Proteins on microbial identification: past achievements, present state-of-the-art, and future challenges

The use of chemical analysis of microbial components, including proteins, became an important achievement in the 80’s of the last century to the microbial identification. This led a more objective microbial identification scheme, called chemotaxonomy, and the analytical tools used in the field are mainly 1D/2D gel electrophoresis, spectrophotometry, high-performance liquid chromatography, gas chromatography, and combined gas chromatography-mass spectrometry. The Edman degradation reaction was also applied to peptides sequence giving important insights to the microbial identification. The rapid development of these techniques, in association with knowledge generated by DNA sequencing and phylogeny based on rRNA gene and housekeeping genes sequences, boosted the microbial identification to an unparalleled scale. The recent results of mass spectrometry (MS), like Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight (MALDI-TOF), for rapid and reliable microbial identification showed considerable promise. In addition, the technique is rapid, reliable and inexpensive in terms of labour and consumables when compared with other biological techniques. At present, MALDI-TOF MS adds an additional step for polyphasic identification which is essential when there is a paucity of characters or high DNA homologies for delimiting very close related species. The full impact of this approach is now being appreciated when more diverse species are studied in detail and successfully identified. However, even with the best polyphasic system, identification of some taxa remains time-consuming and determining what represents a species remains subjective. The possibilities opened with new and even more robust mass spectrometers combined with sound and reliable databases allow not only the microbial identification based on the proteome fingerprinting but also include de novo specific proteins sequencing as additional step. These approaches are pushing the boundaries in the microbial identification field.

Caracterização do microbioma e dos perfis de resistência nos afluentes e efluentes de ETAR

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Engenharia Clínica)

Diversity and capacity to promote maize growth of bacteria isolated from the Amazon region

ABSTRACT Maize plants can establish beneficial associations with plant growth-promoting bacteria. However, few studies have been conducted on the characterization and inoculation of these bacteria in the Amazon region. This study aimed to characterize endophytic bacteria isolated from maize in the Amazon region and to assess their capacity to promote plant growth. Fifty-five bacterial isolates were obtained from maize grown in two types of ecosystems, i.e., a cerrado (savanna) and a forest area. The isolates were characterized by the presence of the nifH gene, their ability to synthesize indole-3-acetic acid (IAA) and solubilize calcium phosphate (CaHPO4), and 16S rRNA partial gene sequencing. Twenty-four bacteria contained the nifH gene, of which seven were isolated from maize plants cultivated in a cerrado area and seventeen from a forest area. Fourteen samples showed the capacity to synthesize IAA and only four solubilized calcium phosphate. The following genera were found among these isolates: Pseudomonas; Acinetobacter; Enterobacter; Pantoea; Burkholderia and Bacillus. In addition, eight isolates with plant growth-promoting capacity were selected for a glasshouse experiment involving the inoculation of two maize genotypes (a hybrid and a variety) grown in pots containing soil. Inoculation promoted the development of the maize plants but no significant interaction between maize cultivar and bacterial inoculation was found. A high diversity of endophytic bacteria is present in the Amazon region and these bacteria have potential to promote the development of maize plants.

Growth of sulfate reducing bacteria on the methanogenic inhibitor BES

The metabolism of methanogenic archaea is inhibited by 2-bromoethanesulfonate (BES). Methane production is blocked because BES is an analog of methyl-coenzyme M and competes with this key molecule in the last step of methanogenesis. For this reason, BES is commonly used in several studies to avoid growth of acetoclastic and hydrogenotrophic methanogens [1]. Despite its effectiveness as methanogenic inhibitor, BES was found to alter microbial communities’ structure, to inhibit the metabolism of non-methanogenic microorganisms and to stimulate homoacetogenic metabolism [2,3]. Even though sulfonates have been reported as electron acceptors for sulfate- and sulfite-reducing bacteria (SRB), only one study described the reduction of BES by complex microbial communities [4]. In this work, a sulfate-reducing bacterium belonging to Desulfovibrio genus (98 % identity at the 16S rRNA gene level with Desulfovibrio aminophilus) was isolated from anaerobic sludge after several successive transfers in anaerobic medium containing BES as sole substrate. Sulfate was not supplemented to the anaerobic growth medium. This microorganism was able to grow under the following conditions: on BES plus H2/CO2 in bicarbonate buffered medium; on BES without H2/CO2 in bicarbonate buffered medium; and on BES in phosphate buffered medium. The main products of BES utilization were sulfide and acetate, the former was produced by the reduction of sulfur from the sulfonate moiety of BES and the latter likely originated from the carbon backbone of the BES molecule. BES was found, in this study, to represent not only an alternative electron acceptor but also to serve as electron donor, and sole carbon and energy source, supporting growth of a Desulfovibrio sp. obtained in pure culture. This is the first study that reports growth of SRB with BES as electron donor and electron acceptor, showing that the methanogenic inhibitor is a substrate for anaerobic growth.

Who is who in anaerobic oil biodegradation?

[Excerpt] Anaerobic bioremediation is an important alternative for the common aerobic cleanup of subsurface petroleum-contaminated soil and water. Microbial communities involved in anaerobic oil biodegradation are scarcely studied, and only few mechanisms of anaerobic hydrocarbons degradation are described. In this work, microbial degradation of aliphatic hydrocarbons (AHC) was studied by using culture-dependent and culture-independent approaches. Hexadecane and hexadecene-degrading microbial communities were enriched under sulfate-reducing and methanogenic conditions. The microorganisms present in the enriched cultures were identified by 16S rRNA gene sequencing. (...)

Optimization of peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria: the effect of pH, dextran sulfate and probe concentration

Fluorescence in situ hybridization (FISH) is a molecular technique widely used for the detection and characterization of microbial populations. FISH is affected by a wide variety of abiotic and biotic variables and the way they interact with each other. This is translated into a wide variability of FISH procedures found in the literature. The aim of this work is to systematically study the effects of pH, dextran sulfate and probe concentration in the FISH protocol, using a general peptide nucleic acid (PNA) probe for the Eubacteria domain. For this, response surface methodology was used to optimize these 3 PNA-FISH parameters for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). The obtained results show that a probe concentration higher than 300 nM is favorable for both groups. Interestingly, a clear distinction between the two groups regarding the optimal pH and dextran sulfate concentration was found: a high pH (approx. 10), combined with lower dextran sulfate concentration (approx. 2% [w/v]) for Gram-negative species and near-neutral pH (approx. 8), together with higher dextran sulfate concentrations (approx. 10% [w/v]) for Gram-positive species. This behavior seems to result from an interplay between pH and dextran sulfate and their ability to influence probe concentration and diffusion towards the rRNA target. This study shows that, for an optimum hybridization protocol, dextran sulfate and pH should be adjusted according to the target bacteria.

Anaerobic oxidation of methane associated with sulfate reduction in a natural freshwater gas source

The occurrence of anaerobic oxidation of methane (AOM) and trace methane oxidation (TMO) was investigated in a freshwater natural gas source. Sediment samples were taken and analyzed for potential electron acceptors coupled to AOM. Long-term incubations with 13C-labeled CH4 (13CH4) and different electron acceptors showed that both AOM and TMO occurred. In most conditions, 13C-labeled CO2 (13CO2) simultaneously increased with methane formation, which is typical for TMO. In the presence of nitrate, neither methane formation nor methane oxidation occurred. Net AOM was measured only with sulfate as electron acceptor. Here, sulfide production occurred simultaneously with 13CO2 production and no methanogenesis occurred, excluding TMO as a possible source for 13CO2 production from 13CH4. Archaeal 16S rRNA gene analysis showed the highest presence of ANME-2a/b (ANaerobic MEthane oxidizing archaea) and AAA (AOM Associated Archaea) sequences in the incubations with methane and sulfate as compared with only methane addition. Higher abundance of ANME-2a/b in incubations with methane and sulfate as compared with only sulfate addition was shown by qPCR analysis. Bacterial 16S rRNA gene analysis showed the presence of sulfate-reducing bacteria belonging to SEEP-SRB1. This is the first report that explicitly shows that AOM is associated with sulfate reduction in an enrichment culture of ANME-2a/b and AAA methanotrophs and SEEP-SRB1 sulfate reducers from a low-saline environment.

