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HIV-1 is a global pandemic with about 39 million people infected. In India, 2.9 million people are infected and about 2 lakh new infections have been reported last year. To date, there is no cure for HIV/AIDS. Current treatment, which is associated with serious side effects, only delays the onset of AIDS and death. Thus, HIV/AIDS is responsible for a global health concern imposing significant healthcare costs, especially in low- and middle-income regions such as India and Africa, and a marked loss of quality of life to infected individuals. Understanding factors impacting vaccine design and drug development via mathematical modelling of HIV-1 transmission, evolution and pathogenesis and discerning the subtype and region specific differences are a crucial part of the overall strategy of reducing the burden of HIV/AIDS. The strain dominant in India is HIV-1 subtype C (HIV-1C). Treatment guidelines have largely been based on studies on HIV-1 subtype B (HIV-1B), dominant in the west. In this thesis, we have attempted to understand the dynamics of the spread of HIV-1C, leading to new guidelines and intervention strategies applicable to India. We have for the first time estimated the basic reproductive ratio, R0, of HIV-1 subtype C (HIV-1C), a proxy for its fitness and virulence, using clinical data of infected patients from India. We employed measurements of viral load decay dynamics during treatment and estimated R0, and the critical efficacy, εc, for successful treatment of HIV-1C infection. Clinical data showed that the viral load in patients in India was significantly higher than in the west. Yet, in 6 months following the start of treatment, 87.5% had undetectable viral load, indicating an excellent response to ART, comparable to the west. We analyzed the clinical data using a mathematical model and estimated the median R0 to be 5.3. The corresponding εc was ∼0.8. These estimates of R0 and εc are smaller than current estimates for HIV-1B, suggesting that HIV-1C exhibits lower in vivo fitness compared to HIV-1B, which allows successful treatment despite high baseline viral loads. New treatment guidelines thus emerge that are less stringent than in the west. HIV-1C is far more prevalent globally than HIV-1B. This is surprising in light of our findings above of a lower fitness of HIV-1C than HIV-1B. To understand this observation, we next developed a mechanistic paradigm of HIV-1 transmission. HIV-1 has been hypothesized to optimize its transmission potential (TP) in an infected population by modulating its steady state viral load (VSS), a robust marker of virulence. The mechanism of this optimization is paradoxical and poorly understood given that HIV-1 mutates rapidly in vivo in response to selection pressure by the host immune system. We hypothesize that the HIV-1 TP is not solely a function of VSS as proposed earlier, but a function of two variables - VSS and R0, which function such that R0 is optimized within an infected individual in response to the immune system while VSS is optimized across individuals such that transmission is optimized. On this TP(VSS, R0) landscape, we find that HIV-1C lies closer to the optimum than HIV-1B, suggesting an explanation for the global spread of HIV-1C. This leads to the intriguing implication that the lower virulence of HIV-1C may be because it has evolved more along the TP(VSS, R0) landscape than HIV-1B. Lastly, we examined the role of recombination on HIV-1 adaptation. Following transmission, HIV-1 adapts in the new host by acquiring mutations that allow it to escape from the host immune response at multiple epitopes. It also reverts mutations associated with epitopes targeted in the transmitting host but not in the new host. Moreover, escape mutations are often associated with additional compensatory mutations that partially recover fitness costs. It is unclear whether recombination expedites this process of multi-locus adaptation. To elucidate the role of recombination, we constructed a detailed population dynamics model that integrates viral dynamics, host immune response at multiple epitopes through cytotoxic T lymphocytes, and viral evolution driven by mutation, recombination, and selection. Using this model, we computed the expected waiting time until the emergence of the strain that has gained escape and compensatory mutations against the new host’s immune response, and reverted these mutations at epitopes no longer targeted. We found that depending on the underlying fitness landscape, shaped by both costs and benefits of mutations, adaptation proceeds via distinct dominant pathways with different effects of recombination, in particular distinguishing escape and reversion. Specifically, recombination tends to delay adaptation when a purely uphill fitness landscape is accessible at each epitope, and accelerate it when a fitness valley is associated with each epitope. Our study points to the importance of recombination in shaping the adaptation of HIV-1 following its transmission to new hosts, a process central to T cell-based vaccine strategies.

