Leaf litter decomposition in lowland tropical forests represents a significant flux of carbon (C) to the atmosphere, and is controlled by both extrinsic site conditions and intrinsic litter traits. However, there is a gap in the understanding about the relative importance of these two factors, and of the role of interactions between them. Global change drivers, such as mean annual precipitation (MAP) change and soil nitrogen (N) fertilisation by deposition, could affect both pathways simultaneously. In order to predict the response of the global C cycle to future change, a further understanding of such interactions is required, and is the focus of this thesis. Using a range of experimental factorial studies, in the field and laboratory, in mature tropical forests in Panama, the relative and interactive effects on decomposition of MAP, soil N and phosphorus (P) availability, litter species identity, and litter N and P status, were determined. Leaf litter species identity was a significant predictor of decomposition across the landscape, whilst soil C:N ratio was more important than MAP. Within species, elevated P concentration and decreased N:P ratio in litter was associated with decreased C mineralisation. Increased soil N availability altered microbial community composition, which increased decomposition of some leaf litter types. The results highlight litter traits as an important driver of decomposition via species identify and intra-species leaf litter chemistry. Also, the implications of decomposer activity and composition for decomposition will depend on litter traits. This thesis contributes valuable research evidence to augment current understanding of the importance of litter traits, and their interactions with decomposers, as a pathway through which global change drivers could affect the C cycle in tropical forests.

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This research is motivated by the need to conserve tropical montane cloud forests (TMCFs) as a biodiversity hotspot threatened by environmental change. A defining feature ofTMCFs is frequent cloud immersion, which also provides moisture to the ecosystem in the dry season. Therefore, TMCFs may be sensitive to any changes in the height or frequency of cloud. The thesis consists of four papers using a combination of field and satellite-based estimations of cloud heights and frequencies with reanalysis data to investigate cloud climatology, trends and variability for a TMCF in SE Peru. The first paper uses satellite-based cloud observations from the International Satellite Cloud Climatology Project (ISCCP) (1983 to 2008), MODIS (Moderate Resolution Imaging Spectroradiometer) (2000 to 2009) and ground-based o~i'rvations to characterise cloud frequency at local and regional scales. The study area is divided into highlands (or puna), eastern slope and lowland zones to investigate spatial variability in the seasonal/diurnal cycles. Greater amplitude annual cycles and an early dry season minimum were found for the puna. For the lowlands, the minimum occurred in the late dry season except in the early morning. The second paper examines differences in interannual variability of cloud frequency between the three zones and its relationship with SSTs. Cloud frequencies are correlated with SSTs areas in the Pacific, Indian Ocean and tropical Atlantic, revealing differences between zones in the SST region of highest correlation, which also varies with season. Composites of cloud frequency, circulation and moisture flux for four combinations of high and low SSTs in the tropical North Atlantic and tropical Pacific suggest that high(low) SST anomalies in these regions are associated with reduced(increased) cloud frequency in all zones in both MAM and SON. Significant decreasing trends are found for the lowlands in January, March and September and in March on the eastern slope. The third uses radiosonde observations from the field site with station data from four elevations and cloud top heights from MODIS to investigate seasonal, diurnal and intra-seasonal variability of atmospheric structure and its relationship with cloud height and frequency. On a seasonal basis the cloud base height varies by approximately 400 m and top height by approximately 4000 m resulting in a minimum relative humidity in September at lower elevations but in June at higher elevations on the slope. Diurnal variability is dominated by daytime upslope and night-time downslope flows. The direction of mid to upper level winds are a dominant feature of intra-seasonal variability and influence inversion frequency, cloud height and frequency in all zones. The final paper compares direct observational methods (photographs, infrared thermometer and disappearance time of the radiosonde), with profile-based methods using relative humidity or temperature thresholds or gradients to estimate the positions of cloud boundaries. Methods to estimate cloud base height using the MODIS Cloud Product were also tested but potential applications were found to be limited. A method is proposed for cloud base height estimation involving consensus estimates from three methods that could be applied on long time scales. 11

The Janzen-Connell (JC) hypothesis is a leading explanation for plant-species diversity in tropical forests. It predicts that host specialist natural enemies drive the disproportionate mortality of con specific juveniles close to adults, particularly when density is high. The survival of heterospecifics is thought to be unaffected because apparent competition is generally weak or absent. Consequently, if the JC effect is sufficiently intense, adults will not be replaced by conspecific individuals and species turnover will be promoted at forest sites, which has the potential to greatly enhance diversity. This thesis first demonstrates experimentally that natural enemies are capable of driving overcompensating density dependence in the seedlings of a tropical tree and that these natural enemies do not generate apparent competition. The potential for these short-term processes to develop into long-term recruitment inhibition is assessed by showing that adults are rarely replaced by con specific individuals, using Barro Colorado Island 50 ha plot datatset. However, self-replacement rates are shown to vary with landscape-scale abundance, adult-tree size and growth form. Finally, the diversity enhancing potential of self-replacement inhibition is measured using a simulation model in which the strength of density dependence is manipulated and the JC mechanism is compared to several alternative mechanisms for enhancing coexistence.

