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A mesocosm experiment was carried out in a Norwegian fjord near Bergen in May 2006, with the main objective being the study of the effects of increasing concentrations of atmospheric CO2 (and associated effects such as increased acidification) on blooms of natural marine coastal plankton. Three mesocosms were bubbled with CO2(g) to achieve a high (~700ppm) CO2 concentration (pH ~7.8) to simulate predicted future conditions as a result of rising atmospheric CO2 concentrations. Another three mesocosms were treated as controls and bubbled with ambient air to represent a near pre-industrial scenario (atmospheric CO2 concentration ~300ppm, surface seawater pH ~8.15). Blooms in the mesocosms were stimulated by the addition of nutrients at a near-Redfield ratio ([N:P] ≈ [16:1]), and scientific measurements and analyses were carried out over the course of the blooms for approximately one month. Of particular interest in this study were the autotrophic plankton. The diversity and activities of these microorganisms under the two treatments was therefore investigated. By designing and using new degenerate primers specifically targeting ‘Green-type’ (Form IA and IB), ‘Red-type’ (Form IC and ID) and Form II RuBisCO, analysis of primary producers was carried out using PCR and either gDNA or cDNA (mRNA) templates from key time points spanning the complete duration of the blooms throughout the mesocosm experiment. Over 1250 novel RuBisCO large subunit sequences have been fully annotated and deposited in the NCBI GenBank® database. These sequences revealed distinct changes in the diversity of primary producers both over the courses of the blooms and between treatments. Particularly striking was the effect of acidification on the community structure of the eukaryotic picoplankton, Prasinophytes. A clade of prasinophytes closely related to Micromonas pusilla showed a distinct preference for the high CO2 conditions; a laboratory-based experiment confirmed the high tolerance of Micromonas pusilla to lower pH. Conversely, a clade related to Bathycoccus prasinos was almost entirely excluded from the high CO2 treatments. Clades of form II RuBisCO-containing dinoflagellates were also abundant throughout the experiment in both treatments. The high similarity of some of these clades to the toxin-producing species Heterocapsa triquetra and Gonyaulax polyedra, and apparent high tolerance of some clades to high CO2 conditions, is perhaps cause for concern in a high CO2 world and demands further research. In parallel with the RubisCO work, new primers were designed that target the gene encoding the Fe protein of nitrogenase (NifH). 82 Bergen genomic nifH sequences have been annotated and submitted to GenBank®. These sequences include those from organisms related to Alpha, Beta, and Gammaproteobacteria, and Cluster II and Cluster III sequences that align most closely with anaerobic Bacteria, Gram positive, and/or sulphur-reducing Bacteria. The biggest surprise, however, was the apparent abundance and significance of a Rhodobacter sphaeroides-like microorganism throughout the duration of the experiment in both treatments. Whilst this clade was unsurprisingly absent in the RuBisCO cDNA libraries, all but two of 128 nifH cDNA clones analysed were identical to the gene from Rhodobacter sphaeroides. This shows that this clade was potentially fixing N2 throughout the entire experiment, even in the presence of combined N added to both sets of mesocosms at the start of the experiment. A group of Rhodobacter sphaeroides-like microorganisms present at Bergen may therefore have been an unexpected source of new N during the experiment and contributed to the maintenance of the mesocosm communities as nutrients became depleted. One organism dominated the autotrophic communities after the blooms in both treatments. Synechococcus spp. Form IA rbcL clones most closely related to the coastal strain Synechococcus sp. strain CC9902 were recovered throughout the experiment but were particularly numerous toward the end of the experiment and dominated the “Green-type” libraries at this time. Initially, rbcL clones from these cyanobacteria were mostly derived from the ambient CO2 mesocosms but were equally distributed between treatments by the end of the experiment. This suggests that cyanobacteria related to strain CC9902 may be less tolerant of elevated CO2 (which was greatest at the beginning rather than the end of the experiment). However, despite the mesocosms being Pi-limited at the end of the experiment, several Synechococcus species (including those related to strain CC9902 and another coastal strain, CC9311) thrived. Following on from this observation, Pi uptake and assimilation mechanisms in a Synechococcus species were investigated in the laboratory. This led to the sequencing and characterisation of a pstS gene from the marine cyanobacterium Synechococcus sp. WH 8103. Unlike conventional pstS, it was discovered that the pstS II gene in this organism is constitutively expressed and unresponsive to or only weakly regulated by Pi supply. The use of PstS/pstS as a marker for P-limitation in natural samples, therefore, should be interpreted with caution.

