Bioindicators of soil quality in coffee organic cultivation systems

The objective of this work was to assess the effect of different coffee organic cultivation systems on chemical and biological soil characteristics, in different seasons of the year. The following systems were evaluated: coffee intercropped with one (CJ1), two (CJ2) or three (CJ3) pigeon pea (Cajanus cajan) alleys; coffee planted under full sun (CS); area planted with sweet pepper and snap bean in a conventional tillage system (AC); and secondary forest area (FFR). Row spacing in CJ1, CJ2, CJ3 and CS was 2.0x1.0, 2.8x1.0, 3.6x1.0, and 2.8x1.0 m, respectively. Soil samples were collected at 10-cm depth, during the four seasons of the year. The results were subjected to analysis of variance, principal component analysis, and redundancy analysis. There was an increase in edaphic macrofauna, soil basal respiration, and microbial quotient in the summer. Total macrofauna density was greater in CJ2 followed by CJ3, CS, CJ1, AC and FFR; Coleoptera, Formicidae, and Isoptera were the most abundant groups. There are no significant differences among the areas for soil basal respiration, and the metabolic quotient is higher in CJ1, CJ3, and FFR. Microbial biomass carbon and the contents of K, pH, Ca+Mg, and P show greater values in AC.

Soil biological attributes in pastures of different ages in a crop-livestock integrated system

The objective of this work was to evaluate the effect of the pasture (Urochloa brizantha) component age on soil biological properties, in a crop-livestock integrated system. The experiment was carried out in a Brazilian savannah (Cerrado) area with 92 ha, divided into six pens of approximately 15 ha. Each pen represented a different stage of the pasture component: formation, P0; one year, P1; two years, P2; three years, P3; and final with 3.5 years, Pf. Samples were taken in the 0-10 cm soil depth. The soil biological parameters - microbial biomass carbon (MBC), microbial biomass respiration (C-CO2), metabolic quotient (qCO2), microbial quotient (q mic), and total organic carbon (TOC) - were evaluated and compared among different stages of the pasture, and between an adjacent area under native Cerrado and another area under degraded pasture (PCD). The MBC, q mic and TOC increased and qCO2 reduced under the different pasture stages. Compared to PCD, the pasture stages had higher MBC, q mic and TOC, and lower qCO2. The crop-livestock integrated system improved soil microbiological parameters and immobilized carbon in the soil in comparison to the degraded pasture.

Microbial communities in Cerrado soils under native vegetation subjected to prescribed fire and under pasture

The objective of this work was to evaluate the effects of fire regimes and vegetation cover on the structure and dynamics of soil microbial communities, through phospholipid fatty acid (PLFA) analysis. Comparisons were made between native areas with different woody covers ("cerrado stricto sensu" and "campo sujo"), under different fire regimes, and a 20-year-old active palisadegrass pasture in the Central Plateau of Brazil. Microbial biomass was higher in the native plots than in the pasture, and the highest monthly values were observed during the rainy season in the native plots. No significant differences were observed between fire regimes or between communities from the two native vegetation types. However, the principal component (PC) analysis separated the microbial communities by vegetation cover (native x pasture) and season (wet x dry), accounting for 45.8% (PC1 and PC3) and 25.6% (PC2 and PC3), respectively, of the total PLFA variability. Changes in land cover and seasonal rainfall in Cerrado ecosystems have significant effects on the total density of soil microorganisms and on the abundance of microbial groups, especially Gram-negative and Gram-positive bacteria.

Microbiological and chemical attributes of a Hapludalf soil with swine manure fertilization

The objective of this work was to evaluate the microbiological and chemical attributes of a soil with a seven‑year history of urea and swine manure application. In the period from October 2008 to October 2009, soil samples were collected in the 0-10 cm layer and were subjected to the treatments: control, without application of urea or manure; and with the application of urea, pig slurry, and deep pig litter in two doses, in order to supply one or two times the recommended N doses for the maize (Zea mays)/black oat (Avena strigosa) crop succession. The carbon of the microbial biomass (MB‑C) and the basal respiration (C‑CO2) were analyzed, and the metabolic (qCO2) and microbial quotient (qmic) were calculated with the obtained data. Organic matter, pH in water, available P and K, and exchangeable Ca and Mg were also determined. The application of twice the dose of deep pig litter increases the MB‑C and C‑CO2 values. The qmic and qCO2 are little affected by the application of swine manure. The application of twice the dose of deep pig litter increases the values of pH in water and the contents of available P and of exchangeable Ca and Mg in the soil.

Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry.

Biocides are widely used for domestic hygiene, agricultural and industrial applications. Their widespread use has resulted in their introduction into the environment and raised concerns about potential deleterious effects on aquatic ecosystems. In this study, the toxicity of the biocides triclosan, penconazole and metalaxyl were evaluated with the freshwater bacterium Caulobacter crescentus and with a freshwater microbial community using a combination of single- and double-stain flow cytometric assays. Growth of C.  crescentus and the freshwater community were repressed by triclosan but not by penconazole or metalaxyl at concentrations up to 250 μM. The repressive effect of triclosan was dependent on culture conditions. Caulobacter crescentus was more sensitive to triclosan when grown with high glucose at high cell density than when grown directly in sterilized lake water at low cell density. This suggests that the use of conventional growth conditions may overestimate biocide toxicity. Additional experiments showed that the freshwater community was more sensitive to triclosan than C.  crescentus, with 10 nM of triclosan being sufficient to repress growth and change the phylogenetic composition of the community. These results demonstrate that isolate-based assays may underestimate biocide toxicity and highlight the importance of assessing toxicity directly on natural microbial communities. Because 10 nM of triclosan is within the range of concentrations observed in freshwater systems, these results also raise concerns about the risk of introducing triclosan into the environment.

Accurate and early diagnosis of orthopedic device-related infection by microbial heat production and sonication.

Proper and rapid diagnosis of orthopedic device-related infection is important for successful treatment. Sonication has been shown to improve the diagnostic performance. We hypothesized that the combination of sonication with a novel method called microcalorimetry will further improve and accelerate the diagnosis of implant infection. We prospectively included 39 consecutive patients (mean age 59 years, 62% males) at our institution from whom 29 orthopedic prostheses and 10 osteosynthesis material were explanted. The explanted device was sonicated. The resulting sonication fluid was analyzed using microcalorimetry. Using standardized criteria to define orthopedic device-related infection, 12 cases (31%) were defined as infected. In all, positive periprosthetic tissue cultures were found. The sensitivity and specificity of microcalorimetry of sonication fluid were 100% and 97%, respectively. Mean time to detection, defined as time to reach a rising heat flow signal of 20 µW measured after equilibiration needed to get accurate measurement, was 10.9 h. In summary, microcalorimetry of sonication fluid is a reliable and a fast method in detecting the presence of microorganisms in orthopedic device-related infection. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:1700-1703, 2013.

Simulation of stromatolite growth using diffusion-limited aggregation and a discrete model of biogeochemical exchanges in microbial mat

