Thesis: Ph. D., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 213-240). / Life is ubiquitous in the environment and an important mediator of Earth's carbon cycle, but quantifying the contribution of microbial biomass and its metabolic fluxes is difficult, especially in spatially and temporally-remote environments. Microbes leave behind an often scarce, unidentifiable, or nonspecific record on geologic timescales. This thesis develops and employs novel geochemical and genetic approaches to illuminate diagnostic signals of microbial metabolisms. Field studies, laboratory cultures, and computational models explain how methanogens produce unique nonequilibrium methane clumped isotopologue (1 3CH3D ) signals that do not correspond to growth temperature. Instead, [Delta]13CH3D values may be driven by enzymatic reactions common to all methanogens, the C-H bond inherited from substrate precursors including acetate and methanol, isotope exchange, or environmental processes such as methane oxidation. The phylogenetic relationship between substrate-specific methyl-corrinoid proteins provides insight into the evolutionary history of methylotrophic methanogenesis. The distribution of corrinoid proteins in methanogens and related bacteria suggests that these substrate-specific proteins evolved via a complex history of horizontal gene transfer (HGT), gene duplication, and loss. Furthermore, this work identifies a previously unrecognized HGT involving chitinases (ChiC/D) distributed between fungi and bacteria (~650 Ma). This HGT is used to tether fossil-calibrated ages from within fungi to bacterial lineages. Molecular clock analyses show that multiple clades of bacteria likely acquired chitinase homologs via HGT during the late Neoproterozoic into the early Paleozoic. These results also show that, following these HGT events, recipient terrestrial bacterial clades diversified ~400-500 Ma, consistent with established timescales of arthropod and plant terrestrialization. Divergence time estimates for bacterial lineages are broadly consistent with the dispersal of chitinase genes throughout the microbial world in direct response to the evolution and expansion of detrital-chitin producing groups including arthropods. These chitinases may aid in dating microbial lineages over geologic time and provide insight into an ecological shift from marine to terrestrial systems in the Proterozoic and Phanerozoic eons. Taken together, this thesis may be used to improve assessments of microbial activity in remote environments, and to enhance our understanding of the evolution of Earth's carbon cycle. / by Danielle S. Gruen / Ph. D.

Lakes play a major role in the global carbon (C) cycle, despite making up a small area of earth’s surface. Lakes receive, transport and process sizable amounts of C, emitting a substantial amount of the greenhouse gases, carbon dioxide (CO2) and methane (CH4), into the atmosphere. Ice-covered lakes are particularly sensitive to climate change, as future reductions to the duration of lake ice cover will have profound effects on the biogeochemical cycling of C in lakes. It is still largely unknown how reduced ice cover duration will affect CO2 and CH4 emissions from ice-covered lakes. Thus, the primary aim of this thesis was to fill this knowledge gap by monitoring the spatial and temporal dynamics of CO2 and CH4 in ice-covered lakes. The results of this thesis demonstrate that below ice CO2 and CH4 were spatially and temporally variable. Nutrients were strongly linked to below ice CO2 and CH4 oxidation variations across lakes. In addition, below ice CO2 was generally highest in small shallow lakes, and in bottom waters. Whilst below ice CH4 was elevated in surface waters near where bubbles from anoxic lake sediment were trapped. During the ice-cover period, CO2 accumulation below ice was not linear, and at ice-melt incomplete mixing of lake waters resulted in a continued CO2 storage in bottom waters. Further, CO2 transported from the catchment and bottom waters contributed to high CO2 emissions. The collective findings of this thesis indicate that CO2 and CH4 emissions from ice-covered lakes will likely increase in the future. The strong relationship between nutrients and C processes below ice, imply that future changes to nutrient fluxes within lakes will influence the biogeochemical cycling of C in lakes. Since catchment and lake sediment C fluxes play a considerable role in below ice CO2 and CH4 dynamics, changes to hydrology and thermal stability of lakes will undoubtedly alter CO2 and CH4 emissions. Nevertheless, ice-covered lakes constitute a significant component of the global C cycle, and as such, should be carefully monitored and accounted for when addressing the impacts of global climate change.

