Constraining the interpretation of 2-methylhopanoids through genetic and phylogenetic methods

Hopanoids are a class of sterol-like lipids produced by select bacteria. Their preservation in the rock record for billions of years as fossilized hopanes lends them geological significance. Much of the structural diversity present in this class of molecules, which likely underpins important biological functions, is lost during fossilization. Yet, one type of modification that persists during preservation is methylation at C-2. The resulting 2-methylhopanoids are prominent molecular fossils and have an intriguing pattern over time, exhibiting increases in abundance associated with Ocean Anoxic Events during the Phanerozoic. This thesis uses diverse methods to address what the presence of 2-methylhopanes tells us about the microbial life and environmental conditions of their ancient depositional settings. Through an environmental survey of hpnP, the gene encoding the C-2 hopanoid methylase, we found that many different taxa are capable of producing 2-methylhopanoids in more diverse modern environments than expected. This study also revealed that hpnP is significantly overrepresented in organisms that are plant symbionts, in environments associated with plants, and with metabolisms that support plant-microbe interactions; collectively, these correlations provide a clue about the biological importance of 2-methylhopanoids. Phylogenetic reconstruction of the evolutionary history of hpnP revealed that 2-methylhopanoid production arose in the Alphaproteobacteria, indicating that the origin of these molecules is younger than originally thought. Additionally, we took genetic approach to understand the role of 2-methylhopanoids in Cyanobacteria using the filamentous symbiotic Nostoc punctiforme. We found that hopanoids likely aid in rigidifying the cell membrane but do not appear to provide resistance to osmotic or outer membrane stressors, as has been shown in other organisms. The work presented in this thesis supports previous findings that 2-methylhopanoids are not biomarkers for oxygenic photosynthesis and provides new insights by defining their distribution in modern environments, identifying their evolutionary origin, and investigating their role in Cyanobacteria. These efforts in modern settings aid the formation of a robust interpretation of 2-methylhopanes in the rock record.

The vertical distribution of zooplankton in the Goggausee (the influence of algae and Chaoborus flavicans) [Translation from: Carinthia II 166/186 373-385, 1976]

The Goggausee, a small, shallow, meromictic lake(700m long, 150m wide, max. depth=12m, mean depth=6m), was the site of a week long study (19-26 May 1974) of the limnology department of the University of Vienna. The study comprised pollen analysis and palaeolimnological studies on the one hand, as well as a stock- taking of physiochemical factors, primary production, bacteria, zooplankton, zoo benthos and fish on the other. This paper studies the zooplankton of the lake. The Goggausee is a meromictic lake, with its anoxic deep water, that restricts the vertical distribution of most zooplankton. The aim of the study was to pursue the vertical distribution of the rotifers and Crustacea. Density of individuals, biomass, percentages of zooplankton together and crustaceans and rotifers as groups. Special consideration is given to the the Dipteran Chaoborus flavicans.

Physiological ecology of the ciliated protozoon Loxodes

Loxodes faces special problems in living close to the oxic-anoxic boundary. In tightly-stratified ponds like Priest Pot its optimum environment may be quite narrow and it can be displaced by the slightest turbulence. Loxodes cannot sense an O sub(2) gradient directly but its ability to perceive gravity allows it to make relatively long vertical migrations. It is also sensitive to light and oxygen and it uses these environmental cues to modulate the parameters of its random motility: in the dark, it aggregates at a low O sub(2) tension and in bright light it aggregates in anoxic water. The oxic-anoxic boundary is also a zone where O sub(2) may be a scarce and transient resource, but Loxodes) can switch to nitrate respiration and exploit the pool of nitrate that often exists close to the base of the oxycline.

