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Ilustraciones, tablas Los microorganismos del suelo en bosques y páramos son ejes claves en el mantenimiento de los ecosistemas por sus actividades de descomposición, nutrición de plantas e intervención en los ciclos biogeoquímicos. En esta investigación se recolectaron muestras de suelo en cuatro localidades en la cordillera central de los Andes en el Valle del Cauca, Colombia siguiendo un gradiente altitudinal entre los 1000 y 3800 msnm. Seguidamente se secuenciaron el gen 16S de ARNr para bacterias y la región ITS1 para hongos empleando metabarcoding. Los análisis de composición taxonómica de microorganismos mostraron variaciones de abundancias a través del gradiente altitudinal, siendo las bacterias Acidobacteriota y Proteobacteriota favorecidas en las mayores alturas y Actinobacteria, Firmicutes y Verrucomicrobia en las menores elevaciones. En hongos, Ascomycota tuvo asignación máxima de lecturas en la mayor elevación, Basidiomycota tendió a dominar en las dos menores altitudes y Mortierellomycota reportó la mayoría de sus lecturas en elevaciones intermedias. Las tendencias de esas clasificaciones presentaron relaciones con parámetros fisicoquímicos del suelo como el carbono orgánico, nitrógeno y pH. El índice de Shannon indicó alta diversidad de bacterias y hongos (>3) en todas las localidades, presentándose un patrón de “U” invertida con máximos de diversidad en la reserva el Pailón a 2400 msnm. Además, se evidenciaron asociaciones de géneros de microorganismos con plantas dentro de los ecosistemas y anotaciones funcionales predictivas diferenciales a través el gradiente. Concluimos que las comunidades de bacterias y hongos del suelo difirieron en estructura y diversidad conforme variaron factores preponderantes para los microorganismos edáficos. (Texto tomado de la fuente) Soil microorganisms in forests and páramos are key axes in the maintenance of ecosystems due to their decomposition activities, plant nutrition and intervention in biogeochemical cycles. In this research, soil samples were collected in four localities in the central Andes mountain range in Valle del Cauca, Colombia, following an altitudinal gradient between 1000 and 3800 masl. The 16S rRNA gene for bacteria and the ITS1 region for fungi were sequenced using metabarcoding. Analysis of the taxonomic composition of microorganisms showed variations in abundance across the altitudinal gradient, with Acidobacteriota and Proteobacteriota being favored at higher altitudes and Actinobacteria, Firmicutes and Verrucomicrobia at lower elevations. In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations and Mortierellomycota reported most of their readings at intermediate elevations. Trends in these classifications showed relationships with soil physicochemical parameters such as organic carbon, nitrogen and pH. The Shannon index indicated high diversity of bacteria and fungi (>3) in all localities, presenting an inverted "U" pattern with maximum diversity in the Pailón reserve at 2400 masl. In addition, associations of microorganism genera with plants within the ecosystems and differential predictive functional annotations across the gradient were evidenced. We conclude that soil bacterial and fungal communities differed in structure and diversity as factors preponderant for edaphic microorganisms varied. Maestría Las localidades del estudio fueron el parque natural regional El Vínculo (bosque seco tropical, 1000 msnm), el parque natural regional Mateguadua (bosque seco tropical, 1200 msnm), la reserva de la sociedad civil El Pailón (bosque andino, 2400 msnm) y distrito regional de manejo integrado páramo Las Domínguez (páramo, 3800 msnm) (Figura 1). En cada localidad se conformaron tres parcelas de 10 m x 10 m, separadas entre sí por 20 metros (12 parcelas en total). Para análisis microbiano, de cada parcela se obtuvieron tres muestras de suelo en tubos falcon de 15 mL de los primeros 25 centímetros de profundidad (36 muestras en total). Además, se recolectaron tres muestras de un kilogramo de suelo en los mismos puntos para análisis fisicoquímico y se realizó una caracterización taxonómica de las plantas presentes en el área de las parcelas. Las muestras de suelo se transportaron al laboratorio de Biología Molecular de la Universidad Nacional de Colombia sede Palmira, en donde se mantuvo el suelo para el análisis microbiano a -80 °C hasta la extracción del ADN Ciencias Agropecuarias.Sede Palmira

Las VI Jornadas Científicas del Museo Nacional de Ciencias Naturales (MNCN-CSIC) fueron celebradas el 17 y 18 de abril de 2023 en Madrid. En ellas tuvieron lugar 3 sesiones plenarias de 45 minutos, 21 charlas de 15 minutos y 31 charlas de 5 minutos. Finalizaron con mesa redonda sobre "El futuro de la carrera investigadora en el Museo".