Estudio de las sustancias antimicrobianas producidas por los microorganismos integrantes de la microbiota de terneros jóvenes

El uso desmedido de antibióticos, en especial en los animales que son destinados al consumo humano, produjo la aparición de cepas bacterianas resistentes y favoreció la presencia de residuos de esas sustancias en los alimentos. Esta situación ha sido relacionada con la aparición de alergias, trastornos gastrointestinales y otros problemas que han puesto en riesgo la salud de la población y han promovido una presión creciente de los consumidores y de los entes reguladores para que el sector de la producción de alimentos no utilice antimicrobianos y evite la presencia de sus residuos. El objetivo del trabajo es evaluar la capacidad de las sustancias con actividad antimicrobiana, producida por la microbiota natural, para inhibir el desarrollo de bacterias patógenas responsables de causar enfermedades en terneros jóvenes. Se utilizarán bacterias ácido lácticas autóctonas aisladas a partir de intestinos (duodeno, yeyuno, íleon, colon y ciego), cavidad bucal de terneros de crianza artificial y de vagina de vacas en la etapa pre-parto y que forman parte del cepario del Laboratorio de Análisis de Alimentos, DSPV. Los microorganismos que demuestren capacidad para producir sustancias antimicrobianas serán identificados utilizando técnicas moleculares (amplificación del 16S rRNA, secuenciación y comparación en bases de datos). Las sustancias producidas por los microorganismos serán purificadas antes de analizar su capacidad inhibitoria. Posteriormente, se evaluará el efecto de los agentes físicos (temperatura) y químicos (solventes orgánicos, ácidos, tripsina, proteinasa K y pepsina) sobre dicha capacidad.

Caracterización de la calidad del agua y de la ictiofauna de tres embalses de la cuenca del Rio Tercero (Córdoba, Argentina). Characterization of water quality and ichthyofauna in three reservoirs in Río Tercero basin (Córdoba, Argentina).

Los embalses constituyen reservorios de agua artificiales que se forman para brindar múltiples propósitos. La generación de energía, la provisión de agua para consumo y riego, la atenuación de crecientes y los usos recreacionales, figuran como los más destacados. La calidad del agua y el grado de eutrofización, condicionan la realización de diferentes usos con consecuencias directas e indirectas para la Salud Pública y el recurso íctico. La eutrofización es precisamente uno de los problemas más recurrentes en los embalses de la provincia de Córdoba. Las hipótesis son: 1-El incremento en la concentración de nutrientes, principalmente fósforo y nitrógeno, favorecen la producción de florecimientos algales, con consecuencias negativas sobre la sociedad y el ambiente; 2 - El estrés ambiental producto del grado de eutrofización de los embalses aumenta la susceptibilidad de Odontesthes bonariensis, situación que contribuye al desarrollo de parásitos y a la disminución de su condición corporal. Los objetivos generales del proyecto son: a) Evaluar la variabilidad temporal y espacial de la calidad del agua de tres embalses de la cuenca del río Tercero; b) Estudiar diferentes características biológicas de la ictiofauna presente. Los reservorios a estudiar son Arroyo Corto (64,57W, 32,22S; 357 ha), Río Tercero (64,38W, 32,17S; 4600 ha) y Piedras Moras (64,28W, 32,18S; 830 ha). La superficie, cantidad de tributarios y características limnológicas que presentan estos embalses son contrastantes. Se determinará de manera estacional y en diferentes sitios de muestreo de cada embalse la calidad del agua para distintos usos, a través de análisis físico-químicos y biológicos según metodología estándar, realizando mediciones in situ y en laboratorio. Se evaluará el grado de eutrofia de los reservorios a través de la concentración de nutrientes, clorofila-a y transparencia de agua. Para evaluar la distribución espacial de clorofila-a se integraran SIG-sensores remotos y se determinarán modelos geoestadísticos para predecir florecimientos algales su composición y su relación con riesgos potenciales para la salud y el recurso íctico. Se determinará la diversidad y riqueza de la ictiofauna y la abundancia poblacional (captura por unidad de esfuerzo), la condición corporal, el crecimiento y el estado sanitario del pejerrey O. bonariensis. Para ello se utilizaran artes de pesca pasivos (red de enmalle, trasmallo), activos (red de arrastre) y aparejos de pesca (espineles). Por último, se determinará la abundancia y distribución de Limnoperma fortunei en el embalse Río Tercero. Los resultados obtenidos permitirán evaluar la calidad del agua, el estado trófico y prevenir los riesgos para la salud pública y animal en una de las cuencas de alto impacto antrópico del país. Por su parte, se obtendrán datos sobre distribución, ecología y condición de la ictiofauna, permitiendo el uso sustentable del recurso pesquero. Se obtendrán herramientas que facilitarán la gestión sistémica y la toma de decisiones en el manejo del recurso agua, su saneamiento y la determinación de áreas críticas de riesgo.