Inland waters receive substantial amounts of organic carbon from adjacent watersheds. Only about half of the carbon exported from inland waters reaches the oceans, while the remainder is lost en route. This thesis identifies flocculation as an important and significant fate of carbon in the boreal landscape. Flocculation reallocates organic carbon from the dissolved state into particles which are prone to settle. Thus, flocculation relocates organic carbon from the water column to the sediment. The dissolved organic carbon (DOC), mainly originating from terrestrial sources, in a set of Swedish lakes was found to determine the extent of sedimentation of particulate organic carbon. A major fraction of the settling particles were of allochthonous origin. This implies that allochthonous DOC was the precursor of the settling matter in these lakes. The gross sedimentation was of the same magnitude as the evasion of carbon dioxide to the atmosphere. Sunlight, especially in the photosynthetically active region, stimulated flocculation of DOC. The effect of light appeared to involve a direct photochemical reaction. Iron was involved in the flocculation but it could not be unravelled whether the iron catalyzes the flocculation or just co-precipitates with the settling matter. Microbial activity was identified as the main regulator of the flocculation rates. Accordingly, alteration of temperature, oxygen concentration and pH did not affect flocculation only indirectly, via their effects on microbial metabolism. A comparison of fluorescence characteristics of organic matter collected in sediment trap and in the sediment surface layer revealed that autochthonous organic carbon was preferentially lost in the sediments while allochthonous matter increased. The recalcitrant nature of the flocculated matter could favour sequestration of this matter in the lake sediment. Hence, the lakes will act as sinks of organic carbon due to a slower mineralization of the flocculated matter in the sediments.

Thesis (MScAgric)--University of Stellenbosch, 2002. / ENGLISH ABSTRACT: Cellulose, a ~-1,4-linked polymer of glucose, is the most abundant renewable carbon source on earth. It is well established that efficient degradation of cellulose requires the synergistic action of three categories of enzymes: endoglucanases (EG), cellobiohydrolases (CBH) and ~-glucosidases. ~-Glucosidases are a heterogenous group of enzymes that display broad substrate specificity with respect to hydrolysis of cellobiose and different aryl- and alkyl-ê-u-glucosides. They not only catalyse the final step in the saccharification of cellulose, but also stimulate the extent of cellulose hydrolysis by relieving the cellobiose mediated inhibition of EG and CBH. The ability to utilize cellobiose is widespread among gram-negative, gram-positive, and Archaea bacterial genera. Cellobiose phosphoenolpyruvate- dependent phosphotransferase systems (PTS) have been reported in various bacteria, including: Bacillus species. In this study, we have used a cellobiose chromophore analog, p-nitrophenyl- ~-D-glucopyranoside (pNPG), to screen a Bacillus pumilus genomic library for cellobiose utilization genes that are functionally expressed in Escherichia coli. Cloning and sequencing of the most active clone with subsequent sequence analysis allowed the identification of four adjacent open reading frames. An operon of four genes (celBACH), encoding a cellobiose phosphotransferase system (PTS): enzyme II (encoded by celB, celA and celC) and a ó-phospho-f-glucosidase (encoded by celH) was derived from the sequence data. The amino acid sequence of the celH gene displayed good homology with ~-glucosidases from Bacillus halodurans (74.2%), B. subtilis (72.7%) and Listeria monocytogenes (62.2%). .As implied by sequence alignments, the celH gene product belongs to family 1 of the glycosyl hydrolases, which employ a retaining mechanism of enzymatic bond hydrolysis. In vivo PTS activity assays concluded that the optimal temperature and pH at which the recombinant E. coli strain hydrolysed pNPG were pH 7.5 and 45°C, respectively. Unfortunately, at 45°C the