Les comunitats microbianes com a bioindicadors de l'estat dels agroecosistemes

Les pràctiques agronòmiques modernes i l'ús excessiu de fertilitzants químics en les últimes dècades han minimitzat el contingut de matèria orgànica de molts sòls agrícoles. L'interès actual per desenvolupar una agricultura sostenible, ha recuperat la utilització d'esmenes orgàniques, residus animals i vegetals, per la seva capacitat per millorar la salut general de les plantes i dels sòls agrícoles. En el cultiu de l'alvocat, especialment en el cultiu ecològic, la utilització d'esmenes orgàniques és una pràctica molt estesa que sembla estar reportant molts beneficis. Investigadors del Grup de Microbiologia Ambiental de la UAB en col·laboració amb investigadors del Departament de Microbiologia de la Universitat de Màlaga han estudiat l'efecte de la pràctica agrícola i de l'aplicació de diferents esmenes orgàniques sobre la microbiota del sòl de cultius d'alvocat.Las prácticas agronómicas modernas y el uso excesivo de fertilizantes químicos en las últimas décadas han minimizado el contenido de materia orgánica de muchos suelos agrícolas. El interés actual en desarrollar una agricultura sostenible, ha propiciado la utilización de enmiendas orgánicas, residuos animales y vegetales, por su capacidad para mejorar la salud general de las plantas y los suelos agrícolas. En el cultivo del aguacate, especialmente en el cultivo ecológico, la utilización de enmiendas orgánicas es una práctica muy extendida que parece estar reportando muchos beneficios. Investigadores del Grupo de Microbiología Ambiental de la UAB en colaboración con investigadores del Departamento de Microbiología de la Universidad de Málaga han estudiado el efecto de la práctica agrícola y de la aplicación de diferentes enmiendas orgánicas sobre la microbiota del suelo de cultivos de aguacate