During a volcanic eruption, the extrusion of lava onto surfaces destroys biological activity creating virgin land surfaces. Through time this new land will be subject to soil formation and colonisation under relatively similar climatic conditions and parent materials. Soils formed from volcanic deposits present a unique opportunity to study microbial community development. Soils at different developmental stages and differing in vegetation cover were selected from four locations on the slopes of Mount Etna, Sicily. Three main research objectives were determined in order to test the hypothesis that the microbial communities from soils at later stages of development would have a greater biomass, be more diverse, be more efficient at utilising carbon sources and recover from an environmental disturbance at a greater rate. A field experiment was conducted to ascertain the long term in situ catabolic abilities of the microbial communities in each soil and to establish the effects of litter mixing on decomposition rate. Litter bags containing either Genista aetnensis (Etnean Broom), Pinus nigra (Corsican Pine) or a mixture of the two were buried at each of the sites and their decomposition monitored over a 2.5 year period. PLFA diversity, community composition and function was assessed for each of the soils. The soils were also subject to a disturbance and the recovery of key community parameters was monitored over a six month period in order to establish each soil community’s resistance and resilience to disturbance. A laboratory experiment was conducted in order to investigate functional diversity and decomposition functions of each soil community using a range of simple and complex substrates. The relationship between PLFA diversity and functional diversity was also investigated. No correlation was found between soil C and N contents, microbial biomass or soil respiration and soil developmental stage and there was no detectable difference in litter bag mass loss between the soil types. No non- additive effects were noted in mixed litters. The more developed soil had a greater PLFA diversity and PLFA biomass however the more developed soil was not more resistant or resilient to disturbance. Developed soils showed greater catabolic diversity compared with less developed soils broadly correlating with PLFA diversity. Despite increased PLFA diversity and functional diversity in the more developed soils, residue decomposition in situ was unaffected. Reduced PLFA diversity and community complexity did not result in reduced function. Soils at different developmental stages had similar catabolic responses and were able to degrade simple and complex substrates to a similar degree. Microbial diversity in soil has the potential to be very high thus resulting in a high rate of functional redundancy i.e. many species within the same community which have the same functional role. It is possible that only a few key functional groups present within the soil community contribute to the main decomposition function within the soil and were able to maintain function during perturbation. Both Etna soils had similar PLFA’s present in similar concentrations and these groups in general were maintained during disturbance. This suggests that total microbial community diversity may not be as important to community function as the presence of key functional groups.

Concentrations of dissolved organic carbon (DOC) measured within water bodies have been increasing on a global scale over the last two decades. Changes in temperature and rainfall have been shown to increase the production and export of DOC from catchments with peat soils in the UK (Freeman et al., 2001). However it is not clear whether increases in DOC concentrations are caused by production increases induced by temperature changes or by a greater incidence of high flows induced by rainfall changes. Increases in both temperature and rainfall have been predicted in Scotland over the next few decades (Kerr et al., 1999) which may further increase current DOC concentrations and exports. The implications of this include both a decrease in water quality and an increase in mobility of metals in upland water bodies. The overall aim of the thesis is to determine if the relationship between dissolved organic carbon (DOC) concentrations and discharge has changed over a 20 year period in small stream catchments in Scotland, in order to better understand the role of hydrology, in driving changes in DOC concentration. To achieve this streams draining two coniferous forest sites and one moorland site were monitored intensively between June 2004 and February 2006. Analysis of the relationship between DOC and discharge, within the catchments, identified the importance of the amount of precipitation falling on the catchment, antecedent precipitation and season, on the concentration of DOC that was measured within the stream. Models were then developed using variables to represent these drivers in terms of both the production (seasonal sine values and 14 day average temperatures) and movement (log of discharge (log Q), days since previous storm event and rising or falling stage) of DOC. In the Ochil Hills catchment, the best predictive model, used 4 hour average discharge and 1 day average 30cm soil temperatures (R2= 0.88). In the Duchray and Elrig catchments, the best predictive models produced used discharge and seasonal sine values; the strength of the model was greater in the Elrig (R2= 0.80) than the Duchray (R2= 0.48) catchment. The strength of the regression models produced highlighted the importance of precipitation in the movement of DOC to the stream and temperature variables representing production in the surrounding catchment. To determine if dissolved organic carbon (DOC) concentrations had changed within the three study catchments, since previous research was conducted at the same sites in the early 1980s and 1990s (Grieve, 1984a; Grieve, 1994), then regression analysis conducted in the previous research was repeated, so changes in the DOC and discharge relationship could be identified. Analysis of the Ochil Hills regression equations identified higher log of discharge and lower temperature and seasonal sine values in the present study (2004-06), when compared to the previous study (1982-83). This suggests that more DOC is now available for movement from the soil, and that the difference between winter and summer DOC production has decreased, potentially because of increasing temperatures. This would explain the limited increase in DOC concentration within the Ochil Hills stream. In the Duchray and Elrig streams, a large increase in DOC was identified at all discharges when all the models produced were compared between the two sampling periods (1989-90 and 2004-06). The increasing trend in DOC concentrations is too large to have been produced by change in temperature alone and it is suggested that the measured reduction in acidic deposition has resulted in the increased DOC concentrations measured in the Duchray and Elrig. The results from this research have identified that concentrations of DOC have increased in Scottish streams over the last 20 years and that the increases in DOC have been induced, potentially by temperature changes in climate. However, changes in temperature are not the only driver of this change as the reduction in acidic deposition is potentially more important, specifically in areas with base poor geology such as the Duchray and Elrig catchments.

