Academic literature on the topic 'Microbial bioindicators'

Water ecosystems are constantly under the pressure of a high number of biotic and abiotic factors, and their action leads to the occurrence of fluctuations in species and populations. The specific response of organisms to external pressures leads to the reorganization of ecosystems, with qualitative and quantitative changes. The aim is to identify the microbial groups with the highest potential in the waste waters. Data were collected during 2015-16 in Bistrita. Identifying the bioindicators quality of microorganisms and their importance in ecosystems was done by comparing them with international databases. The use of microorganisms as bioindicators involves knowing the requirements for one or more environmental variables. The concept refers to the ability of microorganisms to accumulate pollutants. Flagellates are tolerant to acidity and react quickly and with sensitivity to environmental stress by inhibiting their movement. The multiplication of flagellates and filamentous bacteria is manifested through water disturbance and foam production.

This study was developed within the framework of a broad international project, ‘Ecological water quality assessment of the Alcantara (Italy), James (USA) and Guadalfeo (Spain) rivers using bioindicators’, established by the Center for Integrative Mediterranean Studies (CIMS), a collaborative research centre consisting of the University of Messina – Italy, Virginia Commonwealth University – USA, and the University of Cordoba – Spain. The primary objective of the study was the validation of a multi-disciplinary ecological approach at different taxonomic levels for biomonitoring of the Alcantara River (Sicily, Italy) using bioindicators. This study examined the primary physical, chemical and biological features of the river through an interdisciplinary and synoptic approach using bioindicators that included riparian plant physiology, the microbial, zooplanktonic and macroinvertebrate assemblages, Coleoptera (Insecta) and river hydrology. Sampling of the river and riparian areas was conducted at sites from the river’s headwaters to the mouth. The study provided information on the ecological status of the Alcantara River along its course and tested the use of a variety of bioindicators, rather than a single biotic or physicalattribute, to determine the river’s health.

The phylum Arthropoda is one of the most diverse groups under the terrestrial surface comprising different classes of insects that occupy different environments. Some groups have a close relationship with the habitat they occupy, responding significantly to changes in the environment, thus indicating the level of change in the environment by their presence or absence. The present study aimed to demonstrate the importance of edaphic fauna as a bioindicator of environmental quality. This is a bibliographic review based on specialized consultation of scientific articles in the databases Google Scholar, SciELO-Scientific Electronic Library and ResearchGate. The studies found that environmental quality can be measured from the diversity and abundance of arthropods that live and perform their functions in the soil. Macrofauna influences important soil chemical and physical processes such as nutrient cycling, structuring and homogenization, and increased productivity, among others. The mesofauna, besides acting on soil properties, acts on the regulation of microbial populations, is sensitive to changes and responds promptly. The groups Acari, Collembola, Coleoptera, Hymenoptera and Araneae are indicated in several studies as potential bioindicators because they are commonly sampled in different environments. The factors identified as conditioning factors of the presence of these groups are environmental heterogeneity, type of vegetation cover and availability of litter, applied management system, seasonality, soil characteristics, and anthropic activities, among others. In short, because they respond quickly, the changes are considered to be efficient biological indicators; therefore, knowing the diversity of species and their degree of interaction with the environment allows us to analyze the effects of anthropic modifications in ecosystems.

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.

The research was looking for the quick response of soil's microbiota to soil changes caused by management systems, changes to which biological indicators of soil quality are sensitive. In this context, this study aimed to evaluate the impacts of seven soil management systems, including in on hand covers of Pennisetum glaucum (PG), Avena strigosa (AS), Stizolobium aterrimum (SA), EF Pisum sativum (PS) + Avena strigosa (AS), and on the other hand, No soil tillage with gypsum application (NTSG), No soil tillage with scarification (NTSS) and No soil tillage (NTS), on soil quality bioindicators. The bioindicators recorded from top soil samples were collected from the first 10 cm at pre-planting, at pre-flowering and at post-harvest of the soybean, from July 2014 to March 2015 were Total organic carbon (TOC), Soil microbial biomass carbon (SMBC), Soil basal respiration, Respiratory coefficient (qCO2), Microbial coefficient (qMIC), and its relationship with soybean yields. The seven treatments were arranged in the field according to a completely randomized experimental, Analysis of variance (Anova) for each of the bioindicators and comparison of treatment mean values using Tukey test at 5% probability were carried out. SA, the AS+PS consortium and the no-tillage system led to significant improvement of the biological attributes of the soil. The management systems did not change the yield of soybean grain.

ABSTRACT16S rRNA gene molecular analysis elucidated the spatiotemporal distribution of bacterial biofilm communities along a water quality gradient. Multivariate statistics indicated that terrestrial runoff, in particular dissolved organic carbon and chlorophyllaconcentrations, induced shifts of specific bacterial communities between locations and seasons, suggesting microbial biofilms could be suitable bioindicators for water quality.

Challenges to the reclamation of pyritic mine tailings arise from in-situ acid generation that severely constrains natural revegetation. While microbial communities that participate in acid generation through iron and sulfur (FeS) oxidation in acidic aquatic environments are well studied, relatively little information is available concerning the initial dynamics of in-situ soil acidification due to microbial FeS oxidation that occur in moderately acidic conditions. This research characterizes the taxonomic composition and behavior of microbial FeS oxidizing communities across a pH gradient from moderately acidic to highly acidic environmental conditions. We combine results from a 7-year compost-assisted phytostabilization field study with a controlled microcosm enrichment experiment that was conducted in an artificial soil matrix to follow the influence of pH on development of the soil microbiome. Microcosm results show that biological activity significantly increases the acidification rate in moderately acidic pH conditions in comparison to abiotic controls. Taxonomic profiles of the microbial communities in the microcosms and from the field study reveal that populations associated with both heterotrophic and lithotrophic activity (Alicyclobacillaceae, Acetobacteraceae and Xanthomonadaceae) dominate during acidification in moderately acidic conditions. These results suggest that chemoheterotrophs are an important element of the microbial community that help enable, directly and indirectly, lithotrophic FeS oxidation across moderately acidic conditions. Taken together, this research suggests that shifts of microbial populations associated with pH transitions have the potential to be used as bioindicators of the present and future status of the phytostabilization process.

Le sol représente le support de la production agricole. A l’interface avec les autres compartiments de la biosphère, il remplit de nombreuses fonctions essentielles à la fourniture de services écosystémiques nécessaires au bien-être de nos sociétés. C’est aussi une ressource non renouvelable dont les propriétés physicochimiques et biologiques ont été altérées par le développement de l’agriculture intensive. La prise de conscience actuelle de cet état de fait a révélé la nécessité de définir de nouveaux modes de gestion adaptés à la préservation et à l’utilisation durable des sols. Elle a ainsi marqué l’entrée dans l’ère de l’agroécologie qui prône un modèle de production optimisant notamment les services rendus par la biodiversité afin de réduire le recours aux intrants et à l’utilisation d’énergie. Pour atteindre cet objectif, le développement d’une gamme d’indicateurs permettant d’évaluer les pratiques/systèmes agricoles en rendant compte de la qualité biologique du sol est donc indispensable. Cette thèse, dont l’objectif est de contribuer au développement de bioindicateurs microbiens de la qualité du sol, s’inscrit dans ce contexte agroécologique. Le choix de travailler sur les communautés microbiennes se justifie pleinement dans cette problématique car elles sont (i) présentes avec une forte densité et diversité dans tous les environnements, (ii) fortement impliquées dans le fonctionnement biologique et les services rendus par le sol, et (iii) elles répondent de façon très sensible aux changements des conditions environnementales en termes de modification de biomasse, de structure/diversité et d’activité. Elles offrent donc un potentiel important en termes de développement de bioindicateurs. Ce travail a porté plus précisément sur l’évaluation de deux indicateurs complémentaires : (i) la biomasse moléculaire microbienne et (ii) la diversité taxonomique microbienne. Dans une première partie nous avons éprouvé la robustesse de ces deux indicateurs en évaluant les biais associés à chacune des étapes techniques des procédures mises en œuvre pour leur mesure. Nous avons ensuite utilisé ces deux indicateurs dans différents contextes agronomiques pour évaluer leur pertinence. Un premier travail a ainsi consisté à suivre la réhabilitation du patrimoine microbien, par l’implantation d’une culture à vocation énergétique, d’un sol pollué irrigué pendant une centaine d’années par des eaux usées. Une seconde application a porté sur l’étude de l’impact de différentes pratiques agricoles sur les communautés microbiennes selon l’intensité du travail du sol (labour vs. travail réduit), la gestion des résidus de culture (export vs. restitution), et le type de culture (annuelle vs. pérenne).Les résultats montrent que la biomasse moléculaire microbienne et la diversité taxonomique obtenue par séquençage massif sont deux bioindicateurs robustes et sensibles pour décrire la qualité microbiologique des sols agricoles dans des contextes très variés. Ces deux indicateurs permettent de mettre en évidence aussi bien des perturbations des sols que l’impact positif de pratiques innovantes. Ils peuvent donc représenter des outils performants pour l’évaluation des systèmes agricoles, aidant à une amélioration de leur mode de gestion et, à long terme, permettant une utilisation durable des ressources fournies par ces sols
Soil is the support of agricultural production. It performs many functions essential to the provision of ecosystem services necessary for the well-being of our societies. Soil physicochemical and biological properties have been altered by the development of intensive agriculture while it is a non-renewable resource, revealing the need to develop new management practices suitable for the sustainability of soil quality. This also marked the entry into the “Agroecology” era, which promotes the development of new agricultural systems optimizing services provided by biodiversity to reduce the use of inputs and energy use. To achieve this aim, the development of a range of indicators to assess the impact of agricultural practices on the biological quality of the soil is essential. This thesis, which aims to contribute to the development of microbial bio-indicators of soil quality, is a part of this agroecological context. The choice to work on microbial communities is fully justified because they are (i) present with a high abundance and diversity in all environments, (ii) heavily involved in biological functioning and the soil ecosystem services, (iii) they respond very sensitive to changes in environmental conditions in terms of biomass, diversity and activity. They therefore have significant potential in terms of bio-indicators of development. This work has focused specifically on the evaluation of two complementary bioindicators: (i) the microbial molecular biomass and (ii) the microbial taxonomic diversity. In a first part we tested the robustness of these two bioindicators by assessing the biases associated with each of the procedure technical steps used for their measurement. We then used these bioindicators in different agricultural contexts to assess their sensitivity. A first work has followed the rehabilitation of microbial patrimony of a polluted soil irrigated for a hundred years by sewage, by implanting a bioenergy crop. A second application has focused on the impact of different agricultural practices on microbial communities depending on the intensity of tillage (tillage vs. reduced tillage), management of crop residues (export vs. restitution), and the crop type (annual vs. perennial). Results highlighted that microbial molecular biomass and microbial taxonomic diversity achieved by high throughput sequencing are both robust and sensitive bioindicators to describe the microbiological quality of agricultural soils in very different contexts. Both bioindicators allow evidencing soil disturbances but also the positive impact of innovative practices. They may therefore represent powerful tools for the assessment of agricultural systems, helping to improve their long term management, allowing a sustainable use of resources provided by soils

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wastewater use in agricultural soils has been adapted as an important pratice for agriculture. Due to the reduction of the availability of the quality of water resources is becoming increasingly important to add value to the use of water. The swine wastewater is rich in organic matter, composed of various elements of chemical origin, physical and biological. Its addition in soil and water resources without previous studies and knowledge of its components, can cause changes in the soil, contamination of surface and groundwater, biology changes in these environments, as well as the contribution and accumulation of groups of microorganisms in the environment, including pathogens. Most studies on swine wastewater, mainly in Brazil, are restricted to its physical and chemical components, evaluating its impact directly on the ground, water bodies or in plant productivity. Few studies focus on the microbial composition of this type of waste and especially on the risk of environmental contamination by pathogenic microorganisms or even on the impact of this element in the soil microbial community. Thus these animal manure may have an important role as initiators of infectious diseases in animals and humans. Thus, this thesis consists of two papers. In the first article, a study was done to check the bacterial composition present in swine wastewater, and to verify the possibility of eliminating these microorganisms through the main anaerobic treatment systems used in Brazil. It was evaluated in particular pathogenic microorganisms of gastrointestinal origin of the pigs and microbial environmental markers. The wastewater samples were taken from pig farms that use bio-manure storage tanks and digesters as treatment methods for the waste. The results clearly showed the presence of biomarkers and pathogens in swine wastewater. Despite the possibility of decrease of certain microbial groups throughout the stages of the treatment process, no elimination of pathogens in either treatment systems. Thus, demonstrates the possibility of the spread of pathogens and microorganisms in the environment. In the second paper, the objective was to evaluate the effect of application of swine wastewater associated with mineral fertilizer in agriculture, after a long time of application of swine wastewater in the soil microbial community. Thus, samples were collected from soils after 18 production culture cycles, with the application of wastewater from pig farms and assessed the quantitative effects (basal respiration, microbial biomass and metabolic quotient) and qualitative (DGGE, biodiversity indices, correlation between the chemical conditions and soil microbial activity) in the soil microbial community. The results showed that the application of swine wastewater, especially after long time and in higher concentrations, can change the dynamics of soil microbial community, impacting the dump site. The results of these studies show the need for further studies to apply this type of waste in agricultural soils, in order to minimize the risk of environmental contamination and/ or spread of pathogens.
A utilização de água residuária em solos agrícolas vem sendo praticada como importante opção para agricultura. Devido à redução na disponibilidade de recursos hídricos, a reutilização de água residuária vem ganhando espaço na agricultura com a agregação de valor para o uso de água. A água residuária da suinocultura é rica em matéria orgânica, composta por diferentes elementos de origem química, física e biológica. Sua adição no solo e recursos hídricos, sem estudos prévios e conhecimento de seus componentes, pode provocar contaminação de águas superficiais e subterrâneas, alterações da biologia destes ambientes, bem como o aporte e acúmulo de grupos de microrganismos no ambiente, incluindo patógenos. A maior parte dos estudos sobre água residuária da suinocultura, principalmente no Brasil, se restringe aos seus componentes físicos e químicos, avaliando seu impacto diretamente sobre o solo, corpos d´agua ou na produtividade vegetal. Poucos estudos se concentram na composição microbiana deste tipo de resíduo e principalmente sobre o risco de contaminação ambiental por microrganismos patogênicos ou mesmo sobre o impacto deste elemento na comunidade microbiana do solo. Desta forma estes dejetos animais podem apresentar importante papel como iniciadores de doenças infecciosas em animais e seres humanos. Este trabalho de tese é constituído de dois artigos. No primeiro artigo, foi feito um estudo para verificar a composição bacteriana presente na água residuária da suinocultura, bem como verificar a possibilidade de eliminação destes microrganismos através dos principais sistemas de tratamento anaeróbicos utilizados no Brasil. Foram avaliados em especial os microrganismos patogênicos, de origem gastrointestinal dos suínos e bioindicadores microbianos. As amostras de água residuária utilizadas foram provenientes de granjas que utilizavam de sistemas anaeróbicos com esterqueiras e biodigestores no tratamento do resíduo. Os resultados obtidos mostraram claramente a presença de coliformes, mesofilos aeróbios, bolores e leveduras, enterococos e patógenos na água residuária da suinocultura. Apesar da possibilidade de decréscimo de determinados grupos microbianos ao longo das etapas dos processos de tratamento, não houve eliminação de patógenos em nenhum dos dois sistemas de tratamento, o que pode possibilitar a disseminação de microrganismos e patogenos no meio ambiente. No segundo artigo, o objetivo foi avaliar o efeito da aplicação da água residuária da suinocultura associada a adubação mineral, em área agrícola, após longo tempo de aplicação, na comunidade bacteriana do solo. Assim, foram coletadas amostras de solo com 18 ciclos de produção, com aplicação de água residuária de suinocultura e avaliados os efeitos quantitativos (respiração basal, biomassa microbiana e quociente metabólico) e qualitativos (DGGE) na comunidade bacteriana do solo. Os resultados mostraram que a aplicação de água residuária da suinocultura, principalmente após longo tempo e em concentrações maiores, pode alterar a dinâmica da comunidade bacteriana do solo, impactando no local de despejo. Os resultados dos artigos mostram a necessidade de maiores estudos para aplicação deste tipo de resíduo na agricultura, a fim de minimizar os riscos de contaminação ambiental e ou disseminação de patógenos.

the society is highly concerned on life quality, mostly in terms of environment and health. The environmental issues are emergencial in the social agenda to the extent that the human being exploitis the natural resources beyond its regenerative capacity. In this context, the soil biodiversity may constitute an excellent indicator to monitor environmental shifts. In ecosystems such as the Caatinga biome, the major one in the Brazilian Semi-arid Region, the deforestation and the forest fires are still common practices for land farming preparation. This current research investigated the effect of agricultural practices on the soil microbial community, in an agro-ecological dairy system developed for small stockholder farms within the Caatinga biome of N. Sr.ª da Glória-SE. For this purpose, some parameters were used such as enzymatic activity, total microbial population and the DNA analysis of the soil microbial community. These microbial bioindicators were applied to four agro-forestry-pasture systems: reforested areas with the tree legume sabiá (Mimosa caesalpiniaefolia ); pastures of grass (Urocloa moçambisensis); pastures of Gliricidia sepium; palm crop (Opuntia ficus indica), cultivated in adensed rows; and undisturbed native Caatinga grassland, used as control. For the determination of the total soil microbial activity, the hydrolysis of fluorescein diacetate (FDA) method was used. For the determination of the total microbial population it was used the soil dilution technique in to plates containing selective culture media for fungi, bacteria and actinomycetes. The molecular microbial profile was determined by the Amplified Ribosomal DNA Restriction Analysis (ARDRA), extracting the DNA directly from soil and amplifing ribosomal DNA from fungi and bacteria in a polimerase reaction (PCR). The hydrolysis of FDA indicates microbial activity in all agro-forestry-pasture systems. The highest microbiological activity was found in soil under Gliricidia sepium: 0,605 g FDA hydrolyzed min-1 g-1 soil. The total microbial population, indicated that the soil under the palm crop harbours the highest fungi and actinomycete populations: 21 e 127 ufc x 10g/soil, respectively. The highest soil bacteria population, were found in the Caatinga and Gliricidia sepium: 32 e 28 ufc x 10g/soil, respectively. ARDRA was as a powerful tool for the microbial community profile analysis. The Hinf I restriction enzyme disclosed that the genetic structure of the fungi 18S region in the soil under Caatinga revealed a divergent community when compared to the other treatments. The 16S region digested by the Hae III enzyme, disclosed two distinct groups: one with a 100% similarity of the bacterial genetic structure including the soils under reforested areas and under Caatinga; and the others with a 100 % of genetic similarity including the soils under the palm, pastures and Gliricidia sepium. The three parameters (microbial activity, total microbial population and the molecular profile determined by ARDRA) used in this research constituted good bioindicators, since they allowed to detect alterations influenced by different soil managements, indicating the efficiency of the agro-forestry-pasture systems for the preservation and restoration of soil in the Semi-Arid biome.
A sociedade contemporânea preocupa-se, cada vez mais, com a qualidade de vida, retratada, principalmente, em termos de ambiente e saúde. A emergência da questão do ambiente na agenda social é, em grande parte, conseqüência da extensão em que a humanidade hoje se apropria dos recursos naturais, às vezes muito além da capacidade regenerativa da natureza. Dentro deste contexto, a biodiversidade presente nos solos constitue um excelente mediador das condições biológicas do meio ambiente. Nos ecossistemas do bioma Caatinga, o principal ecossistema existente na região do Semi-árido, o desmatamento e as queimadas são ainda práticas comuns no preparo da terra para a agropecuária. Com o presente trabalho objetivou-se conhecer o efeito de práticas agrícolas sobre a comunidade microbiana, em diferentes sistemas agroecológicos de produção de leite para propriedades de base familiar, e em solos do ecossistema original (Caatinga) (testemunha), no município de N. Sr.ª da Glória-SE. Utilizaram-se como parâmetros a atividade microbiológica, a população microbiana total e a análise de DNA da comunidade microbiana do solo. Estes bioindicadores microbiólogicos foram aplicados à quatro tipos de estruturas agrossilvipastoris: áreas reflorestadas com leguminosas arbóreas - sabiá (Mimosa caesalpiniaefolia ); pastagens cultivadas com capim Urocloa mosambicensis; palma forrageira (Opuntia ficus-indica), cultivada em fileiras adensadas; cercas vivas forrageiras de Gliricidia sepium. Para a determinação da atividade microbiológica total foi utilizado o método de hidrólise de diacetato de fluoresceína (FDA). Para a determinação da população total foi utilizado o método de diluição de solo em meios seletivos para fungos, bactérias e actinomicetos. O perfil molecular da comunidade microbiana foi determinado por ARDRA (Amplified Ribossomal DNA Restriction Analysis), extraindo-se o DNA diretamente do solo e submetendo-o à reação de polimearase em cadeia (PCR) com os primers da região conservada do DNA ribossomal para fungos e bactérias. A hidrólise de diacetato de fluoresceína indicou atividade biológica em todos os agroecossistemas, sendo que esta foi superior em solos sob cultivo de Gliricidia sepium, que apresentou 0,605 g FDA hidrolisada min-1 g-1 de solo. Os resultados da população microbiana, indicaram que o solo sob a palma foi o que mais favoreceu a densidade populacional de fungos e actinomicetos: 21 e 127 ufc x 10g/solo, respectivamente. Quanto à população de bactérias, o solo sob a Caatinga e Gliricidia sepium se destacaram apresentando 32 e 28 ufc x 10g/solo, respectivamente. ARDRA se revelou também um marcador promissor para comparar a comunidade microbiana presente nestes solos. Os produtos amplificados, digeridos pela enzima Hinf I, revelaram que a região 18 S diferenciou a estrutura genética da comunidade fúngica no solo sob a caatinga em relação a todos demais tratamentos. Já a região 16 S digerida pela enzima Hae III, discriminou dois grupos distintos: um grupo com 100% de similaridade na estrutura genética bacteriana incluindo o solo sob áreas reflorestadas e o solo sob a caatinga; e outro grupo, com 100 % de similaridade genética incluindo solo sob a palma, o solo sob pastagens e o solo sob Gliricidia sepium. Portanto, os três parâmetros utilizados neste trabalho: atividade microbiológica, população microbiana total e o perfil molecular determinado por ARDRA constituíram-se bons bioindicadores, pois estes detectaram alterações provocadas por diferentes manejos do solo, permitindo avaliar a eficiência da estrutura agrossilvipastoril para a preservação e recomposição do solo no Semi-Árido.

Less than 10% of the world’s domestic wastewater is disinfected prior to discharge into surface waters; therefore, human exposure to diverse wastewater-related pathogens results in millions of cases of illness each year. Among the enteric pathogens, viruses represent an important group of emerging pathogens and are frequently the cause of food- and water-borne outbreaks of illness. Although the World Health Organization and many government agencies mandate the use of bacterial indicators to identify poor microbial water quality, it is well known that these indicators poorly correlate with fecal pollution contamination events and risk of disease. The field of public health-related environmental microbiology has made significant advances over the last twenty years; however, there is still a need for improved methods to identify poor microbial water quality and manage health risks associated with water-related activities (e.g., recreation, shellfish harvesting, irrigation). Furthermore, it is imperative to effectively detect fecal pollution in the environment as well as determine the extent of pathogen removal during (waste)water treatment to meet the Sustainable Development Goals associated with water and food security as well as the water reuse recommendations by the U.S. National Research Council. This dissertation directly addressed the need to identify an improved viral indicator by exploring the application of pepper mild mottle virus (PMMoV), a virus of dietary origin that is extremely abundant in human feces, as a surrogate for enteric viruses in diverse settings and contexts. Using a reverse transcription quantitative polymerase chain reaction (RT-qPCR) method, PMMoV was compared with other indicators, index surrogates, and reference pathogens for assessing surface water quality in a developed country (Appendix A) and developing country context (Appendix B and C). In addition, the applicability of PMMoV as a (waste)water treatment process indicator was demonstrated in natural treatment systems in developing countries (Appendix C and D) and artificial treatment systems (Appendix E). In all settings, PMMoV always co-occurred with at least one reference pathogen, index organism, and/or indicator; additionally, PMMoV was detected more frequently and in higher concentrations than other reference pathogens and indicators. Three investigations also associated PMMoV detection with predicted human health risks greater than the health benchmark for recreation and water reuse activities (Appendix A, C, and D). Additionally, PMMoV facilitated an improved understanding of virus-particle interactions in wastewater treatment pond systems (Appendix D) and allowed for an improved understanding of virus removal with respect to riverbank filtration systems and wastewater reuse in agriculture (Appendix C). PMMoV was established as a valuable component of the microbial source tracking toolbox in Costa Rica (Appendix B) and appeared to be useful in Bolivia (Appendix C). Finally, a paradigm shift in (waste)water management is occurring, in which routine monitoring is being replaced by a more holistic approach that includes sanitary surveys, targeted water quality monitoring, and exploratory quantitative microbial risk assessment. To support and complement this paradigm shift, field-based, laboratory-free methods are needed to identify and/or infer the presence of enteric viruses (Appendix F). Collectively, all the investigations presented here confirm the use of PMMoV as a surrogate for enteric viruses; however, its utility depends on the context and research question.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Alguns queijos frescos como o Minas frescal e a ricota, apresentam elevada atividade de água e diversidade nutricional, fatores que propiciam a proliferação e o desenvolvimento de microbiota oportunista, prejudicando a qualidade e a integridade destes produtos. Diversos microrganismos são propostos como bioindicadores de contaminação da matéria-prima e/ou do produto pronto para o consumo. Para evitar quaisquer fontes de contaminação é imprescindível a adoção de Boas Práticas de Fabricação (BPF), as quais podem ser avaliadas por meio da aplicação do formulário check-list. Nesse contexto, este estudo objetivou avaliar as condições higiênico-sanitárias e adequações quanto às BPF, em uma indústria de laticínios de pequeno porte, produtora de queijos Minas frescal e ricota, localizada em São José do Rio Preto – SP, por meio do monitoramento microbiológico, físico-químico, e aplicação de check-list. Foram realizadas análises, conforme o fluxograma de fabricação, nas seguintes etapas: água, leite pasteurizado, coalho, massa, soro, superfície palmar dos manipuladores e tanque de coagulação, e queijos Minas frescal e ricota logo após o processamento (t0) e com cinco dias de vida de prateleira (t5). Tais etapas foram monitoradas quanto à qualidade microbiológica, por meio da determinação do Número Mais Provável (NMP) de coliformes totais e termotolerantes; contagem de Staphylococcus coagulase positiva e bactérias aeróbias mesófilas; pesquisa de Escherichia coli, Salmonella spp. e Listeria monocytogenes. A contagem de bactérias aeróbias mesófilas foi efetuada apenas nas amostras de água. As análises de determinação do NMP de coliformes totais, termotolerantes foram realizadas para todas as amostras. A contagem de Staphylococcus aureus, pesquisa de Escherichia coli e de Salmonella spp., foram efetuadas para todas as amostras citadas...
Some fresh cheeses as Minas frescal and ricota present high water activity and nutritional diversity, factors that permit the proliferation and the development of opportunist microrganisms, damaging the quality and integrity of these products. Several microrganisms are proposed as bioindicators of raw material and/or product ready for consumption contamination. To avoid any contamination source it`s indispensable to adopt Good Manufacturing Practices (GMP), which may be evaluated by application of checklist form. According to the presented, this study had the objective of evaluate the hygienic sanitary conditions and adequacies, in relation to the GMP, at a small dairy industry; which produces ricota and Minas frescal cheeses, located in São José do Rio Preto - SP by the physical-chemical and microbiological monitoring and check-list application. The analyses were done according to the following production stages: water, pasteurized milk, curd, mass, sour, manipulator hands, coagulation tank, ricota and Minas frescal cheese right after the processing (t0) and with five days of shelf-life (t5). Such stages were monitored in relation to the microbiological quality by the determination of the Most Probable Number (MPN) of total and thermotolerant coliforms; mesophilic aerobic bacteria and Staphylococcus aureus counting; research of Escherichia coli, Salmonella spp. and Listeria monocytogenes. The counting of mesophilic aerobic bacteria was done only in the water samples. The analyses of the determination of the MPN of total and thermotolerant coliforms were done for all samples. The counting of Staphylococcus aureus, Escherichia coli and Salmonella spp. research were done for all samples except water. The analysis of Listeria monocytogenes was done only for Minas frescal and ricotta cheeses. For the water analysis it was verified that 3 samples (25%) presented... (Complete abstract click electronic access below)

Orientador: Fernando Leite Hoffmann
Banca: Crispin Humberto Garcia Cruz
Banca: Walkíria Hanada Viotto
Banca: Roberto da Silva
Resumo: Alguns queijos frescos como o Minas frescal e a ricota, apresentam elevada atividade de água e diversidade nutricional, fatores que propiciam a proliferação e o desenvolvimento de microbiota oportunista, prejudicando a qualidade e a integridade destes produtos. Diversos microrganismos são propostos como bioindicadores de contaminação da matéria-prima e/ou do produto pronto para o consumo. Para evitar quaisquer fontes de contaminação é imprescindível a adoção de Boas Práticas de Fabricação (BPF), as quais podem ser avaliadas por meio da aplicação do formulário check-list. Nesse contexto, este estudo objetivou avaliar as condições higiênico-sanitárias e adequações quanto às BPF, em uma indústria de laticínios de pequeno porte, produtora de queijos Minas frescal e ricota, localizada em São José do Rio Preto - SP, por meio do monitoramento microbiológico, físico-químico, e aplicação de check-list. Foram realizadas análises, conforme o fluxograma de fabricação, nas seguintes etapas: água, leite pasteurizado, coalho, massa, soro, superfície palmar dos manipuladores e tanque de coagulação, e queijos Minas frescal e ricota logo após o processamento (t0) e com cinco dias de vida de prateleira (t5). Tais etapas foram monitoradas quanto à qualidade microbiológica, por meio da determinação do Número Mais Provável (NMP) de coliformes totais e termotolerantes; contagem de Staphylococcus coagulase positiva e bactérias aeróbias mesófilas; pesquisa de Escherichia coli, Salmonella spp. e Listeria monocytogenes. A contagem de bactérias aeróbias mesófilas foi efetuada apenas nas amostras de água. As análises de determinação do NMP de coliformes totais, termotolerantes foram realizadas para todas as amostras. A contagem de Staphylococcus aureus, pesquisa de Escherichia coli e de Salmonella spp., foram efetuadas para todas as amostras citadas... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Some fresh cheeses as Minas frescal and ricota present high water activity and nutritional diversity, factors that permit the proliferation and the development of opportunist microrganisms, damaging the quality and integrity of these products. Several microrganisms are proposed as bioindicators of raw material and/or product ready for consumption contamination. To avoid any contamination source it's indispensable to adopt Good Manufacturing Practices (GMP), which may be evaluated by application of checklist form. According to the presented, this study had the objective of evaluate the hygienic sanitary conditions and adequacies, in relation to the GMP, at a small dairy industry; which produces ricota and Minas frescal cheeses, located in São José do Rio Preto - SP by the physical-chemical and microbiological monitoring and check-list application. The analyses were done according to the following production stages: water, pasteurized milk, curd, mass, sour, manipulator hands, coagulation tank, ricota and Minas frescal cheese right after the processing (t0) and with five days of shelf-life (t5). Such stages were monitored in relation to the microbiological quality by the determination of the Most Probable Number (MPN) of total and thermotolerant coliforms; mesophilic aerobic bacteria and Staphylococcus aureus counting; research of Escherichia coli, Salmonella spp. and Listeria monocytogenes. The counting of mesophilic aerobic bacteria was done only in the water samples. The analyses of the determination of the MPN of total and thermotolerant coliforms were done for all samples. The counting of Staphylococcus aureus, Escherichia coli and Salmonella spp. research were done for all samples except water. The analysis of Listeria monocytogenes was done only for Minas frescal and ricotta cheeses. For the water analysis it was verified that 3 samples (25%) presented... (Complete abstract click electronic access below)
Mestre

A Araucaria angustifolia, conhecida como Pinheiro-do-Paraná é uma espécie ameaçada de extinção no Brasil, está inserida num bioma rico em biodiversidade, a Mata Atlântica, e muito pouco se conhece sobre os atributos microbiológicos dessas florestas. Este trabalho teve como objetivo avaliar potenciais atributos microbiológicos do solo e algumas variáveis ambientais (atributos químicos, físicos e efeito sazonal), a fim de estabelecer bioindicadores de qualidade do solo em Florestas de Araucária. Os estudos foram conduzidos em dois parques estaduais localizados em diferentes regiões do Estado de São Paulo, no município de Campos do Jordão (Parque Estadual de Campos do Jordão - PECJ), nos municípios de Apiaí e Iporanga (Parque Estadual Turístico do Alto Ribeira - PETAR) e também no município de Barra do Chapéu. Foram escolhidas três áreas no PETAR: FN floresta nativa de araucária, ND floresta de araucária com distúrbio antropogênico e PL plantio de araucária; e quatro áreas foram selecionadas no PECJ: FN floresta nativa de araucária, ND floresta de araucária com distúrbio antropogênico, PL plantio de araucária e PF plantio de araucária com ocorrência de fogo acidental. Ao acaso, foram selecionadas quinze árvores de araucária por área e sob a copa de cada uma delas foram retiradas amostras na profundidade de 0 a 20 cm, nas épocas seca e de chuva. Foram avaliados os atributos microbiológicos: arilsulfatase (ARIL), fosfatase ácida (FOSF), -glicosidase (GLIC), desidrogenase (DESID), nitrogênio (NBM) e carbono da biomassa microbiana (CBM), Número Mais Provável (NMP) de amonificantes (AMO), nitritadores (NITRI), nitratadores (NITRA) e desnitrificantes (DESN), respiração basal (RESP), respiração induzida por substrato (RIS), quociente metabólico (qCO2) e microbiano (qMIC). Além disso, foram estabelecidos perfis de ácidos graxos ligados a ésteres de fosfolipídios (EL-PLFAs) e o perfil de capacidade de utilização de substratos de carbono (Biolog). Alguns parâmetros químicos foram avaliados (pH, H++Al3+, Al3+, Ca2+, Mg2+, K+, P, S, N, carbono orgânico total e a capacidade de troca catiônica) e físicos (teores de argila, silte e areia). Verificou-se que o PL do PETAR e PF do PECJ foram relacionados aos atributos microbiológicos ARIL, DESN, CBM e qMIC nos dois períodos. A partição da variabilidade revelou que a atividade microbiana foi influenciada mais pelas variáveis físico-quimicas do solo do que pelas áreas e épocas de coleta. Foram identificados perfis de ácidos graxos semelhantes aos aqui obtidos, PETAR e PECJ, em um trabalho anterior no PECJ, o que pode ser indicação de um padrão de EL-PLFA próprio do ecossistema de araucária. Os ácidos graxos 10Me18:0 (actinobactéria), a relação ácido graxo saturado/insaturado (sat/insat), o consumo dos substratos -metil-D-glicosídeo e o ácido 2-hidroxibenzóico foram também relacionados às áreas PL (PETAR) e PF (PECJ) nos períodos avaliados. Já os ácidos graxos 18:19c (fungo) e 16:17c (bactéria Gram-), o consumo dos substratos glicose-1-fosfato, -D-lactose e ácido -hidroxibutírico estavam relacionados às áreas impactadas dos dois parques durante os períodos de seca e chuva. Portanto, esses atributos microbiológicos são potenciais indicadores de qualidade do solo em Florestas de Araucária, no entanto, novas avaliações são necessárias para as devidas validações dos bioindicadores e monitoramento dessas áreas.
Araucaria angustifolia, also called Brazil Pine, is an endangered species in Brazil. It is part of one of the richest ecosystems in biodiversity, the Atlantic Forest, and little is known about the soil microbiological attributes in this forest. The objective was to evaluate the potential of the soil microbiological attributes and some environmental variables (physical-chemical properties and seasonal effect) to act as bioindicators of soil quality in Araucaria Forests. This study was undertaken in two different state parks in the São Paulo State, in Campos do Jordão county (Campos do Jordão State Park - PECJ), and in Apiaí and Iporanga counties (Alto Ribeira Touristic State Park - PETAR) and also in Barra do Chapéu county. Three areas were surveyed in PETAR: FN Native Araucaria forest, ND Native Araucaria forest with anthropogenic disturbance, and PL Reforested Araucaria; and four areas in PECJ: FN Native Araucaria forest, ND Native Araucaria forest with anthropogenic disturbance; PL Reforested Araucaria, and PF Araucaria reforestation submitted to an accidental fire. Fifteen Araucaria trees were selected at random in each area and the soil and roots were sampled at 0 20 cm depth, in two contrasting seasons (dry and wet). The microbiological attributes evaluated were: arylsulfatase (ARIL), acid phosphatase (FOSF), -glucosidase (GLIC), dehydrogenase (DESID), carbon (CBM) and nitrogen microbial biomass (NBM), most probable number (NMP) of bacterial ammonium oxidizers (AMO), nitrite oxidizers (NITRI), nitrate oxidizers (NITRA) and denitrifiers (DESN), basal microbial respiration (RESP), substrate induced respiration (RIS), and metabolic (qCO2) and microbial quotient (qMIC). Additionally we determined the phospholipid fatty acid profiles (ELPLFA) and the community level physiological profile (Biolog). Some chemical attributes were evaluated (pH, H++Al3+, Al3+, Ca2+, Mg2+, K+, P, S, CEC, C/N ratio, total organic carbon (COT), total nitrogen (NT), as well as some physical ones (soil texture: clay, sand and silt contents). There was a high correlation between the PL of PETAR and the PF of PECJ and the microbiological attributes ARIL, DESN, CBM and qMIC in both periods. The partitioning of the variability evidenced that microbial activity was influenced in a higher degree by the physical-chemical properties of soil than by study areas or periods. We identified similar fatty acid profiles in PETAR and PECJ and they were also similar to the ones found in a previous work in PECJ, what could indicate a specific EL-PLFA pattern in the Araucaria ecosystem. The fatty acids 10Me18:0 (actinobacteria), the saturated/unsaturated fatty acid ratio (sat/insat), the substrate utilization of -methyl-D-glucoside and 2-hydroxybenzoic acid were also related to PL (PETAR) and PF (PECJ), in both periods. The 18:19c fatty acid (fungi) and 16:17c (Gram-), the glucose-1-phosphate, -D-lactose and -hydroxybutyric acid were C-source for microbial communities of the impacted areas in both parks during the wet and dry periods. Therefore, these attributes are potential microbial indicators of soil quality in Araucaria forests, however, new evaluations are required to confirm these biomarkers and to monitor these areas.

Le développement de nouvelles technologies pour le recyclage des eaux usées est une priorité pour les régions arides et semi-arides tels que les pays du bassin méditerranéen. L'objectif de ce travail a été, dans un premier temps, de développer un système de traitement tertiaire des eaux usées en testant l'efficacité de diodes électroluminescentes émettant des UV-A et/ou des UV-C (DEL-UV) sur l'inactivation de souches bactériennes indicatrices de pollution fécale (Escherichia coli et Enterococcus faecalis) puis sur des effluents urbains, en étudiant la diminution des pollutions microbiennes et chimiques. Cette première étape a mis en évidence l'efficacité accrue du couplage UV-A et UV-C, permettant d'obtenir une eau de qualité répondant aux exigences législatives relatives à la réutilisation des eaux usées pour l'irrigation. La deuxième partie de ce travail était l'étude de l'impact de l'arrosage avec des eaux usées traitées par DEL-UV sur les paramètres du sol et sur le devenir de certain polluant aromatiques dans les sols (anthracène et carbamazépine). L'arrosage avec des eaux usées traitées par DEL-UV ne modifie pas la composition chimique de la matière organique de sol, l'activité catabolique globale des microorganismes, et le nombre et la diversité de bactéries indicatrices de pollution fécale par rapport au sol arrosé avec de l'eau d'irrigation. Certaines activités enzymatiques liées à la dégradation de la matière organique augmentent dans les sols arrosés avec des eaux usées traitées par DEL-UV, montrant que la matière organique apportée par l'effluent est activement dégradée par les microorganismes
The development of new technologies for wastewater reuse is a priority for arid and semi-arid areas such as Mediterranean countries. The objective of this work was, firstly, to develop a system for tertiary treatment of wastewaters testing LEDs emitting UV-A and / or UV-C (UV LEDs) on fecal indicator inactivation (Escherichia coli and Enterococcus faecalis) and then on urban effluents, by studying the decrease in both microbial and chemical pollution. This first step has highlighted a higher efficiency of this system when UV UV-A and UV-C are coupled. Wasterwaters with quality meeting the statutory requirements for the reuse of wastewater for irrigation were obtained and used in the second part of this work was to study the impact of watering with UV-LED- treated wastewaters on soil parameters and on the fate of pollutants (anthracene and carbamazepine) in soils. Watering with UV-LED treated wastewater does not change the chemical composition of soil organic matter, the global catabolic activity of soil microorganisms, and the number and diversity of fecal indicators compared to control (irrigation water). Certain enzymatic activities related to the degradation of organic matter increased in soil watered with UV-LED treated wastewater, showing that the organic matter added by the effluent is actively degraded by microorganisms. In addition, aromatic pollutants are oxidized two to three times faster in soils watered with UV-LED treated wastewater

Microorganisms are the most important bioindicators of the environment and ecological risk assessment. The impact of the no-till farming system in combination with microbial preparations needs to be studied and is an urgent task aimed at preserving fertility. The aim of our study was to determine the effect of pre-sowing inoculation with complex microbial preparations (CMP) and farming systems (no-till and conventional farming system) on the microbocenosis of the rhizosphere of Triticum aestivum L. in the Crimean Steppe. Microbiological analysis of the rhizosphere showed a significant increase in the number of actinobacteria (twice). The number of micromycetes, among which there are many pathogens of various plant diseases, decreased under direct sowing by 23 % as a result of inoculation and amounted to 21.5 thousand CFU/g of soil. The number of cellulose-destroying microorganisms that form soil fertility increased under the influence of microbial preparations by 23 % under conventional farming system (10.0 thousand CFU/g of soil); by 20 % under no-till (15.4 thousand CFU/g of soil). Thus, it was found that the use of microbial preparations under both farming techniques contributed to an increase in the number of microorganisms of most ecological-trophic groups that participate in the transformation of nitrogen in the rhizosphere, enhanced enzymatic processes, reduced the development of pathogenic microbiota and, consequently, contributed to improving the state of soil biocenosis.