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1.
Appl Microbiol Biotechnol ; 103(20): 8315-8326, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418052

RESUMO

The cell culture medium is an intricate mixture of components which has a tremendous effect on cell growth and recombinant protein production. Regular cell culture medium includes various components, and the decision about which component should be included in the formulation and its optimum amount is an underlying issue in biotechnology industries. Applying conventional techniques to design an optimal medium for the production of a recombinant protein requires meticulous and immense research. Moreover, since the medium formulation for the production of one protein could not be the best choice for another protein, hence, the most suitable media should be determined for each recombinant cell line. Accordingly, medium formulation becomes a laborious, time-consuming, and costly process in biomanufacturing of recombinant protein, and finding alternative strategies for medium development seems to be crucial. In silico modeling is an attractive concept to be adapted for medium formulation due to its high potential to supersede laboratory examinations. By emerging the high-throughput datasets, scientists can disclose the knowledge about the effect of medium components on cell growth and metabolism, and via applying this information through systems biology approach, medium formulation optimization could be accomplished in silico with no need of significant amount of experimentation. This review demonstrates some of the applications of systems biology as a powerful tool for medium development and illustrates the effect of medium optimization with system-level analysis on the production of recombinant proteins in different host cells.


Assuntos
Bactérias/metabolismo , Biotecnologia/métodos , Meios de Cultura/química , Eucariotos/metabolismo , Proteínas Recombinantes/metabolismo , Biologia de Sistemas/métodos , Bactérias/crescimento & desenvolvimento , Eucariotos/crescimento & desenvolvimento
2.
ISME J ; 13(9): 2196-2208, 2019 09.
Artigo em Inglês | MEDLINE | ID: mdl-31053831

RESUMO

Although it is widely recognized that cyanobacterial blooms have substantial influence on the plankton community in general, their correlations with the whole community of eukaryotic plankton at longer time scales remain largely unknown. Here, we investigated the temporal dynamics of eukaryotic plankton communities in two subtropical reservoirs over a 6-year period (2010-2015) following one cyanobacterial biomass cycle-the cyanobacterial bloom (middle 2010), cyanobacteria decrease (late 2010-early 2011), non-bloom (2011-2014), cyanobacteria increase, and second bloom (late 2014-2015). The eukaryotic community succession that strongly correlated with this cyanobacterial biomass cycle was divided into four periods, and each period had distinct characteristics in cyanobacterial biomass and environments in both reservoirs. Integrated co-occurrence networks of eukaryotic plankton based on the whole study period revealed that the cyanobacterial biomass had remarkably high network centralities, and the eukaryotic OTUs that had stronger correlations with the cyanobacterial biomass exhibited higher centralities. The integrated networks were also modularly responded to different eukaryotic succession periods, and therefore correlated with the cyanobacterial biomass cycle. Moreover, sub-networks based on the different eukaryotic succession periods indicated that the eukaryotic co-occurrence patterns were not constant but varied largely associating with the cyanobacterial biomass. Based on these long-term observations, our results reveal that the cyanobacterial biomass cycle created distinct niches between persistent bloom, non-bloom, decrease and increase of cyanobacteria, and therefore associated with distinct eukaryotic plankton patterns. Our results have important implications for understanding how complex aquatic plankton communities respond to cyanobacterial blooms under the changing environments.


Assuntos
Cianobactérias/crescimento & desenvolvimento , Eucariotos/crescimento & desenvolvimento , Plâncton/crescimento & desenvolvimento , Biomassa , Cianobactérias/classificação , Cianobactérias/genética , Cianobactérias/isolamento & purificação , Ecossistema , Eucariotos/classificação , Eucariotos/genética , Eucariotos/isolamento & purificação , Eutrofização , Filogenia , Plâncton/classificação , Plâncton/genética , Plâncton/isolamento & purificação
3.
Microbiome ; 7(1): 33, 2019 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-30813951

RESUMO

BACKGROUND: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons. RESULTS: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions. CONCLUSIONS: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.


