Snoeijs. The new species are compared with N. perminuta Grunow, a common brackish-water species.

The work in this thesis deals with (1) the effects of woody debris on stream channel morphology and retention of organic material, and (2) the dynamics of woody debris and its relation to riparian forest history and composition. The studied stream reaches are situated in mature, productive forests in the boreal zone of Sweden. Wood variables were important predictors of the frequency of debris dams, pool area, the proportion of pools formed by wood, and variation in the bankfull channel width. Pools formed by woody debris were mainly created by damming and had larger surface areas and residual depths than pools formed by other agents. Stream reaches intersecting old-growth forest (with minor influence of forest management) had coarser and longer woody debris pieces, greater amounts of wood, more debris dams, and wood-formed pools compared to streams surrounded by forests influenced by selective logging. The influence of past forest management on the quality and quantity of woody debris in streams were analyzed by using dendrochrnological methods. Selective loggings and absence of forest fires after 1831 resulted in lower input rates and a gradual replacement of pine by sruce over time. Residence times in stream channels of woody debris (&gt;10 cm in basal diameter) were long and the oldest dated pieces of pine and spruce were over 300 and 100 years, respectively. Dynamics of woody debris were explored by comparing wood volumes and characteristics between stream channels and their riparianforests and between old growth and managed sites. Wood volumes recorded in the stream channels exceeded, but were related to, the volumes found in the riparian forests. Limited input of woody debris by bank cutting and absence of slope processes suggest that recruitment processes of woody debri to stream channels are similar as in riparian forests and slow decay in channels results in greater volumes. The retentiveness of organic material in stream channels was examined by using release and capture experiments in multiple reaces during varying discharges using different sizes of leaf mimics. Sixty eight percent of the variation in retention was explained by a multiple regression model including discharge and leaf mimic siz. Between 44 and 80% of the variation in retention among reaches was explained by channel constraint, gravel coverage, and woody debris variables as the most important. Estimates from a partial least squares (PLS) model suggest an increase in mean transport distances by 22 to 53% in managed forest streams compared to old growth conditions and in a low wood scenario, mean transport distances increased by 38 to 99% with larger increases for higher discharges and larger particle sizes. To regain more pristine conditions of stream channels, management and restoration are needed to increase the amount of woody debris that recreates lost channel structures and increaes the retention of organic material.

The brood-nosed pipefish Syngnathus typhle is a pipefish with reversed sex roles. Males prefer to mate with large and ornamented females and females compete for partners. It has previously been shown that males mate more randomly when water becomes turbid. In the Baltic Sea eutrophication has become a severe problem with turbid waters as one consequence. Turbidity makes visual cues less effective and thus weakens sexual selection in species using vision to discriminate between partners. It also affects mate encounter rates in species using vision to find each other. A lower mate encounter rate means a weakening of sexual selection and that individuals mate more randomly. One way to compensate for lower visibility would be to use olfactory cues instead. In this study I investigated whether S. typhle could use olfactory cues to discriminate between sexes. I found no support that they could use olfactory cues to find a partner.