Ensambles de arqueas y bacterias en la Zona de Mínimo Oxígeno del ecosistema de surgencia de Chile central determinados mediante biomarcadores orgánicos

Indexación: Web of Science; Scielo.Organic biomarkers were used to investigate the influence of seasonal changes in oxygenation and water chemistry on the distribution of archaea and bacteria in the water column and surface sediments of the continental shelf off central Chile (ca. 36°S), an area influenced by seasonal upwelling and the development of an oxygen minimum zone. We were interested in establishing if occurrence of archaea and bacteria responds to oxygenation and water chemistry for which we analyzed archaeal isoprenoid (i) and bacterial branched (br) glycerol dialkyl glycerol tetraethers (GDGTs). Our results combined with molecular data from a year round observational program at the same sampling site and depths indicatives the occurrence and dominance of the marine pelagic group Thaumarchaeota. Changes in the distribution of iGDGTs might be explained by (i) the presence of archaeal populations in sub-oxic waters, phylogenetically different from those in surface water, (ii) changes in the relative contribution of Euryarchaeota with depth, and (iii) a relationship between Thaumarchaeota and environmental factors other than temperature. Branched GDGTs were more abundant in the upper, oxic layer during the non-upwelling season, may be a result of higher river runoff, whereas their diversity was higher within sub-oxic waters. Our results indicate a vertical segregation of iGDGTs and brGDGTs, with predominance of archaeal biomarkers during the low productivity season.Se utilizaron biomarcadores orgánicos en para investigar la influencia de cambios estacionales en los niveles de oxigenación y la química del agua sobre la distribución de arqueas y bacterias en la columna de agua y los sedimentos superficiales de la plataforma continental frente a Chile central, un área influenciada por surgencia estacional asociada al desarrollo de una zona de mínimo oxígeno. Nuestro interés es establecer si la ocurrencia de arquea y bacteria responde a la oxigenación y química del agua para lo cual analizamos gliceroles dialquil gliceroles tetra-éteres (GDGTs) isoprenoides arqueanos (i) y ramificados bacterianos (r). Nuestros resultados, combinados con datos moleculares de observaciones durante un año en el mismo lugar y profundidades del sitio de estudio indican la presencia y dominancia del grupo arqueano marino- pelágico Thaumarchaeota. Los cambios observados en la distribución de iGDGTs podrían explicarse por (i) la presencia de poblaciones de arqueas marinas en la capa de agua sub-óxica, filogenéticamente diferentes a las de aguas superficiales, (ii) cambio en la contribución relativa de Euryarchaeota con profundidad, y (iii) una relación entre Thaumarchaeota y factores ambientales distintos a la temperatura. Los GDGTs ramificados fueron más abundantes en la capa óxica superior durante el periodo de no-surgencia, tal vez influenciado por la alta descarga de ríos, mientras que su diversidad fue más alta en el agua sub-óxica. Nuestros resultados indican una segregación vertical de los GDGTs isoprenoides y ramificados, con el predominio de biomarcadores arqueanos durante el periodo de baja productividad.http://ref.scielo.org/vq5y7

Archaeal and bacterial assemblages in the Oxygen Minimum Zone of the upwelling ecosystem off Central Chile as determined by organic biomarkers

Organic biomarkers were used to investigate the infl uence of seasonal changes in oxygenation and water chemistry on the distribution of archaea and bacteria in the water column and surface sediments of the continental shelf off central Chile (ca. 36°S), an area infl uenced by seasonal upwelling and the development of an oxygen minimum zone. We were interested in establishing if occurrence of archaea and bacteria responds to oxygenation and water chemistry for which we analyzed archaeal isoprenoid (i) and bacterial branched (br) glycerol dialkyl glycerol tetraethers (GDGTs). Our results combined with molecular data from a year round observational program at the same sampling site and depths indicatives the occurrence and dominance of the marine pelagic group Thaumarchaeota. Changes in the distribution of iGDGTs might be explained by (i) the presence of archaeal populations in sub-oxic waters, phylogenetically different from those in surface water, (ii) changes in the relative contribution of Euryarchaeota with depth, and (iii) a relationship between Thaumarchaeota and environmental factors other than temperature. Branched GDGTs were more abundant in the upper, oxic layer during the non-upwelling season, may be a result of higher river runoff, whereas their diversity was higher within sub-oxic waters. Our results indicate a vertical segregation of iGDGTs and brGDGTs, with predominance of archaeal biomarkers during the low productivity season. KEYWORDS: Glycerol dialkyl glycerol tetraethers (GDGTs); archaea; bacteria; oxygen minimum zone; upwelling; Chil

Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis

Development of a Multiplex PCR Assay for Genotyping the Fish Pathogen Piscirickettsia salmonis Through Comparative Genomics

Piscirickettsia salmonis is a bacterial pathogen that severely impact the aquaculture in several countries as Canada, Scotland, Ireland, Norway, and Chile. It provokes Piscirickettsiosis outbreaks in the marine phase of salmonid farming, resulting in economic losses. The monophyletic genogroup LF-89 and a divergent genogroup EM-90 are responsible for the most severe Piscirickettsiosis outbreaks in Chile. Therefore, the development of methods for quick genotyping of P. salmonis genogroups in field samples is vital for veterinary diagnoses and understanding the population structure of this pathogen. The present study reports the development of a multiplex PCR for genotyping LF-89 and EM-90 genogroups based on comparative genomics of 73 fully sequenced P. salmonis genomes. The results revealed 2,322 sequences shared between 35 LF-89 genomes, 2,280 sequences in the core-genome of 38 EM-90 genomes, and 331 and 534 accessory coding sequences each genogroup, respectively. A total of 1,801 clusters of coding sequences were shared among all tested genomes of P. salmonis (LF-89 and EM-90), with 253 and 291 unique sequences for LF-89 and EM-90 genogroups, respectively. The Multiplex-1 prototype was chosen for reliable genotyping because of differences in annealing temperatures and respective reaction efficiencies. This method also identified the pathogen in field samples infected with LF-89 or EM-90 strains, which is not possible with other methods currently available. Finally, the genome-based multiplex PCR protocol presented in this study is a rapid and affordable alternative to classical sequencing of PCR products and analyzing the length of restriction fragment polymorphisms

Stress Tolerance-Related Genetic Traits of Fish Pathogen Flavobacterium psychrophilum in a Mature Biofilm

Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease and rainbow trout fry syndrome, and hence this bacterium is placed among the most important salmonid pathogens in the freshwater aquaculture industry. Since bacteria in biofilms differ substantially from free-living counterparts, this study sought to find the main differences in gene expression between sessile and planktonic states of F. psychrophilum LM-02-Fp and NCMB1947T, with focus on stress-related changes in gene expression occurring during biofilm formation. To this end, biofilm and planktonic samples were analyzed by RNA sequencing to detect differentially expressed candidate genes (DECGs) between the two growth states, and decreasing the effects of interstrain variation by considering only genes with log2-fold changes ≤ −2 and ≥ 2 at Padj-values ≤ 0.001 as DECGs. Overall, 349 genes accounting for ~15% of total number of genes expressed in transcriptomes of F. psychrophilum LM-02-Fp and NCMB1947T (n = 2327) were DECGs between biofilm and planktonic states. Approximately 83 and 81% of all up- and down-regulated candidate genes in mature biofilms, respectively, were assigned to at least one gene ontology term; these were primarily associated with the molecular function term “catalytic activity.” We detected a potential stress response in mature biofilms, characterized by a generalized down-regulation of DECGs with roles in the protein synthesis machinery (n = 63, primarily ribosomal proteins) and energy conservation (seven ATP synthase subunit genes), as well as an up-regulation of DECGs involved in DNA repair (ruvC, recO, phrB1, smf, and dnaQ) and oxidative stress response (cytochrome C peroxidase, probable peroxiredoxin, and a probable thioredoxin). These results support the idea of a strategic trade-off between growth-related processes and cell homeostasis to preserve biofilm structure and metabolic functioning. In addition, LDH-based cytotoxicity assays and an intraperitoneal challenge model for rainbow trout fry agreed with the transcriptomic evidence that the ability of F. psychrophilum to form biofilms could contribute to the virulence. Finally, the reported changes in gene expression, as induced by the plankton-to-biofilm transition, represent the first transcriptomic guideline to obtain insights into the F. psychrophilum biofilm lifestyle that could help understand the prevalence of this bacterium in aquaculture settings

Living in the oxygen minimum zone: A metabolic perspective Viviendo en la zona de mínimo de oxígeno: Una perspectiva metabólica

Respiration is a key variable to understand the flux of energy and matter in any ecosystem. In fact, ecosystem respiration is a critical component of the carbon cycle and might be important in regulating biosphere response to global climate change. Respiration is the basic process used by the biota to yield energy from the degradation of organic matter for their survival needs, its measurement provides an estimate of the minimum energy needed by the organism. Accordingly, the total respiration of an aquatic community can be equated to the minimum energy needed to maintain its organized living structure and function. Despite its importance, community respiration has been a process scarcely studied in the ocean and only during the 90's has become more relevant. In fact, whereas aerobic metabolism has been scarcely studied in ocean systems, anaerobic metabolism, especially at the community level of organization, has been largely neglected.<br>La respiración es la variable clave para comprender el flujo de energía y materia en cualquier ecosistema. De hecho, la respiración del ecosistema es un componente critico del ciclo del carbono y podría ser importante en la regulación de la respuesta de la biosfera al cambio climático. La respiración es el proceso básico usado por la biota en la obtención de energía de la degradación de la materia orgánica para satisfacer sus necesidades de supervivencia; su medición entrega un estimado de la cantidad mínima de energía que necesita el organismo. De acuerdo con esto, la respiración total de la comunidad acuática puede ser igualada a la energía mínima que necesita para mantener su estructura vital y su funcionamiento. A pesar de su importancia, la respiración comunitaria es un proceso escasamente estudiado en el océano y solo a partir de los 90's ha pasado a ser relevante. De hecho, mientras el metabolismo aeróbico ha sido escasamente estudiado en los sistemas oceánicos, el metabolismo anaeróbico, especialmente al nivel de organización de la comunidad, ha sido mayoritariamente descuidado

DataSheet_1_Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm.pdf

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.</p

DataSheet_2_Collective behavior and virulence arsenal of the fish pathogen Piscirickettsia salmonis in the biofilm realm.pdf

Piscirickettsiosis is a fish disease caused by the Gram-negative bacterium Piscirickettsia salmonis. This disease has a high socio-economic impact on the Chilean salmonid aquaculture industry. The bacterium has a cryptic character in the environment and their main reservoirs are yet unknown. Bacterial biofilms represent a ubiquitous mechanism of cell persistence in diverse natural environments and a risk factor for the pathogenesis of several infectious diseases, but their microbiological significance for waterborne veterinary diseases, including piscirickettsiosis, have seldom been evaluated. This study analyzed the in vitro biofilm behavior of P. salmonis LF-89T (genogroup LF-89) and CA5 (genogroup EM-90) using a multi-method approach and elucidated the potential arsenal of virulence of the P. salmonis LF-89T type strain in its biofilm state. P. salmonis exhibited a quick kinetics of biofilm formation that followed a multi-step and highly strain-dependent process. There were no major differences in enzymatic profiles or significant differences in cytotoxicity (as tested on the Chinook salmon embryo cell line) between biofilm-derived bacteria and planktonic equivalents. The potential arsenal of virulence of P. salmonis LF-89T in biofilms, as determined by whole-transcriptome sequencing and differential gene expression analysis, consisted of genes involved in cell adhesion, polysaccharide biosynthesis, transcriptional regulation, and gene mobility, among others. Importantly, the global gene expression profiles of P. salmonis LF-89T were not enriched with virulence-related genes upregulated in biofilm development stages at 24 and 48 h. An enrichment in virulence-related genes exclusively expressed in biofilms was also undetected. These results indicate that early and mature biofilm development stages of P. salmonis LF-89T were transcriptionally no more virulent than their planktonic counterparts, which was supported by cytotoxic trials, which, in turn, revealed that both modes of growth induced important and very similar levels of cytotoxicity on the salmon cell line. Our results suggest that the aforementioned biofilm development stages do not represent hot spots of virulence compared with planktonic counterparts. This study provides the first transcriptomic catalogue to select specific genes that could be useful to prevent or control the (in vitro and/or in vivo) adherence and/or biofilm formation by P. salmonis and gain further insights into piscirickettsiosis pathogenesis.</p