Microbial Community Responses to Environmental Perturbation

Microorganisms mediate many biogeochemical processes critical to the functioning of ecosystems, which places them as an intermediate between environmental change and the resulting ecosystem response. Yet, we have an incomplete understanding of these relationships, how to predict them, and when they are influential. Understanding these dynamics will inform ecological principles developed for macroorganisms and aid expectations for microbial responses to new gradients. To address this research goal, I used two studies of environmental gradients and a literature synthesis.

With the gradient studies, I assessed microbial community composition in stream biofilms across a gradient of alkaline mine drainage. I used multivariate approaches to examine changes in the non-eukaryote microbial community composition of taxa (chapter 2) and functional genes (chapter 3). I found that stream biofilms at sites receiving alkaline mine drainage had distinct community composition and also differed in the composition of functional gene groups compared with unmined reference sites. Compositional shifts were not dominated by groups that could benefit from mining associated increases of terminal electron acceptors; two-thirds of responsive taxa and functional gene groups were negatively associated with mining. The majority of subsidies and stressors (nitrate, sulfate, conductivity) had no consistent relationships with taxa or gene abundances. However, methane metabolism genes were less abundant at mined sites and there was a strong, positive correlation between selenate reductase gene abundance and mining-associated selenium. These results highlighted the potential for indirect factors to also play an important role in explaining compositional shifts.

In the fourth chapter, I synthesized studies that use environmental perturbations to explore microbial community structure and microbial process connections. I examined nine journals (2009–13) and found that many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant. No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure. Together, the findings suggested that few publications report statistically testing structure-process links; but when tested, links often occurred yet shared few commonalities in linked processes or structures and the techniques used for measuring them.

Although the research community has made progress, much work remains to ensure that the vast and growing wealth of microbial informatics data is translated into useful ecological information. In part, this challenge can be approached through using hypotheses to guide analyses, but also by being open to opportunities for hypothesis generation. The results from my dissertation work advise that it is important to carefully interpret shifts in community composition in relation to abiotic characteristics and recommend considering ecological, thermodynamic, and kinetic principles to understand the properties governing community responses to environmental perturbation.

The Quantum Mitochondrion and Optimal Health

A sufficiently complex set of molecules, if subject to perturbation, will self-organise and show emergent behaviour. If such a system can take on information it will become subject to natural selection. This could explain how self-replicating molecules evolved into life and how intelligence arose. A pivotal step in this evolutionary process was of course the emergence of the eukaryote and the advent of the mitochondrion, which both enhanced energy production per cell and increased the ability to process, store and utilise information. Recent research suggest that from its inception life embraced quantum effects such as “tunnelling” and “coherence” while competition and stressful conditions provided a constant driver for natural selection. We believe that the biphasic adaptive response to stress described by hormesis – a process that captures information to enable adaptability, is central to this whole process. Critically, hormesis could improve mitochondrial quantum efficiency, improving the ATP/ROS ratio, while inflammation, which is tightly associated with the aging process, might do the opposite. This all suggests that to achieve optimal health and healthy ageing, one has to sufficiently stress the system to ensure peak mitochondrial function, which itself could reflect selection of optimum efficiency at the quantum level.

Nme Gene Family Evolutionary History Reveals Pre-Metazoan Origins and High Conservation between Humans and the Sea Anemone, Nematostella vectensis

Background: The Nme gene family is involved in multiple physiological and pathological processes such as cellular differentiation, development, metastatic dissemination, and cilia functions. Despite the known importance of Nme genes and their use as clinical markers of tumor aggressiveness, the associated cellular mechanisms remain poorly understood. Over the last 20 years, several non-vertebrate model species have been used to investigate Nme functions. However, the evolutionary history of the family remains poorly understood outside the vertebrate lineage. The aim of the study was thus to elucidate the evolutionary history of the Nme gene family in Metazoans. Methodology/Principal Findings: Using a total of 21 eukaryote species including 14 metazoans, the evolutionary history of Nme genes was reconstructed in the metazoan lineage. We demonstrated that the complexity of the Nme gene family, initially thought to be restricted to chordates, was also shared by the metazoan ancestor. We also provide evidence suggesting that the complexity of the family is mainly a eukaryotic innovation, with the exception of Nme8 that is likely to be a choanoflagellate/metazoan innovation. Highly conserved gene structure, genomic linkage, and protein domains were identified among metazoans, some features being also conserved in eukaryotes. When considering the entire Nme family, the starlet sea anemone is the studied metazoan species exhibiting the most conserved gene and protein sequence features with humans. In addition, we were able to show that most of the proteins known to interact with human NME proteins were also found in starlet sea anemone. Conclusion/Significance: Together, our observations further support the association of Nme genes with key cellular functions that have been conserved throughout metazoan evolution. Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of key developmental and cellular processes.

L’exploitation d’un modèle de levure présentant une déficience de l’absorption des anthracyclines révèle qu’une protéine de Caenorhabditis elegans, OCT-1, est un transporteur fonctionnel d’anthracyclines

