Geomicrobiology: Low life

Mascarelli, Amanda

doi:10.1038/459770a

Cited by 18 publications

(5 citation statements)

References 12 publications

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“…Microorganisms play a crucial role in soil genesis by facilitating mineralization not only for soil organic matter (Leigh Mascarelli, ) but also for prevalent and persistent pollutants, such as polyaromatic hydrocarbons (PAH) and heterocyclic aromatic compounds (Lu et al ., ). Such compounds are common additives in crude oil and industrial chemical products, such as dyes, flavouring compounds, plasticizers, perfumes, pesticides and insect repellent as well as, more recently, microelectronics, printed circuit boards, silk screen printing devices, optical disks and black colour tube matrices (Kästner, ; Chae et al ., ).…”

Section: The Half‐saturation (Michaelis) Coefficient (Km) Catalytic mentioning

confidence: 97%

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters

Martínez-Martínez

Lores

Peña-García

et al. 2014

Microbial Biotechnology

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Herein, we applied a community genomic approach using a naphthalene-enriched community (CN1) to isolate a versatile esterase (CN1E1) from the α/β-hydrolase family. The protein shares low-to-medium identity (≤ 57%) with known esterase/lipase-like proteins. The enzyme is most active at 25–30°C and pH 8.5; it retains approximately 55% of its activity at 4°C and less than 8% at ≥ 55°C, which indicates that it is a cold-adapted enzyme. CN1E1 has a distinct substrate preference compared with other α/β-hydrolases because it is catalytically most active for hydrolysing polyaromatic hydrocarbon (phenanthrene, anthracene, naphthalene, benzoyl, protocatechuate and phthalate) esters (7200–21 000 units g−1 protein at 40°C and pH 8.0). The enzyme also accepts 44 structurally different common esters with different levels of enantio-selectivity (1.0–55 000 units g−1 protein), including (±)-menthyl-acetate, (±)-neomenthyl acetate, (±)-pantolactone, (±)-methyl-mandelate, (±)-methyl-lactate and (±)-glycidyl 4-nitrobenzoate (in that order). The results provide the first biochemical evidence suggesting that such broad-spectrum esterases may be an ecological advantage for bacteria that mineralize recalcitrant pollutants (including oil refinery products, plasticizers and pesticides) as carbon sources under pollution pressure. They also offer a new tool for the stereo-assembly (i.e. through ester bonds) of multi-aromatic molecules with benzene rings that are useful for biology, chemistry and materials sciences for cases in which enzyme methods are not yet available.

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Section: The Half‐saturation (Michaelis) Coefficient (Km) Catalytic mentioning

confidence: 97%

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters

Martínez-Martínez

Lores

Peña-García

et al. 2014

Microbial Biotechnology

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“…Claude ZoBell, considerado o pai da microbiologia marinha, teve um papel fundamental no estudo da dinâmica microbiana, sendo seus artigos citados até os dias atuais em trabalhos publicados por diversos autores (p. ex. Jannasch & Jones 1959, Paul & Morita 1971, Watson et al 1977, Meyer-Reil et al 1978, Deming & Colwell 1982, Deflaun & Mayer 1983, Rowe & Deming 1985, Boetius et al 1996, Mascarelli 2009.…”

Section: Figure 1 Number Of Articles Published Between 1990 and Septunclassified

Análise De Abundância Bacteriana No Estudo Da Ecologia Microbiana De Sedimentos Marinhos

Carvalho

Paranhos

2010

Oecol. Austr.

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Os ecossistemas de mar profundo representam cerca de 65% da superfície do planeta e desempenham um papel importante na produção de biomassa e nos ciclos biogeoquímicos em uma escala global. Estes processos são amplamente mediados por procariotos bentônicos, os quais utilizam detritos orgânicos para a produção de biomassa e respiração. Por este motivo, os sedimentos marinhos se configuram como importante matriz biológica e tem grande relevância na ecologia do sistema de mar profundo. No tempo geológico, eventos que ocorrem neste compartimento, como a degradação de matéria orgânica, afetam profundamente a composição química do oceano e da atmosfera. Devido à sua importância e complexidade, o sistema de mar profundo e a sua microbiota associada têm sido objeto de inúmeros estudos ao longo dos últimos 50 anos, especialmente na última década. Os parâmetros mais comumente analisados nos sedimentos são abundância bacteriana, biomassa e atividade metabólica. Diversas metodologias podem ser utilizadas na análise da atividade microbiana em sedimentos, entre elas a incorporação de aminoácidos marcados com 14 C ou ³H e a medida da respiração bacteriana. A análise de biomassa frequentemente exige a determinação prévia da abundância bacteriana, tornando imprescindível que a quantificação da microbiota do sedimento seja realizada de forma correta. A separação das células das partículas de sedimento e sua apropriada desagregação são necessárias para aplicações de microscopia de epifluorescência e para a análise por citometria em fluxo. O uso otimizado das técnicas de extração e análise e sua avaliação de modo combinado com outros parâmetros microbianos possibilitará um maior entendimento do papel desenvolvido pelos organismos procariotos nos oceanos do mundo. Palavras-chave: Bactérias de mar profundo; abundância; biomassa; matéria orgânica; métodos de extração de bactérias. ABSTRACT ANALYSIS OF BACTERIAL ABUNDANCE IN THE STUDY OF MICROBIAL ECOLOGY OF MARINE SEDIMENTS. Deep-sea ecosystems cover about 65% of the Earth's surface and play an important part in biomass production and biogeochemical cycles on a global scale. These processes are largely mediated by benthic prokaryotes which use organic detritus for biomass production and respiration. Therefore marine sediments are configured as important biological matrix and play a prominent role in the ecology of the system of the deep sea. Events that occur in this compartment as organic matter degradation profoundly affect the chemical composition of the ocean and atmosphere in geological time. Due to its importance and complexity, the system of deep sea and its associated microorganisms have been the object of numerous studies in the last 50 years, especially in the last decade. Bacterial abundance, biomass and metabolic activity are the parameters most commonly measured in the sediments. Several methodologies can be used in microbial activity analysis of sediments, including the amino acids labeled with 14 C or ³H incorporation and the measurement of bacterial respiration. The bio...

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“…This last issue is of relevance, given the large diversity of sediment and soil types, salinities, geographies, climates, and type and level of nutrients and contaminants and the fact that consortia of microorganisms can be viewed as a highly diverse [3,4], metabolically adaptable, rapidly renewable, and metabolically flexible ecosystems. By adapting their metabolism to highly variable environmental constrains, including pollution diversity and level, they are effective in terms of controlling geochemical cycles [5].…”

Section: Introductionmentioning

confidence: 99%

Protein Extraction from Contaminated Soils and Sediments

Pozo

Martínez-Martínez

Ferrer

2014

Springer Protocols Handbooks

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Greasy molecules such as crude oil and polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and easily accumulate in soils and marine sediments. They may primarily be considered as an ecological problem, but at the same time constituted a factor influencing microbial populations and the biodegradation processes they mediate. Several strategies have been used to study the relationship between the PAHs input and ecosystem functioning and population structure. Among them, the preparation of protein extracts becomes overriding to obtain information about microbial function and for inferring active set of reactions associated to proteins being expressed. However, apart from the technical limitations for protein identifications, the isolation of microbial proteins from soil or sediments constitutes per se a key step, which should be optimized. Here we describe several methods for efficient extraction of proteins from contaminated soils or sediments. Such methods allow obtaining high protein yields which could be used for shotgun proteomic approaches or any kind of proteomic approach, including enzymatic activity tests. These approaches include those based on the direct extraction of proteins from raw samples and those based on the separation of microbial cells from material prior protein extraction. Although the majority of described methods are performed under denaturing conditions, we also provided details about approaches to obtain protein in native state, which could be used for biochemical tests.

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Geomicrobiology: Low life

Cited by 18 publications

References 12 publications

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters

Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters

Análise De Abundância Bacteriana No Estudo Da Ecologia Microbiana De Sedimentos Marinhos

Protein Extraction from Contaminated Soils and Sediments

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