Assuntos
Eucariotos/crescimento & desenvolvimento , Fertilizantes/análise , Nitrogênio/efeitos adversos , Bactérias/efeitos dos fármacos , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Produtos Agrícolas/crescimento & desenvolvimento , Eucariotos/efeitos dos fármacos , Eucariotos/isolamento & purificação , Fungos/efeitos dos fármacos , Fungos/crescimento & desenvolvimento , Fungos/isolamento & purificação , Filogenia , Solo/química , Microbiologia do Solo
4.
Environ Pollut ; 244: 314-322, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30343232

RESUMO

Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 µg L-1), medium (10 µg L-1) and high (20 µg L-1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.


Assuntos
Eucariotos/crescimento & desenvolvimento , Processos Heterotróficos/efeitos dos fármacos , Invertebrados/crescimento & desenvolvimento , Processos Fototróficos/efeitos dos fármacos , Plâncton/crescimento & desenvolvimento , Prata/toxicidade , Poluentes Químicos da Água/toxicidade , Animais , Ecossistema , Luz
5.
Mol Ecol Resour ; 19(2): 426-438, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30576077

RESUMO

While in recent years environmental DNA (eDNA) metabarcoding surveys have shown great promise as an alternative monitoring method, the integration into existing marine monitoring programs may be confounded by the dispersal of the eDNA signal. Currents and tidal influences could transport eDNA over great distances, inducing false-positive species detection, leading to inaccurate biodiversity assessments and, ultimately, mismanagement of marine environments. In this study, we determined the ability of eDNA metabarcoding surveys to distinguish localized signals obtained from four marine habitats within a small spatial scale (<5 km) subject to significant tidal and along-shore water flow. Our eDNA metabarcoding survey detected 86 genera, within 77 families and across 11 phyla using three established metabarcoding assays targeting fish (16S rRNA gene), crustacean (16S rRNA gene) and eukaryotic (cytochrome oxidase subunit 1) diversity. Ordination and cluster analyses for both taxonomic and OTU data sets show distinct eDNA signals between the sampled habitats, suggesting dispersal of eDNA among habitats was limited. Individual taxa with strong habitat preferences displayed localized eDNA signals in accordance with their respective habitat, whereas taxa known to be less habitat-specific generated more ubiquitous signals. Our data add to evidence that eDNA metabarcoding surveys in marine environments detect a broad range of taxa that are spatially discrete. Our work also highlights that refinement of assay choice is essential to realize the full potential of eDNA metabarcoding surveys in marine biodiversity monitoring programs.


Assuntos
Organismos Aquáticos/classificação , Biota , Código de Barras de DNA Taxonômico , Ecossistema , Eucariotos/classificação , Metagenômica , Movimentos da Água , Organismos Aquáticos/genética , Organismos Aquáticos/crescimento & desenvolvimento , Análise por Conglomerados , DNA Ribossômico/química , DNA Ribossômico/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Eucariotos/genética , Eucariotos/crescimento & desenvolvimento , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
6.
Environ Microbiol ; 20(10): 3876-3889, 2018 10.
Artigo em Inglês | MEDLINE | ID: mdl-30209866

RESUMO

Protists have fundamental ecological roles in marine environments and their diversity is being increasingly explored, yet little is known about the quantitative importance of specific taxa in these ecosystems. Here we optimized a newly developed automated system of image acquisition and image analysis to enumerate minute uncultured cells of different sizes targeted by fluorescence in situ hybridization. The automated counting routine was highly reproducible, well correlated with manual counts, and was then applied on surface and deep chlorophyll maximum samples from the Malaspina 2010 circumnavigation. The three targeted uncultured taxa (MAST-4, MAST-7 and MAST-1C) were found in virtually all samples from several ocean basins (Atlantic, Indian and Pacific) in fairly constant cell abundances, following typical lognormal distributions. Their global abundances averaged 49, 23 and 7 cells ml-1 , respectively, and altogether the three groups accounted for about 10%-20% of heterotrophic picoeukaryotes. Our innovative high-throughput cell counting routine allows for the first time a direct assessment of the biogeographic distribution of small protists (< 5 µm) and shows the ubiquity in sunlit oceans of three bacterivorous taxa, suggesting their key roles in marine ecosystems.