Les anthracyclines, comme la doxorubicine (DOX) ou la daunorubicine (DNR), sont utilisées dans le traitement d’une grande variété de cancers allant des lymphomes, au cancer du sein, en passant par certaines leucémies. Encore aujourd’hui, beaucoup pensent que les anthracyclines entrent dans les cellules par diffusion passive, toutefois, la plupart de ces mêmes personnes sont d’accord pour dire que la p-glycoprotéine est responsable d’exporter ces molécules hors de la cellule. Mais pourquoi une molécule aurait besoin d’un transporteur pour sortir de la cellule, et pas pour y entrer ? Qu’est-ce qui ferait que la diffusion passive fonctionnerait dans un sens, mais pas dans l’autre, d’autant que l’entrée des anthracyclines dans les cellules est très rapide ? Nous pensons qu’il existe bel et bien un transporteur responsable de faire passer les anthracyclines du milieu extracellulaire au cytoplasme, et nous voulons développer un modèle de levure qui permettrait de déterminer si une protéine, un transporteur, issue d’un autre organisme eucaryote est en mesure de transporter la DOX à l’intérieur de la cellule. Pour ce faire, nous avons rassemblé un groupe de mutants présentant une déficience dans l’absorption d’autres molécules chargées positivement telles que la bléomycine ou le NaD1 et avons déterminé le taux d’absorption de DOX de chacun de ces mutants. Les simples mutants sam3Δ ou dur3Δ n’ont montré qu’une faible réduction de l’absorption de DOX, voire, aucune, par rapport à la souche parentale. Si le double mutant sam3Δdur3Δ a montré une réduction relativement importante de l’absorption de DOX, c’est le mutant agp2Δ qui présentait la plus grande réduction d’absorption de DOX, ainsi qu’une résistance notable à son effet létal. Nous avons utilisé, par la suite, ce mutant pour exprimer, à l’aide d’un vecteur d’expression, une protéine du ver Caenorhabditis elegans, OCT-1 (CeOCT-1). Les résultats ont montré que cette protéine était en mesure de restaurer l’absorption de DOX, compromise chez le mutant agp2Δ ainsi que d’augmenter la sensibilité de la souche parentale à son effet létal, lorsqu’exprimée chez celle-ci. Cela suggère que CeOCT-1 est un transporteur fonctionnel de DOX et contredit également le dogme selon lequel les anthracyclines entrent dans les cellules par diffusion passive.

L’exploitation d’un modèle de levure présentant une déficience de l’absorption des anthracyclines révèle qu’une protéine de Caenorhabditis elegans, OCT-1, est un transporteur fonctionnel d’anthracyclines

Les anthracyclines, comme la doxorubicine (DOX) ou la daunorubicine (DNR), sont utilisées dans le traitement d’une grande variété de cancers allant des lymphomes, au cancer du sein, en passant par certaines leucémies. Encore aujourd’hui, beaucoup pensent que les anthracyclines entrent dans les cellules par diffusion passive, toutefois, la plupart de ces mêmes personnes sont d’accord pour dire que la p-glycoprotéine est responsable d’exporter ces molécules hors de la cellule. Mais pourquoi une molécule aurait besoin d’un transporteur pour sortir de la cellule, et pas pour y entrer ? Qu’est-ce qui ferait que la diffusion passive fonctionnerait dans un sens, mais pas dans l’autre, d’autant que l’entrée des anthracyclines dans les cellules est très rapide ? Nous pensons qu’il existe bel et bien un transporteur responsable de faire passer les anthracyclines du milieu extracellulaire au cytoplasme, et nous voulons développer un modèle de levure qui permettrait de déterminer si une protéine, un transporteur, issue d’un autre organisme eucaryote est en mesure de transporter la DOX à l’intérieur de la cellule. Pour ce faire, nous avons rassemblé un groupe de mutants présentant une déficience dans l’absorption d’autres molécules chargées positivement telles que la bléomycine ou le NaD1 et avons déterminé le taux d’absorption de DOX de chacun de ces mutants. Les simples mutants sam3Δ ou dur3Δ n’ont montré qu’une faible réduction de l’absorption de DOX, voire, aucune, par rapport à la souche parentale. Si le double mutant sam3Δdur3Δ a montré une réduction relativement importante de l’absorption de DOX, c’est le mutant agp2Δ qui présentait la plus grande réduction d’absorption de DOX, ainsi qu’une résistance notable à son effet létal. Nous avons utilisé, par la suite, ce mutant pour exprimer, à l’aide d’un vecteur d’expression, une protéine du ver Caenorhabditis elegans, OCT-1 (CeOCT-1). Les résultats ont montré que cette protéine était en mesure de restaurer l’absorption de DOX, compromise chez le mutant agp2Δ ainsi que d’augmenter la sensibilité de la souche parentale à son effet létal, lorsqu’exprimée chez celle-ci. Cela suggère que CeOCT-1 est un transporteur fonctionnel de DOX et contredit également le dogme selon lequel les anthracyclines entrent dans les cellules par diffusion passive.

Prevalence and genetic diversity of Blastocystis in family units living in the United States

The human gut is host to a diversity of microorganisms including the single-celled microbial eukaryote Blastocystis. Although Blastocystis has a global distribution, there is dearth of information relating to its prevalence and diversity in many human populations. The mode of Blastocystis transmission to humans is also insufficiently characterised, however, it is speculated to vary between different populations. Here we investigated the incidence and genetic diversity of Blastocystis in a US population and also the possibility of Blastocystis human-human transmission between healthy individuals using family units (N = 50) living in Boulder, Colorado as our sample-set. Ten of the 139 (~ 7%) individuals in our dataset were positive for Blastocystis, nine of whom were adults and one individual belonging to the children/adolescents group. All positive cases were present in different family units. A number of different Blastocystis subtypes (species) were detected with no evidence of mixed infections. The prevalence of Blastocystis in this subset of the US population is comparatively low relative to other industrialised populations investigated to date; however, subtype diversity was largely consistent with that previously reported in studies of European populations. The distribution of Blastocystis within family units indicates that human-human transmission is unlikely to have occurred within families that participated in this study. It is not unexpected that given the world-wide variation in human living conditions and lifestyles between different populations, both the prevalence of Blastocystis and its mode of transmission to humans may vary considerably.