Dissertations / Theses on the topic 'Oligotrophic bacteria'

Lakes are important global ecosystems and many of them are nutrient-poor (unproductive). Especially in northern boreal latitudes, lakes may be heavily subsidized by terrestrial organic material (t-OM) from peat layers in the catchment. Thus, in addition to heterotrophic bacteria and phytoplankton, zooplankton may also use the particulate fraction of peat layer t-OM (t-POM) as a potential food source in those systems. Inputs of t-OM in northern latitudes are anticipated to increase in the future due to increasing precipitation and temperature. As t-OM is a good substrate for bacterial growth and as bacteria can often outcompete phytoplankton for inorganic nutrients, the proportions of heterotrophic bacteria and phytoplankton are expected to change in unproductive lakes. This may have pronounced impacts on zooplankton population dynamics. The aim of my thesis was to investigate how changes in food quality and quantity will affect metazoan zooplankton performance in unproductive lakes. Three laboratory studies assessed the quality of specific food components (phytoplankton, bacteria and peat layer t-POM) and their effects on Daphnia survival, growth and reproduction. Further, a mesocosm study with a full natural plankton community tested the predictions of the Light:Nutrient-Hypothesis in an unproductive clear water lake in situ by adding carbon and inorganic nutrients and changing light availability. I found that pure bacterial (Pseudomonas sp.) or t-POM diets could not sustain Daphnia populations, even though both were readily ingested. Daphnids needed at least 10-20% phytoplankton (Rhodomonas) in the diet to survive and even higher proportions (≥ 50%) were necessary for the production of viable offspring. Further, I showed that the dilution of non-limiting concentrations of Rhodomonas with increasing proportions of Pseudomonas or t-POM led to decreased Daphnia performance. Both Pseudomonas and t-POM lack essential biochemicals (fatty acids and sterols). In contrast, mineral nutrient limitation only occurred on t-POM-dominated diets as evidenced by a labeling experiment that showed Daphnia can incorporate carbon and phosphorus from Rhodomonas and Pseudomonas with similar efficiencies. Thus, peat layer t-POM was a lower quality food than Pseudomonas. This was corroborated by the finding that intermediate additions of Pseudomonas to limiting amounts of Rhodomonas supported increased Daphnia survival, growth and reproduction while t-POM additions had no beneficial effect. My results suggest that high terrestrial stable isotope signals in metazoan zooplankton are most likely derived from t-OM that is channeled tohigher trophic levels via the microbial loop (i.e. heterotrophic bacteria and/or bacterivorous protozoa) but not from direct metazoan feeding on t-POM. Furthermore, bacteria may serve as an important supplement to zooplankton diets when phytoplankton abundance is low. However, a sufficient proportion of high quality phytoplankton is always necessary to fulfil mineral and especially biochemical requirements of zooplankton in unproductive aquatic systems. The results of the mesocosm study showed that the Light:Nutrient-Hypothesis is not applicable to unproductive clear water systems in which the phytoplankton community is dominated by mixotrophs. In the face of the theoretical predictions, low light levels led to decreased zooplankton biomass. This was most likely caused by a shift in the algal community composition towards less edible taxa. Another reason may have been a weakening of the microbial loop. This is in line with the results of the laboratory studies that point out the importance of the microbial food web for zooplankton nutrition in unproductive lakes.

Recent studies have characterized coastal estuarine systems as important components of the global carbon cycle. This study investigated carbon cycling through the microbial loop of Florida Bay by use of bacterial growth efficiency calculations. Bacterial production, bacterial respiration, and other environmental parameters were measured at three sites located along a historic phosphorus-limitation gradient in Florida Bay and compared to a relatively nutrient enriched site in Biscayne Bay. A new method for measuring bacterial respiration in oligotrophic waters involving tracing respiration of 13C-glucose was developed. The results of the study indicate that 13C tracer assays may provide a better means of measuring bacterial respiration in low nutrient environments than traditional dissolved oxygen consumption-based methods due to strong correlations between incubation length and δ13C values. Results also suggest that overall bacterial growth efficiency may be lower at the most nutrient limited sites.