Las zonas húmedas mediterráneas juegan un papel muy importante en los ciclos biogeoquímicos, ya que la presencia de agua, de forma constante o transitoria, favorece unas altas tasas metabólicas. Respecto al ciclo del carbono, los humedales mediterráneos se ven activamente involucrados en la captación o en la emisión de gases de efecto invernadero carbonados (C-GEI) hacia la atmósfera, concretamente el dióxido de carbono y el metano. Esta relevancia de los humedales en el ciclo del carbono se debe, en parte, a la actividad de las comunidades de procariotas que habitan en el agua y en el sedimento de las zonas húmedas, puesto que la abundancia y versatilidad metabólica de los procariotas les otorgan el papel de actores principales en los flujos de carbono de estos ecosistemas. No obstante, los humedales mediterráneos no son homogéneos, sino que corresponden a diferentes tipos que muestran una serie de características ecológicas específicas, las cuales pueden influir tanto en la estructura como en los metabolismos del carbono de las comunidades de procariotas que habitan en dichos humedales. El objetivo principal de esta tesis ha consistido en determinar el papel que tienen las características ambientales que determinan cada tipo de humedal, junto a su estado de conservación, en la estructuración y los metabolismos del carbono de las comunidades de procariotas que habitan en las aguas y en los sedimentos de lagunas representativas de las grandes categorías de humedales mediterráneos. Los resultados de esta tesis demuestran que las características ecológicas de los diferentes tipos de humedales influyen profundamente en la estructura de las comunidades de procariotas que los habitan, de forma que cada tipo de humedal y estado de conservación mostró una serie de taxones característicos de procariotas. La salinidad fue la variable ambiental que más influenció la estructura de dichas comunidades, aunque otras variables como la alcalinidad para las comunidades de procariotas del agua y el pH y el carbonato para las del sedimento también fueron relevantes. Por otra parte, y además del tipo de humedal, la sinergia entre su estado de conservación y la estacionalidad fue determinante en la estructuración de las comunidades de procariotas del agua, pero ejerció un efecto mucho más modesto en las comunidades del sedimento, al ser este un ambiente más estable. La relación entre las tasas de los principales metabolismos relacionados con el carbono y la inferencia molecular de su potencial metabólico fue compleja, ya que dependió del balance entre diferentes metabolismos microbianos y la abundancia relativa de los grupos de procariotas involucrados en dichos metabolismos. Además, en esta tesis se determinó experimentalmente la influencia de la temperatura en el incremento de la actividad de las arqueas metanógenas y consecuentemente en las emisiones de metano de los humedales estudiados. Los resultados de esta tesis demuestran la importancia de combinar medidas de la actividad metabólica in situ con estudios moleculares de las comunidades de procariotas para entender mejor los flujos de carbono y de gases de efecto invernadero en los humedales mediterráneos, y con ello su papel potencial en la mitigación del cambio climático Mediterranean wetlands play a very important role in biogeochemical cycles, as the presence of water, either constantly or transiently, favours high metabolic rates. Regarding the carbon cycle, Mediterranean wetlands are actively involved in the uptake or emission of carbon-greenhouse gases (C-GHGs) from/into the atmosphere, namely carbon dioxide and methane. This relevance of wetlands in the carbon cycle is due, in part, to the activity of the prokaryotic communities that inhabit the water and sediment of wetlands, since the abundance and metabolic versatility of prokaryotes make them key players in the carbon fluxes of these ecosystems. However, Mediterranean wetlands are not all equal, but instead correspond to different ecological types displaying a number of type-specific ecological characteristics, which can influence in both the structure and carbon metabolisms of the prokaryotic communities inhabiting these wetlands. The main objective of this thesis has been determining the role of the typical ecological characteristics of each type of wetland, together with its conservation status, in the structuration and carbon metabolisms of the prokaryote communities inhabiting the waters and sediments of representative wetlands among the different types of Mediterranean wetlands. The results of this thesis demonstrate that the ecological characteristics of the different wetland types deeply influence the structure of their prokaryotic communities, in such a way that each wetland type and conservation status showed a series of characteristic prokaryotic taxa. Salinity was the environmental variable that most influenced the prokaryotic community structure, although other variables such as alkalinity for water and pH and carbonate for sediments were also relevant. On the other hand, in addition to the wetland type, the synergy between wetland conservation status and seasonality was a determining factor in structuring the water prokaryotic assemblages but had a much more modest effect on sediment communities, as this is a more stable environment. The relationship between the rates of the main carbon-related metabolisms and the molecular inference of their metabolic potential was complex, as it depended on the balance between different microbial metabolisms and the relative abundance of the groups of prokaryotes involved in these metabolisms. Furthermore, in this thesis, the influence of temperature on the increase of the activity of methanogenic archaea and consequently on methane emissions from the studied wetlands was experimentally determined. The results of this thesis demonstrate the importance of combining in situ measurements of metabolic activity with molecular studies of prokaryotic communities to better understand the carbon and greenhouse gases fluxes in Mediterranean wetlands, and thus their potential role in climate change mitigation.

No estamos solos. Bacterias, hongos, parásitos y virus habitan cualquier parte de nuestro organismo y pueden cumplir funciones biológicas importantes, bien sea benéficas o dañinas. Conocerlos es fundamental para un manejo adecuado. Con las herramientas que utiliza el Grupo de Investigaciones Microbiológicas se pueden identificar la presencia del microorganismo y los marcadores moleculares de interés para la salud, como los relacionados con la resistencia a antibióticos, lo que aporta una información muy útil para el manejo de los pacientes. We are not alone. Bacteria, fungi, parasites and viruses inhabit any part of our body and can perform important biological functions, either beneficial or harmful. Knowing them is essential for proper management. With the tools used by the Microbiological Research Group, the presence of the microorganism and molecular markers of interest for health, such as those related to antibiotic resistance, can be identified, which provides very useful information for patient management.

