Ana Isabel López-Archilla

Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain

We studied the correlation between physicochemical and biological characteristics of an acidic river, the Tinto River, in Southwestern Spain. The Tinto River is an extreme environment characterized by its low pH (mean of 2.2) and high concentrations of heavy metals (Fe 2.3 g/L, Zn 0.22 g/L, Cu 0.11 g/L). These extreme conditions are the product of the metabolic activity of chemolithotrophic microorganisms, including iron- and sulfur-oxidizing bacteria, that can be found in high concentrations in its waters. The food chain in the river is very constrained and exclusively microbial. Primary productivity in the Tinto River is the sum of photosynthetic and chemolithotrophic activity. Heterotrophic bacteria and fungi are the major decomposers and protists are the major predators. A correlation analysis including the physicochemical and biological variables suggested a close relationship between the acidic pH values and abundance of both chemolithotrophic bacteria and filamentous fungi. Chemolithotrophic bacteria correlated with the heavy metals found in the river. A principal component analysis of the biotic and abiotic variables suggested that the Tinto River ecosystem can be described as a function of three main groups of variables: pH values, metal concentrations, and biological productivity.

A Comparative Ecological Study of Two Acidic Rivers in Southwestern Spain

A bstractWe have analyzed select physicochemical and biological characteristics of two acidic rivers, the Tinto and the Odiel, located in the Pyritic Belt of Southwestern Spain. Despite a common geography and geochemistry, they exhibit important differences. Most of the measured physicochemical parameters, especially pH and those related to conductivity (heavy metal concentrations), showed more extreme values in the Tinto than in the Odiel. However, it was at the microbiological level (fungal and bacterial populations) where both rivers showed the most important differences according to the statistical analysis of principal components. Lithoautotrophic bacteria were more abundant in the more acidic Tinto River and fungal diversity varied significantly from one river to the other.

ECOSYSTEM METABOLISM IN A MEDITERRANEAN SHALLOW LAKE (LAGUNA DE SANTA OLALLA, DOÑANA NATIONAL PARK, SW SPAIN)

Santa Olalla is a Mediterranean permanent coastal shallow lake, with high annual solar irradiation and warm water temperature throughout the year. Ecosystem metabolism, chlorophyll a concentrations, and physical and chemical features were studied in the Santa Olalla lake from March 1998 to February 2000. Gross primary productivity (GPP) and community respiration (CR) were determined using a modification of the one-station diel oxygen change method. Chlorophyll a, Secchi depth, and total phosphorous and nitrogen reveal Santa Olalla to be a hypereutrophic system. Values of GPP and CR were very high (average 7.88 g O2 m−2 d−1 and 8.52 g O2 m−2 d−1, respectively). Principal components analysis and a multiple regression model showed photosynthetically active radiation and soluble reactive phosphorus to be the main factors that control primary production in Santa Olalla. Also, the annual and interannual variation of water level in Santa Olalla seems to be an important factor that influences the ecological processes of this system. Mean net daily metabolism during a hydrologic period was not statistically different from 0 (0.008 g O2 m−2 d−1, p=0.99), and the average P/R ratio was not statistically different from 1 (1.164, p=0.343). These results suggest that the primary productivity was balanced with community respiration in Santa Olalla lake. The high values of metabolic rates and low nutrient concentrations in this aquatic ecosystem suggest a quick recycling of nutrients, which were assimilated almost instantaneously after mineralization.

Spatiotemporal distribution of microbial communities in a coastal, sandy aquifer system (Doñana, SW Spain).

The aquifer system of Doñana (SW Spain) represents the most important freshwater source in the Doñana Natural Area. Its spatiotemporal dynamics favours the hydrological connection between surface and subsurface ecosystems, and promotes matter fluxes among the different terrestrial and aquatic systems present here. This aquifer has been intensively studied from a hydrogeological point of view but little is known from an ecological perspective. In order to understand the ecological roles played by microbial communities in this system, we conducted a long-term seasonal study of bacterial abundance, cell biomass, bacterial biomass and functional activities over a 2-year period. Bacterial abundance ranged between 2.11 +/- 1.79 x 10(5) and 8.58 +/- 6.99 x 10(7) bacteria mL(-1) groundwater, average cell biomass was estimated to be 77.01 +/- 31.56 fgC and bacterial biomass varied between 8.99 +/- 4.10 x 10(-2) and 5.65 +/- 0.70 microgC mL(-1). Iron-related bacteria showed the highest activities among the functional groups studied. Moreover, among the variables that usually control spatial distributions of microbial communities in aquifer systems, depth did not have a relevant effect on this aquifer, at least in the range of depths studied, but grain size, probably due to its direct effects on hydrogeological parameters, such as permeability or porosity, appeared to exert moderate control, principally in terms of bacterial abundance. Finally, significant seasonal differences in the means of these microbiological variables were also observed; temperature seems to be the main factor controlling the temporal distribution of microbial communities in this aquifer system.