Of the organic matter in soils typically < 1% by weight is dissolved in the soil solution (dissolved organic matter; DOM). DOM is a continuum of molecules of various sizes and chemical structures which has largely been operationally defined as the fraction of total organic carbon in an aqueous solution that passes through a 0.45 µm filter. Although only representing a relatively small proportion, it represents the most mobile part of soil organic carbon and is probably enriched with highly labile compounds. DOM acts as a source of nutrients for both soil and aquatic micro-organisms, influences the fate and transport of organic and inorganic contaminants, presents a potential water treatment problem and may indicate the mobilisation rate of key terrestrial carbon stores. The objective of this research was to ascertain some of the biologically relevant characteristics of soil DOM and specifically to determine: (1) the influence of method and time of extraction of DOM from the soil on its biochemical composition and concentration; (2) the dynamics of DOM biodegradation; and, (3) the effects of repeated applications of trace amounts of DOM on the rate of soil carbon mineralization. To examine the influence of method and time of extraction on the composition and concentration of DOM, soil solution was collected from a raised peat bog in Central Scotland using water extraction, field suction lysimetry, and centrifugation techniques on a bimonthly basis over the period of a year (Aug 2003 – Jun 2004). Samples were analysed for dissolved organic carbon (DOC), dissolved organic nitrogen (DON), protein, carbohydrate and amino acid content. For all of the sampled months except June the biochemical composition of DOC varied with extraction method, suggesting the biological, chemical and/or physical influences on DOC production and loss are different within the differently sized soil pores. Water-extractable DOC generally contained the greatest proportion of carbohydrate, protein and/or amino acid of the three extraction methods. Time of extraction had a significant effect on the composition of water- and suction-extracted DOC: the total % carbohydrate + protein + amino acid C was significantly higher in Oct than Dec, Feb and Jun for water-extracted DOC and significantly greater in Dec than Aug, Apr and Jun for suction-extracted DOC. There was no significant change in the total % carbohydrate + protein + amino acid C of centrifuge-extracted DOC during the sampled year. Time of extraction also had a significant effect on the % protein + amino acid N in water- and centrifuge-extracted DON: Oct levels were significantly higher than Feb for water-extracted DON and significantly higher in Aug and Apr for centrifuge-extracted DON. Concentrations of total DOC and total DON were also found to be dependent on time of extraction. DOC concentrations showed a similar pattern of variation over the year for all methods of extraction, with concentrations relatively constant for most of the year, rising in April to reach a peak in Jun. DON concentrations in water- and centrifuge-extracted DON peaked later, in Aug. There were no significant seasonal changes in the concentration of suction-extracted DON. A lack of correlation between DOC and DON concentrations suggested that DOC and DON production and/or loss are under different controls. Laboratory-based incubation experiments were carried out to examine the dynamics of DOC biodegradation. Over a 70 day incubation period at 20oC, the DOM from two types of peat (raised and blanket) and four samples of a mineral soil (calcaric gleysol), each previously exposed to a different management strategy, were found to be comprised of a rapidly degradable pools (half-life: 3 – 8 days) and a more stable pool (half-life: 0.4 to 6 years). For all soil types/treatments, excepting raised peat, the total net loss of DOC from the culture medium was greater than could be accounted for by the process of mineralization alone. A comparison between net loss of DOC and loss of DOC to CO2 and microbial biomass determined by direct microscopy suggested that at least some of the differences between DOC mineralised and net DOC loss were due to microbial assimilation and release. Changes in the microbial biomass during the decomposition process showed proliferation followed by decline over 15 days. The protein and carbohydrate fractions showed a complex pattern of both degradation and production throughout the incubation. The effects of repeated applications of trace amounts of litter-derived DOC on the rate of carbon mineralization over a 35 day period were investigated in a laboratory based incubation experiment. The addition of trace amounts of litter-derived DOC every 7 and 10.5 days appeared to ‘trigger’ microbial activity causing an increase in CO2 