Oligotrophic ecosystems can be loosely defined as environments that exhibit low ambient nutrient levels. During my thesis, I used 454 DNA pyrosequencing of partial 16S rDNA to explore the bacterial diversity in three different oligotrophic environments, including A. surface desert soil, B. Asian sandstorm dust and C. a section of the city of Paris's drinking water distribution system.A. Arid regions represent nearly 30% of the Earth's terrestrial surface. The living conditions at the surface of deserts are a challenge for microorganisms, as there is little available water and/or carbon, a very large range of temperatures and high exposure to UV irradiation from the Sun. In surface sand samples from two large Asian deserts, unexpectedly large bacterial diversity residing was revealed. Sequences belonging to the Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria phyla were the most abundant. An increase in phylotype numbers with increasing C/N ratio was noted, suggesting a possible role in the bacterial richness of these desert sand environments.B. Desert sandstorms are a meteorological phenomenon which have been postulated affect the Earth's climate and public health. We examined the particle-associated (dust and sand-associated) bacterial populations of atmospheric sand in the absence (as control) and presence of sandstorms in five Asian cities. Greater than 90% of the sequences can be classified as representing bacteria belonging to four phyla: Proteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. Principal component analyses showed that the sandstorm-associated bacterial populations were clustered by sampling year, rather than location. Members belonging to nine bacterial genera (Massilia, Planococcus, Carnobacterium, Planomicrobium, Pontibacter, Pedobacter, Lysobacter, Sanguibacter, Ohtaekwangia) were observed to increase in sand-associated samples from sandstorms, versus the controls. C. We characterized the bacterial communities in three water and three biofilm samples from one part of the Parisian drinking water distribution system. A dramatic change in bacterial population in the water during flow through the distribution system from the water treatment plant to the exit from the reservoir was found. The richness of the bacterial population was reduced from the water treatment plant to the reservoir (from 336 to 165 OTUs for water samples leaving the reservoir and from 947 to 275 for biofilm samples in the network). Several OTUs belonging to pathogenic genera were detected in our samples, mostly in the biofilm samples, thus suggesting that the biofilms may be an important source of bacteria during water distribution to the consumers.

This dissertation examines the bacterial diversity of hyperarid and arid regions of the Atacama Desert, Chile, as a first step towards understanding the global biogeochemical significance of arid-land microbial communities. The specific objectives were to characterize bacterial diversity and infer the possible metabolic potential of these bacterial communities, and to evaluate the influence of moisture exposure on community structure. In addition, the strengths and limitations of available tools for probing microbial diversity and activity in terrestrial ecosystems were characterized for their application to extreme oligotrophic communities. Preliminary PCR-DGGE analysis of a west-east elevational transect from the Pacific Ocean near Antofagasta to the western slopes of the central Andes indicated that bacterial communities along this transect belonged to two distinct community types: 1) hyperarid (700 - 2000 m) and 2) arid (2500 - 4500 m) communities that included both vegetated and unvegetated regions. Subsequent diversity analysis of these two regions revealed novel but distinct communities in both regions. A greater diversity was observed in the unvegetated arid regions than in the unvegetated hyperarid areas. The unvegetated arid sites were characterized by a bacterial community harboring a combination of radiotolerant and halotolerant heterotrophs as wells as diverse phylotypes closely related to chemolithoautotrophs. These rare phylotypes may be uniquely adapted to arid ecosystems. Molecular tools evaluated for community diversity analysis included PCR-DGGE, Sanger-clone and 454-pyrosequencing analysis of 16S rRNA gene libraries, and the use of reverse transcriptase quantitative PCR (RT-qPCR) for quantifying the impact of environmental variables on the metabolic activity of a specific organism. These techniques were evaluated using the ecosystems of the Atacama Desert as well as model ecosystems designed to address specific questions. Molecular tools are invaluable to the study of microbial ecology because they facilitate the study of fastidious organisms that are difficult or impossible to culture, but the analysis presented in this dissertation demonstrates that each of these methods has limitations and biases which must be acknowledged to avoid inaccurate conclusions from skewed results. The most complete picture of the taxonomic and functional profile of a microbial community is obtained by employing a combination of molecular techniques.