Estudi de la biocenosi dels tapissos microbians del delta de l?Ebre

S'estudià la microzonació de la comunitat de microorganismes que composa els tapissos microbians del delta de l'Ebre mitjançant tècniques de microcòpia òptica i de microscòpia electrònica. Els tapissos microbians estudiats presentaven característiques diferents (nombre de laminacions, composició d'espècies, etc.). La laminació superior estava formada per diversos organismes fotosintètics oxigènics on dominaven les diatomees pinnades, arribant a densitats de 7,3·107 cel·cm?3. S'identificaren 12 gèneres, dels quals els més abundants foren Nitzschia, Navicula, Amphora i Mastogloia. En la laminació superficial també s'hi podien observar cianobacteris, tant filamentosos com cocoides dels quals Lyngbya aestuarii és un dels cianobacteris filamentosos més abundants que s'hi va trobar. A la segona laminació el microorganisme dominant era el cianobacteri Microcoleus chthonoplastes, que podia presentar entre 5 i més de 20 tricomes per beina. La tercera laminació pigmentada no la presentaven tots els tapissos microbians estudiats, i en els que s'observà podia variar l'espècie de microorganisme dominant. Així, el microorganisme més abundant d'aquesta laminació, en el punt de mostreig P1, era el bacteri fototròfic anoxigènic Chromatium gracile. En canvi, en el P3 el microorganisme predominant fou una nova espècie de la família Chromatiaceae, de 4,16 µm d'ample per 5,98 µm de longitud, que acumulava sofre intracel·lular i tenia el sistema intracitoplasmàtic de membranes de tipus lamel·lar. També s'hi observà la presència d'un microorganisme fototròfic filamentós embeinat, que tenia un sistema intracitoplasmàtic de membranes (ICM) de tipus lamel·lar. En la zona superior de la laminació rosa, es va observar la presència del bacteri quimiolitotròfic Beggiatoa sp i al davall de la zona fòtica, on el sediment era de color negre es van detectar bacteris reductors de sulfat dels gèneres Desulfovibrio, Desulfococcus i Desulfotomaculum.Se estudió la microzonación de la comunidad de microorganismos que forman los tapetes microbianos del delta del Ebro mediante técnicas de microscopía óptica y electrónica. Los tapetes microbianos estudiados presentaban características distintas (número de capas, composición de especies, etc.). La laminación superior estaba formada por diversos organismos fotosintéticos oxigénicos donde dominaban las diatomeas pennadas, llegando a densidades de 7,3·107 cel·cm?3. Se identificaron 12 géneros, entre los más abundantes estaban Nitzschia, Navicula, Amphora y Mastogloia. En la primera capa también se observaron cianobacterias, tanto filamentosas como cocoides, siendo Lyngbya aestuarii una de las cianobacterias filamentosas más abundantes que se detectaron. En la segunda laminación el microorganismo dominante era Microcoleus chthonoplastes, que podía presentar entre 5 y más de 20 tricomas por vaina. La tercera laminación pigmentada no la presentaban todos los tapetes estudiados, y en aquellos en los que se observó podía variar la especie de microorganismo dominante. La especie más abundante en esa laminación, en el punto de muestreo P1, era la bacteria fototrófica anoxigénica Chromatium gracile. Sin embargo, en el P3 el microorganismo predominante era una nueva especie de la familia Chromatiaceae, de 4,16 µm de diámetro por 5,98 µm de longitud, que acumulaba azufre intracelular y el sistema intracitoplasmático de membranas (ICM) era de tipo lamelar. También se observó la presencia de un microorganismo fototrófico filamentoso envainado, con un sistema ICM lamelar. En la zona superior de la laminación rosa, se observó la presencia de la bacteria quimiolitotrófica Beggiatoa sp. y por debajo de la zona fótica, donde el sedimento era de color negro se detectaron bacterias reductoras de sulfato pertenecientes a los géneros Desulfovibrio, Desulfococcus y Desulfotomaculum.The microzonation of microorganisms in the microbial mats of the Ebro Delta was studied by light microscopy andscanning and transmission electron microscopy. Microbial mats showed differences in species composition, number and colour of layers, etc. Oxygenic photosynthetic organisms grew on the surface of the mat. In this layer, the community consisted predominantly of pennate diatoms, reaching densities of 7.3·107 cel·cm?3. Twelve genera of diatoms were identified, and the most abundant were Nitzschia, Navicula, Amphora and Mastogloia. Coccoid cyanobacteria and filamentous cyanobacteria were also identified in the upper layer of the mat, where the predominant filamentous cyanobacterium was Lyngbya aestuarii. The dominant microorganism in the second layer was the filamentous cyanobacterium Microcoleus chthono plastes, which contained 5-20 trichomes within the common sheath. The third layer was not present in all the microbial mats studied, and when it was present the dominant species could be different in different sampling sites. In sampling site P1 the dominant microorganism was the anoxygenic phototrophic bacterium Chromatium gracile. But in site P3 the dominant microorganism in the purple third layer was a new species belonging to the Chromatiaceae (4,16 µm in diameter and 5,98 µm in length; the intracytoplasmic membrane system (ICM) was lamellar; and in the presence of sulphide and light, globules of sulphur are formed inside these cells). Another sheathed filamentous phototrophic microorganism with a lamellar ICM was also observed in this layer. Between the Microcoleus layer and the purple layer, the chemolithotrophic bacterium Beggiatoa sp. was found. Below the photic zone, in the black sediment, sulphate reducing bacteria belonging to the genera Desulfovibrio, Desulfococcus and Desulfotomaculum were identified

Sulfide fluxes in a microbial mat from the Ebro Delta, Spain

The sulfur cycle of Ebro Delta microbial mats was studied in order to determine sulfide production and sulfide consumption. Vertical distribution of two major functional groups involved in the sulfur cycle, anoxygenic phototrophic bacteria and dissimilatory sulfate-reducing bacteria (SRB), was also studied. The former reached up to 2.2 ×108 cfu cm-3 sediment in the purple layer, and the latter reached about 1.8×105 SRB cm-3 sediment in the black layer. From the changes in sulfide concentrations under light-dark cycles it can be inferred that the rate of H2S production was 6.2 μmol H2S cm-3 day-1 at 2.6 mm, and 7.6 μmol H2S cm-3 day-1 at 6 mm. Furthermore, sulfide consumption was also assessed, determining rates of 0.04, 0.13 and 0.005 mmol l-1 of sulfide oxidized at depths of 2.6, 3 and 6 mm, respectively

Seasonal microbial ribotype shifts in the sulfurous karstic lakes Cisó and Vilar, in northeastern Spain

