Involvement of several transcriptional regulators in the differential expression of tfd genes in Cupriavidus necator JMP134

Cupriavidus necator JMP134 has been extensively studied because of its ability to degrade chloroaromatic compounds, including the herbicides 2,4-dichlorophenoxyacetic acid (2,4-D) and 3-chlorobenzoic acid (3-CB), which is achieved through the pJP4-encoded chlorocatechol degradation gene clusters: tfdCIDIEIFI and tfdDIICIIEIIFII. The present work describes a different tfd-genes expression profile depending on whether C. necator cells were induced with 2,4-D or 3-CB. By contrast, in vitro binding assays of the purified transcriptional activator TfdR showed similar binding to both tfd intergenic regions; these results were confirmed by in vivo studies of the expression of transcriptional lacZ fusions for these intergenic regions. Experiments aimed at investigating whether other pJP4 plasmid or chromosomal regulatory proteins could contribute to the differences in the response of both tfd promoters to induction by 2,4-D and 3-CB showed that the transcriptional regulators from the benzoate degradation pathway, CatR1 and CatR2, affected 3-CB- and 2,4-D-related growth capabilities. It was also determined that the ISJP4-interrupted protein TfdT decreased growth on 3-CB. In addition, an ORF with 34% amino acid identity to IclR-type transcriptional regulator members and located near the tfdII gene cluster module was shown to modulate the 2,4-D growth capability. Taken together, these results suggest that tfd transcriptional regulation in C. necator JMP134 is far more complex than previously thought and that it involves proteins from different transcriptional regulator families. [Int Microbiol 2009; 12(2):97-106

Correction to: Detection of the phycotoxin pectenotoxin-2 in waters around King George Island, Antarctica

A correction to this paper has been published: https://doi.org/10.1007/s00300-021-02834-3</jats:p

Detection of the phycotoxin pectenotoxin-2 in waters around King George Island, Antarctica

In order to set a base line for the observation of planktonic community changes due to global change, protistan plankton sampling in combination with phycotoxin measurements and solid phase adsorption toxin tracking (SPATT) was performed in two bays of King George Island (KGI) in January 2013 and 2014. In addition, SPATT sampling was performed in Potter Cove during a one-year period from January 2014 until January 2015. Known toxigenic taxa were not firmly identified in plankton samples but there was microscopical evidence for background level presence of Dinophysis spp. in the area. This was consistent with environmental conditions during the sampling periods, especially strong mixing of the water column and low water temperatures that do not favor dinoflagellate proliferations. Due to the lack of significant abundance of thecate toxigenic dinoflagellate species in microplankton samples, no phycotoxins were found in net tow samples. In contrast, SPATT sampling revealed the presence of dissolved pectenotoxin-2 (PTX-2) and its hydrolyzed form PTX-2 seco acid in both bays and during the entire one-year sampling period. The presence of dissolved PTX in coastal waters of KGI is strong new evidence for the presence of PTX-producing species, i.e., dinoflagellates of the genus Dinophysis in the area. The presence of phycotoxins and their respective producers, even at the low background concentrations found in this study, may be the seed of possible proliferations of these species under changing environmental conditions. Furthermore, phycotoxins can be used as chemotaxonomic markers for a very specific group of plankton thus allowing to track the presence of this group over time.Fil: Krock, Bernd. Alfred Wegener Institut-Helmholtz Zentrum für Polarund Meeresforschung; AlemaniaFil: Schloss, Irene Ruth. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Austral de Investigaciones Científicas; Argentina. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Universidad Nacional de Tierra del Fuego; ArgentinaFil: Trefault, Nicole. Universidad de Santiago de Chile; ChileFil: Tillmann, Urban. Alfred Wegener Institut-Helmholtz Zentrum für Polarund Meeresforschung; AlemaniaFil: Hernando, Marcelo Pablo. Comisión Nacional de Energía Atómica; ArgentinaFil: Deregibus, Dolores. Ministerio de Relaciones Exteriores, Comercio Interno y Culto. Dirección Nacional del Antártico. Instituto Antártico Argentino; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Antoni, Julieta Silvina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Almandoz, Gaston Osvaldo. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo; ArgentinaFil: Hoppenrath, Mona. Alfred Wegener Institut-Helmholtz Zentrum für Polarund Meeresforschung; Alemani

Next Generation Sequencing and mass spectrometry reveal high taxonomic diversity and complex phytoplankton-phycotoxins patterns in Southeastern Pacific fjords

In fjord systems, Harmful Algal Blooms (HABs) not only constitute a serious problem when affecting the wildlife and ecosystems, but also human health and economic activities related to the marine environment. This is mostly due to a broad spectrum of toxic compounds produced by several members of the phytoplankton. Nevertheless, a deep coverage of the taxonomic diversity and composition of phytoplankton species and phycotoxin profiles in HAB prone areas are still lacking and little is known about the relationship between these fundamental elements for fjord ecosystems. In this study, a detailed molecular and microscopic characterization of plankton communities was performed, together with an analysis of the occurrence and spatial patterns of lipophilic toxins in a HAB prone area, located in the Southeastern Pacific fjord region. Microscopy and molecular analyses based on the 18S rRNA gene fragment indicated high diversity and taxonomic homogeneity among stations. Four toxigenic genera were identified: Pseudo-nitzschia, Dinophysis, Prorocentrum, and Alexandrium. In agreement with the detected species, liquid chromatography coupled with mass spectrometry revealed the presence of domoic acid (DA), pectenotoxin-2 (PTX-2), dinophysistoxin-2 (DTX-2), and 13-desmethyl spirolide C (SPX-1). Furthermore, a patchy distribution among DA in different net haul size fractions was found. Our results displayed a complex phytoplankton-phycotoxin pattern and for the first time contribute to the characterization of high-resolution phytoplankton community composition and phycotoxin distribution in fjords of the Southeastern Pacific region

Bacteria Isolated From the Antarctic Sponge Iophon sp. Reveals Mechanisms of Symbiosis in Sporosarcina, Cellulophaga, and Nesterenkonia

Antarctic sponges harbor a diverse range of microorganisms that perform unique metabolic functions for nutrient cycles. Understanding how microorganisms establish functional sponge–microbe interactions in the Antarctic marine ecosystem provides clues about the success of these ancient animals in this realm. Here, we use a culture-dependent approach and genome sequencing to investigate the molecular determinants that promote a dual lifestyle in three bacterial genera Sporosarcina, Cellulophaga, and Nesterenkonia. Phylogenomic analyses showed that four sponge-associated isolates represent putative novel bacterial species within the Sporosarcina and Nesterenkonia genera and that the fifth bacterial isolate corresponds to Cellulophaga algicola. We inferred that isolated sponge-associated bacteria inhabit similarly marine sponges and also seawater. Comparative genomics revealed that these sponge-associated bacteria are enriched in symbiotic lifestyle-related genes. Specific adaptations related to the cold Antarctic environment are features of the bacterial strains isolated here. Furthermore, we showed evidence that the vitamin B5 synthesis-related gene, panE from Nesterenkonia E16_7 and E16_10, was laterally transferred within Actinobacteria members. Together, these findings indicate that the genomes of sponge-associated strains differ from other related genomes based on mechanisms that may contribute to the life in association with sponges and the extreme conditions of the Antarctic environment

Detection of the phycotoxin pectenotoxin-2 in waters around King George Island, Antarctica

In order to set a base line for the observation of planktonic community changes due to global change, protistan plankton sampling in combination with phycotoxin measurements and solid phase adsorption toxin tracking (SPATT) was performed in two bays of King George Island (KGI) in January 2013 and 2014. In addition, SPATT sampling was performed in Potter Cove during a one-year period from January 2014 until January 2015. Known toxigenic taxa were not firmly identified in plankton samples but there was microscopical evidence for background level presence of Dinophysis spp. in the area. This was consistent with environmental conditions during the sampling periods, especially strong mixing of the water column and low water temperatures that do not favor dinoflagellate proliferations. Due to the lack of significant abundance of thecate toxigenic dinoflagellate species in microplankton samples, no phycotoxins were found in net tow samples. In contrast, SPATT sampling revealed the presence of dissolved pectenotoxin-2 (PTX-2) and its hydrolyzed form PTX-2 seco acid in both bays and during the entire one-year sampling period. The presence of dissolved PTX in coastal waters of KGI is strong new evidence for the presence of PTX-producing species, i.e., dinoflagellates of the genus Dinophysis in the area. The presence of phycotoxins and their respective producers, even at the low background concentrations found in this study, may be the seed of possible proliferations of these species under changing environmental conditions. Furthermore, phycotoxins can be used as chemotaxonomic markers for a very specific group of plankton thus allowing to track the presence of this group over time.Este artículo tiene una corrección (ver "Documentos relacionados").Facultad de Ciencias Naturales y Muse

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (&gt;30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world's countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome