Influence of Hydrologic History on Nitrogen Cycling in Lake Sediments

Water quality is declining in freshwater lakes around the world due to environmental change and anthropogenic activities that threaten the physical, ecological, and geochemical integrity of freshwater ecosystems. Excess N and P in lakes can cause eutrophication, a major driver of water quality impairment that leads to excessive algal growth, or harmful algal blooms (HABs), and poses risks to recreation, fisheries, and public drinking water. Water level fluctuations in lakes are expected to become more frequent and intense as climate change increases periods of drought and alters precipitation patterns, and fluctuations may stimulate biogeochemical reactions in littoral sediments that add or remove bioavailable nutrients and impair water quality in lakes. This study assessed the effect of drying and rewetting on nitrogen cycling in littoral sediments at Utah Lake, a shallow, hypereutrophic lake in Utah, USA. Nitrogen fluxes were assessed during dry summer conditions and transitional fall conditions in three field sampling campaigns across three zones (saturated, littoral, and upland) with different hydrologic histories. Sediment and water samples were analyzed for bioavailable nutrients (sediment nitrate, and sediment ammonium) and sediment nitrogen cycling (denitrification, mineralization, nitrification, and microbial biomass C and N). Our results showed considerable variability across zones. High levels of sediment ammonium were found in the lake zones and in winter across all zones, while high levels of nitrate and rates of mineralization were found in the upland zones. Carbon availability sediment moisture, and pH strongly influenced these results. We hypothesize that if lake levels decrease and more sediments are exposed, there is potential for bioavailable nutrients to leach into the groundwater and contribute to internal nitrogen loading. The results of this study will contribute to the creation of an internal nutrient loading budget of Utah Lake. With this data, we will better understand the relationships between external and internal nutrient loading to Utah Lake. From there, the most significant sources of nutrients to the lake will be identified and we can begin to reduce nutrient loads in order to manage eutrophication

Bacterial and Archaeal Communities Change With Intensity of Vegetation Coverage in Arenized Soils From the Pampa Biome

Arenization occurs in regions that present sandy soils with normal rainfall levels. Predatory use of environmental sources, the dissolution of arenitic rocks and reworking of non-consolidated surface sands intensify this degradation scenario. Thus, this work aimed to evaluate the impact of the arenization process in the Brazilian Pampa Biome and how this phenomenon affects the soil microbial and plant communities. For this purpose, three arenized areas in Southern Brazil (Pampa Biome) were selected and, in each one, three sampling points were studied: arenized (ARA), arenized to grassland transition (AGT), and grassland (GRA) areas. In the three sampling points, soils presented low levels of nutrients, organic matter, mud and pH acidic in all regions but, the presence of vegetation coverage in AGT and GRA areas preserved the topsoil structure. Our study related ARA with bacterial families Alcaligenaceae, Pseudomonadaceae, and Xanthomonadaceae. AGT with bacterial families Bacillaceae and Burkholderiaceae, and plant species Melinis repens (Willd.) Zizka and Paspalum stellatum Humb. and Bonpl. ex Flüggé, and GRA with bacterial families Koribacteraceae, Hyphomicrobiaceae, and Chthoniobacteraceae, and plant species Croton subpannosus Müll.Arg. ex Griseb., Piptochaetium montevidense (Spreng.) Parodi and Elyonurus sp. The three studied areas (as well as sampling points) present soils extremely poor in nutrients with sandy texture, and the bacterial and plant composition well known to be resistant to environmental stresses were dominant. The vulnerability of these areas causes a degradation scenario, which is worsened by agricultural activities. However, in general, this phenomenon is a natural process that occurs mainly due to soil characteristics (poor soils) and climatic variations

Microbial regulation of pesticide degradation coupled to carbon turnover in the detritusphere

