130,504 research outputs found
How steep is my seep? Seepage in volcanic lakes - hints from numerical simulations
No full textThe existence and survival of volcanic lakes require the accomplishment of a delicate balance between meteoric recharge, evaporation, and water loss by infiltration within the volcanic edifice, commonly referred to as seepage. A deep-seated, volcanic component may participate to a variable extent to the lake’s evolution, depending on volcanic activity. In this work, we apply a numerical model of hydrothermal fluid circulation to study the interaction between the hot volcanic gases and the shallow lake water. We focus on the conceptual model developed for Poás volcano (Costa Rica), where a shallow magma intrusion drives the hydrothermal activity underneath and around the crater lake. Numerical simulations are carried out to assess the role of relevant system properties, including rock permeability, reservoir conditions, lake geometry, and meteoric recharge. Our results suggest that vertical seepage can be severely hindered by the ascent of volcanic gases, whereas horizontal infiltration through the vertical lake walls may ensure a long-term water loss. Our simulations also show that the permeability distribution, especially around the lake, determines the overall pattern of circulation affecting the development and spatial distribution of hot springs and fumaroles, and ultimately controlling the evolution of the lake
A photographic method for detailing the morphology of the floor of a dynamic crater lake: the El Chicho´n case (Chiapas, Mexico)
No full textThe active volcano El Chicho´n (Chiapas,
Mexico) hosts a shallow acidic crater lake. During the
period 2001–2007, 26 photographs of the crater lake were
taken from the same spot at the eastern crater rim,*160 m
above the crater floor. The size of the lake was extremely
variable. Using a GPS track from around the lake shore as a
reference, 26 digitized lake outlines were corrected
simultaneously for the perspective angle. The corrected
lake outlines were superposed, leading to a ‘‘morphological
map’’ of a large section of the lake bottom. This map
provides insight into the erosive–sedimentary regime of the
lake floor. The inner section of the lake is more stable due
to the precipitation of sealing clays. This is probably one of
the reasons why the El Chicho´n crater lake has never disappeared
during the past 28 years. The sealing clays at the
lake bottom can be considered the superficial analog of
impermeable clay caps at the depths of hydrothermal systems.
The photographic procedure presented here may be
useful for other limnological and (volcanic) lake studies
aimed at describing lake morphology, and for eventually
deducing the surface area and volume of the lake.Published225-2331.3. TTC - Sorveglianza geodetica delle aree vulcaniche attiveJCR Journalrestricte
Major and trace element geochemistry of neutral and acidic thermal springs at El Chichón volcano, Mexico. Implications for monitoring of the volcanic activity
No full textFour groups of thermal springs with temperatures from 50 to 80 °C are located on the S–SW–W slopes of El Chichón volcano, a composite dome-tephra edifice, which exploded in 1982 with a 1 km wide, 160 m deep crater left. Very dynamic thermal activity inside the crater (variations in chemistry and migration of pools and fumaroles, drastic changes in the crater lake volume and chemistry) contrasts with the stable behavior of the flank hot springs during the time of observations (1974–2005). All known groups of hot springs are located on the contact of the basement and volcanic edifice, and only on the W–SW–S slopes of the volcano at almost same elevations 600–650 m asl and less than 3 km of direct distance from the crater. Three groups of near-neutral (pH≈6) springs at SW–S slopes have the total thermal water outflow rate higher than 300 l/s and are similar in composition. The fourth and farthest group on the western slope discharges acidic (pH≈2) saline (10 g/kg of Cl) water with a much lower outflow rate (b10 l/s). Water–rock interaction modeling of main types of the El Chichón thermal waters using regular log Q/K graphs (saturation indices vs temperature) showed maximum equilibrium temperature slightly higher than 200 °C. Acidic waters are equilibrated with some clay minerals at about 120 °C. Three main sources of the salinity of thermal water are suggested on the basis of mixing plots and isotopic data: a magmatic source for CO2, boron, sulfur and a limited part of Cl; volcanic rock source for the major cations and trace elements; the oil-bearing evaporitic basement source (oil-field brine?) for NaCl, Br, a part of Ca and some trace elements. All flank thermal springs end up in the river Rio Magdalena that has a variable seasonal flow rates from 4 to 20 m3/s. Any changes in the chemistry of springs must notably change the composition of the streams draining hot springs and eventually, Rio Magdalena. A monthly geochemical monitoring of Rio Magdalena and streams draining main hot springs would be a useful tool for surveying the activity of the volcano
Microbiological survey of el Chichon volcanic lake by cultivation - dependent and - indipendent techniques
No full textVolcanic environments belong to the so-called “extreme environments” where the environmental stressors for the living biota are represented by acidic pH, moderate to high temperatures and high concentrations of chemicals like heavy metals. The investigation of microbial life in volcanic environments is of great interest. Thermoacidophilic microorganisms have potential biotechnological applications and, moreover, their ecophysiological study can give insights about the origin of life on our planet, since volcanic environments are considered analogous to the early Earth.