"Où peut-on trouver des microbes, et comment survivent-ils dans ces lieux ?" sont des questions essentielles afin de comprendre la vie sur Terre. Les populations bactériennes du sol sont connues pour jouer un rôle important dans les cycles biogéochimiques, l'entretien des sols, les effets climatiques et l'agriculture.Dans ce travail, j'ai utilisé la technique de pyroséquençage, via le produit d’une PCR d’ADNr 16S amplifiée extraite d’ADN totale, afin de révéler les populations bactériennes présentes dans quatre environnements inhabituels et oligotrophes différents:A. Les écosystèmes saumâtres sont largement distribués sur Terre et sont représentés par des systèmes aquifères salés et des sols salins. Nous avons examiné la composition bactérienne des sédiments des estuaires, sols saumâtres et des échantillons de sol sablonneux de la région de Camargue, échantillonnés pendant deux années consécutives. Les membres appartenant au phylum Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria et Actinobactéries ont été trouvés principalement dans les sols et sédiments. Nous avons constaté que les membres de ces groupes bactériens étaient associés principalement à des bactéries halophiles, sulfatoréductrices (SRB), nitratoréductrices et coliformes, dont leurs proportions ont probablement été affectées par la salinité et leurs localisations géographiques.B. Les bactéries associées à la rhizosphère des plantes sont connues pour jouer un rôle essentiel dans les cycles biogéochimiques, la nutrition des plantes et la lutte biologique contre les maladies végétales. Nous avons examiné les populations bactériennes de la rhizosphère du riz (Oryza sativa) en fin de croissance dans la région de la Camargue en 2013 et 2014. Les populations bactériennes les plus abondantes se sont révélées être des membres appartenant au phylum Proteobacteria, Acidobacteria, Chloroflexi et Gemmatimonadetes. Les genres bactériens auxquels appartiennent ces différents phylums sont connus pour participer dans des processus biogéochimiques du sol, tel que la nitrification, la dénitrification, l'oxydation, ainsi que comme agents de control biologique. Les proportions bactériennes trouvées varient considérablement en fonction de leur localisation géographique et selon l’année d’échantillonnage.C. Nous avons examiné les sols de surface de "Padza de Dapani" situés sur l'île de Mayotte au large de la côte est de l'Afrique, car cette région n’est pas un vrai désert, mais y ressemble due à l’érosion du sol. Les sols de Mayotte sont acides, oligotrophes et minéralisées, et leur population bactérienne principale appartient aux phylums des Actinobactéries, Proteobacteria et Acidobacteria. Un fait intéressant, les membres des genres Acinetobacter, Arthrobacter, Burkholderia et Bacillus sont prédominants dans nos échantillons, comme observé dans des déserts (asiatiques) chauds et jouant probablement un rôle dans la minéralisation des sols, expliquant la désertification.D. Les régions arides de la Terre constituent &gt; de 30% de la surface continentale et les sols oligotrophes sont soumis à des facteurs environnementaux difficiles tels que la faible pluviométrie moyenne annuelle, l'exposition aux UV et les grandes fluctuations de température. Nous avons examiné les populations bactériennes présentes dans la rhizosphère des plantes pionnières et les sols de surface du désert de Jizan d'Arabie Saoudite. Les phylums bactériens les plus abondants appartiennent aux groupes des Bacteroidetes, Proteobacteria et Firmicutes qui diffèrent entre la rhizosphère des plantes étudiées par rapport à la surface du sol, à l'exception de la plante "Panicum Turgidum" qui contient des proportions élevées (70%) des membres appartenant au genre Flavobacterium<br>“What microbes are where, and how do they live there” is now an essential question to understand life on Earth, even when comparing seemingly similar ecosystems in different locations. Soil bacterial populations are known to play important roles in biogeochemical cycles, soil maintenance, climatic effects and agriculture. I used pyrosequencing of PCR amplified 16S rDNA from total extracted DNA in order to reveal the bacterial populations living in four different unusual and oligotrophic environments: A. Saline areas are widely distributed on Earth’s and are represented by both saline lakes and saline soils. We examined the bacterial composition of estuary sediments, brackish and sandy soil samples from the Camargue region (Rhône delta in southern France) sampled in two consecutive years. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Acidobacteria and Actinobacteria phyla were found principally in saline sediment and soil samples. We found that members from these phyla were associated principally to halophilic bacteria, sulphate reducing bacteria (SRB), nitrate reducing bacteria and coliforms, and that their varying proportions were likely affected by salinity and geographical location. B. Bacterial populations associated with the rhizosphere of plants are known to play essential roles in biogeochemical cycles, plant nutrition and disease biocontrol. We examined the bacterial populations of the rhizosphere of rice (Oryza sativa) growing in the Camargue region in 2013 and 2014. The most abundant bacterial populations were found to be members belonging to the Proteobacteria, Acidobacteria, Chloroflexi and Gemmatimonadetes phyla. The genera members belong these phyla were found to participate in soil biogeochemical processes such as nitrification, denitrification, oxidation, as well as act as biocontrol agents. The bacterial populations were found to significantly vary by geographical location as well by year of collection. C. We examined the surface soils from “Padza de Dapani” on the island of Mayotte off the east coast of Africa, as this region is not a true (hot) desert, but resembles one due to extensive soil erosion. In the acidic, oligotrophic and mineralized soil samples from Mayotte, members of the Actinobacteria, Proteobacteria and Acidobacteria phyla dominated the bacterial populations. Interestingly, members of the genera Acinetobacter, Arthrobacter, Burkholderia and Bacillus were found to be predominant in our samples, as is also observed in hot (Asian) deserts and may play roles in soil mineral weathering, thus helping to understand desertification processes. D. Earth’s arid regions comprise &gt;30% of the continental surface and the oligotrophic soils are subjected to harsh environmental factors such as low average annual rainfall, high UV exposure and large temperature fluctuations. We examined the bacterial populations present in the rhizosphere of pioneer plants and surface soils in the Jizan desert of Saudi Arabia. The most abundant bacterial phyla belonged to the Bacteroidetes, Proteobacteria and Firmicutes phyla that were different between the rhizosphere of plant versus these from surface sand, with the exception of the plant “Panicum Turgidum”, which contain in its rhizosphere high proportions (70%) of members belonging to the Flavobacterium genus

Given the high salinity, prevailing annual high temperatures, and ultra-oligotrophic conditions in the Red Sea isolation and characterization of important microbial groups thriving in this environment is important in understanding the ecological significance and metabolic capabilities of these communities. By using a high-­throughput cultivation technique in natural seawater amended with minute amounts of nutrients, members of the rare biosphere (PS1), methylotrophic Betaproteobacteria (OM43), and the ubiquitous and abundant SAR11 group (Pelagibacterales), were isolated in pure culture. Phylogenetic analyses of Red Sea isolates along with comparative genomics with close representatives from disparate provinces revealed ecotypes and genomic differentiation among the groups. Firstly, the PS1 alphaproteobacterial clade was found to be present in very low abundance in several metagenomic datasets form divergent environments. While strain RS24 (Red Sea) harbored genomic islands involved in polymer degradation, IMCC14465 (East (Japan) Sea) contained unique genes for degradation of aromatic compounds. Secondly, methylotrophic OM43 bacteria from the Red Sea (F5, G12 and H7) showed higher similarities with KB13 isolate from Hawaii, forming a ‘H-­RS’ (Hawaii-­Red Sea) cluster separate from HTCC2181 (Oregon isolate). HTCC2181 members were shown to prevail in cold, productive coastal environments and had an nqrA-­F system for energy generation by sodium motive force. On the contrary, H-­RS cluster members may be better adapted to warm and oligotrophic environments, and seem to generate energy by using a proton-­translocating NADH:Quinone oxidoreductase (complex I; nuoA-­N subunits). Moreover, F5, G12, and H7 had unique proteins related to resistance to UV, temperature and salinity, in addition to a heavy metal ‘resistance island’ as adaptive traits to cope with the environmental conditions in the Red Sea. Finally, description of the Red Sea Pelagibacterales isolates from the Ia (RS39) and Ib (RS40) subgroups, principally revealed unique putative systems for iron uptake and myo-inositol utilization in RS39, and a potential phosphonates biosynthetic pathway present in RS40. The findings presented here reflect how environments influence the genomic repertoire of microbial communities and shows novel metabolisms and putative pathways as unique adaptive qualities in diverse microbes encompassing from rare to predominant bacterioplankton groups from the Red Sea.