Geoquímica orgânica aplicada à formação Irati, área de Herval, Rio Grande do Sul (RS), bacia do Paraná

Esta dissertação tem por objetivo o estudo geoquímico detalhado em poço da Bacia do Paraná, mais especificamente na cidade de Herval (RS), visando preencher algumas das lacunas existentes em termos de geoquímica orgânica da Formação Irati. Com base nos dados de carbono orgânico total, enxofre total, resíduo insolúvel, raios-gama, isótopos de carbono da matéria orgânica, pirólise Rock-Eval e biomarcadores individualizaram-se dez unidades quimioestratigráficas. Biomarcadores foram usados na caracterização dos ambientes deposicionais, na discriminação da origem da matéria orgânica e da influência da litologia. O ambiente deposicional das unidades A, B, C é óxico com salinidade normal. O topo da unidade B representa a superfície de inundação máxima, onde os valores de COT aumentam. Com base nos biomarcadores caracterizou-se um paleoambiente deposicional com alguma tendência anóxica. Nas unidades D e G ocorrem os folhelhos intercalados com carbonatos. Nestas, a concentração de COT é acima de 1%, porém, somente na unidade G há bom potencial gerador para gás e condensado. As unidades E e I apresentam elevados teores de carbono orgânico total, chegando a 16%. Os dados de pirólise Rock-Eval indicam um bom a excelente potencial gerador para óleo e gás. Os dados isotópicos possibilitaram a divisão da Formação Irati, no poço em estudo, em três ciclos. O primeiro, da base para o topo, corresponde ao Membro Taquaral, os outros dois correspondem ao Membro Assistência. No Membro Assistência o δ13C varia de acordo com a salinidade, aumento da produtividade primária e da preservação da matéria orgânica (anoxia).

L'oxygène dissous en Lagune Ebrié: Influences de l'hydroclimat et des pollutions

The hydrology of the Ebrie coastal lagoon in Abidjan area is summarized. The authors describe the oxygenation in that area during the two extreme seasons of the hydrological cycle: the low-water season (March-April) and the high-water season (Sept-Oct). The influences of the continental and oceanic waters, photosynthesis, exchanges with the atmosphere and pollution are considered. The oxigen consumption of primary organic pollution represents from 9 to 12% of the content of the waters that circulates in the area. It is geographically very heterogeneous. The central basin, swept by strong marine and fresh water currents, shows a rather high level of water oxygenation. In the peripheric bays, water circulation and mixing are less important and pollution accelerates the natural eutrophic processes. During the low-water season, a vertical stratification is responsible for a bottom anoxic layer and the deposit of reduced organic silts. On the contrary, supersaturations, up to 200%, are recorded on the surface layer. During the high-water season the break of the vertical stratification sets the loose reduced silts into suspension and partly reoxygenates the bottom waters. A classification of the different areas, based on the oxygen vertical profiles is proposed.

Natural Variation In Recovery From A Short Period Of Anoxia Due To A cGMP-Dependent Protein Kinase in Drosophila melanogaster

[EN] Protein Kinase G (PKG) or cGMP-dependent protein kinases (PKG) have been shown to play an important role in resistance to abiotic stressors such as high temperatures or oxygen deprivation in Drosophila melanogaster. In Drosophila, the foraging gene encodes a PKG; natural variants for this gene exist, which differ in the level of expression of PKG: rovers (forR allele) which express high PKG levels, and sitters (forS allele) which express lower PKG levels. This project explores the differences in recovery from short periods of anoxia between natural variants (focusing on forS2, flies with a sitter gene in a rover background), as well as mutants with insertions in the foraging gene and RNAi recombinants that show a reduced PKG expression. The parameters measured were time to recovery and level of activity after anoxia. The results showed lower activity after anoxia in sitters than in rovers, reflecting a worse recovery from the anoxic coma in flies with lower PKG levels.