Untersuchungsgegenstand der vorliegenden Dissertation sind biomassebasierte Kohlen (Biokohlen, biochar), welche für eine langfristige Kohlenstoffspeicherung in Böden mit dem gleichzeitigen Ziel der zusätzlichen Bodenverbesserung hergestellt werden. Die Auswahl der Kohlen umfasste Kohlen aus Pyrolyse- und hydrothermale Carbonisierung (HTC). In dieser Arbeit werden einige zentrale Phänomene, die bei deren Ausbringung in einem bestehenden Bodenökosystem auftreten können, nähergehend untersucht. Einerseits beeinflusst das fremde Material den Stoffwechsel und die Abundanz und Vielfalt innerhalb der mirkobiellen Gemeinschaft im Boden; im Gegenzug spielen die Mikroorganismen eine aktive Rolle beim Abbau des neuen Substrats. Diese beiden Aspekte sind größer Bedeutung, um bewerten zu können, wie erfolgsversprechend der Einsatz einer bestimmten Kohle im Boden hinsichtlich der Langlebigkeit, der gewünschten Ertragseffekte sowie möglicher Nebenwirkungen ist. Daraus ergeben sich die beiden folgenden zwei Fragestellungen, auf die diese Arbeit fokusiert ist: • Welche Faktoren beeinflussen die Abbaubarkeit der Kohlen im Boden? • Welche Wirkungen haben die Kohlen auf die Bodenatmung, auf den Boden-C-Gehalt, auf die mikrobielle Abundanz und auf die Dynamik der mikrobiellen Gemeinschaft? Als mögliche Einflussgrößen für die Abbaubarkeit der Kohlen wurden die Art der Kohlenherstellung, eine mögliche Nachbehandlung, der Alterungsprozess sowie die Zugabe einer Nährstoff- und einer labilen Kohlenstoffquelle getestet. Für diese Studie wurden Pyrolyse- und HTC-Kohlen aus Mais-Silage in einen Sandboden ausgebracht. Grundlage aller Versuche war die Untersuchung der Respirationsdynamik in unterschiedlichen Boden-Kohle-Gemischen, die durch Infrarotspektrometrie ermittelt wurde. Sie diente als Indikator für die mikrobielle Aktivität und dem daraus resultierenden Abbau der Substrate. Ergänzend wurde am Anfang und am Ende jedes Versuchs der Boden-Kohlenstoffgehalt gemessen. Die Versuche erfolgten auf verschiedenen Skalen: • Kurzzeit-Laborinkubationen (10 Tage) unter konstanten klimatischen Bedingungen in einem automatisch gesteuerten Durchflusssystem, an das das Messgerät direkt angeschlossen wurde. • Parzellenversuch (2 Jahre) im Freiland im Nordwesten Brandenburgs, bei dem die Bestimmung der Bodenatmung mittels wiederholter Beprobung aus auf der Ackerfläche gestellten geschlossenen Hauben erfolgte. In einer Laborinkubation wurde zusätzlich eine qPCR (quantitative Echtzeit Polymerase Kettenreaktion) zur Bestimmung der Abundanz ausgewählter mikrobieller Gruppen eingesetzt. Im Feldversuch wurde außerdem die Abundanz der stabilen Kohlenstoff-Isotopen (12C und 13C) im Boden und im freigesetzten CO2 ermittelt, um den Abbau der Kohlen vom Abbau des bodenorganischen Kohlenstoffs, der durch die Kohlen beeinflusst sein kann (priming), zu unterscheiden. Die Ergebnisse bestätigen die erhöhte Stabilität beider Kohlen im Vergleich zum Ausgangsmaterial, vor allem für die Pyrolyse-Kohle, deren Abbau sowohl im Labor als auch im Freiland am langsamsten erfolgte. Bei beiden Kohlen sank die Abbaubarkeit mit ihrer Alterung. Anhand der Abbauraten im zweiten Jahr des Feldversuchs wurden für die Pyrolyse- und HTC-Kohle Halbwertszeiten von 81 bzw. 60 Jahren ermittelt. Im Gegensatz zur Pyrolyse-Kohle wies der Abbau der HTC-Kohle eine komplexere Dynamik auf, was im Lauf der 10-tägigen Inkubationsversuche mit einer Verschiebung der mikrobiellen Gemeinschaft einherging. Im ersten Jahr des Freilandversuchs kam es bei der HTC-Kohle zur Ausgasung flüchtiger und leicht abbaubarer Kohlenstoffverbindungen, wodurch die Stabilität im Folgejahr deutlich erhöht wurde. Eine Nachbehandlung der Kohlen durch anaerobe Fermentierung führte zu einer deutlichen Verminderung der kurzzeitigen Ausgasung bei HTC-Kohle, sowohl im Freiland als auch im Labor, jedoch zu einer