Depuis la découverte d’archées capables d’oxyder l’ammoniac en milieu aérobie, de nombreuses études ont mesuré en simultané les taux de nitrification et la diversité des organismes oxydant l’ammoniac dans la colonne d’eau des milieux marins. Malgré l’importance globale des lacs d’eau douce, beaucoup moins d’études ont fait la même chose dans ces milieux. Dans cette étude, nous avons évalué l’importance de la nitrification et caractérisé la communauté microbienne responsable de la première étape limitante de la nitrification dans un lac tempéré durant une année entière. L’utilisation de traceur isotopique 15NH4 nous a permis de mesurer des taux d’oxydation d’ammoniac à deux profondeurs dans la zone photique tout au long de l’année. Les taux d’oxydation d’ammoniac varient de non détectable à 333 nmol L-1 j-1 avec un pic d’activité sous la glace. De toutes les variables environnementales mesurées, la concentration d’ammonium dans la colonne d’eau semble avoir le plus grand contrôle sur les taux d’oxydation d’ammoniac. Nous avons détecté la présence d’archées (AOA) et de bactéries oxydante d’ammoniac (BOA) à l’aide de tests par réaction en chaîne de la polymérase (PCR) ciblant une partie du gène ammoniac monoxygénase (amoA). Les AOA et les BOA ont été détectées dans la zone photique du lac, cependant seules les AOA étaient omniprésentes durant l’année. Le séquençage du gène amoA des archées révèle que la majorité des AOA dans le lac sont membres du groupe phylogénétique Nitrosotalea (également appelé SAGMGC-1 ou groupe I.1a associé), ce qui confirme la pertinence écologique de ce groupe dans les eaux douces oligotrophes. Globalement, nos résultats indiquent l’hiver comme étant un moment propice pour l’oxydation de l’ammoniac dans les lacs tempérés. Cette étude fournit un point de référence pour la compréhension du processus d’oxydation de l’ammoniac dans les petits lacs oligotrophes.<br>Since the discovery that some archaea are able to oxidize ammonia aerobically, several studies have focused on measuring nitrification rates and identifying the diversity of planktonic ammonia oxidizers in marine systems. Despite the global importance of freshwater lakes, far fewer studies have done the same in these ecosystems. Here we investigated the importance of nitrification and characterize the microbial community catalyzing the first rate-limiting step of nitrification over an annual cycle in a temperate lake. The measurements of ammonia oxidation rates, using the 15NH4+ isotope tracer method, at two depths in the photic zone show that this process occurred throughout the entire year in the lake. Rates of ammonia oxidation ranged from undetectable to 333 nmol L-1 d-1 with a peak of activity during winter. Off all environmental variables measured, ammonium concentrations in the water-column seem to have the strongest effect on the magnitude of ammonia oxidation rates. We detected the presence of ammonia-oxidizing archaea (AOA) and bacteria (AOB) using polymerase chain reaction (PCR) assays targeting part of the ammonia monooxygenase (amoA) gene. Both AOA and AOB were detected in the photic zone of the lake, although only AOA were omnipresent over the year. The sequencing of archaeal amoA genes reveals that most of the AOA in the lake are members of the Nitrosotalea cluster (also referred as SAGMGC-1 or group I.1a associated), which confirms the ecological relevance of this cluster in oligotrophic freshwaters. Altogether, our results indicate that winter may be a critical time for ammonia oxidation in temperate lakes and provide a baseline for the understanding of ammonia oxidation in small oligotrophic lakes.