Involvement of microbial mats in delayed decay: An experimental essay on fish preservation

ABSTRACT Microbial mats have been implicated in exceptional fossil preservation. Few analyses have addressed how these complex-multilayered biofilms promote fossil preservation. The sequence of changes during decay of neon tetra fish were tracked up to 27 months, and their decomposition in mats was compared against nonmat sediments (control fish). Statistically significant differences in quantitative variables (length, width, and thickness) are provided (ANOVA test, in all cases, P < 0.001). Changes in the qualitative features (body-head, fins, scale connection, and eye and body coloration) were phenetically analyzed resulting in two clusters and highlighting that notable differences in decay began at day 15. Mat fish show a delayed decomposition maintaining the external and internal body integrity, in which soft organs were preserved after 27 months as shown by Magnetic Resonance Imaging. We discuss how the organization, structure, and activity of this community are interrelated, favoring exceptional preservation. Microbial mats entomb the fish from the earliest stages, forming a Ca-rich coat over the carcass while embedding it in an anoxic condition. This quick entombment provides important protection against abiotic and/or biotic agents.

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites

Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

Spreading topsoil encourages ecological restoration on embankments: soil fertility, microbial activity and vegetation cover.

The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the original substrate should be previously assessed on a site by site basis.

Preservation in microbial mats: mineralization by a talc-like phase of a fish embedded in a microbial sarcophagus

Microbial mats have been repeatedly suggested to promote early fossilization of macroorganisms. Yet, experimental simulations of this process remain scarce. Here, we report results of 5 year-long experiments performed onfish carcasses to document the influence of microbial mats on mineral precipitation during early fossilization. Carcasses were initially placed on top of microbial mats. After two weeks, fishes became coated by the mats forming a compact sarcophagus, which modified the microenvironment close to the corpses. Our results showed that these conditions favoured the precipitation of a poorly crystalline silicate phase rich in magnesium. This talc-like mineral phase has been detected in three different locations within the carcasses placed in microbial mats for more than 4 years: 1) within inner tissues, colonized by several bacillary cells; 2) at the surface of bones of the upper face of the corpse buried in the mat; and 3) at the surface of several bones such as the dorsal fin which appeared to be gradually replaced by the Mg-silicate phase. This mineral phase has been previously shown to promote bacteria fossilization. Here we provide first experimental evidence that such Mg-rich phase can also be involved in exceptional preservation of animals.

THE IMPACT OF MICROBIAL MATS AND THEIR MICROENVIRONMENTAL CONDITIONS IN EARLY DECAY OF FISH

Abstract:  This study provides experimental evidence confirming the significance of microbial mat presence in controlling the spatial and temporal development of chemical microenvironments which become established inside and outside decaying fish carcasses. Dissolved oxygen (DO) and pH profiles were monitored over 1,000 days with microelectrodes positioned inside and adjacent to carcasses. In the vicinity of fish, the DO varied from an oxygenated green upper layer to an anoxic bottom stratum and the pH was alkaline. Inside the fish, the DO and the pH were decoupled during the first week, in that anoxia remained constant and the pH decreased and became acidic. Once covered by the mat, the fish carcass turned oxic and pH returned to alkaline levels. This novel second phase occurred from day 90 to three years and would likely remain after this time. Based on the fish soft tissue quality at the end of the experiment, we discuss whether oxic-alkaline microenvironmental conditions could promote organic preservation and long-term mineralization.

Microbial Activities in a Coastal, Sandy Aquifer System (Doñana Natural Protected Area, SW Spain)

We conducted a seasonal research of the activities of microbial communities in a coastal, sandy aquifer system located in the Doñana Natural Protected Area (SW, Spain). Groundwaters from 30 piezometers were sampled over a two-year period. The proportion of active microbial biomass ranged from 0.02 to 6.36% of the total microbial biomass, while the active microbial biomass ranged from 7.42 10 −3 2.20 10 −4 to 17.30 3.71 ngC mL −1 . Bacterial carbon production, measured through the incorporation of [ 3 H]leucine into cellular proteins, showed a mean value of 0.18 0.72 ngC mL −1 h −1 in all wells and all seasons. Bacterial growth rates ranged from 0.03 to 87.26 days. These activities exhibited spatiotemporal patterns. Temperature and the presence of nutrients and organic matter appear to be important factors controlling these patterns. However, hydrogeological flows, both local and regional, seemed to constitute the most important factor determining these spatiotemporal patterns, probably because the distribution of nutrients in aquifer systems is mainly controlled by these hydrogeological flows. The well-known hydrological flows connecting surface waters and groundwaters in Doñana support the assumption that both water compartments form a unique entity (called hydroecosystem), which functions as a whole. Consequently, not only microbial processes in surface waters can influence ecological processes in groundwaters, the characteristics of surface waters can also be affected by groundwater chemical processes, among others, mediated by the activities of microbial communities.