langfristigen Reduktion der Stabilität beider Kohlen: die ermittelten Halbwertszeiten für die fermentierte Pyrolyse- und HTC-Kohle nach dem zweiten Jahr des Feldversuchs betrugen 14 bzw. 13 Jahren. Die Wirkung der unbehandelten Kohlen auf die Abundanz der untersuchten mikrobiellen Gruppen im C-armen Boden war stark reduziert im Vergleich zum Ausgangsmaterial, und unter C-reichen Bedingungen kam es zu einer Hemmung der Aktivitätssteigerung. Die Zugabe leicht verfügbaren Kohlenstoffs wie Glukose zum reinen Boden in einem Inkubationsversuch steigerte die Bodenatmung erheblich und erhöhte die Variationsbreite der mikrobiellen Gemeinschaft. In Gegenwart der Kohlen war dies allerdings weniger stark ausgeprägt. Bei Zugabe mineralischen Stickstoffs in Gegenwart von Kohlen wurde hingegen keine signifikante Veränderung der Bodenatmung nachgewiesen. Die Inkubationsversuche haben es ermöglicht, die Kurzzeitdynamik der Bodenatmung und die Anpassung der mikrobiellen Gemeinschaft nach Zugabe der Kohlen und zusätzlicher C- und N-Quellen nachzuweisen. Im Freilandversuch konnte die Abbaudynamik von Kohlenstoffverbindungen unter Praxisbedingungen untersucht werden und durch die Messung der stabilen Isotope differenzierte Aussagen über die langfristige Stabilität von zugesetzten Kohlen und der bodenorganischen Substanz getroffen werden. Eine langfristige Festlegung von Kohlenstoff ist im Boden in Form von Biokohlen ist möglich. Allerdings hängt die Dauer der Festlegung von einer Vielzahl von Faktoren wie der Art der Ausgangsstoffe, den Prozessbedingungen, den Interaktionen zwischen Kohlepartikeln und Bodenorganismen und nicht zuletzt der Versuchsdauer ab. Während Kurzzeitversuche eine gute Möglichkeit darstellen, um die Effekte veränderter Bedingungen im Boden aufzuzeigen, kann die Kohlestabilität im Boden und damit das C-Sequestrierungspotenzial am zuverlässigsten nur in Langzeitstudien im Freiland abgeschätzt werden. / The object of the present thesis is charred biomass (biochar) produced for double aim of carbon storage in soil and improvement of soil properties. The chosen chars included chars from pyrolysis and hydrothermal carbonisation (HTC). The present work investigates closely some basic phenomena which can occur upon application of chars into an existing soil ecosystem: on the one hand, the allochthonous material affects the metabolism and the relative abundance of different microbial groups; on the other hand the microorganisms play an active role in the degradation of the new substrate. These two aspects are crucial to evaluate the suitability of the application of a specific char in the soil, particularly as concerns its stability, the length of time the char remains in the soil, the expected effects on crop yields, as well as possible side effects on the soil ecosystem. Based on this, two research questions arise which have been investigated in this thesis: • What factors affect the degradability of chars in soil? • How do the chars influence soil respiration, soil carbon content, microbial abundance and the dynamics of the microbial community? The production process, a post-treatment, the ageing process as well as the addition of a source of nutrients and a source of labile carbon were assessed as possible factors in determining the degradability of chars. For the present study, pyrolysis char and HTC char from maize silage were applied to a sandy soil. The basis of all experiments was an investigation of the respiration dynamics in different soil/char mixtures, measured through an infrared spectrometer, which was used to track the microbial activity and the substrate degradation. As a complement, soil carbon was also measured at the beginning and at the end of each experiment. The investigations were performed at different scales: • Short-term laboratory incubations (10 days) under constant climatic conditions in an automatic multi-channel flowthrough system, with direct plug-in for the measurement instrument. • A plot-wise investigation (2 years) in an agricultural field in North-West Brandenburg, where the soil respiration was measured by a repeated sampling from static chambers placed hermetically on the field. For one incubation study, qPCR (qunatitative real time polymerase chain reaction) was additionally applied to determine the abundance of selected microbial groups. Moreover, for the field investigation the abundance of stable carbon isotopes (12C und 13C) in the soil and in the released CO2 was recorded, to