CelBACH-associated activity of the recombinant strain was only stable for 20 minutes. It was also shown that the enzyme complex is very sensitive to glucose. Since active growing cells metabolise glucose very rapidly this feature is not a significant problem. Constitutive expression of the B. pumilus celBACH genes in E. coli enabled the host to efficiently metabolise cellobiose as a carbon source. However, cellobiose utilization was only achievable in the presence ofO.01% glucose. This phenomenon could be explained by the critical role of phosphoenolpyruvate (PEP) as the phosphate donor in PTS-mediated transport. Glucose supplementation induced the glycolytic pathway and subsequently the availability of PEP. Furthermore, it could be concluded that the general PTS components . (enzyme I and HPr) of E. coli must have complemented the CelBACH system from B. pumilus to allow functionality of the celBACH operon, in the recombinant E. coli host. / AFRIKAANSE OPSOMMING: Sellulose (' n polimeer van p-l,4-gekoppelde glukose) is die volopste bron van hernubare koostof in die natuur. Effektiewe afbraak van sellulose word deur die sinnergistiese werking van drie ensiernklasse bewerkstellig: endoglukanases (EG), sellobiohidrolases (CBH) en P-glukosidases. p-Glukosidases behoort tot 'n heterogene groep ensieme met 'n wye substraatspesifisiteit m.b.t. sellobiose en verskeie ariel- and alkiel-ê-n-glukosidiesc verbindings. Alhoewel hierdie ensieme primêr as kataliste vir die omskakeling van sellulose afbraak-produkte funksioneer, stimuleer hulle ook die mate waartoe sellulose hidroliese plaasvind deur eindprodukinhibisie van EG en CBH op te hef. Sellobiose word algemeen deur verskeie genera van die gram-negatiewe, gram-positiewe en Archae bakterieë gemetaboliseer. Die sellobiose-spesifieke fosfoenolpirovaatfosfotransportsisteem (PTS) is reeds is in verskeie bakterië, insluitende die Bacillus spesies, beskryf. In hierdie studie word die sifting van 'n Bacillus pumilus genoombiblioteek m.b.V. 'n chromofoor analoog van sellobiose, p-nitrofeniel-p-o-glukopiranosied (pNPG), vir die teenwoordigheid van gene wat moontlike sellobiose-benutting in Escherichia coli kan bewerkstellig, beskryf. Die DNA-volgorde van die mees aktiewe kloon is bepaal en daaropvolgende analiese van die DNA-volgorde het vier aangrensende oopleesrame geïdentifiseer. 'n Operon (celBACH), bestaande uit vier gene, wat onderskeidelik vir die ensiem II (gekodeer deur celB, celA en celC) en fosfo-B-glukosidase (gekodeer deur celH) van die sellobiose-spesifieke PTS van B. pumilus kodeer, is vanaf die DNA-volgorde afgelei. Die aminosuuropeenvolging van die celH-geen het goeie homologie met P-glukosidases van Bacillus halodurans (74.2%), B. subtilis (72.7%) en Listeria monocytogenes (62.2%) getoon. Belyning van die DNA-volgordes het aangedui dat die celH geenproduk saam met die familie 1 glikosielhidrolases gegroepeer kan word. Hierdie familie gebruik 'n hidrolitiese meganisme waartydens die stoigiometriese posisie van die anomeriese koolstof behou word. PTS-aktiwiteit van die rekombinante E. coli ras, wat die celBACH gene uitdruk, is in vivo bepaal. Die optimale temperatuur en pH waarby die rekombinante ras pNPG hidroliseer, is onderskeidelik pH 7.5 en 45°C. Alhoewel die ensiernkompleks baie sensitief is vir glukose, is dit nie 'n wesenlike probleem nie, omdat aktief groeiende E. coli selle glukose teen 'n baie vinnige tempo benut. Die celBACH operon het onder beheer van 'n konstitiewe promotor in E coli die rekombinante gasheer in staat gestelom sellobiose as 'n koolstofbron te benut. Die benutting van sellobiose word egter aan die teenwoordigheid van 'n lae konsentrasie glukose (0.01 %) gekoppel. Hierdie verskynsel dui op die kritiese rol van fosfoenolpirovaat (PEP) as die fosfaatdonor gedurende PTS-gebaseerde transport. Glukose speel waarskynlik 'n rol in die indusering van glikoliese, en sodoende die produksie van PEP as tussenproduk. Verder kan afgelei word dat die algemene PTS komponente (ensiem I en HPr) van E. coli die B. pumilis CelBACH-sisteem komplementeer en derhalwe funksionering van die celBACH operon in E. coli toelaat.