Historical nitrogen and phosphorus loadings to the northern Gulf of Mexico

Primary productivity in many coastal systems is nitrogen (N) limited; although, phytoplankton productivity may be limited by phosphorus (P) seasonally or in portions of an estuary. Increases in loading of limiting nutrients to coastal ecosystems may lead to eutrophication (Nixon 1996). Anthropogenically enhanced eutrophication includes symptoms such as loss of seagrass beds, changes in algal community composition, increased algal (phytoplankton) blooms (Richardson et al. 2001), hypoxic or anoxic events, and fish kills (Bricker et al. 2003).

Assessment of some physico-chemical parameters of River Ogun (Abeokuta, Ogun State, southwestern Nigeria) in comparison with national and international standards

This study assessed the physico-chemical quality of River Ogun, Abeokuta, Ogun state, Southwestern Nigeria. Four locations were chosen spatially along the water course to reflect a consideration of all possible human activities that are capable of changing the quality of river water. The water samples were collected monthly for seven consecutive months (December 2011 – June 2012) at the four sampling stations. pH, air temperature (℃), water temperature (℃), conductivity (µs/cm) and total dissolved solids (mg/L) were conducted in-situ with the use of HANNA Combo pH and EC multi meter Hi 98129 and Mercury-in-glass thermometer while dissolved oxygen (mg/L), nitrate (mg/L), phosphate (mg/L), alkalinity (mg/L) and hardness (mg/L) were determined ex-situ using standard methods. Results showed that dissolved oxygen, hydrogen ion concentration, total hardness and nitrate were above the maximum permissible limit of National Administration for Food, Drugs and Control (NAFDAC), Standard Organization of Nigeria (SON), Federal Environmental Protection Agency (FEPA), United States Environmental Protection Agency (USEPA), European Union (EU) and World Health Organization (WHO) for drinking water during certain months of the study period. Results also showed that water temperature and conductivity were within the permissible limits of all the standards excluding FEPA. However, total dissolved solids and alkalinity were within the permissible limits of all the standards. Adejuwon and Adelakun, (2012) also reported similar findings on Rivers Lala, Yobo and Agodo in Ewekoro local government area of Ogun state, Nigeria. Since most of the parameters measured were above the maximum permissible limits of the national and international standards, it can be concluded that the water is unfit for domestic uses, drinking and aquacultural purposes and therefore needs to be treated if it is to be used at all. The low dissolved oxygen values for the first four months was too low i.e. < 5 mg/L. This is most likely as a result of the amount of effluents discharged into the river. To prevent mass extinction of aquatic organisms due to anoxic conditions, proper regulations should be implemented to reduce the organic load the river receives.

Geochemical evidence for enhanced upwelling and organic productivity during the late Quaternary on the continental margin of northern California

EXTRACT (SEE PDF FOR FULL ABSTRACT): Laminated sediments are preserved in upper Pleistocene sections of cores collected on the continental slope at water depths within the present oxygen-minimum zone from at least as far north as the Klamath River and as far south as Point Sur. Comparison of sediment components in the laminae with those delivered to sediment traps as pelagic marine "snow" show the dark/light lamination couplets are indeed annual (varves). ... The presence of carbon-, sulfur-, and metal-rich sediments, as well as lack of bioturbation, all support the theory that the oxygen-minimum zone in the northeastern Pacific Ocean was more intense - in fact, anoxic - during the late Pleistocene in response to greater coastal upwelling and higher organic productivity.

Sea surface temperature and paleo-El Niño events in Santa Barbara Basin, AD 1841-1941

Like pages of a "natural coastal diary", successive layers of anoxic varved sediment in the central Santa Barbara Basin have been used by paleoceanographers to reconstruct aspects of past coastal climate. This report focuses on the end of the "Little Ice Age" (15th to 19th century) and on the beginning of this century, a period known to encompass extreme climate excursions and weather events in the Santa Barbara Basin and other parts of Southern California. El Niño events are known to disrupt Southern California's coastal ecosystems and to cause anomalous weather conditions, but El Niño events in Southern California before 1990 have been largely undocumented.