Many soil functions, such as nutrient cycling or pesticide degradation, are controlled by microorganisms. Dynamics of microbial populations and biogeochemical cycling in soil are largely determined by the availability of carbon (C). The detritusphere is a microbial hot spot of C turnover. It is characterized by a concentration gradient of C from litter (high) into the adjacent soil (lower). Therefore, this microhabitat is very well suited to investigate the influence of C availability on microbial turnover. My thesis aimed at the improved understanding of biochemical interactions involved in the degradation of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) coupled to C turnover. In the detritusphere gradients of organic matter turnover from litter into the adjacent soil could be identified. Increased C availability, due to the transport of dissolved organic substances from litter into soil, resulted in the boost of microbial biomass and activity as well as in the acceleration of MCPA degradation. Fungi and bacterial MCPA-degraders benefited most from litter-C input. Accelerated MCPA degradation was accompanied by increased incorporation of MCPA-C into soil organic matter. The experimental results show that the transport of dissolved organic substances from litter regulates C availability, microbial activity and finally MCPA degradation in the detritusphere. In general, litter-derived organic compounds provide energy and resources for microorganisms. The following possible regulation mechanisms were identified: i) Litter might directly supply the co-substrate alpha-ketoglutarate (or surrogates) required for enzymatic oxidation of MCPA by bacterial MCPA degraders. Alternatively it might provide additional energy and resources for production and regeneration of the needed co-substrate. ii) Additional litter-C might alleviate substrate limitation of enzyme production by bacteria and bacterial consortia resulting in an increased activity of specific enzymes attacking MCPA. iii) Litter-derived organic substances might stimulate MCPA degradation via fungal co-metabolism by unspecific extracellular enzymes, either directly by inducing enzyme production, or by supplying primary substrates that provide the energy consumed by co-metabolic MCPA transformation. A new biogeochemical model abstracts these regulation mechanisms in such a way that C availability controls physiological activity, growth, death and maintenance of microbial pools. Based on a global sensitivity analysis, 41% (n=33) of all considered parameters and input values were classified as very important and important. These mainly include biokinetic parameters and initial values. The calibration of the model allowed to validate the implemented regulation mechanisms of accelerated MCPA degradation. The Pareto-analysis showed that the model structure was adequate and the identified parameter values were reasonable to reproduce the observed dynamics of C and MCPA. The model satisfactorily matched observed abundances of gene-markers of total bacteria and specific MCPA degraders. However, it underestimated the steep increase of fungal ITS fragments, most probably because this gene-marker is only inadequately suited as a measure of fungal biomass. The model simulations indicate that soil fungi primarily benefit from low-quality C, whereas bacterial MCPA-degraders preferentially use high-quality C. According to the simulations, MCPA was predominantly transformed via co-metabolism to high-quality C. Subsequently, this C was primarily assimilated by bacterial MCPA-degraders. The highest turnover of litter-derived C occurred by substrate uptake for microbial growth. Input and microbial turnover of litter-C stimulated MCPA degradation mainly in a soil layer at 0-3 mm distance to litter. As a consequence of this, a concentration gradient of MCPA formed, which triggered the diffusive upward transport of MCPA from deeper soil layers into the detritusphere. The results of the three studies suggest: The detritusphere is a biogeochemical hot spot where microbial dynamics control matter cycling. The integrated use of experiments and mathematical modelling gives detailed insight into matter cycling and dynamics of microorganisms in soil. Microbial communities need to be explicitly considered to understand the regulation of soil functions.Viele Bodenfunktionen, wie zum Beispiel die Umsetzung von Nährstoffen oder der Abbau von Pestiziden, werden massgeblich durch Mikroorganismen gesteuert. Die Verfügbarkeit von Kohlenstoff (C) bestimmt dabei signifikant die Dynamik der mikrobiellen Biomasse