[eng] Understanding the mechanisms and processes driving biological com- munities assembly, i.e. determining why a specific community is found under certain circumstances, is one of the fundamental questions in ecology. The potential effect of the different assembly processes (selection, dispersal and ecological drift, together with speciation which operates at evolutionary timescales) has been studied over multiple systems and types of organisms, proposing a complex equilibrium with a variable dominance of either stochastic or deterministic assembly processes. In this PhD thesis, we aimed to reach a deep understanding on the processes and mechanisms driving microbial communities assembly using a highly dynamic system of ephemeral saline lakes potentially interconnected by dispersal processes as study model. Ephemeral saline lakes are a perfect scenario to assess the effect of variable selective pressure (promoted by wide salinity fluctuations) and the potential effect on complementary assembly processes as dispersal and ecological drift. The study of these processes across environ- mental, spatial and temporal scales may offer a mechanistic understanding on how assembly processes interact to determine communities diversity. Along three consecutive hydrological cycles, we characterized the monthly dynamics of the aquatic microbiome inhabiting 14 ephemeral salt lakes in the Monegros Desert (NE Spain). These systems experienced severe variations in water volume along the hydrological cycle, which promote wide salinity fluctuations from freshwater to salt-saturation. The inhabiting bacterial, archaeal and microeukaryal communities were characterized by high-throughput sequencing of the 16S and 18S rRNA genes, respectively. We assessed the effect of increasing salinity concentrations in the diversity and composition of microbial communities, together with ecological and metabolic effects. Next, we analyzed the ephemeral lakes from a metacommunity perspective to investigate the role of the different assembly processes along the hydrological cycle and their interactions to shape the observed dynamics. As expected, we noticed that increasing salinity gradients strongly deter- mined microbial communities compositions. While a taxonomic replacement was observed in the bacterial communities driven by mass extinctions followed by colonization by better-adapted halophilic groups, eukaryal communities suffered a severe environmental filtering which produced a simplified assembly dominated by a few halophilic groups, mainly the photosynthetic algae Dunaliella and Navicula. Conversely, the rich archaeal assemblage of Monegros become more abundant as lakes reached hypersaline concentrations. Through a novel genomic trait-based approach we set up the transition from stochasticity to deterministic assembly describing a consistent threshold at salinities c.a. 5%. Beyond this threshold, increasing selective pressure reduced the potential colonization success among lakes, but also the potential colonization by allochthonous microbes from other biomes as sediments and soils. Potential interspecies interactions along the salinity gradient were addressed by a network analysis that showed that increasing selective pressure, and the associated transition from generalists to specialists groups, reduced competition and did not promote facilitative associations. Overall, the multiscale assessment of the deterministic and stochastic assembly processes in the Monegros ephemeral lacustrine system, together with the previous vast knowledge on both the ecology and microbiology of saline system and the physiological effects of salinity gradients, allowed us to describe the biological assembly from an unusual combination of mechanistic and integrative points of view., [spa] Comprender los mecanismos y los procesos que impulsan el ensamblaje de las comunidades biológicas, es decir, determinar por qué se encuentra una comunidad específica en determinadas circunstancias, es una de las cuestiones fundamentales en ecología. El efecto potencial de los diferentes procesos de ensamblaje (selección, dispersión y deriva ecológica, junto con la especiación que opera a escalas de tiempo evolutivas) se ha estudiado en múltiples sistemas y organismos, proponiendo un equilibrio complejo con un predominio variable de los procesos de ensamblaje estocásticos y deterministas. En esta tesis doctoral, nuestro objetivo es comprender los procesos y mecanismos que impulsan el ensamblaje de las comunidades microbianas utilizando un sistema de lagos salinos efímeros altamente dinámicos y potencialmente interconectados por procesos de dispersión como modelo de estudio. Los lagos salinos efímeros son un escenario perfecto para evaluar el efecto de una presión selectiva variable (promovida por las amplias fluctuaciones de salinidad) y el efecto potencial sobre los procesos de ensamblaje complementarios como la dispersión y la deriva ecológica. El estudio de estos procesos a través de múltiples escalas ambientales, espaciales y temporales puede ofrecer una comprensión mecanicista de cómo los diferentes procesos interactúan para determinar el ensamblaje de las comunidades. A lo largo de tres ciclos hidrológicos consecutivos, caracterizamos la dinámica mensual del microbioma acuático de 14 lagos salinos efímeros del desierto de Monegros (NE de España). Estos sistemas experimentaron severas variaciones en el volumen de agua a lo largo del ciclo hidrológico, los cuales promueven amplias fluctuaciones de salinidad que van desde agua dulce hasta la saturación de sales. Las comunidades de bacterias, arqueas y microeucariotas que habitan estos lagos se caracterizaron mediante la secuenciación masiva de los genes 16S y 18S rRNA, respectivamente. Evaluamos el efecto del aumento de la salinidad en la diversidad y composición de las comunidades microbianas, junto con los efectos ecológicos y metabólicos. A continuación, analizamos los lagos efímeros desde una perspectiva de metacomunidad para evaluar el papel de los diferentes procesos de ensamblaje, así como sus interacciones, para originar las dinámicas observadas a lo largo del ciclo hidrológico. Como se esperaba, observamos que la composición de las comunidades microbianas está fuertemente determinada por el aumento de los niveles de salinidad. Mientras que se observó una reemplazo taxonómico en las comunidades bacterianas, impulsado por extinciones masivas seguidas de la colonización por grupos halófilos mejor adaptados, las comunidades de eucariotas sufrieron un severo filtrado ambiental que dio lugar a un ensamblaje simplificado dominado por unos pocos grupos halófilos, principalmente las algas fotosintéticas Dunaliella y Navicula. Por el contrario, el rico y diverso ensamblaje de arqueas presente en los Monegros se hizo más abundante a medida que los lagos alcanzaban concentraciones hipersalinas. Mediante un novedoso enfoque basado en los rasgos genómicos, identificamos la transición de un ensamblaje dominado por procesos estocásticos a un ensamblaje determinista, describiendo un umbral consistente a salinidades c.a. 5%. Más allá de este umbral, el aumento de la presión selectiva redujo el éxito potencial de los procesos de colonización entre los lagos, pero también la colonización potencial por parte de microorganismos alóctonos provenientes de otros biomas como sedimentos y suelos. Las potenciales interacciones entre especies a lo largo del gradiente de salinidad se abordaron mediante un análisis de redes que mostró que el aumento de la presión selectiva, y la transición asociada de grupos generalistas a especialistas, redujo la competencia y no promovió la facilitación entre especies. En general, el análisis multiescala de los procesos de ensamblaje deterministas y estocásticos en el sistema de lagos efímeros de Monegros, junto con los amplios conocimientos previos sobre la ecología y microbiología de los sistemas salinos y los efectos fisiológicos de los gradientes de salinidad, nos permitieron describir el ensamblaje de las comunidades desde una inusual combinación de puntos de vista mecanicistas e integradores.

Submitted by Ana Paula Corrêa Moneda (ana.moneda@unesp.br) on 2022-05-17T21:31:39Z No. of bitstreams: 1 DISSERTAÇÃO FINALIZADA.pdf: 5365809 bytes, checksum: 8b52808b47401a43984fc756347985a5 (MD5) Approved for entry into archive by Laudicélia Martins Arantes (lm.arantes@unesp.br) on 2022-05-18T11:52:31Z (GMT) No. of bitstreams: 1 moneda_apc_me_jabo.pdf: 5365809 bytes, checksum: 8b52808b47401a43984fc756347985a5 (MD5) Made available in DSpace on 2022-05-18T11:52:31Z (GMT). No. of bitstreams: 1 moneda_apc_me_jabo.pdf: 5365809 bytes, checksum: 8b52808b47401a43984fc756347985a5 (MD5) Previous issue date: 2022-05-06 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) A cultura da cana de açúcar (Saccharum spp.) envolve atividades agrícolas e industriais de extrema importância para a obtenção de produtos e subprodutos que movimentam fortemente a economia e possuem impactos no meio ambiente. Na agricultura convencional é comum a aplicação de fertilizantes, pesticidas e demais produtos agroquímicos de origem sintética, além de uma intensiva exploração dos recursos naturais, como o solo. Uma prática alternativa, o cultivo orgânico visa maior sustentabilidade e equilíbrio das relações ecológicas aliado a conservação ambiental. Poucos estudos avaliaram o impacto desses dois sistemas contrastantes de manejo na composição e estrutura da microbiota rizosférica. Neste trabalho, utilizamos o sequenciamento em larga-escala dos genes 16S rRNA (V3 e V4) e o Espaçador Interno Transcrito (ITS2) oriundos de amostras coletadas da rizosfera de plantas de cana-de-açúcar cultivadas em condições de campo para a identificação de procariotos e fungos, respectivamente. Os filos mais comuns encontrados foram Proteobacteria e Ascomycota. Ao todo, obtivemos 14 táxons bacterianos e 60 táxons fúngicos diferencialmente abundantes e a presença de grupos taxonômicos essenciais, promotores de crescimento de plantas. Nas redes de coocorrência, táxons chaves sugestivamente alteram a estrutura das comunidades microbianas. Na predição funcional, se destacam vias metabólicas envolvidas em processos estruturais e biológicos dos microbiomas. Nossos resultados, evidenciam que o tipo de manejo empregado determina de forma sútil a composição, diversidade e estrutura dessa microbiota. The cultivation of sugarcane (Saccharum spp.) involves agricultural and industrial activities of extreme importance to obtain products and by-products that strongly move the economy and have impacts on the environment. In conventional agriculture, it is common to apply fertilizers, pesticides and other agrochemicals of synthetic origin, in addition to intensive exploitation of natural resources, such as soil. An alternative practice, organic cultivation aims at greater sustainability and balance of ecological relationships combined with environmental conservation. Few studies have evaluated the impact of these two contrasting management systems on the composition and structure of the rhizospheric microbiota. In this work, we used the large-scale sequencing of the 16S rRNA genes (V3 and V4) and the Internal Transcript Spacer (ITS2) from samples collected from the rhizosphere of sugarcane plants grown under field conditions to identify prokaryotes and fungi, respectively. The most common phyla found were Proteobacteria and Ascomycota. Altogether, we obtained 14 bacterial taxa and 60 differentially abundant fungal taxa and the presence of essential taxonomic groups that promote plant growth. In co-occurrence networks, key taxa suggestively alter the structure of microbial communities. In functional prediction, metabolic pathways involved in structural and biological processes of microbiomes stand out. Our results show that the type of management employed subtly determines the composition, diversity and structure of this microbiota. 145962/2019-9 Fapesp nº. 2017/09008-5

O uso de agrot?xicos em atividades rurais gera impacto no meio ambiente, sendo poss?vel encontrar ind?cios de contamina??o por esses compostos em amostras de diferentes ambientes aqu?ticos. H? relatos de adapta??es de bact?rias ? presen?a de agrot?xicos e de resist?ncia cruzada entre essas mol?culas e antimicrobianos. O Sistema Aqu?fero Guarani (SAG) ? um dos mais importantes sistemas hidrost?ticos da por??o sul da Am?rica do Sul. Como parte de um projeto anterior, 23 isolados bacterianos foram obtidos de amostras de ?gua do SAG de tr?s regi?es de intensa agricultura do estado do Rio Grande do Sul (RS, Brasil). O presente estudo investigou a suscetibilidade desses isolados bacterianos a pesticidas e antimicrobianos. A maioria dos isolados foi identificada como pertencente aos g?neros Bacillus, Lysinibacillus ou Pseudomonas. Tamb?m foi poss?vel observar um exemplar de Enterococcus, Leuconostoc e Staphylococcus. Todos os isolados foram expostos a um gradiente de concentra??o de herbicida ? base de ?cido diclorofenoxiac?tico (1,2 ?g/mL, 1,5 ?g/mL e 1,2 ?g/mL) e herbicida ? base de glifosato (4 ?g/mL, 6 ?g/mL e 8 ?g/mL), separadamente, por 45 h a 25?C. Al?quotas de 5 h, 20 h, 30 h e 45 h dos tratamentos foram analisadas para estimativa de sobreviv?ncia (contagens de unidades formadoras de col?nia por mL). Os isolados apresentaram resposta bastante heterog?nea aos tratamentos com herbicidas, dentre os quais 19 foram tolerantes ou altamente tolerantes a pelo menos uma concentra??o de um herbicida. Os isolados de Nova Palma (Quarta Col?nia) mostraram um valor m?dio de sobreviv?ncia m?xima (SM) a ambos os herbicidas significativamente superior ao de doutras regi?es. Al?m disso, o tipo resposta dos isolados a ambos os herbicidas mostrou uma correla??o positiva significativa. Os 13 isolados que foram identificados como Bacillus, Lysinibacillus, Pseudomonas e Enterococcus tamb?m foram submetidos a testes de suscetibilidade a antimicrobianos, utilizando os m?todos de disco difus?o e microdilui??o. Destes, 7 apresentaram resist?ncia a pelo menos um f?rmaco, muitos destes com valores de MIC acima do valor de corte para resist?ncia. Os isolados de Pseudomonas foram os que apresentaram resist?ncia ao maior n?mero de antimicrobianos testados. Integrando os dados, os isolados com o maior e o menor ?ndice de m?ltipla resist?ncia a antibi?ticos (MRA) apresentaram valores altos e baixos de SM aos herbicidas, respectivamente. Uma an?lise de componentes principais tamb?m mostrou que o padr?o de resposta aos antimicrobianos parece estar relacionado ?s caracter?sticas taxon?micas dos isolados, o que n?o foi observado para a resposta aos herbicidas. Nossos dados indicam que herbicidas e antimicrobianos podem favorecer a propaga??o de algumas popula??es bacterianas do SAG e prejudicar a manuten??o de outras. Desta forma, estes dados servem como evid?ncias de que tais estressores est?o potencialmente alterando a estrutura das comunidades microbianas em ambientes naturais. Eles tamb?m destacam a import?ncia de estudar os microrganismos desses ambientes como potenciais indicadores e/ou remediadores de impacto ambiental derivado de atividades humanas. The use of pesticides in rural activities induces an impact on the environment, and it is possible to find evidence of contamination by these compounds in samples from different aquatic environments. There are reports of adaptations of bacteria to the presence of pesticides and of cross-resistance between these compounds and antimicrobial drugs. The Guarani Aquifer System (GAS) is one of the most important hydrostatic systems in the southern portion of South America. As part of a previous project, 23 bacterial isolates were obtained from GAS water samples from three agriculture-intensive regions of the state of Rio Grande do Sul (RS, Brazil). The present study investigated the susceptibility of these bacterial isolates to pesticides and antimicrobials. Most isolates were identified as belonging to the genera Bacillus, Lysinibacillus or Pseudomonas. It was also possible to observe one representative of Enterococcus, Leuconostoc and Staphylococcus. They were all exposed to a concentration gradient of 2,4-Dichlorophenoxyacetic acid-based herbicide (1.2 ?g/mL, 1.5 ?g/mL and 1.2 ?g/mL) and glyphosate-based herbicide (4 ?g/mL, 6 ?g/mL and 8 ?g/mL), separately, for 45 h at 25?C. Aliquots from 5 h, 20 h, 30 h and 45 h treatments were analyzed for survival estimation (colony-forming unit/mL counts). The isolates presented a very heterogeneous response to the herbicides? treatments, among which 19 were tolerant or highly tolerant to at least one concentration of one herbicide. The isolates from Nova Palma (Quarta Col?nia) showed mean values of maximum survival (MS) for both herbicides significantly higher than those from other regions. Furthermore, the response of isolates to both herbicides showed a significant positive correlation. The 13 isolates that were identified as Bacillus, Lysinibacillus, Pseudomonas and Enterococcus were also submitted to antimicrobial susceptibility tests, using disk diffusion and microdilution methods. Among these, 7 presented resistance to at least one drug, many of which presented MIC values above the breakpoint value for resistance. The Pseudomonas isolates showed resistance to the highest number of antimicrobials tested. Integrating the data, the isolates with the highest and the lowest index of multiple antibiotic resistance (MAR) showed high and low values of MS to herbicides, respectively. A principal component analysis also showed that the pattern of response to antimicrobials seemed to be related to the taxonomic characteristics of the isolates, which was not observed for the response to herbicides. Our data indicate that herbicides and antimicrobials may favor the propagation of some GAS bacterial populations, harming the maintenance of others. In this context, these data serve as evidence that such stressors are potentially altering the structure of microbial communities in natural environments. They also highlight the importance of studying the microorganisms in these environments as potential indicators and/or remediators of environmental impact from human activities. Conselho Nacional de Pesquisa e Desenvolvimento Cient?fico e Tecnol?gico - CNPq

The aim of present study is to characterize the resistance and virulence profile of enterococci isolated from aquaculture excavated ponds and masonry tanks (6 samples) in southern Brazil. Samples were cultured in selective medium, 10 colonies were randomly selected from each sample, which were identified by MALDI-TOF and tested against 13 antimicrobials. The presence of resistance (tetL, tetM, tetS, ermB and msrC) and virulence (ace, esp, agg, cylA and gelE) genes were determined by PCR. A total of 79 enterococci were identified, and Entecococcus faecalis (44.3%) and E. casseliflavus (36.7%) were the most prevalent species isolated. Sixty-five strains (82.3%) were resistant to at least one of the antimicrobials tested, whereas 27 (34.2%) strains were multiresistant. The overall percentages of antimicrobial resistant isolates were: 58.2% to rifampicin, 40.5% to fluoroquinolones, 36.7% to erythromycin and 30.4% to tetracycline. The tetL and tetM genes were found in 57.7% of the tetracycline-resistant strains; and msrC in 31.01% of erythromycin-resistant strains. The most frequently detected virulence factors were ace and gelE genes. Although limited to a single farm, these data suggest that aquaculture may be a reservoir of resistant and virulent enterococci. This study is the first step towards enhancing our understandingof distribution, resistance and virulence profile in enterococci isolated from fish farming environments in the south Brazil. Resumo O objetivo do estudo apresentado é caracterizar o perfil de resistência e virulência de enterococos isolados de viveiros escavados e tanques de alvenaria (6 amostras) de uma pisicultura no Sul do Brasil. As amostras foram cultivadas em meio seletivo, 10 colônias foram selecionadas aleatoriamente de cada amostra, que foram identificadas por MALDI-TOF e testadas contra 13 antimicrobianos. A presença de genes de resistência (tetL, tetM, tetS, ermB e msrC) e virulência (ace, esp, agg, cylA e gelE) foi determinada por PCR. Foram identificados 79 enterococos, sendo Entecococcus faecalis (44,3%) e E. casseliflavus (36,7%) as espécies mais frequentes isoladas. Sessenta e cinco cepas (82,3%) eram resistentes a pelo menos um dos antimicrobianos testados, enquanto 27 (34,2%) eram multirresistentes. As porcentagens gerais de isolados resistentes a antimicrobianos foram: 58,2% para rifampicina, 40,5% para fluoroquinolonas, 36,7% para eritromicina e 30,4% para tetraciclina. Os genes tetL e tetM foram encontrados em 57,7% das cepas resistentes à tetraciclina; e msrC em 31,01% das cepas resistentes à eritromicina. Os fatores de virulência mais comumente detectados foram ace e gelE. Embora limitados a uma única fazenda, esses dados indicam que a aquicultura pode ser uma fonte de enterococos resistentes e virulentos. Este estudo é o primeiro passo para melhorar nosso entendimento da distribuição, resistência e perfil de virulência em enterococos isolados de ambientes de piscicultura no sul do Brasil.

Tubastraea coccinea is an azooxanthellate coral species recorded in the Indian and Atlantic oceans and is presently widespread in the southwestern Atlantic with an alien status for Brazil. T. coccinea outcompete other native coral species by using a varied repertoire of biological traits. For example, T. coccinea has evolved potent venom capable of immobilizing and digesting zooplankton prey. Diversification and modification of venom toxins can provide potential adaptive benefits to individual fitness, yet acquired alteration of venom composition in cnidarians is poorly understood as the adaptive flexibility affecting toxin composition in these ancient lineages has been largely ignored. We used quantitative high‐throughput proteomics to detect changes in toxin expression in clonal fragments of specimens collected and interchanged from two environmentally distinct and geographically separate study sites. Unexpectedly, despite global changes in protein expression, there were no changes in the composition and abundance of toxins from coral fragments recovered from either site, and following clonal transplantation between sites. There were also no apparent changes to the cnidome (cnidae) and gross skeletal or soft tissue morphologies of the specimens. These results suggest that the conserved toxin complexity of T. coccinea co‐evolved with innovation of the venom delivery system, and its morphological development and phenotypic expression are not modulated by habitat pressures over short periods of time. The adaptive response of the venom trait to specific predatory regimes, however, necessitates further consideration., Toxin complexity in the alien coral Tubastraea coccinea is conserved and co‐evolved with innovation of the venom delivery system. Morphological development of the coral and phenotypic expression of the venom and delivery system is not modulated by habitat pressures over short periods of time.

En el trabajo se realiza un analisis de alfa y beta diversidad de la composición bacteriana de 6 puntos del distrito de riego La Ramada, a partir de abundancias medidas posterior a la clasificación taxonómica realizada en 3 herramientas. El incremento de la población humano y su actividad asociada, han tenido impacto en la composición bacteriana de muchos ambientes, entre ellos los entornos acuáticos. Se ha reportado que en cuerpos de agua como ríos, lagos, lagunas y efluentes de plantas de tratamiento de aguas residuales, se presentan mayor abundancia bacterias presentes en el tracto gastrointestinal. Se han realizado trabajos donde han reportado la presencia de Salmonella, E. coli, Bacteroides, Bifiodobacterium y otros Bacteroidetes en el río Bogotá. En este trabajo se caracterizó la composición de la comunidad microbiana acuática de muestras tomadas en seis lugares en el distrito de riego La Ramada, a partir de secuenciación dirigida al gen del ARNr 16s. Las bacterias identificadas con las distintas herramientas dan cuenta que la actividad humana puede tener un impacto negativo en la calidad del agua, consistente con trabajos previos. Al Ministerío de Ciencia, Tecnología e Innovación. Proyecto ¿Identificación de contaminantes emergentes y microbiológicos, análisis metagenómico bacteriano y perfil de resistencia a antibióticos en aguas de riego y hortalizas de la Sabana occidental de Cundinamarca, código 110180763785¿. Magíster en Biología Computacional Maestría

Microbial diversification is driven by geographic and ecological factors, but how the relative importance of these factors varies among species, geographic scales, and habitats remains unclear. Streptomyces, a genus of antibiotic-producing, spore-forming, and widespread bacteria, offers a robust model for identifying the processes underlying population differentiation. We examined the population structure of 37 Streptomyces olivaceus strains isolated from various sources, showing that they diverged into two habitat-associated (free-living and insect-associated) and geographically disparate lineages. More frequent gene flow within than between the lineages confirmed genetic isolation in S. olivaceus. Geographic isolation could not explain the genetic isolation; instead, habitat type was a strong predictor of genetic distance when controlling for geographic distance. The identification of habitat-specific genetic variations, including genes involved in regulation, resource use, and secondary metabolism, suggested a significant role of habitat adaptation in the diversification process. Physiological assays revealed fitness trade-offs under different environmental conditions in the two lineages. Notably, insect-associated isolates could outcompete free-living isolates in a free-iron-deficient environment. Furthermore, substrate (e.g., sialic acid and glycogen) utilization but not thermal traits differentiated the two lineages. Overall, our results argue that adaptive processes drove ecological divergence among closely related streptomycetes, eventually leading to dispersal limitation and gene flow barriers between the lineages. S. olivaceus may best be considered a species complex consisting of two cryptic species. China Ocean Mineral Resources R&D Association/[DY135-B2-02]/CONRA/China National Natural Science Foundation of China/[32070001 and 91751118]/NSFC/China RV KEXUE/[KEXUE2019GZ05]//China Chinese Academy of Sciences/[KEXUE2019GZ05]/CAS/China Universidad de Costa Rica/[801-B0-530]/UCR/Costa Rica UCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Estructuras Microscópicas (CIEMIC) UCR::Vicerrectoría de Docencia::Ingeniería::Facultad de Ingeniería::Escuela de Ciencias de la Computación e Informática

Background Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST. Results In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as ‘ocean’. The ‘Quick Search’ and ‘Advanced Search’ tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the MarineMetagenomeDB web app to select estuarine metagenomes for potential large-scale microbial biogeography studies. Conclusion The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/.

Boza is a traditional low-alcohol fermented beverage from the Balkan Peninsula, frequently explored as a functional food product. The product is rich in Lactic Acid Bacteria (LAB) and some of them can produce bacteriocins. In this study, a sample of Boza from Belogratchik, Bulgaria, was analyzed for the presence of bacteriocinogenic LAB, and after analyses by RAPD-PCR, three representative isolates were characterized by genomic analyses, using whole genome sequencing. Isolates identified as Pediococcus pentosaceus ST75BZ and Pediococcus pentosaceus ST87BZ contained operons encoding for bacteriocins pediocin PA-1 and penocin A, while isolate identified as Pediococcus acidilactici ST31BZ contained only the operon for pediocin PA-1 and a CRISPR/Cas system for protection against bacteriophage infection. The antimicrobial activity of bacteriocins produced by the three isolates was inhibited by treatment of the cell-free supernatants with proteolytic enzymes. The produced bacteriocins inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp., among other tested species. The levels of bacteriocin production varied from 3200 to 12,800 AU/ml recorded against L. monocytogenes 104, 637 and 711, measured at 24 h of incubation at 37 °C. All bacteriocins remained active after incubation at pH 2.0–10.0. The activity mode of the studied bacteriocins was bactericidal, as determined against L. monocytogenes 104, 637 and 711. In addition, bactericidal activity was demonstrated using a cell leakage β-galactosidase assay, indicating a pore formation mechanism as a mode of action. The present study highlights the importance of combining genomic analyses and traditional microbiological approaches as way of characterizing microbial interactions in fermented foods.

ANII: POS_NAC_2016_1_129862

Published Online: 27 September, 2021, The high complexity found in microbial communities makes the identification of microbial interactions challenging. To address this challenge, we present OrtSuite, a flexible workflow to predict putative microbial interactions based on genomic content of microbial communities and targeted to specific ecosystem processes. The pipeline is composed of three user-friendly bash commands. OrtSuite combines ortholog clustering with genome annotation strategies limited to user-defined sets of functions allowing for hypothesis-driven data analysis such as assessing microbial interactions in specific ecosystems. OrtSuite matched, on average, 96% of experimentally verified KEGG orthologs involved in benzoate degradation in a known group of benzoate degraders. We evaluated the identification of putative synergistic species interactions using the sequenced genomes of an independent study that had previously proposed potential species interactions in benzoate degradation. OrtSuite is an easy-to-use workflow that allows for rapid functional annotation based on a user-curated database and can easily be extended to ecosystem processes where connections between genes and reactions are known., This work was funded by the Helmholtz Young Investigator grant VH-NG-1248 Micro “Big Data.”, info:eu-repo/semantics/publishedVersion

Las comunidades bacterianas presentes en el tracto gastrointestinal (TGI) de las aves son de vital importancia ya que contribuyen a su sanidad y nutrición. Además, cobran relevancia dado que las mismas pueden ser transferidas a suelos agrícolas cuando los residuos de la producción aviar son utilizados como enmiendas orgánicas. En la presente tesis se utilizaron técnicas de secuenciación masiva de amplicones del gen ARNr 16S con el objetivo de caracterizar estas comunidades bacterianas. Primeramente, se realizó un meta-análisis comparando la composición bacteriana del TGI de aves de diferentes países. Los resultados obtenidos mostraron el papel de la locación geográfica como modulador de la composición microbiana de ciegos permitiendo describir la "microbiota local" argentina. Además, se evaluaron los efectos de diferentes aditivos dietarios a escala experimental y comercial, encontrándose patrones diferenciales de modulación para cada aditivo, con un incremento en la relación Firmicutes/Bacteroidetes en los animales alimentados con taninos, debido a la mayor proporción de bacterias del orden Clostridiales. Finalmente, se describieron poblaciones de bacterias presentes en los residuos avícolas y el impacto que éstos producen en los agroecosistemas, particularmente en suelos agrícolas. Si bien la aplicación de guano y cama de pollo no mostró efectos significativos sobre la estructura de las comunidades bacterianas del suelo, se encontraron aumentos importantes en los valores de fósforo total y extractable, así como efectos fitotóxicos. Por este motivo, el guano fue tratado mediante compostaje y digestión anaeróbica encontrándose en cada enmienda obtenida, grupos taxonómicos y funcionales vinculados a cada tipo de tratamiento. Además, esto redujo el exceso de nutrientes y bacterias patógenas, permitiendo su utilización de forma segura, sin poner en riesgo la salud humana, animal ni vegetal, y disminuyendo el riesgo de contaminación de napas y cursos de agua. The bacterial communities present in the gastrointestinal tract (GIT) of birds are of vital importance as they contribute to their health and nutrition. In addition, they are relevant since can be transferred to agricultural soils when the waste of avian production are used as organic amendments. In the present study, metabarcoding of 16S rRNA gene was used in order to characterize these bacterial communities. First, a meta-analysis was carried out comparing the bacterial composition of the GIT of birds from different countries. The results obtained showed the role of the geographic location as a modulator factor of the microbial composition of cecum, allowing the Argentine "local microbiota" to be described. In addition, the effects of different dietary additives were evaluated on an experimental and commercial scale, finding differential modulation patterns for each additive, with an increase in the Firmicutes/Bacteroidetes ratio in animals fed with tannins, due to the higher proportion of bacteria of the order Clostridiales. Finally, bacteria communities present in poultry waste and the impact they produce on agroecosystems, particularly on agricultural soils, were described. Although the application of poultry manure and chicken litter did not show significant effects on the structure of the soil bacterial communities, significant increases were found in the values of total and extractable phosphorus, as well as phytotoxic effects. For this reason, the poultry manure was treated by composting and anaerobic digestion, finding in each amendment obtained, taxonomic and functional groups linked to each type of treatment. In addition, this reduced the excess of nutrients and pathogenic bacteria, allowing their use in a safe way, without putting human, animal, or plant health at risk, and reducing the risk of contamination of water courses. Fil: Pin Viso, Natalia Daniela. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina.

Ce numéro de la Revue d’Anthropologie des Connaissances interroge et met en perspective la notion, récemment apparue dans le champ des sciences sociales des microbes et plus largement dans les études multispécifiques, de « tournant microbien ». Après en avoir rappelé la définition, ainsi que celles de notions qui lui sont associées, cette introduction les discute en les resituant au sein de traditions négligées des sciences naturelles et d’une plus vaste littérature de sciences sociales. Ceci permet d’une part de remobiliser une variété de récits et d’approches des relations humains/microbes qui précède ce prétendu tournant, d’autre part de souligner des points de vigilance quant aux promesses qui l’accompagnent. Relativiser la nouveauté et les promesses de ce « tournant » ne vise pas à disqualifier cette notion, mais à la resituer au sein d’infrastructures de pratiques et de savoirs plus larges, afin d’en proposer une reprise attentive aux conditions et conséquences politiques de ce tournant. This issue of the Revue d'Anthropologie des Connaissances questions and puts into perspective the notion of a "microbial turn," which has appeared recently in the microbial social sciences field and more broadly in multispecies studies. After reiterating their definition and the definition of some associated notions, this introduction discusses them by contextualizing them within certain neglected traditions of the natural sciences and of a broader literature in the social sciences. This allows the authors to reengage on the one hand with a variety of narratives and approaches regarding human/microbe relationships that preceded this so-called turn, and on the other hand to highlight focal points of attention in regard to the promises attached to them. This effort to relativize the novelty and the promises of this "turn" is not intended to disqualify this notion, but to relocate it within infrastructures of wider practices and knowledge, in order to propose that it be taken up whilst giving careful attention to the conditions and political consequences of this turn. Este número de la Revue d’Anthropologie des Connaissances cuestiona y pone en perspectiva la noción de «giro microbiano», surgida recientemente en el ámbito de las ciencias sociales de los microbios y, a nivel más amplio, en los estudios multiespecíficos. Tras recordar su definición y las nociones asociadas, esta introducción las aborda en el contexto de tradiciones olvidadas en las ciencias naturales y de una literatura más amplia de las ciencias sociales. Esto permite, por un lado, movilizar de nuevo una variedad de narrativas y enfoques de las relaciones entre los seres humanos y los microbios que preceden a este llamado «giro» y, por otro lado, subrayar puntos de vigilancia respecto a las promesas que lo acompañan. Relativizar la novedad y las promesas de este «giro» no pretende descalificar este concepto, sino resituarlo dentro de infraestructuras más amplias de prácticas y conocimientos, para proponer una continuación atenta a las condiciones y consecuencias políticas de este giro.

Este número de la Revue d’Anthropologie des Connaissances cuestiona y pone en perspectiva la noción de «giro microbiano», surgida recientemente en el ámbito de las ciencias sociales de los microbios y, a nivel más amplio, en los estudios multiespecíficos. Tras recordar su definición y las nociones asociadas, esta introducción las aborda en el contexto de tradiciones olvidadas en las ciencias naturales y de una literatura más amplia de las ciencias sociales. Esto permite, por un lado, movilizar de nuevo una variedad de narrativas y enfoques de las relaciones entre los seres humanos y los microbios que preceden a este llamado «giro» y, por otro lado, subrayar puntos de vigilancia respecto a las promesas que lo acompañan. Relativizar la novedad y las promesas de este «giro» no pretende descalificar este concepto, sino resituarlo dentro de infraestructuras más amplias de prácticas y conocimientos, para proponer una continuación atenta a las condiciones y consecuencias políticas de este giro. Ce numéro de la Revue d’Anthropologie des Connaissances interroge et met en perspective la notion, récemment apparue dans le champ des sciences sociales des microbes et plus largement dans les études multispécifiques, de « tournant microbien ». Après en avoir rappelé la définition, ainsi que celles de notions qui lui sont associées, cette introduction les discute en les resituant au sein de traditions négligées des sciences naturelles et d’une plus vaste littérature de sciences sociales. Ceci permet d’une part de remobiliser une variété de récits et d’approches des relations humains/microbes qui précède ce prétendu tournant, d’autre part de souligner des points de vigilance quant aux promesses qui l’accompagnent. Relativiser la nouveauté et les promesses de ce « tournant » ne vise pas à disqualifier cette notion, mais à la resituer au sein d’infrastructures de pratiques et de savoirs plus larges, afin d’en proposer une reprise attentive aux conditions et conséquences politiques de ce tournant. This issue of the Revue d'Anthropologie des Connaissances questions and puts into perspective the notion of a "microbial turn," which has appeared recently in the microbial social sciences field and more broadly in multispecies studies. After reiterating their definition and the definition of some associated notions, this introduction discusses them by contextualizing them within certain neglected traditions of the natural sciences and of a broader literature in the social sciences. This allows the authors to reengage on the one hand with a variety of narratives and approaches regarding human/microbe relationships that preceded this so-called turn, and on the other hand to highlight focal points of attention in regard to the promises attached to them. This effort to relativize the novelty and the promises of this "turn" is not intended to disqualify this notion, but to relocate it within infrastructures of wider practices and knowledge, in order to propose that it be taken up whilst giving careful attention to the conditions and political consequences of this turn.