Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach

Temperate coniferous forests sustain the highest levels of biomass of all terrestrial ecosystems and belong to the major carbon sinks on Earth. However, the community composition and its functional diversity depending on the habitat have yet to be unveiled. Here, we analyzed the proteomes from litter, plant roots, rhizosphere, and bulk soil in a temperate coniferous forest at two time points to improve the understanding of the interplay between bacterial and eukaryotic communities in different habitats. Our metaproteomic approach yielded a total of 139,127 proteins that allowed to differentiate the contribution of microbial taxa to protein expression as well as the general functionality based on KEGG Orthology in each habitat. The pool of expressed carbohydrate-active enzymes (CAZymes) was dominated by fungal proteins. While CAZymes in roots and litter targeted mostly the structural biopolymers of plant origin such as lignin and cellulose, the majority of CAZymes in bulk and rhizosphere soil targeted oligosaccharides, starch, and glycogen. Proteins involved in nitrogen cycling were mainly of bacterial origin. Most nitrogen cycling proteins in litter and roots participated in ammonium assimilation while those performing nitrification were the most abundant in bulk and rhizosphere soil. Together, our results indicated niche differentiation of the microbial involvement in carbon and nitrogen cycling in a temperate coniferous forest topsoil

Al-Bustān. Las fincas aristocráticas y la construcción de los paisajes periurbanos de al-Ándalus y Sicilia

Navarro Palazón, Julio, editorLa presente publicación se enmarca en el Proyecto I+D+i «Almunias medievales en el Mediterráneo: Historia y conservación de los paisajes culturales periurbanos» (PID2019-111508GB-I00, dirigido por Julio Navarro Palazón), del Ministerio de Ciencia e Innovación. Agencia Estatal de Investigación. Proyectos de I+D+i, de los Programas Estatales de Generación de Conocimiento y fortalecimiento Científico y Tecnológico del Sistema de I+D+i y de I+D+i Orientada a los Retos de la Sociedad, del Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020. Esta obra es también un fruto destacado del trabajo realizado en el marco de la Unidad Asociada de I+D+i Patrimonio Cultural Árabe e Islámico, Consejo Superior de Investigaciones Científicas-Universidad de Granada, a través de la Escuela de Estudios Árabes de Granad

Causes of Transition from Democracy to Totalitarism

Additional file 6: Table S2. Summary of proteins annotated as substrate-binding proteins (SBP) from ATP-binding cassette (ABC) transporters detected in the proteomes of Paenibacillus O199. Annotation was performed with RAST

Environmentally relevant concentrations of silver nanoparticles diminish soil microbial biomass but do not alter enzyme activities or microbial diversity

The increasing use of silver nanoparticles (AgNPs) due to their well-known antimicrobial activity, has led to their accumulation in soil ecosystems. However, the impact of environmental realistic concentrations of AgNPs on the soil microbial community has been scarcely studied. In this work, we have assessed the impact of AgNPs, that mimic real concentrations in nature, on tropical soils cultivated with Coffea arabica under conventional and organic management systems. We evaluated the biomass, extracellular enzyme activities, and diversity of the soil microbial community, in a microcosm experiment as a function of time. After seven days of incubation, we found an increase in microbial biomass in an AgNPs-concentration-independent manner. In contrast, after 60-day-incubation, there was a decrease in Gram+ and actinobacterial biomass, in both soils and all AgNPs concentrations. Soil physico-chemical properties and enzyme activities were not affected overall by AgNPs. Regarding the microbial community composition, only some differences in the relative abundance at phylum and genus level in the fungal community were observed. Our results suggest that environmental concentrations of AgNPs affected microbial biomass but had little impact on microbial diversity and may have little effects on the soil biogeochemical cycles mediated by extracellular enzyme activities.El uso cada vez mayor de nanopartículas de plata (AgNP) debido a su conocida actividad antimicrobiana, ha provocado su acumulación en los ecosistemas del suelo. Sin embargo, el impacto de las concentraciones ambientales realistas de AgNP en la comunidad microbiana del suelo ha sido escasamente estudiado. En este trabajo, hemos evaluado el impacto de los AgNP, que imitan concentraciones reales en la naturaleza, en suelos tropicales cultivados con Coffea arabica bajo sistemas de manejo convencionales y orgánicos. Evaluamos la biomasa, las actividades de las enzimas extracelulares y la diversidad de la comunidad microbiana del suelo, en un experimento de microcosmos en función del tiempo. Después de siete días de incubación, encontramos un aumento en la biomasa microbiana de una manera independiente de la concentración de AgNP. Por el contrario, después de 60 días de incubación, hubo una disminución en la biomasa Gram + y actinobacteriana, tanto en los suelos como en todas las concentraciones de AgNP. Las propiedades físico-químicas del suelo y las actividades enzimáticas no se vieron afectadas en general por los AgNP. Con respecto a la composición de la comunidad microbiana, solo se observaron algunas diferencias en la abundancia relativa a nivel de filo y género en la comunidad fúngica. Nuestros resultados sugieren que las concentraciones ambientales de AgNP afectaron la biomasa microbiana, pero tuvieron poco impacto en la diversidad microbiana y pueden tener pocos efectos en los ciclos biogeoquímicos del suelo mediados por actividades de enzimas extracelulares.Universidad Nacional, Costa RicaInstituto Tecnológico de Costa RicaUniversidad Estatal a Distancia, Costa RicaEscuela de Ciencias BiológicasEscuela de Químic

Microhabitat heterogeneity associated with Vanilla spp. and its influences on the microbial community of leaf litter and soil

Open AccessThe impact of forest microhabitats on physiochemical properties of the soil and that of microbial communities on tropical soils remain poorly understood. To elucidate the effect of tropical forest stand on leaf litter and soil microbial communities, we studied enzyme activities, microbial biomass, and diversity in three distinct microhabitats in terms of plant richness, diameter at breast height (DBH), and physiochemical properties of soil and litter, each associated with a different Vanilla sp. In the soil, positive correlations were found between electrical conductivity (EC) and total organic carbon (TOC) with phosphatase activity, and between nitrogen (N) and water-soluble carbon (WSC) content with urease activity (UA). In the litter, the water content was positively correlated with bacterial and fungal biomass, and N and WSC contents were positively correlated with fungal biomass. Positive correlations were found between plant richness and UA in the soil, plant richness and fungal biomass in the soil and litter, and DBH and fungal biomass in the litter. Amplicon sequencing revealed differences between microhabitats in the relative abundance of some fungal and bacterial taxa and in the bacterial community composition of both litter and soil. Bacterial richness and diversity were different between microhabitats, and, in litter samples, they were negatively correlated with DBH and plant richness, respectively. By contrast, none of the soil and litter physiochemical properties were significantly correlated with microbial diversity. Our results show that significant shifts in enzyme activity, microbial biomass, and diversity in the microhabitats were driven by key abiotic and biotic factors depending on the soil or litter sample type.El impacto de los microhábitats forestales sobre las propiedades fisicoquímicas del suelo y el de las comunidades microbianas en los suelos tropicales sigue siendo poco conocido. Para dilucidar el efecto del rodal del bosque tropical sobre la hojarasca y las comunidades microbianas del suelo, estudiamos las actividades enzimáticas, la biomasa microbiana y la diversidad en tres microhábitats distintos en términos de riqueza de plantas, diámetro a la altura del pecho (DAP) y propiedades fisicoquímicas del suelo y basura, cada uno asociado con una Vanilla sp. En el suelo, se encontraron correlaciones positivas entre la conductividad eléctrica (CE) y el carbono orgánico total (TOC) con la actividad de la fosfatasa, y entre el contenido de nitrógeno (N) y carbono soluble en agua (WSC) con la actividad de la ureasa (UA). En la hojarasca, el contenido de agua se correlacionó positivamente con la biomasa bacteriana y fúngica, y los contenidos de N y WSC se correlacionaron positivamente con la biomasa fúngica. Se encontraron correlaciones positivas entre la riqueza vegetal y la AU en el suelo, la riqueza vegetal y la biomasa fúngica en el suelo y la hojarasca, y el DAP y la biomasa fúngica en la hojarasca. La secuenciación de amplicones reveló diferencias entre microhábitats en la abundancia relativa de algunos taxones de hongos y bacterias y en la composición de la comunidad bacteriana de la hojarasca y el suelo. La riqueza y diversidad de bacterias fueron diferentes entre los microhábitats y, en las muestras de hojarasca, se correlacionaron negativamente con el DAP y la riqueza de plantas, respectivamente. Por el contrario, ninguna de las propiedades fisicoquímicas del suelo y la hojarasca se correlacionó significativamente con la diversidad microbiana. Nuestros resultados muestran que los cambios significativos en la actividad enzimática, la biomasa microbiana y la diversidad en los microhábitats fueron impulsados ​​por factores abióticos y bióticos clave según el tipo de muestra de suelo o hojarasca.Centro Nacional de Alta Tecnología, Costa RicaUniversidad Nacional, Costa RicaAsociación Nacional de Vainilleros Unidos, Costa RicaUniversidad de Murcia, EspañaInstitute of Microbiology of the CAS, República ChecaEscuela de Ciencias BiológicasEscuela de Químic

Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach

Temperate coniferous forests sustain the highest levels of biomass of all terrestrial ecosystems and belong to the major carbon sinks on Earth. However, the community composition and its functional diversity depending on the habitat have yet to be unveiled. Here, we analyzed the proteomes from litter, plant roots, rhizosphere, and bulk soil in a temperate coniferous forest at two time points to improve the understanding of the interplay between bacterial and eukaryotic communities in different habitats. Our metaproteomic approach yielded a total of 139,127 proteins that allowed to differentiate the contribution of microbial taxa to protein expression as well as the general functionality based on KEGG Orthology in each habitat. The pool of expressed carbohydrate-active enzymes (CAZymes) was dominated by fungal proteins. While CAZymes in roots and litter targeted mostly the structural biopolymers of plant origin such as lignin and cellulose, the majority of CAZymes in bulk and rhizosphere soil targeted oligosaccharides, starch, and glycogen. Proteins involved in nitrogen cycling were mainly of bacterial origin. Most nitrogen cycling proteins in litter and roots participated in ammonium assimilation while those performing nitrification were the most abundant in bulk and rhizosphere soil. Together, our results indicated niche differentiation of the microbial involvement in carbon and nitrogen cycling in a temperate coniferous forest topsoil.This article is published as Robert Starke, Rubén López Mondéjar, Zander Rainer Human, Diana Navrátilová, Martina Štursová, Tomáš Větrovský, Heather M. Olson, Daniel J. Orton, Stephen J. Callister, Mary S. Lipton, Adina Howe, Lee Ann McCue, Christa Pennacchio, Igor Grigoriev, and Petr Baldrian. "Niche differentiation of bacteria and fungi in carbon and nitrogen cycling of different habitats in a temperate coniferous forest: A metaproteomic approach." Soil Biology and Biochemistry (2021): 108170. DOI: 10.1016/j.soilbio.2021.108170.</p