Spatio-temporal changes in two sulfurous lakes from the karstic area of Banyoles (Girona, Spain), holomictic lake Cisó and meromictic lake Vilar, were studied over one year. Samples were collected at different depths from the two lakes on the same days, during each of the four seasons, and several physico-chemical variables (temperature, light, pH, conductivity, sulfide, oxygen concentration, pigment concentrations, etc.) were measured. To fingerprint bacterial populations from each sample, DNA was extracted, bacterial 16S rRNA genes were amplified by PCR, and restriction fragment length polymorphism (RFLP) analyses of the total bacterial 16S rDNAs were performed. Each 16S rDNA pool was independently digested with three restriction endonucleases (AluI, HinfI, and RsaI) and separated electrophoretically. More restriction fragments were obtained from the Lake Vilar samples than from the Lake Cisó samples. Moreover, intrasample and intersample differences were observed in each lake. RFLP patterns were compared by scoring similarities using the Jaccard coefficient and then building a multidimensional scaling (MDS) map from the resulting similarities matrix. In both lakes, results indicated that seasonality was mostly responsible for the observed fluctuations in the RFLP patterns, while the effect of stratification was less pronounced. [Int Microbiol 2005; 8(4):235-242

Estudi de la biocenosi dels tapissos microbians del Delta de l'Ebre

S'estudià la microzonació de la comunitat de microorganismes que composa els tapissos microbians del delta de l'Ebre mitjançant tècniques de microcòpia òptica i de microscòpia electrònica. Els tapissos microbians estudiats presentaven característiques diferents (nombre de laminacions, composició d'espècies, etc.). La laminació superior estava formada per diversos organismes fotosintètics oxigènics on dominaven les diatomees pinnades, arribant a densitats de 7,3·107 cel·cm-3. S'identificaren 12 gèneres, dels quals els més abundants foren Nitzschia, Navicula, Amphora i Mastogloia. En la laminació superficial també s'hi podien observar cianobacteris, tant filamentosos com cocoides dels quals Lyngbya aestuarii és un dels cianobacteris filamentosos més abundants que s'hi va trobar. A la segona laminació el microorganisme dominant era el cianobacteri Microcoleus chthonoplastes, que podia presentar entre 5 i més de 20 tricomes per beina. La tercera laminació pigmentada no la presentaven tots els tapissos microbians estudiats, i en els que s'observà podia variar l'espècie de microorganisme dominant. Així, el microorganisme més abundant d'aquesta laminació, en el punt de mostreig P1, era el bacteri fototròfic anoxigènic Chromatium gracile. En canvi, en el P3 el microorganisme predominant fou una nova espècie de la família Chromatiaceae, de 4,16 µm d'ample per 5,98 µm de longitud, que acumulava sofre intracel·lular i tenia el sistema intracitoplasmàtic de membranes de tipus lamel·lar. També s'hi observà la presència d'un microorganisme fototròfic filamentós embeinat, que tenia un sistema intracitoplasmàtic de membranes (ICM) de tipus lamel·lar. En la zona superior de la laminació rosa, es va observar la presència del bacteri quimiolitotròfic Beggiatoa sp i al davall de la zona fòtica, on el sediment era de color negre es van detectar bacteris reductors de sulfat dels gèneres Desulfovibrio, Desulfococcus i Desulfotomaculum.The microzonation of microorganisms in the microbial mats of the Ebro Delta was studied by light microscopy andscanning and transmission electron microscopy. Microbial mats showed differences in species composition, number and colour of layers, etc. Oxygenic photosynthetic organisms grew on the surface of the mat. In this layer, the community consisted predominantly of pennate diatoms, reaching densities of 7.3·107 cel·cm-3. Twelve genera of diatoms were identified, and the most abundant were Nitzschia, Navicula, Amphora and Mastogloia. Coccoid cyanobacteria and filamentous cyanobacteria were also identified in the upper layer of the mat, where the predominant filamentous cyanobacterium was Lyngbya aestuarii. The dominant microorganism in the second layer was the filamentous cyanobacterium Microcoleus chthono- 114 plastes, which contained 5-20 trichomes within the common sheath. The third layer was not present in all the microbial mats studied, and when it was present the dominant species could be different in different sampling sites. In sampling site P1 the dominant microorganism was the anoxygenic phototrophic bacterium Chromatium gracile. But in site P3 the dominant microorganism in the purple third layer was a new species belonging to the Chromatiaceae (4,16 µm in diameter and 5,98 µm in length; the intracytoplasmic membrane system (ICM) was lamellar; and in the presence of sulphide and light, globules of sulphur are formed inside these cells). Another sheathed filamentous phototrophic microorganism with a lamellar ICM was also observed in this layer. Between the Microcoleus layer and the purple layer, the chemolithotrophic bacterium Beggiatoa sp. was found. Below the photic zone, in the black sediment, sulphate reducing bacteria belonging to the genera Desulfovibrio, Desulfococcus and Desulfotomaculum were identified.Se estudió la microzonación de la comunidad de microorganismos que forman los tapetes microbianos del delta del Ebro mediante técnicas de microscopía óptica y electrónica. Los tapetes microbianos estudiados presentaban características distintas (número de capas, composición de especies, etc.). La laminación superior estaba formada por diversos organismos fotosintéticos oxigénicos donde dominaban las diatomeas pennadas, llegando a densidades de 7,3·107 cel·cm-3. Se identificaron 12 géneros, entre los más abundantes estaban Nitzschia, Navicula, Amphora y Mastogloia. En la primera capa también se observaron cianobacterias, tanto filamentosas como cocoides, siendo Lyngbya aestuarii una de las cianobacterias filamentosas más abundantes que se detectaron. En la segunda laminación el microorganismo dominante era Microcoleus chthonoplastes, que podía presentar entre 5 y más de 20 tricomas por vaina. La tercera laminación pigmentada no la presentaban todos los tapetes estudiados, y en aquellos en los que se observó podía variar la especie de microorganismo dominante. La especie más abundante en esa laminación, en el punto de muestreo P1, era la bacteria fototrófica anoxigénica Chromatium gracile. Sin embargo, en el P3 el microorganismo predominante era una nueva especie de la familia Chromatiaceae, de 4,16 µm de diámetro por 5,98 µm de longitud, que acumulaba azufre intracelular y el sistema intracitoplasmático de membranas (ICM) era de tipo lamelar. También se observó la presencia de un microorganismo fototrófico filamentoso envainado, con un sistema ICM lamelar. En la zona superior de la laminación rosa, se observó la presencia de la bacteria quimiolitotrófica Beggiatoa sp. y por debajo de la zona fótica, donde el sedimento era de color negro se detectaron bacterias reductoras de sulfato pertenecientes a los géneros Desulfovibrio, Desulfo- coccus y Desulfotomaculu

