SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Effects of grassland conversion and tillage intensities on soil microbial biomass, residues and community structure

Agricultural intensification has a strong impact on level of soil organic matter (SOM), microbial biomass stocks and microbial community structure in agro-ecosystems. The size of the microbial necromass C pool could be about 40 times that of the living microbial biomass C pool in soils. Due to the specificity, amino sugar analysis gives more important information on the relative contribution of fungal and bacterial residues to C sequestration potential of soils. Meanwhile, the relationship between microbial biomass and microbial necromass in soil and its ecological significance on SOM are not fully understood and likely to be very complex in grassland soils. This thesis focuses on the effects of tillage, grassland conversion intensities and fertilisation on microbial biomass, residues and community structure. The combined analyses of microbial biomass and residue formation of both fungi and bacteria provided a unique opportunity to study the effect of tillage, grassland conversion and fertilisation on soil microbial dynamics. In top soil at 0-30 cm layer, a reduction in tillage intensity by the GRT and NT treatments increased the accumulation of saprotrophic fungi in comparison with the MBT treatment. In contrast, the GRT and NT treatments promoted AMF at the expense of saprotrophic fungi in the bottom soil layer at 30-40 cm depth. The negative relationship between the ergosterol to microbial biomass C ratio and the fungal C to bacterial C ratio points to the importance of the relationship between saprotrophic fungi and biotrophic AMF for tillage-induced changes in microbial turnover of SOC. One-season cultivation of winter wheat with two tillage events led to a significant loss in SOC and microbial biomass C stocks at 0-40 cm depth in comparison with the permanent grassland, even 5 years after the tillage event. However, the tillage induced loss in microbial biomass C was roughly 40% less in the long-term than in the short-term of the current experiment, indicating a recovery process during grassland restoration. In general, mould board tillage and grassland conversion to maize monoculture promoted saprotrophic fungi at the expense of biotrophic AMF and bacteria compared to undisturbed grassland soils. Slurry application promoted bacterial residues as indicated by the decreases in both, the ergosterol to microbial biomass C ratio and the fungal C to bacterial C ratio. In addition, the lost microbial functional diversity due to tillage and maize monoculture was restored by slurry application both in arable and grassland soils. I conclude that the microbial biomass C/S ratio can be used as an additional indicator for a shift in microbial community. The strong relationships between microbial biomass and necromass indices points to the importance of saprotrophic fungi and biotrophic AMF for agricultural management induced effects on microbial turnover and ecosystem C storage. Quantitative information on exact biomass estimates of these two important fungal groups in soil is inevitably necessary to understand their different roles in SOM dynamics.

Effect of soil structure on temporal and spatial dynamics of bacteria

Soil is a complex heterogeneous system comprising of highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of resident microbiota. A question addressed in this research is how soil structure affects the temporal dynamics and spatial distribution of bacteria. Using repacked microcosms, the effect of bulk-density, aggregate sizes and water content on growth and distribution of introduced Pseudomonas fluorescens and Bacillus subtilis bacteria was determined. Soil bulk-density and aggregate sizes were altered to manipulate the characteristics of the pore volume where bacteria reside and through which distribution of solutes and nutrients is controlled. X-ray CT was used to characterise the pore geometry of repacked soil microcosms. Soil porosity, connectivity and soil-pore interface area declined with increasing bulk-density. In samples that differ in pore geometry, its effect on growth and extent of spread of introduced bacteria was investigated. The growth rate of bacteria reduced with increasing bulk-density, consistent with a significant difference in pore geometry. To measure the ability of bacteria to spread thorough soil, placement experiments were developed. Bacteria were capable of spreading several cm’s through soil. The extent of spread of bacteria was faster and further in soil with larger and better connected pore volumes. To study the spatial distribution in detail, a methodology was developed where a combination of X-ray microtopography, to characterize the soil structure, and fluorescence microscopy, to visualize and quantify bacteria in soil sections was used. The influence of pore characteristics on distribution of bacteria was analysed at macro- and microscales. Soil porosity, connectivity and soil-pore interface influenced bacterial distribution only at the macroscale. The method developed was applied to investigate the effect of soil pore characteristics on the extent of spread of bacteria introduced locally towards a C source in soil. Soil-pore interface influenced spread of bacteria and colonization, therefore higher bacterial densities were found in soil with higher pore volumes. Therefore the results in this showed that pore geometry affects the growth and spread of bacteria in soil. The method developed showed showed how thin sectioning technique can be combined with 3D X-ray CT to visualize bacterial colonization of a 3D pore volume. This novel combination of methods is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