und biogeochemischer Umsetzungsprozesse im Boden. Ein hot spot des mikrobiellen C-Umsatzes ist die Detritusphäre. Sie ist durch einen starken Gradienten der C-Konzentration von der Streu (hoch) in den angrenzenden Boden (niedriger) geprägt. Daher lässt sich der Einfluss der C-Verfügbarkeit auf mikrobielle Umsatzprozesse gerade in der Detritusphäre sehr gut untersuchen. Ziel meiner Dissertation war es, die am gekoppelten Pestizid-Abbau und C-Umsatz beteiligten biogeochemischen Wechselwirkungen in der Detritusphäre besser zu verstehen. Dabei diente das Herbizid 4-Chlor-2-methylphenoxyessigsäure (MCPA) als ein Modell-Xenobiotikum. In der Detritusphäre zeigten sich Gradienten des Stoffumsatzes von der Streu in den angrenzenden Boden. Die erhöhte C-Verfügbarkeit in der Detritusphäre, infolge des Transports gelöster organischer Verbindungen aus der Streu in den Boden, führte zu einem Anstieg der mikrobiellen Biomasse und Aktivität sowie zu einem beschleunigten MCPA-Abbau. Pilze und bakterielle MCPA-Abbauer profitierten am stärksten von eingetragenem Streu-C. Der beschleunigte MCPA-Abbau ging mit verstärktem Einbau von MCPA-C in die organische Bodensubstanz einher. Die experimentellen Ergebnisse zeigen, dass der Transport gelöster organischer Verbindungen aus der Streu die C-Verfügbarkeit und in der Folge sowohl die mikrobielle Aktivität als auch den MCPA-Umsatz im Boden reguliert. Generell stellen eingetragene Verbindungen aus der Streu Energie und Ressourcen für Mikroorganismen zur Verfügung. Als mögliche Regulationsmechanismen wurden identifiziert: i) Streu könnte direkt das Co-Substrat alpha-Ketoglutarat (oder Surrogate) liefern, das für die enzymatische Oxidation von MCPA durch bakterielle MCPA-Abbauer gebraucht wird. Alternativ könnten organische Verbindungen aus der Streu zusätzliche Energie und Ressourcen zur Produktion und Regeneration des benötigten Co-Substrats liefern. ii) Zusätzlicher Streu-C könnte die Substratlimitierung der Enzymproduktion von Bakterien und bakteriellen Konsortien vermindern und in der Folge zu höherer Aktivität von spezifischen MCPA-angreifenden Enzymen führen. iii) Organische Substanzen aus der Streu könnten den co-metabolischen MCPA-Abbau durch unspezifische extrazelluläre Enzyme von Bodenpilzen stimulieren, entweder direkt über die Induktion der Enzymproduktion oder indem aus Primärsubstraten Energie, die für die co-metabolische MCPA-Transformation verbraucht wird, gewonnen werden kann. Ein neues biogeochemisches Modell abstrahiert diese Regulationsmechanismen, indem physiologische Aktivität, Wachstum, Absterben und Erhaltungsstoffwechsel der mikrobiellen Pools durch die C-Verfügbarkeit kontrolliert werden. Auf Basis einer globalen Sensitivitätsanalyse des Modells wurden 41% (n = 33) aller berücksichtigten Parameter bzw. Eingangsgrößen als sehr wichtig und wichtig klassifiziert. Dazu zählten vor allem biokinetische Parameter und Anfangswerte. Die Pareto-Analyse ergab, dass die Modellstruktur geeignet war und sinnvolle Parameterwerte identifiziert werden konnten, um die gemessene Dynamik von C und MCPA abzubilden. Das Modell konnte gemessene Abundanzen bakterieller Gen-Marker zufriedenstellend wiedergeben. Es unterschätzte allerdings den extrem starken Anstieg der pilzlichen ITS-Fragmente, höchstwahrscheinlich weil dieser Gen-Marker nur unzureichend als Maß für die gesamte pilzliche Biomasse geeignet ist. Die Modellsimulationen zeigten, dass Bodenpilze vor allem von C niedriger Qualität profitierten, während bakterielle MCPA-Abbauer bevorzugt C hoher Qualität nutzten. In den Simulationen wurde MCPA überwiegend durch pilzlichen Co-Metabolismus zu C von hoher Qualität umgesetzt. Dieser C wurde anschließend primär von spezifischen bakteriellen MCPA-Abbauern assimiliert. Der größte Umsatz von eingetragenem Streu-C erfolgte durch Substrataufnahme für mikrobielles Wachstum. Eintrag und mikrobieller Umsatz von Streu-C förderte den Abbau von MCPA vor allem in einer Bodenschicht in 0-3 mm Abstand zur Streu. Infolgedessen bildete sich ein Gradient der MCPA-Konzentration aus, der den diffusiven MCPA Transport aus tieferen Bodenschichten in die Detritusphäre antrieb. Die Ergebnisse der Studien zeigen: i) Die Detritusphäre ist ein biogeochemischer hot spot, in dem Stoffumsätze durch die mikrobielle Dynamik kontrolliert werden. ii) Die integrierte Anwendung von Experimenten und mathematischer Modellierung erlaubt einen erweiterten Einblick in die Dynamik von Stoffen und Mikroorganismen im Boden. iii) Mikrobielle Gemeinschaften müssen explizit berücksichtigt werden, um die Regulation von Bodenfunktionen zu verstehen

The role of forest trees and their mycorrhizal fungi in carbonate weathering and phosphorus biogeochemical cycling

Over millions of years, atmospheric CO2 concentrations, and Earth’s climate, are regulated by continental silicate weathering and associated marine carbonate deposition. On this geological timescale, carbonate weathering has no net effect on CO2 drawdown. However, over the coming decades-to-centuries, accelerated weathering of carbonate rocks may provide a sink for anthropogenic CO2 emissions and increase alkalinity flux to the oceans to counteract ocean acidification. Recent experimental evidence strongly supports trees and their associated mycorrhizal fungi as key drivers of silicate mineral weathering; however, their role in the context of carbonate weathering is largely unknown. Carbonate lithology is abundant globally and underlies many boreal and temperate forest ecosystems in the northern hemisphere. If biological enhancement of carbonate weathering by forests occurs, this might presents a new opportunity for CO2 sequestration. This thesis presents results from a 14-month field experiment at the UK's national pinetum investigating carbonate rock weathering under a common climate. Overall, I find original evidence for biotic enhancement of calcite- and dolomite weathering by an evolutionary diverse range of trees that host either arbuscular (AM) or ectomycorrhizal (EM) root-associating fungal symbionts. Recent soil analyses are integrated with a re-interpretation of historic data to provide an 85-year record of in-situ soil development under different forestry species. This study challenges the classic dogma that divergence of properties is driven by the major tree functional groups, angiosperms and gymnosperms. Instead, we find that over decades, mycorrhizal functional type plays a dominant role in determining soil physico- chemical characteristics, and conditions generated by EM fungi are likely to enhance mineral weathering. Field trials next investigated the impact of tree-mycorrhizal functional group on weathering of the four main carbonate rock types (chalk, limestone, marble and dolomite) and a quartz silicate. Under EM trees carbonate rock grain dissolution was 12 times faster that silicate weathering. In the initial 3 months, calcite weathering intensity increased from gymnosperm to angiosperm species and from AM to later, but independently-evolved EM fungal partnerships. More extensive weathering after 6 months, especially within EM forest soils, confirms the importance of these fungi for carbonate mineral dissolution and nutrient mobilisation. This effect is linked to rhizosphere acidification by EM fungi and is confirmed by a parallel study of tree species’ influence on soil chemistry. Both AM and EM fungi facilitate the mobilisation of nutrient elements, which are provided to their host plants in exchange for carbon from photosynthesis. I applied a suite of nanoscale surface analysis techniques (VSI, SEM) to quantify mineral alteration and provide direct evidence for mycorrhizal involvement in carbonate weathering in the field. Fungal hyphae preferentially colonised chalk and quartz silicate grains, which contained the highest concentrations of phosphorus (P), a growth limiting elemental nutrient. P was selectively depleted from silicate grains, especially in EM forest soils, but accumulated on carbonates. Although the origin of this accumulated P remains uncertain, extensive analyses of different potential P-pools indicated it is likely to be inorganic, but accumulated via active microbial import. These findings lead to new insights linking carbonate weathering with phosphorus biogeochemical cycling in soils. Results show that P from the surrounding environment is concentrated on carbonate grains and this potentially provides a renewable P resource accessible to host trees. Overall, this thesis builds new support for the role of mycorrhizal partnerships in shaping soil properties important for accelerating carbonate rock weathering (Chapter 2); presenting the first field-based evidence for the enhancement of carbonate dissolution by tree roots and their associated mycorrhizal partners (Chapters 3-5) and generating new insights into biogeochemical P cycling in soils (Chapter 4). More broadly, these findings suggest targeted reforestation/afforestation with EM-tree taxa on carbonate-rich terrain as a possible regional-scale land management strategy for promoting short-term anthropogenic CO2 sequestration and perhaps helping ameliorate ocean acidification