Distribution of phototrophic populations and primary production in a microbial mat from the Ebro Delta, Spain

Microbial mats arising in the sand flats of the Ebro Delta (Tarragona, Spain) were investigated during the summer season, when the community was highly developed. These mats are composed of three pigmented layers of phototrophic organisms, an upper brown layer mainly composed of Lyngbya aestuarii and diatoms, an intermediate green layer of the cyanobacterium Microcoleus chthonoplastes, and an underlying pink layer of a so-far unidentified purple sulfur bacterium. In the photic zone, oxygenic phototrophs constitute about 58% of total photosynthetic biomass, measured as biovolume, and anoxygenic phototrophs represent 42%. Diatoms constitute 11.8% of the oxygenic biomass, M. chthonoplastes 61.2%, and L. aestuarii and coccoid cyanobacteria 20.6 and 6.4%, respectively. In this laminated community, organic matter has an autochthonous origin, and photosynthesis is the most important source of organic carbon. Oxygen production reaches up to 27.2 mmol O2 m–2 h–1, measured at 1000 μE m–2 s–1 light intensity, whereas oxidation of sulfide in the light has been calculated to be 18.6 mmol S m–2 h–1. This amount represents 26% of the total photosynthetic production in terms of photoassimilated carbon, demonstrating the important role of anoxygenic phototrophs as primary producers in the pink layer of Ebro Delta microbial mats. [Int Microbiol 2004; 7(1):19–25

Microbial community changes induced by Managed Aquifer Recharge activities: linking hydrogeological and biological processes

Managed Aquifer Recharge (MAR) is a technique used worldwide to increase the availability of water resources. We study how MAR modifies microbial ecosystems and its implications for enhancing biodegradation processes to eventually improve groundwater quality. We compare soil and groundwater samples taken from a MAR facility located in NE Spain during recharge (with the facility operating continuously for several months) and after 4 months of no recharge. The study demonstrates a strong correlation between soil and water microbial prints with respect to sampling location along the mapped infiltration path. In particular, managed recharge practices disrupt groundwater ecosystems by modifying diversity indices and the composition of microbial communities, indicating that infiltration favors the growth of certain populations. Analysis of the genetic profiles showed the presence of nine different bacterial phyla in the facility, revealing high biological diversity at the highest taxonomic range. In fact, the microbial population patterns under recharge conditions agree with the intermediate disturbance hypothesis (IDH). Moreover, DNA sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) band patterns revealed the existence of indicator species linked to MAR, most notably Dehalogenimonas sp., Nitrospira sp. and Vogesella sp.. Our real facility multidisciplinary study (hydrological, geochemical and microbial), involving soil and groundwater samples, indicates that MAR is a naturally based, passive and efficient technique with broad implications for the biodegradation of pollutants dissolved in water.Peer ReviewedPostprint (published version