Effects of concentrated viral communities on photosynthesis and community composition of co-occurring benthic microalgae and phytoplankton

Marine viruses have been shown to affect phytoplankton productivity; however, there are no reports on the effect of viruses on benthic microalgae (microphytobenthos). Hence, this study investigated the effects of elevated concentrations of virus-like particles on the photosynthetic physiology and community composition of benthic microalgae and phytoplankton. Virus populations were collected near the sediment surface and concentrated by tangential flow ultrafiltration, and the concentrate was added to benthic and water column samples that were obtained along a eutrophication gradient in the Brisbane River/Moreton Bay estuary, Australia. Photosynthetic and community responses of benthic microalgae, phytoplankton and bacteria were monitored over 7 d in aquaria and in situ. Benthic microalgal communities responded to viral enrichment in both eutrophic and oligotrophic sediments. In eutrophic sediments, Euglenophytes (Euglena sp.) and bacteria decreased in abundance by 20 to 60 and 26 to 66%, respectively, from seawater controls. In oligotrophic sediments, bacteria decreased in abundance by 30 to 42% from seawater controls but the dinoflagellate Gymnodinium sp. increased in abundance by 270 to 3600% from seawater controls, The increased abundance of Gymnodinium sp. may be related to increased availability of dissolved organic matter released from lysed bacteria. Increased (140 to 190% from seawater controls) initial chlorophyll a fluorescence measured with a pulse-amplitude modulated fluorometer was observed in eutrophic benthic microalgal incubations following virus enrichment, consistent with photosystem II damage. Virus enrichment in oligotrophic water significantly stimulated carbon fixation rates, perhaps due to increased nutrient availability by bacterial lysis. The interpretation of data from virus amendment experiments is difficult due to potential interaction with unidentified bioactive compounds within seawater concentrates. However, these results show that viruses are capable of influencing microbial dynamics in sediments.

Antagonistic activity expressed by Shigella sonnei: identification of a putative new bacteriocin

Bacteriocins are antibacterial, proteinaceous substances that mediate microbial dynamics. Bacteriocin production is a highly disseminated property among all major lineages of bacteria, including Shigella. In this paper, we addressed the purification and characterisation of a bacteriocin produced by a Shigella sonnei strain (SS9) isolated from a child with acute diarrhoea. The substance was purified through ammonium-sulphate precipitation and sequential steps of chromatography. The intracellular fraction obtained at 75% ammonium sulphate maintained activity following exposure to pH values from 1-11 and storage at -80ºC for more than two years and was inactivated by high temperatures and proteases. The molecular mass of the purified bacteriocin was determined by mass spectrometry to be 18.56 kDa. The N-terminal sequence of the bacteriocin did not match any other antibacterial proteins described. A putative new bacteriocin produced by S. sonnei has been detected. This bacteriocin may represent a newly described protein or a previously described protein with a newly detected function. Considering that SS9 expresses antagonism against other diarrhoeagenic bacteria, the bacteriocin may contribute to S. sonnei virulence and is potentially applicable to either preventing or controlling diarrhoeal disease.

Características biológicas do solo indicadoras de qualidade após dois anos de aplicação de biossólido industrial e cultivo de milho

A utilização agrícola de biossólidos tem sido muito incentivada, mas, como esses resíduos apresentam composição química variada, o valor agronômico e os efeitos sobre características indicadoras de qualidade do solo precisam ser avaliados caso a caso, a fim de estabelecer normas de segurança para uso desses materiais. Neste trabalho foram avaliadas características biológicas, após a aplicação, por dois anos consecutivos, de doses crescentes (0, 6, 12, 18 e 24 t ha-1 base seca) de um biossólido gerado por uma indústria de fibras e resinas PET e da adubação mineral completa no cultivo de milho, em um Cambissolo distrófico, comparados aos de uma área adjacente, sob Brachiaria sp. e sem cultivo nos últimos 10 anos, usada como referência. Os valores de C e N da biomassa microbiana, a respiração basal e as atividades das enzimas urease e beta-glicosidase e da hidrólise do diacetato de fluoresceína (FDA) aumentaram, enquanto a atividade da fosfatase ácida diminuiu com a elevação das doses de biossólido, porém estas não tiveram efeito sobre o quociente metabólico (qCO2). A diminuição da atividade da fosfatase se deveu ao aumento da disponibilidade de P no solo, não caracterizando efeito adverso da aplicação do biossólido. Com aplicação de 12 t ha-1 de biossólido (recomendação agronômica), a respiração e a hidrólise da FDA foram maiores e a atividade da fosfatase foi menor que a obtida no solo com adubação mineral, mas as demais características avaliadas não diferiram entre estes tratamentos. A colonização micorrízica de Brachiaria sp. não diferiu entre plantas de crescimento espontâneo nas parcelas anteriormente cultivadas com milho e aquelas da área adjacente. Apesar do menor número de esporos, verificou-se enriquecimento de espécies de fungos micorrízicos arbusculares (FMAs) nas parcelas cultivadas. O carbono orgânico (Corg) e a biomassa microbiana apresentaram alta correlação com os demais parâmetros avaliados, indicando que as alterações na quantidade e qualidade da matéria orgânica, promovidas pela aplicação do biossólido, refletiram na dinâmica da microbiota e influenciaram positivamente os parâmetros biológicos de qualidade do solo.

Estabilidade aeróbia de silagens de planta e de grãos úmidos de milho

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Efeitos da contaminação fecal sobre a dinâmica e a estrutura da alça microbiana em areias de praias do litoral norte do estado de São Paulo

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

High alkaline phosphatase activity in phosphate replete waters: The case of two macrotidal estuaries

The occurrence of alkaline phosphatase activity (APA) that hydrolyses organic phosphorus into phosphate (PO4) is commonly related to PO4 deficiency of oceanic, coastal and fresh waters. APA is almost never investigated in PO4-rich estuaries, since very low activities are expected to occur. As a consequence, microbial mineralization of organic phosphorus into PO4 has often been ignored in estuaries. In this study, we examined the importance of potential APA and the associated microbial dynamics in two estuaries, the Aulne and the Elorn (Northwestern France), presenting two different levels of PO4 concentrations. Unexpected high potential APA was observed in both estuaries. Values ranged from 50 to 506 nmol L−1 h−1, which range is usually found in very phosphorus-limited environments. High potential APA values were observed in the oligohaline zone (salinity 5–15) in spring and summer, corresponding to a PO4 peak and a maximum bacterial production of particle-attached bacteria. In all cases, high potential APA was associated with high suspended particulate matter and total particulate phosphorus. The low contribution of the 0.2–1 μm fraction to total APA, the strong correlation between particulate APA and bacterial biomass, and the close relationship between the production of particle-attached bacteria and APA, suggested that high potential APA is mainly due to particle-attached bacteria. These results suggest that the microbial mineralization of organic phosphorus may contribute to an estuarine PO4 production in spring and summer besides physicochemical processes.