Remotely sensed (spectral) phenological data has often been used to characterise and investigate tropical forest ecosystems. The basic assumptions, linking real (biological) and remotely sensed (spectral) phenology, have however rarely been scrutinised and little empirical information from synchronous datasets exists.;This research selected three tropical vegetation communities; each characterised by a different climate, biological phenology and each hypothesised to exhibit a differing spectral phenology. An extensive verification campaign was then initiated to collect phenological data from all three of these sites for an entire phenological cycle. The verification dataset comprised; forest structural parameters, meteorological measurements, litterfall weights, phenological observations (of leaf flushing, senescence and abscission), quantifications of canopy openness and LAI (using hemispherical photography and Ceptometry) and overpass-synchronous radiometry readings.;Large area (1 km2), remotely sensed spectral data was then acquired, for all sites, from the NOAA-14 AVHRR and ERS-2 ATSR-2 satellite sensor systems. An evaluation of the biological significance of the spectral phenological data as then undertaken using two basic methodologies. First, the ground verification data were compared to several commonly used spectral vegetation indices. Next, textural changes, in the spectral landscape, attributed to each verification site were assessed. At two of the monitored sites, spectral phenology was shown to have a strong physiological basis at the scale of the vegetation community. This was attributed to, the pronounced seasonality in the climate at these locations, and, the relative structural simplicity of the vegetation formations. At the third site (a structurally more complex, seasonally-inundated tropical forest) the association between biological and spectral phenology was less conclusive. Clearly further work is required before the scientific community can be certain that all temporal trends, derived from 1km spatial resolution image data, are providing accurate insights into the biological processes, of humid tropical forests, but in general the association between spectral and biological phenology is a strong one.

Spatial patterns of forest trees, stand level effects of cyclones, and factors affecting mortality and growth of individual trees were investigated in 20 experimental plots (0.5 ha) in North Queensland tropical rain forests, Australia. Cyclone disturbance has been recorded in individual plots for 20 times since establishment in 1971. Spatial point patterns of trees were mapped, and pair correlation and mark correlation function were used to investigate relationships between the trees. Effects of cyclones on stand level properties of the forests (total basal area, stem densities, stem size inequality, species diversity, recruitment, mortality) were estimated using generalised additive modelling. Factors affecting individual tree mortality and growth were analysed in generalised mixed effects modelling. The spatial pattern analysis showed minor changes of tree density and tree death in the forest spatial patterns following cyclones. The models revealed that the forest properties were changed significantly. Cyclones decreasing total basal area and increased tree mortality rates and number of abundant species. Higher mortality rates are likely influenced by individual tree characteristics of low wood density, negative growth rates and belonging to particular sets of families. Factors that increase growth rates are include higher crowding effects of tree density, cyclone occurrence, crowding effects by smaller trees, and trees of some families. Slower growth rates are likely influenced by higher wood density, higher surrounding basal area of competing trees and in certain families. From this research, evidence has found for cyclones to be a factor increasing stand level mortality rates but not individual tree mortality. The dynamics from individual trees in mortality and growth, forest spatial patterns and stand level properties has characterised the tropical rain forests of North Queensland in facing frequent cyclone disturbances.

Amazonia contains the largest expanse of tropical forest in the world and is globally significant as a store of carbon, a regulator of climate and an area of high species diversity. The ability of the Amazonian forests to maintain these important ecological functions is however, increasingly under question in light of recent predictions of climate change. There is currently significant uncertainty in model predictions of how Amazonian forests will respond to predicted future climate change. This thesis reports the finding of two field studies, targeted at understanding the responses of two tropical forest carbon fluxes which are poorly simulated in vegetation models, and two modelling studies, which aim to better quantify uncertainty on model predictions of the effects of current and future climate change on the ecological function of Amazonian forests. The responses of forests to varying magnitudes of seasonal changes in climate which occur across Amazonia can give an important insight into the sensitivity of these forests to climate perturbations and changes. Testing the sensitivity of an Amazonian forest in Tambopata, Peru, to seasonal variations in precipitation and temperature, I find that the stem diameter growth of tropical trees is more sensitive to water availability than temperature changes. The vulnerability of trees to reduced soil water varied between tree classes with different functional traits, including wood density, tree height, tree diameter and tree growth rate. Similarly, I find that the respiration flux from tropical dead wood, at a second site in French Guiana, is highly sensitive to variations in water content. I show that these variations in respiration fluxes can be modelled successfully using seasonal variations in soil water content. To date there are few studies which have comprehensively tested vegetation models using ecological data from Amazon forests. Using data assimilation and nine sources of ecological data I estimate the certainty with which we can parameterise a carbon cycle model to represent the effects of a strong dry season on tropical forests. Using this technique I find, that the carbon balance of Amazonian forests can be very sensitive to reductions in water availability, and that these seasonal changes need to be accurately simulated across models to correctly predict annual carbon budgets. The variability in model responses caused by differences in the way processes are structured and parameterised in vegetation models requires better quantification. Using a model inter-comparison I demonstrate that the relative sensitivity of modelled climate-vegetation feedbacks to changes in ambient air temperature and precipitation is highly variable. I find that although the models showed similar directional responses at both the leaf and canopy scale some models showed a greater sensitivity to temperature and others to drought. I therefore demonstrate the need for greater constraint on modelled responses of Amazonian forests to changes in temperature and precipitation. The impact of climate change on Amazonian forests is an important global issue, yet our knowledge is reliant on our ability to understand the uncertainties on our predictions. Using field data to evaluate and to develop model predictions is a valuable way to reduce the uncertainty associated with modelling future change. This thesis presents an investigation of how tropical forests respond to changes in climate and with what certainty we can model these changes in order to predict the response of Amazon forests to predicted future climate change.