A comprehensive theory explaining the relationship between periodic variations in the Earths orbital parameters and the response of the climate system remains elusive. One of the key challenges is that of the Mid-Pleistocene Transition (MPT), during which the dominant mode of glacial/interglacial climatic variability shifted without any corresponding change in the mode of orbital forcing. Subtropical climate on orbital time-scales is sensitive to variability in both the low-latitude ocean/atmosphere circulation regime and the global carbon-cycle (through its effect on atmospheric greenhouse gas levels), both of which may have played a role in the shift in mode of global climate response to orbital forcing during the MPT. This thesis presents a series of multi-proxy (foraminiferal stable isotope and trace-metal) paleoceanographic reconstructions from the subtropical southwest Pacific, as seen in marine sediment core MD06-3018, from 2470m water depth and 23ºS in the New Caledonia Trough, southern Coral Sea. The core age-model, based upon magnetic stratigraphy and orbital tuning, yields a mean sedimentation rate at the site of 20mm/ka and a core-bottom age of 1600ka. The MD06-3018 reconstruction of New Caledonia Trough deep water chemistry, based on benthic 13C measurements, shows that the spatial chemistry gradient within the Southern Ocean between deep waters entering the Tasman Sea and the open Pacific was greater during glacial (relative to interglacial) stages over at least the past 1100ka. This gradient was, however, generally reduced on the >100kyr time-scale across the MPT, consistent with it being a period of reduced deep water ventilation in both hemispheres. The MD06-3018 Mg/Ca-derived reconstruction of subtropical southwest Pacific Sea Surface Temperature (SST) shows glacial/interglacial variability of 2-3ºC but no significant trends on the >100kyr time-scale over the duration of the record. An estimate of the uncertainty associated with the SST reconstruction demonstrates that no significant changes in reconstructed southern Coral Sea mean-annual SST can be identified between interglacial stages across the MPT. It is, therefore, unlikely that regional climatic change constituted the main cause for the observed middle Pleistocene expansion of coral reef systems. The >100kyr time-scale stability of southern Coral Sea SST means that the position of the southern boundary of the Pacific warm pool has also been stable over at least the past 1500ka. Comparison with other low-latitude Pacific reconstructions shows that the early Pleistocene warm pool was consequently more hemispherically asymmetric than its present configuration, with the latter being established by ~1000ka and implying significant changes in meridional atmospheric heat and moisture fluxes prior to the MPT. On orbital time-scales, the SST reconstruction shows a clear shift from dominant 40kyr to 100kyr modes of variability over the MPT, although significant 40kyr structure is also retained into the middle/late Pleistocene. In contrast, reconstructed hydrological cycle variability (based on coupled 18O-Mg/Ca measurements) shows only limited coherence with the obliquity cycle and a stronger relationship with the precession cycle. The decoupling of the reconstructed subtropical SST and hydrological cycle responses places constraints on the extent of orbitally paced fluctuations in the low-latitude ocean/atmosphere system. Instead, comparison of the MD06-3018 SST reconstruction with others from across the lowlatitude Pacific supports a dominant role for greenhouse gas forcing in low-latitude western Pacific glacial/interglacial SST variability across the Pleistocene. The subtropical multi-proxy climate reconstructions presented here show that the timing and sense of long-term (>100kyr time-scale) changes in the low-latitude ocean/atmosphere circulation regime are consistent with that system having been important in the expansion of northern hemisphere ice-volume during the early part of the MPT. However, the subtropical reconstructions also suggest that neither the low-latitude ocean/atmosphere circulation system nor the global carbon-cycle underwent a fundamental change in mode of response to orbital forcing during the transition. Instead, the origin of the 100kyr glacial/interglacial mode was most likely related to thresholds in the dynamics of the expanding northern hemisphere icesheets, leading in turn to the existence of significant inter-hemispheric asymmetry in the orbital time-scale climate response over the middle/late Pleistocene. Summary for Non-Specialists. Over the past five million years of its history, the Earths climate has undergone a series of regular, or nearly regular, fluctuations between warmer and colder states. These fluctuations take tens to hundreds of thousands of years to occur and are known as the ‘glacial/interglacial cycles’ on account of the associated changes in ice-sheet extent in the high-latitudes. The origin of these cycles is widely held to be the regular variations