Estudio de las sustancias antimicrobianas producidas por los microorganismos integrantes de la microbiota de terneros jóvenes.

El uso desmedido de antibióticos, en especial en los animales que son destinados al consumo humano, produjo la aparición de cepas bacterianas resistentes y favoreció la presencia de residuos de esas sustancias en los alimentos. Esta situación ha sido relacionada con la aparición de alergias, trastornos gastrointestinales y otros problemas que han puesto en riesgo la salud de la población y han promovido una presión creciente de los consumidores y de los entes reguladores para que el sector de la producción de alimentos no utilice antimicrobianos y evite la presencia de sus residuos. El objetivo del trabajo es evaluar la capacidad de las sustancias con actividad antimicrobiana, producida por la microbiota natural, para inhibir el desarrollo de bacterias patógenas responsables de causar enfermedades en terneros jóvenes. Se utilizarán bacterias ácido lácticas autóctonas aisladas a partir de intestinos (duodeno, yeyuno, íleon, colon y ciego), cavidad bucal de terneros de crianza artificial y de vagina de vacas en la etapa pre-parto y que forman parte del cepario del Laboratorio de Análisis de alimentos, DSPV. Los microorganismos que demuestren capacidad para producir sustancias antimicrobianas serán identificados utilizando técnicas moleculares (amplificación del 16S rRNA, secuenciación y comparación en bases de datos). Las sustancias producidas por los microorganismos serán purificadas antes de analizar su capacidad inhibitoria. Posteriormente, se evaluará el efecto de los agentes físicos (temperatura) y químicos (solventes orgánicos, ácidos, tripsina, proteinasa K y pepsina) sobre dicha capacidad.

Estudio de las sustancias antimicrobianas producidas por los microorganismos integrantes de la microbiota de terneros jóvenes.

El uso desmedido de antibióticos, en especial en los animales que son destinados al consumo humano, produjo la aparición de cepas bacterianas resistentes y favoreció la presencia de residuos de esas sustancias en los alimentos. Esta situación ha sido relacionada con la aparición de alergias, trastornos gastrointestinales y otros problemas que han puesto en riesgo la salud de la población y han promovido una presión creciente de los consumidores y de los entes reguladores para que el sector de la producción de alimentos no utilice antimicrobianos y evite la presencia de sus residuos. El objetivo del trabajo es evaluar la capacidad de las sustancias con actividad antimicrobiana, producida por la microbiota natural, para inhibir el desarrollo de bacterias patógenas responsables de causar enfermedades en terneros jóvenes. Se utilizarán bacterias ácido lácticas autóctonas aisladas a partir de intestinos (duodeno, yeyuno, íleon, colon y ciego), cavidad bucal de terneros de crianza artificial y de vagina de vacas en la etapa pre-parto y que forman parte del cepario del Laboratorio de Análisis de alimentos, DSPV. Los microorganismos que demuestren capacidad para producir sustancias antimicrobianas serán identificados utilizando técnicas moleculares (amplificación del 16S rRNA, secuenciación y comparación en bases de datos). Las sustancias producidas por los microorganismos serán purificadas antes de analizar su capacidad inhibitoria. Posteriormente, se evaluará el efecto de los agentes físicos (temperatura) y químicos (solventes orgánicos, ácidos, tripsina, proteinasa K y pepsina) sobre dicha capacidad.

Fungi, bacteria and soil pH: the oxalate-carbonate pathway as a model for metabolic interaction

The oxalatecarbonate pathway involves the oxidation of calcium oxalate to low-magnesium calcite and represents a potential long-term terrestrial sink for atmospheric CO2. In this pathway, bacterial oxalate degradation is associated with a strong local alkalinization and subsequent carbonate precipitation. In order to test whether this process occurs in soil, the role of bacteria, fungi and calcium oxalate amendments was studied using microcosms. In a model system with sterile soil amended with laboratory cultures of oxalotrophic bacteria and fungi, the addition of calcium oxalate induced a distinct pH shift and led to the final precipitation of calcite. However, the simultaneous presence of bacteria and fungi was essential to drive this pH shift. Growth of both oxalotrophic bacteria and fungi was confirmed by qPCR on the frc (oxalotrophic bacteria) and 16S rRNA genes, and the quantification of ergosterol (active fungal biomass) respectively. The experiment was replicated in microcosms with non-sterilized soil. In this case, the bacterial and fungal contribution to oxalate degradation was evaluated by treatments with specific biocides (cycloheximide and bronopol). Results showed that the autochthonous microflora oxidized calcium oxalate and induced a significant soil alkalinization. Moreover, data confirmed the results from the model soil showing that bacteria are essentially responsible for the pH shift, but require the presence of fungi for their oxalotrophic activity. The combined results highlight that the interaction between bacteria and fungi is essential to drive metabolic processes in complex environments such as soil.