Tropical forests have existed for up to one hundred million years, and today provide many ecosystem services vital for human well-being. They also harbour great biodiversity, which, in addition to its intrinsic value, plays a key role in the functioning of these ecosystems. Despite their local to global significance, there are still many knowledge gaps concerning the dynamic processes that govern the functioning of tropical forests. Rapid rates of deforestation and landscape conversion, predominantly for logging and industrial agriculture, are limiting the time and opportunity available to collect the information needed to fill these gaps. This research aims to shed light on the long-term ecological functioning of tropical forests, specifically investigating the history of disturbance in these ecosystems and the response of forest vegetation to past perturbations. The carbon-rich tropical peat swamp forests found along the coast of Sarawak, Malaysian Borneo, are a central focus of this study. For these forests in particular, a large deficit of knowledge surrounding their history and unique ecological functioning is coupled with some of the highest conversion rates of all tropical forest ecosystems across the world. In this thesis, palaeoecological data has been used to reconstruct temporal variability in forest vegetation coincident with external perturbations in order to identify changes in the resilience of these ecosystems through time, via indicators such as slowing rates of recovery and reduced regeneration of forest vegetation. Results suggest that tropical forest ecosystems have, for the most part, shown resilience to natural disturbances in the past, ranging from instantaneous localised tree-fall to longer-term regional climatic change; but that recent anthropogenic disturbances, of novel forms and greater intensities, are jeopardizing the potential for forest recovery and thus compromising ecosystem resilience. These findings enhance our understanding of the ecology of tropical peat swamp forests, and tropical forests more broadly. They also provide a context for contemporary tropical forest management, allowing for predictions on future responses to disturbance and enabling more ecologically sustainable landscape planning.

Les forêts tropicales constituent le principal réservoir de biodiversité et de carbone (C). Cependant, la plupart des forêts tropicales, en particulier les forêts de Bornéo en Asie du Sud-Est, subissent une pression intense et sont menacées par des activités anthropiques telles que l'exploitation forestière, l'industrie minière l’agriculture et la conversion en plantations industrielles. En 2010, la superficie des forêts de production de Bornéo était de 26,8 millions d’ha (environ 36% de la superficie totale de l’île, dont 18 millions ha (environ 24%) déjà exploités. Par conséquent, les forêts de production occupent donc une place importante à Bornéo et jouent un rôle essentiel dans la compensation des biens fournis et la maintenance des services écosystémiques, tels que la conservation du C et de la biodiversité.L’exploitation sélective réduit la biomasse aérienne et souterraine par l’élimination de quelques grands arbres, et augmente les stocks de bois mort par des dommages collatéraux. En créant des trouées dans la canopée, le microclimat dans les sous-étages et au sol change localement et accélèrent la décomposition de la litière et de la matière organique. L'importance des dégâts, de l'ouverture de la canopée et de la rapidité du rétablissement du C s'est avéré principalement liée à l'intensité de l'exploitation forestière. Cependant, les évaluations empiriques de l'effet à long terme de l'intensité de l'exploitation forestière sur l'équilibre du C dans les forêts de production restent rares.La présente thèse se concentre principalement sur l'évaluation de l'effet à long terme de l'intensité de l'exploitation forestière sur la séquestration de carbone dans une forêt à Diptérocarpées de Nord Bornéo (District de Malinau, Kalimantan Nord) exploitée en 1999/2000. Cinq principaux réservoirs de C, à savoir le C aérien dans les arbres vivants (AGC), le C souterrain dans les arbres vivants (BGC), le bois mort, la litière et le C organique du sol (SOC) ont été estimés le long d’un gradient d'intensité d'exploitation (0-57% de la biomasse perdue).Nos résultats ont montré que les stocks totaux de C, 16 ans après l'exploitation, variaient de 218 à 554 Mg C ha-1 avec une moyenne de 314 Mg C ha-1. Une différence de 95 Mg C ha-1 a été observée entre une faible intensité d'exploitation forestière (<2,1% de la biomasse initiale perdue) et une intensité d'exploitation élevée (>19%). La plus grande partie du C (environ 77%) était présente dans les arbres vivants, suivie par les stocks du sol (15%), les stocks de bois mort (6%) et une fraction mineure des stocks de litière (1%). L'empreinte de l'intensité de l'exploitation forestière était encore détectable 16 ans après l'exploitation et a été le principal facteur expliquant la réduction des AGC>20, BGC>20, du bois mort et des stocks de C et une augmentation du bois mort. L'intensité de l'exploitation expliquait à elle seule 61%, 63%, 38% et 48% des variations des AGC>20, BGC>20, du bois mort et des stocks de C totaux, respectivement. L'intensité de l'abattage a également réduit considérablement les stocks de SOC dans la couche supérieure de 30 cm. Pour l'ensemble des stocks de SOC (0-100 cm), l'influence de l'intensité de l'exploitation était encore perceptible, en conjonction avec d'autres variables.Nos résultats quantifient l'effet à long terme de l'exploitation forestière sur les stocks de C forestier, en particulier sur les AGC et les bois morts. L'intensité élevée de l'exploitation forestière (réduction de 50% de la biomasse initiale) a réduit les stocks totaux de C de 27%. La récupération de l'AGC était plus faible dans les parcelles d'intensité d'exploitation forestière élevée, ce qui suggère une résilience plus faible de la forêt à l'exploitation forestière. Par conséquent, une intensité d'exploitation forestière inférieure à 20%, devrait être envisagé afin de limiter l'effet à long terme sur les AGC et le bois mort. / Tropical forests are a major reservoir of biodiversity and carbon (C), playing a pivotal role in global ecosystem function and climate regulation. However, most of the tropical forests, especially Bornean forests in Southeast Asia, are under intense pressure and threatened by anthropogenic activities such as logging, mining industry, agriculture and conversion to industrial plantation. In 2010, the area of production forests in Borneo was 26.8 million ha (approx. 36% of the total land area of Borneo) including 18 million ha (approx. 24%) of logged forests. Production forests are thus emerging as a dominant land-use, playing a crucial role in trading-off provision of goods and maintenance of ecosystem services, such as C and biodiversity retention.Selective logging is known to reduce both above- and below-ground biomass through the removal of a few large trees, while increasing deadwood stocks through collateral damages. By creating large gaps in the canopy, microclimates in the understory and on the forest floor change locally speeding up the decomposition of litter and organic matter. The extent of incidental damages, canopy openness, as well as the speed of C recovery, was shown to be primarily related to logging intensity. However, empirical evaluations of the long-term effect of logging intensity on C balance in production forests remain rare.The present thesis aims to assess the long-term effect of logging intensity on C sequestration in a north Bornean Dipterocarp forests (Malinau District, North Kalimantan) logged in 1999/2000. Five main C pools, namely above-ground (AGC) and below-ground (BGC) carbon in living trees, deadwood, litter, and soil organic carbon (SOC) were estimated along a logging intensity gradient (ranging from 0 to 57% of initial biomass removed).Our result showed that total C stocks 16 years after logging, ranged from 218-554 Mg C ha-1 with an average of 314 Mg C ha-1. A difference of 95 Mg C ha-1 was found between low logging intensity (<2.1% of initial biomass lost) and high logging intensity (>19%). Most C (approx. 77%) was found in living trees, followed by soil (15%), deadwood (6%), and a minor fraction in litter (1%). The imprint of logging intensity was still detectable 16 years after logging, and logging intensity thus was the main driver explaining the reduction of AGC>20, BGC>20, deadwood, and total C stocks and an increase in deadwood. Solely, logging intensity explained 61%, 63%, 38%, and 48% of variations of AGC>20, BGC>20, deadwood, and total C stocks, respectively. Logging intensity also significantly reduced SOC stocks in the upper 30 cm layer. For total SOC stocks (0-100 cm), the negative influence of logging intensity was still perceptible, being significant in conjunction with other variables.Our results quantify the long-term effect of logging on forest C stocks, especially on AGC and deadwood. High logging intensity (50% reduction of initial biomass) reduced total C stocks by 27%. AGC recovery was lower in high logging intensity plots, suggesting lowered forest resilience to logging. Our study showed that maintaining logging intensity, below 20% of the initial biomass, limit the long-term effect of logging on AGC and deadwood stocks.