The near-AD 1600 multi-proxy puzzle

EXTRACT (SEE PDF FOR FULL ABSTRACT): A varve chronology with annual resolution (AD 1117-1992) has been developed recently for Santa Barbara Basin. Varve thickness and water content show an exponential trend consistent with expected patterns in the presence of sediment compaction over time. Annual varve thickness was decomposed into orthogonal components using singular spectrum analysis (SSA) to identify and retrieve inter-decadal oscillations. ... This suggests a connection with global-scale decadal cycles identified in the subtropical Pacific gyre circulation and, possibly, with solar-driven phenomena. The near-1600 AD event coincides with (a) a similarly sudden change of state in nearby Santa Monica Basin that triggered the onset of anoxic conditions and the preservation of laminated sediments, (b) an extreme drought over the American Southwest, (c) a transformation of the age structure in a number of forest populations throughout Arizona and New Mexico. Total organic carbon burial flux in Santa Barbara Basin varves also shows a marked change after AD 1600. A possible climatic link is proposed that involves pathways for moisture transport in the Southwest at decadal and longer time scales.

Euglenophytes in aquaculture ponds - their ecology and role in fish production

The ecology of euglenophytes and their role in fish production were studied in 12 small earthen ponds beside the Faculty of Fisheries, BAU from July to November 2001. Four experiments each with three replications were conducted and those were as follows: pond treated with both poultry droppings and cowdung (T1); pond treated with only poultry droppings (T2), and pond treated with only poultry droppings (T3), while the control (T4) where no organic manure was applied. Fishes comprising of rohu (Labeo rohita), catla ( Catla catla), mrigal ( Cirrhinus cirrhosus), silver carp (Hypophthalmichthys molitrix) and silver barb (Barbonymus gonionotus) were stocked at the same stocking density of (10,621 fish/ha) and species ratio (1:1:1:2:2). The stocked fishes were fed with a common supplemental diet comprising of mustard oil cake and rice polish (1:1) at the rate of 4% of body weight per day. The highest cell density of euglenophytes was found in the ponds of T2, where poultry droppings were applied and was followed by T1, where both poultry droppings and cow dung were applied. Higher temperature, nitrate-nitrogen, phosphate-phosphorous and acidic pH were found to be conducive for the bloom of noxious euglenophytes. The bloom was found to use up most of the nutrients resulting in reduction in the growth of beneficial plankters and planktivorous fishes. The SGR (%/day) of catla, rohu and mrigal was lower during heavy bloom period while that of silver carp and silver barb were comparatively higher. The mortality of fishes in a pond of T2 during the bloom period was possibly due to formation of anoxic situation (dissolved oxygen level as low as 0.34 mg/1) in the early mornings through bacterial decomposition of the settled dead individuals or due to the combined effect of anoxic situation and toxic metabolite secretion by the euglenophytes.

Management of euglenophytes in aquaculture ponds for improvement of fish production

Four experiments each with three replications were conducted in 12 experimental ponds to control the euglenophytes bloom viz. treatment 1 (T1, covering of one third of the water surface by duckweed (Lemna minor); treatment 2 (T2), application of 123.5 kg lime/ha/month; treatment 3 (T3), use of both duckweed as in T1 and lime as in T2; treatment 4 (T4) was considered as control where neither duckweed nor lime was applied. Fishes comprising of rohu (Labeo rohita), catla (Catla catla), mrigal ( Cirrhinus cirrhosus), silver carp (Hypophthalmichthys molitrix) and silver barb (Barbonymus gonionotus) were stocked at the rate of 1080 fishes/ha with the species ratio of 8:4:6:9:13, respectively. The lowest cell density of euglenophytes was found in the ponds of T3 followed by T2, and T1. In the ponds of T3, euglenophytes bloom did not occur possibly due to alkaline pH, shade and nutrient absorption by duckweed. Thin bloom was observed in the ponds of T1 where pH was neutral or slightly alkaline. The grazing on euglenophytes by the silver carp and silver barb also had some contribution in controlling the bloom. Growth of fishes was comparatively higher in the ponds of T3 and T1, which might be due to better water quality and availability of adequate food while the lower fish growth as recorded from the ponds of T4 might be due to euglenophytes bloom. Thick bloom inhibited light penetration which hampered photosynthesis and growth of other phytoplankton that are the preferred food of planktivorous fishes. Mortality of fishes in ponds having euglenophytes bloom was possibly due to formation of anoxic situation in the early morning or due to the combined effect of anoxic situation and toxic metabolites secretion by the euglenophytes.