in form of the Earths orbit around the sun. In spite of decades of research, however, no complete ‘orbital theory of climate’ exists, mainly because the patterns of past climate variability, as reconstructed using ‘proxies’ for variables such as surface temperature, is much more complex than that of the orbital variations themselves. It follows that processes within the Earth system, especially those associated with large ice-sheets, the carbon-cycle and the ocean circulation system, act to substantially modify the climate response to the orbital variations. Over the past ten years, new observations from both ice-cores and low-latitude marine sediment cores have suggested that the dominant system(s) involved in setting the Earths response to the orbital variations may potentially be the carboncycle and/or the low-latitude ocean/atmosphere circulation regime rather than highlatitude ice-sheet dynamics, as was generally supposed previously. If this new view is correct, it has profound implications for the general sensitivity of the climate to the carbon-cycle on a range of time-scales - making its evaluation a scientific objective of considerable current importance. This thesis presents a series of reconstructions of aspects of climate and carbon-cycle variability for the subtropical southwest Pacific, as based on proxy measurements in a marine sediment core than spans the past 1,600,000 years at around 5000 year resolution. The key focus is on an interval called the ‘Mid- Pleistocene Transition’, during which time the mode of glacial/interglacial variability changed, indicating a fundamental change in one or more aspects of the response to the orbital forcing. The study site is well placed to investigate variability in both the carbon-cycle and low-latitude ocean circulation over the climatic transition as it lies between the Southern Ocean, a key source of carbon-cycle variability and the equatorial Pacific, where the modern El-Niño system arises. By characterizing variability in these systems, the potential role played by both systems in causing the change in mode of glacial/interglacial variability can be evaluated. The key findings of the thesis are that; firstly, changes in the long-term state of the low-latitude ocean circulation system may well have been important for the expansion of northern hemisphere ice-sheets during the early part of the Mid- Pleistocene Transition. Secondly, it provides further support for a close connection between variability in the carbon-cycle and low-latitude climate on orbital timescales but suggests that there is no clear evidence for either system undergoing a fundamental change in sensitivity to the orbital forcing during the transition.

There is much confidence in the global temperature change and its attribution to human activities. Global climate models have attained unprecedented complexity in representing the climate system and its response to external forcings. However, climate prediction remains a serious challenge and carries large uncertainty, particularly when the scale of interest becomes small. With the increasing interest in regional impact studies for decision-making, one of the urgent tasks is to make a systematic, quantitative evaluation of the expected skill of climate models over a range of spatiotemporal scales. The first part of this dissertation was devoted to this task, with focus on the predictive skill in the linear trend of surface air temperature. By evaluating the hindcasts for the last 120 year period in the form of deterministic and probabilistic predictions, it was found that the hindcasts can reproduce broad-scale changes in the surface air temperature, showing reliable skill at spatial scales larger than or equal to a few thousand kilometers (30° x 30°) and at temporal scales of 30 years or longer. However, their skill remains limited at smaller spatiotemporal scales, where we saw no significant improvement over climatology or a random guess. Over longer temporal scales, the feedbacks from the carbon cycle to atmospheric CO₂ concentration become important. Therefore the rest of the dissertation attempts to find key processes in the climate-carbon cycle feedback using one of the leading land-climate models, the National Center for Atmospheric Research Community Land Model. Evaluation of site-level simulations using field observations from the Amazon forest revealed that the current formulation for drought-related mortality, which lacks the ecophysiological link between short- and long-term drought stress, prevent the model from simulating realistic forest response. Global simulations showed that such dynamics of vegetation strongly influences the control of the nitrogen cycle on vegetation productivity, which then alters the sensitivity of the terrestrial biosphere to surface air temperature. This implies that if the state of the terrestrial biosphere is inconsistent with the simulated climate, either biased or prescribed, then its feedback to anthropogenic forcing could be also inconsistent.

Current estimates of terrestrial carbon (C) fluxes overlook explicit hydrological controls. In this research project, a spatially explicit hydro-ecological model, BEPS-TerrainLab V2.0 was further developed to improve our understanding of the non-linearities associated with various hydro-ecological processes. A modeling study was conducted in a humid boreal ecosystem in north central Quebec, Canada. The sizes and nature of various ecosystem-C-pools were comprehensively reconstructed under a climate change and disturbance scenario prior to simulation in order to ensure realistic biogeochemical modeling. Further, several ecosystem processes were simulated and validated using field measurements for two years. A sensitivity analysis was also performed. After gaining confidence in the model’s ability to simulate various hydrologically controlled ecophysiological and biogeochemical processes and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are currently used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered 2) Implicit, where calculations were based on a bucket-modeling approach 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). From these results it was clear that lateral water flow does play a significant role in the net terrestrial C distribution and it was discovered that non-explicit forms of hydrological representations underestimate the sizes of terrestrial C-sources rather than C-sinks. The scientific implication of this work demonstrates that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological processes due to large topographic variations of the Earth’s surface.

The Amazon rain forest plays an important role in regional and global biogeochemical cycling, but the region may undergo an increase in the frequency and severity of drought conditions driven by global climate change, regional deforestation and fire. The effects of this drought on carbon cycling in the Amazon, particularly below-ground, are potentially large but remain poorly understood. This thesis examines the impacts of seasonal and longer-term drought upon ecosystem carbon allocation and cycling at an Amazon rain forest site with a particular focus upon below-ground processes. Measurements are made at three one-hectare forest plots with contrasting soil type and vegetation structure, to observe responses across a range of Amazon primary forest types. A fourth plot is subjected to partial rainfall exclusion to permit measurement of forest responses to a wider range of soil moisture levels than currently exists naturally. An analysis of the number of samples required to accurately quantify important ecosystem carbon stocks and fluxes is used to guide the sampling strategy at the field site. Quantifying root dynamics, in particular, presents methodological challenges. Thus, I critically review existing methods, and develop techniques to accurately measure root standing biomass and production. Subsequently, these techniques are used to record root responses, in terms of standing biomass, production, morphology, turnover and nutrient content, to variation in soil moisture across the four rain forest plots. There is substantial environmental variation in root characteristics. However, several responses remain consistent across plots: root production of biomass, length, and surface area, is lower where soil is dry, while root length and surface area per unit mass show the opposite pattern. The other major component of the below-ground carbon cycle is soil carbon dioxide efflux. I partition this efflux, on each plot, into contributions from organic ground surface litter, roots and soil organic matter, and investigate abiotic and biotic causes for observed differences within and between plots. On average, the percentage contribution of soil organic matter respiration to total soil carbon dioxide efflux declines during the dry season, while root respiration contribution displays the opposite trend. However, spatial patterns in soil respiration are not directly attributable to variation in either soil moisture or temperature. Instead, ground surface organic litter mass and root mass account for 44 % of observed spatial heterogeneity in soil carbon dioxide efflux. Finally, information on below-ground carbon cycling is combined with aboveround data, of canopy dynamics and stem wood production and mortality, to analyze the potential effects of drought upon carbon cycling in an Amazon forest ecosystem. Comparison of the rainfall exclusion plot with a similar, but unmodified, control plot reveals potentially important differences in tree carbon allocation, mortality, reproduction, soil respiration and root dynamics. The apparent net consequence of these changes is that, under drier conditions, the amount of CO2 moving out of the forest and into the atmosphere is diminished. This synthesis of above-ground and below-ground data advances understanding of carbon cycling in rain forests, and provides information which should allow more accurate modelling of the response of the Amazon region to future drought. Additional measurements at other sites, and of other ecosystem carbon fluxes, should further refine modelling predictions.