Abiotic and biotic influences on acetochlor fate in pristine soils and subsoils

Soil exists as an intricate matrix in which a wide variety of biotic (e.g. enzymes, macro-, micro- fauna) and abiotic (e.g. clay minerals, oxides, humic substances, organo-mineral composites) factors interact, forming a highly dynamic and heterogeneous environment. Upon release into this complex environment, pesticides are subject to a number of processes that result in sorption to soil surfaces, biodegradation/transformation, or leaching. Pesticides leaching through a soil profile to groundwater will be exposed to changing environmental conditions as different horizons with distinct physical and chemical properties are encountered. The way these divergent soil properties influence pesticide degradation and retention needs to be assessed to allow accurate predictions of environmental fate and more efficient management practices. To address this issue, soil cores were taken from two soil profiles (surface textures: silty clay loam and loamy sand), and samples taken from 0-30 cm (surface), 1.0-1.3 m (mid) and 2.7-3.0 m (deep; clay) and 3.9-4.2 m (deep; sand). A variety of soil biotic (microbial numbers, microbial biomass and enzyme activities) and abiotic (pH, organic matter content, texture, CEC) properties were measured for each soil. Microbial numbers and enzyme activities were found to decrease significantly with soil depth and were positively correlated to the organic matter content. An exception was urease activity in the clay soil, under buffered conditions, where a 2.9-fold greater activity was exhibited in the mid soil compared to the surface soil. Although microbial numbers did decrease with soil depth substantial numbers of bacteria were still isolated from the deep soils (direct counts: 5.6 x 108 sand, 4.5 x 108 clay) despite only representing 4.7 and 1.7 % of those in the respective surface soils. Equilibrium sorption and desorption isotherms of 14C-ring-labelled acetochlor revealed that the sorptive behaviour of this pesticide varied with soil depth. The difference in retention capacity with soil depth was strongly correlated to soil organic carbon content. Differential desorption characteristics were also apparent between different particle size fractions, highlighting the influence of microsite variation on pesticide fate in soil, and this was also related to the soil organic carbon content of the fractions. Degradation and sorption processes were coupled in a long-term (100 d) fate study of acetochlor, under laboratory conditions. Acetochlor was shown to dissipate under biotic and sterile conditions, with the formation of a number of environmentally stable metabolites including ethanesulphonic acid and oxanilic acid derivatives. Mineralization was not a major fate process with less than 5 % of the initially applied acetochlor recovered as 14C02. Nonextractable residue formation occurred instantly and rapidly progressed over the initial 21 d of incubation. Nonextractable residues were unevenly distributed between soil size factions, concentrated in the macroaggregate fractions. Nonextractable residue formation was enhanced under biotic conditions for those fractions. Under biotic conditions, DT50 values of 9.32, 12.32 and 12.56 d were determined for acetochlor in clay surface, mid and deep soil, respectively. Further experiments are needed to generate more data, to enable accurate modelling of pesticide fate

Microbial volatile fingerprints : potential use for soil/water diagnostics and correlation with traditional microbial parameters