In June 2009 five sites located into and in proximity of the volcanic lake El Chichón (Chiapas, Mexico) have been sampled from the acidic (pH 2.3) SO4-Cl type crater lake (LE), from the acidic (pH 4.1) SO4-type steam-heated pools (T 42°C) within the Soap Pool field (SP) and from acidic (pH 2.6-3.0) Cl-SO4 type saline thermal springs (T 53-59°C), located ~2 km outside the crater (AS1 and AS8).
Molecular microbiology techniques are independent from cultivation and have the potential to overcome the limitations imposed by the low level of cultivability of environmental bacteria. Denaturing Gradient Gel Electrophoresis (DGGE) applied on the total DNA extracted from the samples demonstrated that i) all the sites were colonised by bacteria, ii) the different environments studied in El Chichón area contained a peculiar microbiota, probably adapted to the specific geochemical context. Basing on DGGE data, the microbiota inhabiting the crater lake resulted dominated by the species Acidithiobacillus thiooxidans, which has sulphur-oxidation energetic metabolism and plays a key role in the sulphur biogeochemical cycle. Sulphur-iron oxidizing bacteria were also cultivated from the SP and AS thermal springs. Bacteria of the order Aquificae were specifically retrieved in the thermal springs external to the crater, represented by Sulfurihydrogenibium azorense, a thermophilic, strictly chemolithoautotrophic species previously isolated from terrestrial hot springs in the Azores, Portugal.
The molecular study was integrated by a cultivation-dependent approach in order to explore the physiological and metabolic properties of the organisms able to colonize such an extreme environment, with particular emphasis on bacteria having plant growth promoting (PGP) activity, since pioneer vascular plants were observed in SP site. Several bacterial species were associated to plant roots, some of them known for their capability to grow in extreme conditions. Tests about their survival at in situ conditions and potential PGP activity are at present undergoing. Several strains showed 1-aminocyclopropane-1-carboxylate (ACC)-deaminase activity, one of the best studied PGP activity, with a role in protecting the plant from environmental stress. The isolates showed, besides ACC-deamminase, also other PGP activities such as phosphate solubilization, dinitrogen fixation, and the production of siderophores.
Molecular and cultivation-based approaches demonstrated that El Chichón crater lake and the associated thermal springs are colonised by a rich microbiota mainly involved in the sulphur and iron biogeochemical cycles, which diversity is selected by the specific geochemical context. Plants adapted to live in this extreme environment are associated with several bacterial species having potential activity of plant growth promotion and stress protection
Risorse utili per l’agricoltura dallo studio della biodiversità microbica
No full textLa rizosfera, il sottile strato di suolo influenzato dalla radice di una pianta, è circa 100 volte più ricco di batteri rispetto al suolo libero circostante. Le radici delle piante producono molecole organiche che possono essere utilizzate come nutrienti dai microrganismi della rizosfera, i quali mostrano un elevata biodiversità, strettamente influenzata dalla specie vegetale e dal suo profilo di essudazione. Piante e rizobatteri si trovano in una associazione mutualistica, dove le piante forniscono nutrienti, nella forma di essudati radicali, ai microrganismi che a loro volta esercitano un effetto benefico sulla crescita vegetale. Questi batteri, chiamati “Plant Growth Promoting Rhizobacteria (PGPR)”, possono influenzare direttamente la pianta fornendo nutrienti biodisponibili o metaboliti che stimolano la crescita vegetale, controllano gli effetti dello stress, promuovono la fertilità del suolo. I PGPR possono anche promuovere indirettamente la crescita della pianta, proteggendola dalle fitopatologie tramite un’azione antagonista nei confronti degli agenti patogeni.
In questo lavoro abbiamo studiato la biodiversità microbica nella rizosfera di piante selvatiche e di interesse agricolo, provenienti da ambienti agricoli e da ambienti estremi. Lo scopo del lavoro era di ottenere in coltura ceppi microbici in grado di colonizzare la rizosfera e/o il sistema vascolare della pianta, aventi forti e polivalenti caratteristiche PGP.