Microbial community changes induced by Managed Aquifer Recharge activities: linking hydrogeological and biological processes

Managed Aquifer Recharge (MAR) is a technique used worldwide to increase the availability of water resources. We study how MAR modifies microbial ecosystems and its implications for enhancing biodegradation processes to eventually improve groundwater quality. We compare soil and groundwater samples taken from a MAR facility located in NE Spain during recharge (with the facility operating continuously for several months) and after 4 months of no recharge. The study demonstrates a strong correlation between soil and water microbial prints with respect to sampling location along the mapped infiltration path. In particular, managed recharge practices disrupt groundwater ecosystems by modifying diversity indices and the composition of microbial communities, indicating that infiltration favors the growth of certain populations. Analysis of the genetic profiles showed the presence of nine different bacterial phyla in the facility, revealing high biological diversity at the highest taxonomic range. In fact, the microbial population patterns under recharge conditions agree with the intermediate disturbance hypothesis (IDH). Moreover, DNA sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) band patterns revealed the existence of indicator species linked to MAR, most notably Dehalogenimonas sp., Nitrospira sp. and Vogesella sp.. Our real facility multidisciplinary study (hydrological, geochemical and microbial), involving soil and groundwater samples, indicates that MAR is a naturally based, passive and efficient technique with broad implications for the biodegradation of pollutants dissolved in water

Are dominant microbial sub-surface communities affected by water quality and soil characteristics?

Subsurface microorganisms must deal with quite extreme environmental conditions. The lack of light, oxygen, and potentially nutrients are the main environmental stresses faced by subsurface microbial communities. Likewise, environmental disruptions providing an unbalanced positive input of nutrients force microorganisms to adapt to varying conditions, visible in the changes in microbial community diversity. In order to test microbial community adaptation to environmental changes, we performed a study in a surface Managed Aquifer Recharge facility, consisting of a settlement basin (two-day residence time) and an infiltration pond. Data on groundwater hydrochemistry, soil texture, and microbial characterization was compiled from surface water, groundwater, and soil samples at two distinct recharge operation conditions. Multivariate statistics by means of Principal Component Analysis (PCA) was the technique used to map the relevant dimensionality reduced combinations of input variables that properly describe the system behavior. The methodology selected allows including variables of different nature and displaying very different range values. Strong differences in the microbial assemblage under recharge conditions were found, coupled to hydrochemistry and grain-size distribution variables. Also, some microbial groups displayed correlations with either carbon or nitrogen cycles, especially showing abundant populations of denitrifying bacteria in groundwater. A significant correlation was found between Methylotenera mobilis and the concentrations of NO3 and SO4, and also between Vogesella indigofera and the presence of DOC in the infiltrating water. Also, microbial communities present at the bottom of the pond correlated with representative descriptors of soil grain size distribution.Peer ReviewedPostprint (author's final draft

Effects of Supplementation with Microminerals on Production Indicators and Blood, Feces, and Urine Traces of Grazing Alpaca (Lama lama)

To analyze the effect of additional microminerals in the diet supplement on weight and diameter of alpaca fiber, the application of three doses of selenium and zinc (0.0; 1.0; and 1.5 cc) on the diet, on CRD factorial arrangement (3 x 2) + (3 x 2), was assessed. The results showed statistically significant differencences for treatments: selenium doses, ages, zinc doses, and for zinc interaction by ages (Se1E2 with 74.33 kg at 90 days, for height at the withers, Zn1E2, averaging 91.33 cm). Fiber length for treatments Se1E1 and Se1E2 averaged 3 cm. For fiber diameter, treatments 1 (Se0E1) and Se1E1, group 1, and treatments Zn0E2 and Zn1E1, group 2, showed the best fiber quality (P < 0.05), averaging 28 microns. Live weight and fiber quality from mature animals based on supplementation with Se and Zn had beneficial effects, which improved phenotypical features of production, like live weight, though residues were found in 3-5 year old animals