Changes in phytoplankton communities and primary production

Lake Victoria is the second largest lake in the world (69000km2) by surface area, but it is the shallowest (69m maximum depth) of the African Great Lakes. It is situated across the equator at an altitude of 1240m and lies in a shallow basin between two uplifted ridges of the eastern and western rift valleys (Beadle 1974). Despite their tropical locations, African lakes exhibit considerable seasonality related to the alteration of warm, wet and cool, dry seasons and the accompanying changes in lucustrine stratification and mixing (Tailing, 1965; 1966; Melack 1979; Hecky& Fee 1981; Hecky& Kling,1981; 1987; Bootsma 1993; Mugidde 1992; 1993). Phytoplankton productivity, biomass and species composition change seasonally in response to variations in light environment and nutrient availability which accompany changes in mixed layer depth and erosion or stabilization of the metalimnion / hypolimnion (Spigel & Coulter 1996; Hecky et al., 1991; Tailing 1987). Over longer, millennial time scales, the phytoplankton communities of the African Great Lakes have responded to variability in the EastAfrican climate (Johnson 1996; Haberyan& Hecky, 1986) which also alters the same ecological factors (Kilham et al., 1986). Recently, over the last few decades, changes in external and or internal factors in Lake Victoria and its basin have had a profound inlluence on the planktic community of this lake (Hecky, 1993; Lipiatou et al., 1996). The lake has experienced 2-10x increases in chlorophyll and 2x increase in primary productivity since Tailing's observations in the early 1960s (Mugidde 1992, 1993). In addition to observed changes in the lake nutrient chemistry (Hecky & Mungoma, 1990; Hecky & Bugenyi 1992; Hecky 1993; Bootsma & Hecky 1993), the deep waters previouslyoxygenated to the sediment surface through most of the year are now regularly anoxic(Hecky et al., 1994).

Effects of sediment anoxia and light on turion germination and early growth of Potamogeton crispus

Potamogeton crispus is a cosmopolitan aquatic species and is widely used as a pioneer species for vegetation restoration of eutrophic lakes. However, many restoration projects applying P. crispus turions have not been successful. Earlier studies focused on effects of light and temperature on turion germination. The purpose of this study was to determine whether sediment anoxia and light interactively affected the turion germination and early growth of P. crispus. Anoxic conditions in the experiment were produced by adding sucrose to the sediment. The germination rate of the turions was 68-73% lower in the highly anoxic condition treatment than in the control. Medium light intensity (10% of natural light at the water surface) was more favorable for germination under slightly anoxic conditions than either low or high light intensity. The growth of newly-formed sprouts was also significantly inhibited by sediment anoxia. Photosynthesis and shoot biomass were reduced under sediment anoxia, whereas total chlorophyll content, root biomass, and soluble protein content were highest in the low anoxic condition treatment. Medium light improved net photosynthesis and biomass production of the sprouts. We conclude that turion germination and sprout growth can be significantly inhibited by sediment anoxia. Medium light intensity may alleviate this inhibition by anoxia, but light has little effect when sediment anoxia is severe. For the purposes of vegetation restoration, more attention should be paid to the role of sediment anoxia, and it is necessary to improve sediment and light conditions for turion germination and early growth of P. crispus in eutrophic lakes. These results will contribute to a more complete understanding of turion germination dynamics of P. crispus and will be useful for future restoration programs.