Sono stati prelevati campioni di rizosfera e radici di piante di interesse agricolo per il bacino del Mediterraneo – peperone, olivo e vite – coltivate in regioni aride – Tunisia ed Egitto – lungo un transetto nord-sud di desertificazione. Sono inoltre state studiate piante selvatiche provenienti da ambienti estremi, suoli ipersalini nella zona degli Chott tunisini e sorgenti calde ed acide in ambiente vulcanico (Messico). È stata quindi costituita una vasta collezione di migliaia di isolati batterici rizosferici ed endofiti, che è tutt’ora in fase di screening per le potenzialità PGP. La collezione presenta elevata diversità tassonomica e diversi ceppi hanno dimostrato polivalenti attività PGP in test in vitro. Gli isolati più promettenti sono in fase di screening in vivo su piante modello. I PGPR isolati dagli ambienti estremi hanno dimostrato di essere adattati a condizioni ambientali non convenzionali, e di avere il potenziale di essere applicati come risorsa biotecnologica per l’agricoltura in regioni calde e/o aride, e suoli degradati.
Esperimenti in planta hanno mostrato che le colture selezionate sono in grado di colonizzare la radice, promuovere la germinazione dei semi e la crescita vegetale e diminuire sensibilmente i livelli di stress idrico. I risultati dimostrano l’elevato potenziale della biodiversità dei microrganismi associati alle radici delle piante, sfruttabili come risorse biotecnologiche applicabili in agricoltura come biofertilizzanti e/o biostimolanti, utili per lo sviluppo di pratiche agricole sostenibili ed “environmental-friendly”
Unravelling extremophiles diversity of volcanic habitats
No full textIntroduction
Acidic habitats of natural origin are broadly distributed on the Earth. Nevertheless little is known about the microbial diversity of these extreme ecosystems, generally originated by volcanic and hydrothermal activities. Since their values of temperature, pH and concentration of chemicals are close to known limits for life, they represent challenging habitats for those microorganisms that normally colonize conventional environments and only a small fraction of Bacteria are expected to thrive in such a harsh type of ecosystem. Extremophiles inhabiting volcanic habitats, including crater lakes and hot springs, are of interest to microbiologists for their potential biotechnological application.
In this study the composition of the microbiome inhabiting acidic water samples collected from six crater lakes located in Costa Rica (Río Cuarto, Hule, Irazú, Botos and Poás) and Mexico (El Chichón) was investigated. Furthermore the bacterial community able to colonize water collected from three different sites of an acidic Icelandic hot-spring was analyzed.
Main purposes of the present work were (i) to explore the phylogenetic diversity of Bacteria adapted to the peculiar physio-chemical conditions and (ii) the understanding of the microbiome’s composition shaping forces in natural acidic waters. In order to overcome the low level of cultivability of environmental bacteria, the Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting technique was applied on the metagenome extracted from the lake waters. Moreover, cultivation dependent methods were applied to investigate the physiological capabilities of the microorganisms that colonize thermal spring field related to the El Chichón volcanic system, where pioneering vascular plants were retrieved. Establishment of tight interplay of microbes and plants are well known to occour in many different type of extreme environments (Puente et al., 2004; Siddikee et al., 2010) For this reason a special attention has been dedicated to plant growth promoting (PGP) rhizobacteria, with the aim of discovering bacteria able to aid the plant to cope with the inhospitable environmental conditions.
Materials and Methods
Water samples were collected in March 2010 at different depths along a vertical profile of the water column from 1 m to the maximum depth for Laguna Hule (H), Río Cuarto (RC) and Botos (B) lakes. Water samples were collected from different sites at the surface layer in the case of Poás, Irazú (LN09, LE09, LE10) and El Chichón (LE, SP, AS8, ASgas) volcanic lakes (December 2009 and March 2010) and from the Icelandic hot-spring (P). Immediately after collection the water samples (0.1 to 0.5 l) have been filtered through Sterivex filters with 0.2-m pore size (Millipore). After adding RNA Later the filters were stored at –20°C until DNA extraction. The rhizosphere of a single individual of vascular plants observed in the acidic (pH 4.1) SO4-type steam-heated pools (T 42°C) within the Soap Pool field (SP) of El Chichón system was collected, stored in a sterile bag and transferred to the laboratory for cultivation experiments.
Temperature, pH, conductivity and redox potential were measured in-situ using a CTD profiler.
For details about the applied molecular and cultivation methods please refer to the manuscript in preparation (Mapelli et al.)
Results and discussion
The geochemistry of some of the Laguna Húle, Río Cuarto, Botos and Poás lakes was deeply studied in the last decades (Tassi et al., 2009), nevertheless few data are available about the microbiome composition of these extreme habitats.
DGGE fingerprinting results showed the highest number of bands in the samples collected along the depth profiles of Laguna Húle and Río Cuarto lake, where the water was characterized by pH ranging from neutrality to slightly acidic value and temperature was comprise between 20 and 26 °C. A low bacterial diversity, revealed by the lowest number of DGGE bands, was observed in the extremely acidic water (pH 0.83) of the Poás lake in accordance to what previously observed in a similar environment (Löhr et al., 2006).
In the case of Botos, Río Quarto and Húle lakes the analyses of the partial 16S rRNA sequences obtained from the excised DGGE bands rarely allowed to find a match higher than 97% of similarity with described species. Chlorobium limicola, a green phototrophic anaerobic bacterium, was identified from samples H15m and H21m, where the redox potential of the water shifted to negative value. The richness of undescribed species mainly belonging to Proteobacteria and Bacteroidetes classes, or which classification is unknown, indicate that novel bacterial species adapted to the peculiar geochemical setting of these crater lakes may inhabit them.
On the other hand most of the partial 16S rRNA sequences detected from the Irazù lake, in addition to those recovered from the Icelandic hot-spring and El Chichón lake, showed higher percentage of similarity to described species previously isolated from analogous environments. The occurrence of bacterial species such as Hydrogenobaculum acidophilum or Acidicaldus organivorans from the acidic high-temperature geothermal waters collected in Iceland is tightly related to the physiochemical condition of these ecosystems. Similar considerations may be done in the case of the El Chichón crater system, where the water in the different investigated sites is characterized by high sulfate concentration. According to DGGE data the microbiome colonizing the El Chichón lake was dominated by the species Acidithiobacillus thiooxidans and Thiomonas intermedia which play a crucial role in the sulphur biogeochemical cycle.
To estimate the overall similarity among the samples a Principal Component Analysis (PCA) has been applied after the conversion of DGGE pattern into line plot profiles. This approach allowed to compare the water samples taking into account the whole bacterial community, including those bands that was not possible to excide from the gels to obtain the 16SrRNA sequences. As stated by the distribution observed for the Botos lake samples (Fig. 1a) and in the cases of the Poás lake sample (Fig. 1b), pH value represent one of the most important factors determining the relationship among the bacterial communities composition. Indeed the role of pH have been widely demonstrated in biogeography of soil (Fierer et al., 2006; Griffiths et al., 2011 ) and it is possible to hypothesize its importance also in the prediction of the microbial community structure of freshwater lake systems. However the results of the multivariate analysis indicated that samples characterized by similar pH value can be distinguished according to the lake of provenance, a fact that likely reflect the microbiome adaption to the specific environmental parameters shaping overall each ecosystem.
In correspondence of the SP site located in the El Chichón volcanic system, pioneer vascular plants were observed. These extremophile plants living at high T (42°C) and low pH (4.1) were associated with PGP rhizobacteria, some of them known for their capability to grow in extreme conditions. In vitro tests evidenced that 13% of the 44 selected PGP strains were effectively able to survive at in situ conditions. Moreover metabolic properties of the selected strains were explored, especially concerning their potential PGP activities. Several strains showed 1-aminocyclopropane-1-carboxylate (ACC)-deaminase activity, one of the best studied PGP activity, with a role in protecting the plant from environmental stress. Noteworthy percentage of the isolates showed also other PGP activities such as phosphate solubilisation (25%), siderophores production (16%) and the ability to affect phytohormones balance producing indole-3-acetic acid (20%).
Conclusions
The analyzed natural acidic ecosystems hosted a bacterial community which composition and richness degree appeared to be strongly related to the extreme geochemical parameters of the water. The use of DGGE fingerprinting showed the presence of 16S rRNA sequences poorly related to any known bacteria in the Botos, Río Cuarto and Húle lakes and indicated that volcanic systems might be considered as a source of novel extremophiles, possibly characterized by interesting biotechnological properties. By the way cultivation experiments allowed to identify rhizobacteria displaying multiple PGP activities. These isolates are able to help pioneer plants to cope with the harsh condition of thermal spring sites of the El Chichón lake. In its entirety the data set obtained in the present study indicate that acidic habitats of volcanic and hydrothermal origin can represent a resource for sustainable agriculture in acidic soils.
References
1. Siddikee M.A., Chauhan P.S., Anandham R., Han G., Sa T. (2010). J. Microbiol. Biotechnol. 20(11): 1577–1584
2. Puente M.E., Li C.Y., Bashan Y., (2004). Plant Biol. 6: 643-650.
3. Löhr A.J., Laverman A.M., Braster M., van Straalen N.M., Röling W.F.M. (2006). Microb. Ecol. 52: 609-618
4. Tassi F., Vaselli O., Fernandez E., Duarte E., Martinez M., delgado Huertas A., Bergamaschi F. (2009). J.Limnol. 68: 193-205
5. Fierer N., Jackson R.B. (2006).PNAS 103 (3): 626-631
6. Griffiths R.I., Thomson B.C., James P., Bell T., Bailey M., Whiteley A.S. (2011). Environ. Microbiol. 13(6): 1642-165
Unravelling extremophiles diversity of volcanic habitats
No full textVolcanic habitats are classified as extreme environments due to their values of pH, temperature and concentration of chemicals, like heavy metals, permanently close to the extreme limits known for life. Due to the potential biotechnological applications of extremophile microorganisms, the investigation of microbial life in volcanic environments is of great interest. Moreover, volcanic environments are dominated by physiochemical conditions considered analogue to those present during the first stages of life on Earth and represent key habitats for astrobiology.
Six volcanic lakes, dominated by different geochemical parameters such as concentration of dissolved gas and salt, were explored. Acidic waters of the El Chichón crater lake and related thermal springs were collected in Mexico, whereas the ultra-acidic lake of Poas volcano, the acidic Botos lagoon, the Irazù crater lake, the Laguna Hule and Rio Cuarto were sampled in Costa Rica.
DNA-fingerprinting techniques allow to overcome the limitations imposed by the low level of cultivability of environmental bacteria. Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting applied on the metagenome extracted from the lake waters demonstrated that i) the sites were colonised by bacteria, ii) the different lakes hosted a peculiar microbiota, likely adapted to the specific environmental conditions. Cultivation-dependent techniques were also applied in order to explore the physiological and metabolic properties of the organisms able to colonize thermal spring field related to the El Chichón volcanic system, where pioneer vascular plants were observed. Special attention has been given to plant growth promoting (PGP) bacteria, with the aim of revealing bacteria able to aid the plant to cope with the harsh environmental conditions. Many different bacterial species were associated to plant roots, some of them known for their capability to grow in extreme conditions. Several strains showed 1-aminocyclopropane-1-carboxylate (ACC)-deaminase activity, one of the best studied PGP activity, with a role in protecting the plant from environmental stress. The isolates showed, besides ACC-deaminase, also other PGP activities such as phosphate solubilization, dinitrogen fixation, and the production of siderophores, potentially promoting plant growth by supplying mineral elements.
The results of molecular fingerprinting and cultivation analyses demonstrated that the analyzed volcanic lakes and the associated thermal springs are colonised by a rich microbiota and that the specific geochemical context is the main driver of the microbial community composition. Moreover, plants adapted to live in the extreme environment of El Chichón lake are associated with several bacterial species having potential activity of plant growth promotion and stress protection
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Geochemical monitoring of volcanic lakes. A generalized box model for active crater lakes
No full text<p>In the past, variations in the chemical contents (SO42&minus;, Cl&minus;, cations) of crater lake water have not systematically demonstrated any relationships with eruptive activity. Intensive parameters (i.e., concentrations, temperature, pH, salinity) should be converted into extensive parameters (i.e., fluxes, changes with time of mass and solutes), taking into account all the internal and external chemical&ndash;physical factors that affect the crater lake system. This study presents a generalized box model approach that can be useful for geochemical monitoring of active crater lakes, as highly dynamic natural systems. The mass budget of a lake is based on observations of physical variations over a certain period of time: lake volume (level, surface area), lake water temperature, meteorological precipitation, air humidity, wind velocity, input of spring water, and overflow of the lake. This first approach leads to quantification of the input and output fluxes that contribute to the actual crater lake volume. Estimating the input flux of the "volcanic" fluid (Qf- kg/s) &ndash;&ndash; an unmeasurable subsurface parameter &ndash;&ndash; and tracing its variations with time is the major focus during crater lake monitoring. Through expanding the mass budget into an isotope and chemical budget of the lake, the box model helps to qualitatively characterize the fluids involved. The (calculated) Cl&minus; content and dD ratio of the rising "volcanic" fluid defines its origin. With reference to continuous monitoring of crater lakes, the present study provides tips that allow better calculation of Qf in the future. At present, this study offers the most comprehensive and up-to-date literature review on active crater lakes.</p>
- …
