A“Dirty” Footprint: Macroinvertebrate diversity in Amazonian Anthropic Soils

International audienceAmazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems. We found 673 morphospecies and, despite similar richness in ADEs (385 spp.) and reference soils (399 spp.), we identified a tenacious pre-Columbian footprint, with 49% of morphospecies found exclusively in ADEs. Termite and total macroinvertebrate abundance were higher in reference soils, while soil fertility and macroinvertebrate activity were higher in the ADEs, and associated with larger earthworm quantities and biomass. We show that ADE habitats have a unique pool of species, but that modern land use of ADEs decreases their populations, diversity, and contributions to soil functioning. These findings support the idea that humans created and sustained high-fertility ecosystems that persist today, altering biodiversity patterns in Amazonia

A "dirty" footprint: macroinvertebrate diversity in Amazonian Anthropic Soils.

Amazonian rainforests, once thought to be pristine wilderness, are increasingly known to have been widely inhabited, modified, and managed prior to European arrival, by human populations with diverse cultural backgrounds. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by pre-Columbian societies with sedentary habits. Much is known about the chemistry of these soils, yet their zoology has been neglected. Hence, we characterized soil fertility, macroinvertebrate communities, and their activity at nine archeological sites in three Amazonian regions in ADEs and adjacent reference soils under native forest (young and old) and agricultural systems

Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots

Submitted by Luciane Willcox ([email protected]) on 2016-10-13T15:09:16Z No. of bitstreams: 1 RNA-seq transcriptional profiling.pdf: 1083112 bytes, checksum: 495932b4bc48644bb23802afc8fea605 (MD5)Approved for entry into archive by Luciane Willcox ([email protected]) on 2016-10-13T15:19:22Z (GMT) No. of bitstreams: 1 RNA-seq transcriptional profiling.pdf: 1083112 bytes, checksum: 495932b4bc48644bb23802afc8fea605 (MD5)Made available in DSpace on 2016-10-13T15:19:22Z (GMT). No. of bitstreams: 1 RNA-seq transcriptional profiling.pdf: 1083112 bytes, checksum: 495932b4bc48644bb23802afc8fea605 (MD5) Previous issue date: 2016-01-22The Brazilian Program of National Science and Technology Institute/INCT for BNFUniversidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, BrasilUniversidade Estadual de Londrina. Departamento de Bioquímica e Biotecnologia, Londrina, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Biologia Celular. Curitiba, PR, Brasil.Instituto Nacional do Câncer. Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Instituto Nacional do Câncer. Coordenação de Pesquisa Clínica. Unidade de Bioinformática. Rio de Janeiro, RJ, Brasil. / Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Genômica Funcional e Bioinformática. Rio de Janeiro, RJ, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Universidade Federal do Paraná. Departamento de Bioquímica e Biologia Molecular. Curitiba, PR, Brasil.Herbaspirillum seropedicae is a diazotrophic and endophytic bacterium that associates with economically important grasses promoting plant growth and increasing productivity. To identify genes related to bacterial ability to colonize plants, wheat seedlings growing hydroponically in Hoagland's medium were inoculated with H. seropedicae and incubated for 3 days. Total mRNA from the bacteria present in the root surface and in the plant medium were purified, depleted from rRNA and used for RNA-seq profiling. RT-qPCR analyses were conducted to confirm regulation of selected genes. Comparison of RNA profile of root attached and planktonic bacteria revealed extensive metabolic adaptations to the epiphytic life style. These adaptations include expression of specific adhesins and cell wall re-modeling to attach to the root. Additionally, the metabolism was adapted to the microxic environment and nitrogen-fixation genes were expressed. Polyhydroxybutyrate (PHB) synthesis was activated, and PHB granules were stored as observed by microscopy. Genes related to plant growth promotion, such as auxin production were expressed. Many ABC transporter genes were regulated in the bacteria attached to the roots. The results provide new insights into the adaptation of H. seropedicae to the interaction with the plant