This project used an electronic nose (E-nose) system composed of an array of 14 nonspecific conducting polymer sensors for soil and water diagnostics, based on qualitative microbial volatile production patterns. It tested the feasibility of using soil microbial volatile fingerprints for detecting and monitoring changes in microbial activity in three soils, as a response to key environmental factors such as temperature (16, 25, 37°C), water potential (-0.7, -2.8 MPa), and nutrient (glucose and wheat straw) inputs. It also investigated their potential use for atrazine detection when applied to soil at usual field application rates (2.5 ppm) as well as for monitoring its bioremediation using the white-rot fungus Trametes versicolor (R26), for up to 24 weeks. Furthermore, statistical correlations were investigated between soil volatile profiles and traditional microbial parameters for characterising microbial communities and their metabolic activities such as respiration, dehydrogenase (DHA) and laccase (LAC) activities, bacterial and fungal colony counts and fungal community structure under different soil conditions. Finally, this study explored the potential of microbial volatile production patterns for monitoring the activity and differentiation of two Streptomyces species (S. aureofaciens A253 and S. griseus A26) in potable water and in soil, as well as the production of geosmin in both environments. Data in this research has demonstrated that the production of volatile organic compounds (VOC) in soil is likely to arise from microbial metabolism. The E-nose was able to detect variations in the patterns of volatile production from soil according to treatments, functioning as indicators of shifts in microbial activity and community structure. The potential for discrimination between soil types in relation to environmental factors and nutrient addition has been demonstrated for the first time using principle component analysis (PCA). Significant (p0.80) between PC1 and soil respiration was particularly relevant, since it indicates that microbial volatile fingerprints, similarly to respiration, respond quickly to changes in soil conditions. The sensor array was also able to detect Streptomyces activity and differentiation as well as discriminate between bacterial species at different concentrations in potable water and in soil. Using this approach, the presence of geosmin was detected in water at 0.5 ppb (below its human odour threshold detection, OTD) and in soil at 100 ppb (OTD not established). This study has, therefore, demonstrated that an E-nose can be employed as a rapid, sensitive, reproducible and non-invasive tool for characterising changes in soil environmental conditions, as well as for monitoring key soil processes such as organic matter decomposition and atrazine degradation. It also suggests that this approach can complement, and perhaps replace, some of these methods for a quick and routine evaluation of the impact of environmental factors on soil microbial communities. Furthermore, this study showed that an E-nose can also be employed for assessing Streptomyces activity and detecting geosmin production at an early stage in water and soil.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

The characterisation and detection of plant Pathogenic streptomycetes in the natural environment

Streptomyces scabies has been attributed to be the causal agent of common scab, a superficial disease of the potato. Confusion over the taxonomic position of the organism arose as a result of the erroneous designation of a type strain that did not match the original description. This confusion was compounded by the deposition of many taxonomically distinct pathogenic strains in culture collections under the name of Streptomyces scabies. These studies attempted to clarify the taxonomic position of this organism. Common scab strains were characterised on the basis of phenotypic variation and hybridization to 16S rRNA probes. Pathogenic strains appeared to conform to three centres of variation similar to the S.albidoflavus, S.rochei and S.diastaticus Streptomyces spp. groups. The pathogenicity of putative pathogens was investigated and the pathogenic basis to the taxonomically heterogeneous group confirmed. Further studies focused on the development and application of approaches to the monitoring and detection of these strains in soil. Strain, ISP5078 has been well characterised and was selected as a model strain to pursue these objectives. Monitoring and detection strategies evaluated included: screening ISP5078 for selective phenotypic markers (such as antibiotic resistance) to assist in its selective recovery from soil and attempting to insert the marker genes xylE (novel to the Streptomyces) and nptll (a kanamycin resistance determinant) into the chromosome of strain ISP5078. Studies were also initiated to apply 16S rRNA targeted oligonucleotide probes to the monitoring of streptomycete inoculants in the natural environment. Studies focused on the development and evaluation of a method for the extraction and recovery of 16S ribosomal RNA from soil and the application of 16S rRNA probes to in situ hybridizations in the analysis of the lifecycle of scab-causing Streptomyces strains in situ. The influence of the potato rhizosphere on common scab strain populations was assessed by applying specific strategies to follow the fate of ISPS078 in sterile soil with and without potato plants. The lifecycle and activity of scab-causing streptomycetes in association with potatoes and soil was investigated using scanning electron microscopy and in situ hybridization

Mechanics of Biomaterials

The mechanical behavior of biomedical materials and biological tissues are important for their proper function. This holds true, not only for biomaterials and tissues whose main function is structural such as skeletal tissues and their synthetic substitutes, but also for other tissues and biomaterials. Moreover, there is an intimate relationship between mechanics and biology at different spatial and temporal scales. It is therefore important to study the mechanical behavior of both synthetic and livingbiomaterials. This Special Issue aims to serve as a forum for communicating the latest findings and trends in the study of the mechanical behavior of biomedical materials