Biodiversity of amoebae and amoebae-resisting bacteria in a drinking water treatment plant

The complex ecology of free-living amoebae (FLA) and their role in spreading pathogenic microorganisms through water systems have recently raised considerable interest. In this study, we investigated the presence of FLA and amoebae-resisting bacteria (ARB) at various stages of a drinking water plant fed with river water. We isolated various amoebal species from the river and from several points within the plant, mostly at early steps of water treatment. Echinamoeba- and Hartmannella-related amoebae were mainly recovered in the drinking water plant whereas Acanthamoeba- and Naegleria-related amoebae were recovered from the river water and the sand filtration units. Some FLA isolates were recovered immediately after the ozonation step, thus suggesting resistance of these microorganisms to this disinfection procedure. A bacterial isolate related to Mycobacterium mucogenicum was recovered from an Echinamoeba-related amoeba isolated from ozone-treated water. Various other ARB were recovered using co-culture with axenic Acanthamoeba castellanii, including mycobacteria, legionella, Chlamydia-like organisms and various proteobacteria. Noteworthy, a new Parachlamydia acanthamoebae strain was recovered from river water and from granular activated carbon (GAC) biofilm. As amoebae mainly multiply in sand and GAC filters, optimization of filter backwash procedures probably offers a possibility to better control these protists and the risk associated with their intracellular hosts

Bacterial community structure of a pesticide-contaminated site and assessment of changes induced in community structure during bioremediation.

The introduction of culture-independent molecular screening techniques, especially based on 16S rRNA gene sequences, has allowed microbiologists to examine a facet of microbial diversity not necessarily reflected by the results of culturing studies. The bacterial community structure was studied for a pesticide-contaminated site that was subsequently remediated using an efficient degradative strain Arthrobacter protophormiae RKJ100. The efficiency of the bioremediation process was assessed by monitoring the depletion of the pollutant, and the effect of addition of an exogenous strain on the existing soil community structure was determined using molecular techniques. The 16S rRNA gene pool amplified from the soil metagenome was cloned and restriction fragment length polymorphism studies revealed 46 different phylotypes on the basis of similar banding patterns. Sequencing of representative clones of each phylotype showed that the community structure of the pesticide-contaminated soil was mainly constituted by Proteobacteria and Actinomycetes. Terminal restriction fragment length polymorphism analysis showed only nonsignificant changes in community structure during the process of bioremediation. Immobilized cells of strain RKJ100 enhanced pollutant degradation but seemed to have no detectable effects on the existing bacterial community structure.

Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi.

Arbuscular mycorrhizal fungi (AMF) are symbiotic soil fungi that are intimately associated with the roots of the majority of land plants. They colonise the interior of the roots and the hyphae extend into the soil. It is well known that bacterial colonisation of the rhizosphere can be crucial for many pathogenic as well as symbiotic plant-microbe interactions. However, although bacteria colonising the extraradical AMF hyphae (the hyphosphere) might be equally important for AMF symbiosis, little is known regarding which bacterial species would colonise AMF hyphae. In this study, we investigated which bacterial communities might be associated with AMF hyphae. As bacterial-hyphal attachment is extremely difficult to study in situ, we designed a system to grow AMF hyphae of Glomus intraradices and Glomus proliferum and studied which bacteria separated from an agricultural soil specifically attach to the hyphae. Characterisation of attached and non-attached bacterial communities was performed using terminal restriction fragment length polymorphism and clone library sequencing of 16S ribosomal RNA (rRNA) gene fragments. For all experiments, the composition of hyphal attached bacterial communities was different from the non-attached communities, and was also different from bacterial communities that had attached to glass wool (a non-living substratum). Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi.