Comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea

Background Metal sulfide mineral dissolution during bioleaching and acid mine drainage (AMD) formation creates an environment that is inhospitable to most life. Despite dominance by a small number of bacteria, AMD microbial biofilm communities contain a notable variety of coexisting and closely related Euryarchaea, most of which have defied cultivation efforts. For this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring AMD archaea. Our analyses targeted members of the Thermoplasmatales and related archaea. These results greatly expand genomic information available for this archaeal order. Results We reconstructed near-complete genomes for uncultivated, relatively low abundance organisms A-, E-, and Gplasma, members of Thermoplasmatales order, and for a novel organism, Iplasma. Genomic analyses of these organisms, as well as Ferroplasma type I and II, reveal that all are facultative aerobic heterotrophs with the ability to use many of the same carbon substrates, including methanol. Most of the genomes share genes for toxic metal resistance and surface-layer production. Only Aplasma and Eplasma have a full suite of flagellar genes whereas all but the Ferroplasma spp. have genes for pili production. Cryogenic-electron microscopy (cryo-EM) and tomography (cryo-ET) strengthen these metagenomics-based ultrastructural predictions. Notably, only Aplasma, Gplasma and the Ferroplasma spp. have predicted iron oxidation genes and Eplasma and Iplasma lack most genes for cobalamin, valine, (iso)leucine and histidine synthesis. Conclusion The Thermoplasmatales AMD archaea share a large number of metabolic capabilities. All of the uncultivated organisms studied here (A-, E-, G-, and Iplasma) are metabolically very similar to characterized Ferroplasma spp., differentiating themselves mainly in their genetic capabilities for biosynthesis, motility, and possibly iron oxidation. These results indicate that subtle, but important genomic differences, coupled with unknown differences in gene expression, distinguish these organisms enough to allow for co-existence. Overall this study reveals shared features of organisms from the Thermoplasmatales lineage and provides new insights into the functioning of AMD communities.United States. Dept. of Energy. Genomics:GTL (Grant DE-FG02-05ER64134)National Science Foundation (U.S.). Graduate Research Fellowshi

Ilex paraguariensis productivity cultivated according light availability

Yerba mate (Ilex paraguariensis) is one of the main income crops in North Eastern Argentina, and is cultivated under traditional open-pit management. Very little information is known about the interaction between tree species and yerba mate. On the hypothesis that shade could affect yerba mate yield and quality, in 2010 two trials have been installed: Trial 1, consociation with tree species and trial 2, interaction under different degrees of artificial shade. In trial 1, up to age seven (7), the productivity of yerba mate has not decreased. In trial 2, the performance is maintained under the different artificial shade levels studied.EEA MontecarloFil: Munaretto, Néstor. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: Barth, Sara Regina. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: Fassola, Hugo Enrique. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: Colcombet, Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: González, Paola. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; ArgentinaFil: Comolli, Luis. Empresa El Rocío S.A.; ArgentinaFil: Schegg, Esteban. Profesional independiente; ArgentinaFil: Loto, Mauro. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Montecarlo; Argentin

Parámetros Productivos de dos Especies de Peces Autóctonos (Piaractus mesopotamicus y Prochilodus lineatus) en un Sistema Acuapónico con Lechuga (Lactuca sativa sp)

Se analizó el comportamiento productivo de dos especies de peces autóctonos bajo un sistema intensivo de producción acuapónica. El sistema contó con cuatro módulos, dos para Pacú: M2 y M3 y dos para Sábalo: M1 y M4. Cada módulo estaba constituido por un tanque de 1000 l para los peces, un tanque sobre elevado de 200 l, que recibía el agua del tanque de peces y un biofiltro de 15 l que drenaba en los sistemas hidropónicos, los cuales tenían una superficie de 4 m2 por módulo y un flujo de agua en el sistema de 2 l/minuto. Los parámetros de calidad de agua (oxígeno, pH, temperatura y conductividad eléctrica) se mantuvieron dentro de valores aceptables para la cría de los peces y para el crecimiento de la lechuga. En la serie nitrogenada (nitrito, nitrato, amonio, amoníaco) se observaron variaciones en los diferentes módulos, sin llegar a valores críticos. Respecto a los índices productivos de los peces, se obtuvo un mejor desempeño en Pacú, obteniéndose después de 37 días de cultivo una biomasa de 6.900 y 6.930 g para los módulos 2 y 3 de Pacú y 4.780 y 5.090g para los módulos 2 y 4 de Sábalo, respectivamente. Para la lechuga, la biomasa total fue de 7.482, 4.872, 8.584 y 10.672 g para los módulos 1, 2, 3 y 4, respectivamente. Los resultados indican que el Pacú es una especie de pez alternativa para la producción de acuaponía

Mariprofundus ferrooxydans PV-1 the First Genome of a Marine Fe(II) Oxidizing Zetaproteobacterium

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 6 (2011): e25386, doi:10.1371/journal.pone.0025386.Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO2, carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.Funding has been provided by the NSF Microbial Observatories Program (KJE, DE), NSF’s Science and Technology Program, by the Gordon and Betty Moore Foundation (KJE), the College of Letters, Arts, and Sciences at the University of Southern California (KJE), and by the NASA Astrobiology Institute (KJE, DE). Advanced Light Source analyses at the Lawrence Berkeley National Lab are supported by the Office of Science, Basic Energy Sciences, Division of Materials Science of the United States Department of Energy (DE-AC02-05CH11231)

Innovations for Sustainability: Pathways to an efficient and post-pandemic future

3rd Report prepared by The World in 2050 initiativ