mineralisation such that extra C mineralised exceeded DOC additions by more than 2 fold. Acceleration in the rate of extra C mineralised 7 days after the second addition suggested that either the microbial production of enzymes responsible for biodegradation and/or an increase in microbial biomass, are only initiated once a critical concentration of a specific substrate or substrates has been achieved. The addition of ‘DOC + nutrients’ every 3.5 days had no effect on the total rate of mineralization. To date DOC has tended to be operationally defined according to its chemical and physical properties. An understanding of the composition, production and loss of DOC from a biological perspective is essential if we are to be able to predict the effects of environmental change on the rate of mineralization of soil organic matter. This research has shown that the pools of DOC extracted, using three different methods commonly used in current research, are biochemically distinct and respond differently to the seasons. This suggests some degree of compartmentalisation of biological processes within the soil matrix. The observed similarities between the characteristics of the decomposition dynamics of both peatland and agricultural DOC suggests that either there is little difference in substrate quality between the two systems or that the microbial community have adapted in each case to maximise their utilisation of the available substrate. The dependency of the concentration and biochemical composition of DOC on the seasons requires further work to ascertain which biotic and/or abiotic factors are exerting control. Published research has focussed on factors such as temperature, wet/dry cycles, and freeze/thawing. The effect of the frequency of doses of trace amounts of DOC on increasing the rate of soil organic C mineralization, evident from this research, suggests that the interval between periods of rainfall may be relevant. It also emphasises how it can be useful to use knowledge of a biological process as the starting point in determining which factors may be exerting control on DOC production and loss.

This study reports forest structure, regeneration and the soil properties from unlogged and logged forest in the Bulungan Research Forest, Malinau District, East Kalimantan, Indonesia. Four sites were compared by using four 1-ha replicate plots in each of primary forest (PF), 5, 10 and 30-yr old logged forest (LF-5, LF-10, LF- 30). The tree species composition differ among forest types, as it was shown that the mean value of similarity indices for all pairs were 0.215 (for the Jaccard index) and 0.353 (for the Sorensen index). The low values for similarities among forest types were most probably caused by low numbers of species shared between each forest type. Both correlation values, r = 0.023 for Jaccard index and r = 0.031 for Sorensen index, showed no strong correlation between the similarity index (C) and the distance between forest types. This supports the use of a chronosequence approach. A total of 914 tree species with ³ 10 cm dbh were recorded from 223 genera and 65 families. There were no significant differences in mean species numbers (166 – 180/ha) among treatments. Mean density of species was lower in LF-5 and LF-10 (501/ha) than in PF or LF-30 (605/ha and 577/ha); similarly to mean basal area (LF-5, 28.5 m2/ha; LF-10, 32.6 m2/ha) vs. PF (45.8 m2/ha) and LF-30 (46.9 m2/ha). Dead wood on the forest floor was significantly higher in LF-10 (75 m3/ha) than in the other treatments. Seedlings (< 2 cm dbh) of 1,022 species were recorded from 408 genera and 111 families. The mean number of tree seedling species ranged between 170-206; the mean density of seedlings was about two-fold lower in LF-10 (2790/ha) than in the other treatments. Saplings (>2 – 9.9 cm dbh) of 802 species belonged to 241 genera and 65 families. There was a high variability in species richness across treatments (89 – 191/ha), but not in stem numbers. The Dipterocarpaceae family was dominant in all treatments, followed by the Euphorbiaceae. The soils were acidic, low in nutrients and had low to very low fertility. Both primary and logged forest areas are marginal or not suitable for sustained production of plantation crops. Logging caused soil compaction in LF-30. Although in terms of number of species and trees, amount of BA, number of saplings and seedlings LF-30 appeared to have satisfied prescriptions for a second harvest, ecologically the forest is far from mature. The Indonesian Selective Cutting and Replanting (TPTI) system may need to be revised to a 35 – 45 year cycle to ensure long-term forest productivity in terms of not only timber but other goods and ecosystem services, the value of which are never quantified in monetary terms, but can be higher than the timber revenue.