Resume : Mieux comprendre les stromatolithes et les tapis microbiens est un sujet important en biogéosciences puisque cela aide à l'étude des premières formes de vie sur Terre, a mieux cerner l'écologie des communautés microbiennes et la contribution des microorganismes a la biominéralisation, et même à poser certains fondements dans les recherches en exobiologie. D'autre part, la modélisation est un outil puissant utilisé dans les sciences naturelles pour appréhender différents phénomènes de façon théorique. Les modèles sont généralement construits sur un système d'équations différentielles et les résultats sont obtenus en résolvant ce système. Les logiciels disponibles pour implémenter les modèles incluent les logiciels mathématiques et les logiciels généraux de simulation. L'objectif principal de cette thèse est de développer des modèles et des logiciels pour aider a comprendre, via la simulation, le fonctionnement des stromatolithes et des tapis microbiens. Ces logiciels ont été développés en C++ en ne partant d'aucun pré-requis de façon a privilégier performance et flexibilité maximales. Cette démarche permet de construire des modèles bien plus spécifiques et plus appropriés aux phénomènes a modéliser. Premièrement, nous avons étudié la croissance et la morphologie des stromatolithes. Nous avons construit un modèle tridimensionnel fondé sur l'agrégation par diffusion limitée. Le modèle a été implémenté en deux applications C++: un moteur de simulation capable d'exécuter un batch de simulations et de produire des fichiers de résultats, et un outil de visualisation qui permet d'analyser les résultats en trois dimensions. Après avoir vérifié que ce modèle peut en effet reproduire la croissance et la morphologie de plusieurs types de stromatolithes, nous avons introduit un processus de sédimentation comme facteur externe. Ceci nous a mené a des résultats intéressants, et permis de soutenir l'hypothèse que la morphologie des stromatolithes pourrait être le résultat de facteurs externes autant que de facteurs internes. Ceci est important car la classification des stromatolithes est généralement fondée sur leur morphologie, imposant que la forme d'un stromatolithe est dépendante de facteurs internes uniquement (c'est-à-dire les tapis microbiens). Les résultats avancés dans ce mémoire contredisent donc ces assertions communément admises. Ensuite, nous avons décidé de mener des recherches plus en profondeur sur les aspects fonctionnels des tapis microbiens. Nous avons construit un modèle bidimensionnel de réaction-diffusion fondé sur la simulation discrète. Ce modèle a été implémenté dans une application C++ qui permet de paramétrer et exécuter des simulations. Nous avons ensuite pu comparer les résultats de simulation avec des données du monde réel et vérifier que le modèle peut en effet imiter le comportement de certains tapis microbiens. Ainsi, nous avons pu émettre et vérifier des hypothèses sur le fonctionnement de certains tapis microbiens pour nous aider à mieux en comprendre certains aspects, comme la dynamique des éléments, en particulier le soufre et l'oxygène. En conclusion, ce travail a abouti à l'écriture de logiciels dédiés à la simulation de tapis microbiens d'un point de vue tant morphologique que fonctionnel, suivant deux approches différentes, l'une holistique, l'autre plus analytique. Ces logiciels sont gratuits et diffusés sous licence GPL (General Public License). Abstract : Better understanding of stromatolites and microbial mats is an important topic in biogeosciences as it helps studying the early forms of life on Earth, provides clues re- garding the ecology of microbial ecosystems and their contribution to biomineralization, and gives basis to a new science, exobiology. On the other hand, modelling is a powerful tool used in natural sciences for the theoretical approach of various phenomena. Models are usually built on a system of differential equations and results are obtained by solving that system. Available software to implement models includes mathematical solvers and general simulation software. The main objective of this thesis is to develop models and software able to help to understand the functioning of stromatolites and microbial mats. Software was developed in C++ from scratch for maximum performance and flexibility. This allows to build models much more specific to a phenomenon rather than general software. First, we studied stromatolite growth and morphology. We built a three-dimensional model based on diffusion-limited aggregation. The model was implemented in two C++ applications: a simulator engine, which can run a batch of simulations and produce result files, and a Visualization tool, which allows results to be analysed in three dimensions. After verifying that our model can indeed reproduce the growth and morphology of several types of stromatolites, we introduced a sedimentation process as an external factor. This lead to interesting results, and allowed to emit the hypothesis that stromatolite morphology may be the result of external factors as much as internal factors. This is important as stromatolite classification is usually based on their morphology, imposing that a stromatolite shape is dependant on internal factors only (i.e. the microbial mat). This statement is contradicted by our findings, Second, we decided to investigate deeper the functioning of microbial mats, We built a two-dimensional reaction-diffusion model based on discrete simulation, The model was implemented in a C++ application that allows setting and running simulations. We could then compare simulation results with real world data and verify that our model can indeed mimic the behaviour of some microbial mats. Thus, we have proposed and verified hypotheses regarding microbial mats functioning in order to help to better understand them, e.g. the cycle of some elements such as oxygen or sulfur. ln conclusion, this PhD provides a simulation software, dealing with two different approaches. This software is free and available under a GPL licence.

Micromorphological characterization and lithification of microbial mats from the Ebro Delta (Spain)

The structural organization of microbial mats from the Ebro Delta (Spain) and their accretion and partial lithification processes were explored using scanning electron microscopy in back-scattered electron mode and low-temperature scanning electron microscopy. Two differentiated zones were distinguished in a transverse section of a fragment taken from the mat at a depth of 2.5 mm. The first consisted of an upper layer in which the dominant microorganisms, Microcoleus spp., actively grew in an embedded slack matrix of exopolysaccharides. Microcoleus filaments were oriented parallel to the surface and to each other, with filaments below arranged perpendicularly to one another but without crossing. Most of the minerals present were allochthonous grains of calcium phosphate biocorroded by cyanobacteria. The second zone was below a depth of 1 mm and made up of accretion layers with large deposits of calcium carbonate and smaller amounts of calcium phosphate of biological origin. The predominance of a particular type of mineral precipitation with a characteristic external shape and/or texture within a zone, e.g., sponge-like deposits of calcium phosphate, appears to depend on the taxa of the prevailing microorganisms

Microbial quality of linseed and fibre hemp plants during growing and harvest seasons

Selostus: Pellavan ja kuituhampun mikrobiologinen laatu kasvukauden aikana