differentiate between the degradation of the chars and the degradation of soil organic carbon, which might be affected by the presence of chars (priming). The results confirm the higher stability of both chars in comparison to the feedstock, in particular for pyrolysis char, whose decay was the slowest both in the laboratory and in the field. The degradability of both chars decreased with their ageing. Based on the decay rates in the second year of the field investigation, decay half-lives for pyrolysis char and HTC char amounted respectively to 81 years and 60 years. Other than pyrolysis char, the degradation of HTC char revealed a more complex dynamics, which was accompanied by a shift of the microbial community within the 10 days incubation. During the first year of the field experiment, an intensive release of volatile and labile compounds took place, which led to an increased stability during the following year. A post-treatment of the chars via anaerobic fermentation led to a reduction in the initial degasing of the HTC char, both in the laboratory and in the field, but also to a decrease in stability for both chars: the calculated half-lives for fermented pyrolysis char and fermented HTC char on the basis of the second year of the field investigation were respectively 14 years and 13 years. The effects of the untreated chars on the abundance of the selected microbial groups in the carbon-poor soil used was also strongly reduced in comparison to the feedstock, while in a situation of carbon abundance a inhibition of the activity increase took place. Addition of readily available carbon in the form of glucose increased soil respiration tremendously and magnified the variation amplitude of the microbial community, which was however much reduced in the presence of chars. Instead, after addition of mineral nitrogen in presence of chars, no significant variation in the soil respiration could be observed. The incubation experiments made it possible to report the short-term dynamics of the soil respiration and the adaptation of the microbial community after application of char and additional carbon and nitrogen sources. In the field experiment the decay dynamics of char compounds could be investigated in a situation of common agricultural practice and the measurement of stable isotopes has given differentiated outcomes about the long-term stability of the added chars and of the soil organic matter. Storage of carbon in the soil in the form of char for a long period is possible. How long carbon can actually be stored depends on a number of factors such as the feedstock, the carbonisation process parameters, the interactions between char particles and soil microorganisms and the duration of the investigation itself. Short-term experiments represent a good possibility to highlight the effects of modified soil conditions, while the stability of char in soil and thus the potential carbon sequestration can be estimate in the most reliable way only through long-term studies in field. / Oggetto della presente tesi sono i carboni prodotti da biomasse (biochar) e utilizzati per lo stoccaggio del carbonio nel suolo e allo stesso tempo come ammendanti per terreni agricoli. I carboni considerati sono derivati da pirolisi o carbonizzazione idrotermale (HTC). Nel presente lavoro vengono esaminati in dettaglio alcuni importanti fenomeni che si possono manifestare in seguito all’applicazione su un ecosistema preesistente nel terreno: da un lato il materiale estraneo influenza il metabolismo della materia organica, l’abbondanza e la varietà all’interno della comunità microbica nel suolo, dall’altro i microorganismi giocano un ruolo fondamentale nella degradazione del nuovo substrato. Questi due aspetti sono essenziali per valutare quanto sia opportuno l’utilizzo di un determinato carbone dal punto di vista della sua longevità, degli effetti attesi sulla resa agricola e di eventuali effetti collaterali sull’ecosistema. Da queste premesse sono emerse le seguenti domande, su cui è focalizzato il presente lavoro: • Quali fattori determinano la degradabilità dei carboni nel suolo? • Che effetti possono avere i carboni sulla respirazione del terreno, sul suo contenuto di carbonio, sull’abbondanza dei microorganismi e sulla dinamica della comunità microbica? Come possibili variabili indipendenti per la degradabilità dei carboni sono state considerate: il processo di produzione, un possibile posttrattamento, l’invecchiamento dei substrati, l’aggiunta