Performance of a horizontal-flow anaerobic immobilized biomass (HAIB) reactor and dynamics of the microbial community during degradation of pentachlorophenol (PCP)

The anaerobic biological treatment of pentachlorophenol (PCP) and methanol as the main carbon source was investigated in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor at 30 +/- 1 degrees C, during a 220-day trial period. The reactor biomass was developed as an attached biofilm on polyurethane foam particles, with 24 h of hydraulic retention time. The PCP concentrations, which ranged from 2.0 to 13.0 mg/L, were controlled by adding synthetic substrate. The HAIB reactor reduced 97% of COD and removed 99% of PCP. The microbial biofilm communities of the HAIB reactor amended with PCP, without previous acclimatization, were characterized by polymerase chain reaction (PCR) and amplified ribosomal DNA restriction analysis (ARDRA) with specific Archaea oligonucleotide primers. The ARDRA technique provided an adequate analysis of the community, revealing the profile of the selected population along the reactor. The biomass activities in the HAIB reactor at the end of the experiments indicated the development of PCP degraders and the maintenance of the population of methanogenic Archaea, ensuring the high efficiency of the system treating PCP with added methanol as the cosubstrate. The use of the simplified ARDRA method enabled us to monitor the microbial population with the addition of high concentrations of toxic compounds and highlighting a selection of microorganisms in the biofilm. (C) 2008 Published by Elsevier Ltd.

Effects of fire on soil nitrogen dynamics and microbial biomass in savannas of Central Brazil

The objective of this work was to study the effects of fire on net N mineralization and soil microbial biomass in burned and unburned cerrado stricto sensu sites. The study was carried out from April 1998 to April 2000. The pH values were significantly higher in the burned site while soil moisture content was significantly higher in the unburned site (P<0.05). The soil C/N ratio was 22/1 and the available NO3-N ranged between 1.5 and 2.8 mg kg-¹ dry weight. However, the NH4-N concentration ranged between 3 and 34 mg kg-1 dry weight in the burned site and between 3 and 22 mg kg-1 dry weight in the unburned site. The NH4-N increased after fire, but no significant changes were observed for NO3-N (P<0.05). The NO3-N accumulation occurred in short periods during the rainy season. The rates of net N mineralization increased during the rainy season while reductions in soil microbial biomass were observed at both sites. This suggested that the peak in microbial activities occurred with the first rain events, with an initial net immobilization followed by net mineralization. Both sites presented the same pattern for mineralization/immobilization, however, the amount of inorganic-N cycled annually in unburned site was 14.7 kg ha-1 per year while the burned site presented only 3.8 kg ha-¹ of inorganic-N, one year after the burning.

Microbial communities in a porphyry copper tailings impoundment and their impact on the geochemical dynamics of the mine waste

The distribution and diversity of acidophilic bacteria of a tailings impoundment at the La Andina copper mine, Chile, was examined. The tailings have low sulfide (1.7% pyrite equivalent) and carbonate (1.4% calcite equivalent) contents and are stratified into three distinct zones: a surface (0-70-80 cm) `oxidation zone' characterized by low-pH (2.5-4), a `neutralization zone' (70-80 to 300-400 cm) and an unaltered `primary zone' below 400 cm. A combined cultivation-dependent and biomolecular approach (terminal restriction enzyme fragment length polymorphism and 16S rRNA clone library analysis) was used to characterize the indigenous prokaryotic communities in the mine tailings. Total cell counts showed that the microbial biomass was greatest in the top 125 cm of the tailings. The largest numbers of bacteria (10(9) g(-1) dry weight of tailings) were found at the oxidation front (the junction between the oxidation and neutralization zones), where sulfide minerals and oxygen were both present. The dominant iron-/sulfur-oxidizing bacteria identified at the oxidation front included bacteria of the genus Leptospirillum (detected by molecular methods), and Gram-positive iron-oxidizing acidophiles related to Sulfobacillus (identified both by molecular and cultivation methods). Acidithiobacillus ferrooxidans was also detected, albeit in relatively small numbers. Heterotrophic acidophiles related to Acidobacterium capsulatum were found by molecular methods, while another Acidobacterium-like bacterium and an Acidiphilium sp. were isolated from oxidation zone samples. A conceptual model was developed, based on microbiological and geochemical data derived from the tailings, to account for the biogeochemical evolution of the Piuquenes tailings impoundment.