Previous pulse-chase experiments have revealed a wide diversity of benthic response patterns to organic matter (OM) input depending on environmental setting, benthic community structure and experimental conditions i.e. quantity and quality of the added OM.  However, the mechanisms and interaction of environmental and biological factors that produce an observed response pattern are poorly understood. The present thesis set out to improve our current understanding on the set of parameters that determine benthic response patterns.  The core of this study was based on two pulse-chase experiments in two bathyal settings: the Faroe-Shetland Channel (FSC) and the SW Cretan slope in the E. Mediterranean (E. Med).  The sub-zero temperatures in the FSC enabled the observation of the benthic response in “slow-motion” and showed that the response is not static but instead might go through various “phases”.  In the warm E. Med, C processing rates were considerably lower compared to previous measurements in adjacent regions.  The discrepancy was attributed to the particularly refractory sedimentary OM at the sampling station with apparent consequences for the physiological state of the bacterial community.  Both experiments showed that bacterial metabolism and its regulation is a key factor determining the reaction of the benthic community to OM inputs.  This thesis provided further understanding on the short-term fate of organic C in deep-sea sediments but also raised certain issues that could be addressed in future studies.

Master of Science / Department of Agronomy / Eduardo Alvarez Santos / Isotope analysis combined with micrometeorological techniques can bring new insights into the mechanisms governing biogeochemical cycles in ecosystems. New field-deployable optical sensors that have recently become available can provide accurate trace gas concentration measurements at sampling rates suitable for micrometeorological measurements. These instruments could help enhance current carbon cycling research efforts. This research will bring new insights into understanding the biophysical processes governing the carbon cycle at the ecosystem scale, which will be crucial for enhancing our future climate change scenario predictions. The impact that land use management has on the carbon cycle components of an ecosystem is an important issue that could be addressed with this new approach. More notably, research is needed to identify how management practices affect the abundance of C₃ and C₄ plant communities in grasslands and to identify how shifts in plant community composition can modify the net ecosystem exchange of CO₂. Chapter 1 of this thesis provides a literature review on the carbon cycle in grasslands, stable isotope analysis in environmental mediums, and the combination of isotope analysis with micrometeorological methods to study carbon exchange at the ecosystem scale. In Chapter 2, we describe the evaluation of the performance for a multi-port sampling system’s measurements of vertical concentration gradients of stable isotopes of CO₂. The results of these analyzes show that the sampling system was suitable to measure vertical gradients of concentration under field conditions. Chapter 3 describes how the sampling system was used to study the isotope exchange in two watersheds at the Konza Prairie Biological station under distinct management conditions. Gradients of isotopes were measured in two adjacent watersheds (K2A and C3SA). The K2A watershed is burned every other year, while the C3SA watershed is in a patch-burn grazing system and is burned every three years. Results show that the sampling system’s performance is adequate for our study. The sampling system was able to detect clear differences in the isotopic composition of nighttime NEE between the watersheds, which is believed to be greatly influenced by C₃ and C₄ plant community composition. Further research is needed to examine the role that other environmental conditions played on altering the isotopic signals of the NEE in each watershed. Additionally, other management practices should be examined using this sampling system to determine their impact on biophysical drivers in the ecosystem, which could subsequently impact the plant community abundance and diversity.