di nutrienti e di carbonio biodisponibile. Per questo studio sono stati applicati carboni derivati da pirolisi e da HTC di insilato di mais in un terreno sabbioso. Il fondamento di tutti gli esperimenti riportati è lo studio della dinamica della respirazione microbica in diverse miscele terreno/carbone, misurata tramite spettroscopia a infrarossi, che vale come tracciante per l’attività microbica e per la degradazione del substrato. In aggiunta è stato periodicamente misurato il contenuto di carbonio nel terreno. Gli esperimenti sono stati condotti su due diverse scale: • Incubazioni in laboratorio (10 giorni) in condizioni climatiche controllate, all’interno di un apparato per la ventilazione a flusso continuo, con presa diretta per lo strumento di misura. • Esperimento in campo parcellizzato (2 anni) nel Brandeburgo nordoccidentale, dove la misura della respirazione è avvenuta per campionamento ripetuto da camere opache poggianti ermeticamente sul suolo. Per una delle incubazioni è stata anche eseguita una qPCR (reazione a catena della polimerasi quantitativa in tempo reale) per quantificare l’abbondanza di determinati gruppi tassonomici di microorganismi. Nel campo è stata inoltre misurata l’abbondanza degli isotopi stabili del carbonio (12C e 13C), sia nel terreno sia nella CO2 liberata, per differenziare la degradazione dei carboni da quella del carbonio organico nel suolo, che in principio può essere influenzata dalla presenza dei carboni (priming). I risultati confermano l’aumentata stabilità di entrambi i carboni in confronto al materiale di partenza, in particolare del carbone pirolitico che si è degradato piú lentamente, sia in laboratorio sia in campo. La degradabilità di entrambi i carboni si è in ogni caso ridotta con l’invecchiamento. Basandosi sulle emissioni del secondo anno della sperimentazione in campo, sono stati calcolati dei tempi di dimezzamento di 81 anni e 60 anni, rispettivamente per il carbone pirolitico e per il carbone da HTC. La degradazione del carbone da HTC ha rivelato una dinamica piú complessa, che testimonia un adattamento della comunità microbica nell’arco dei 10 giorni di incubazione. Nel primo anno in campo è stata rilevata un’elevata emissione di composti volatili e labili, che ha portato a un incremento della stabilità nell’anno seguente. Il posttrattamento dei carboni tramite fermentazione anaerobica ha comportato una notevole riduzione dell’iniziale mineralizzazione del carbone da HTC, ma una diminuzione della stabilità di entrambi i carboni sul lungo periodo: i tempi di dimezzamento calcolati per il carbone pirolitico fermentato e per il carbone da HTC fermentato nel secondo anno dell’esperimento sul campo valgono rispettivamente 14 anni e 13 anni. Nel terreno usato, povero di carbonio, gli effetti dei carboni sull’abbondanza dei gruppi microbici selezionati è stata nettamente ridotta rispetto al materiale non carbonizzato, mentre la reazione all’aggiunta di carbonio labile è stata tendenzialmente inibitoria. Infatti, se l’aggiunta di glucosio ha incrementato considerevolmente la respirazione e l’ampiezza delle variazioni nella comunità microbica, in presenza dei carboni le variazioni sono state fortemente ridotte. L’aggiunta di azoto inorganico non ha invece portato a variazioni apprezzabili nella respirazione. Gli esperimenti basati su incubazioni hanno consentito di determinare la dinamica a breve termine della respirazione e l’adattamento della comunità microbica in seguito ad aggiunta dei carboni e di altre sorgenti di carbonio e azoto. Nell’esperimento su campo si è potuta osservare la dinamica di degradazione dei composti carboniosi in condizioni di prassi agricola e grazie alla misura degli isotopi stabili si sono potuti ottenere risultati differenziati sulla stabilità a lungo termine dei carboni e della sostanza organica del suolo. È quindi possibile immagazzinare il carbonio in modo duraturo nel suolo sotto forma di carbone. La durata stimabile di questo immagazzinamento dipende però da molteplici fattori tra cui la materia prima, il processo di carbonizzazione, le interazioni tra particelle carboniose e microorganismi del suolo e non da ultimo la durata della sperimentazione. Gli esperimenti a breve termine sono un mezzo efficace per rilevare le conseguenze immediate di modifiche del terreno; la stabilità dei carboni e quindi il loro potenziale per il sequestro del carbonio può essere determinata nel modo piú affidabile solo in studi a lungo termine sul campo.