Assuntos
Eucariotos/classificação , Eucariotos/citologia , Microscopia/métodos , Água do Mar/parasitologia , Automação , Ecossistema , Eucariotos/crescimento & desenvolvimento , Eucariotos/isolamento & purificação , Hibridização in Situ Fluorescente , Microscopia/instrumentação , Oceanos e Mares
7.
FEMS Microbiol Ecol ; 94(10)2018 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-30137302

RESUMO

An assessment of the temperature increase effect on processes within the microbial food web provides a better insight into the carbon transfer and energy flow processes in marine environments in the global warming perspective. Modified laboratory dilution experiments that allow simultaneous estimates of protozoan grazing and viral lysis on picoplankton groups (bacteria, Prochlorococcus, Synechococcus and pico-eukaryotic algae) under in situ and 3°C above in situ temperatures were performed at seasonal scale. Picoplankton mortality due to grazing was generally higher than that caused by viral lysis, especially in the cold months. The largest part of HNF carbon demand was satisfied by grazing on bacteria throughout the year. Although ciliates satisfied their carbon demand predominantly through grazing on HNF and bacteria, the role of autotrophic picoplankton (APP) as their prey increased significantly in the cold months. Bacteria constituted the most important host for viruses throughout the year. However, during the warm months, APP groups were also significant hosts for viral infection. Under the warming condition the amount of picoplankton biomass transferred to protozoan grazers exceeded the lysed biomass, suggesting that global warming could further increase picoplankton carbon flow toward higher trophic levels in the Adriatic Sea.


Assuntos
Ciclo do Carbono , Mudança Climática , Cadeia Alimentar , Microbiologia da Água , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Biomassa , Eucariotos/crescimento & desenvolvimento , Eucariotos/metabolismo , Mar Mediterrâneo , Temperatura , Vírus/metabolismo
8.
Protist ; 169(5): 682-696, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30125803

RESUMO

Two closely related new species of centrohelid heliozoans with unusual morphology were studied with light and electron microscopy. Sequences of the 18S rRNA gene were also obtained and secondary structure of 18S rRNA molecule reconstructed. The cells, covered with inner siliceous plate scales formed colonies. The entire colony was surrounded with a thick layer of external scales. Inner scales were tabulate and had a patternless surface, except for the presence of an axial rib. Outer scales had a boat-like (Yogsothoth knorrus gen. nov., sp. nov.) or pot-like (Yogsothoth carteri sp. nov.) shape with an axial rib and numerous conical papillae on the scale surface. Analysis of 18S rRNA gene sequences robustly placed the new taxa within centrohelids, but not in any existing family. Scaled Yogsothoth represents a genetically divergent closest outgroup of Acanthocystida, branching after the supposedly primary non-scaled Marophrys, and together with acanthocystids, forming the novel taxon Panacanthocystida. Reconstruction of presumptive 18S rRNA secondary structure reveals interspecific differences in expansion segments 7 and 9 of Yogsothoth. Analysis of 18S rRNA secondary structure of other centrohelids allowed identification of length increases characteristic for Panacanthocystida location and reconstruction of 18S rRNA elongation in the course of the evolution of this group.


Assuntos
Eucariotos/genética , Evolução Molecular , Eucariotos/química , Eucariotos/classificação , Eucariotos/crescimento & desenvolvimento , Conformação de Ácido Nucleico , Filogenia , RNA Ribossômico 18S/química , RNA Ribossômico 18S/genética
9.
Environ Microbiol ; 20(8): 3042-3056, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29968383

RESUMO

The unicellular Labyrinthulomycete protists have long been considered to play a significant role in ocean carbon cycling. However, their distribution and biogeochemical function remain poorly understood. We present a large-scale study of their spatiotemporal abundance and diversity in the coastal waters of Bohai Sea using flow cytometry and high-throughput sequencing. These protists display niche preferences and episodic higher biomass than that of bacterioplankton with much phylogenetic diversity (> 4000 OTUs) ever reported. They were ubiquitous with a typical abundance range of 100-1000 cells ml-1 and biomass range of 0.06-574.59 µg C L-1 . The observed spatiotemporal abundance variations support the current 'left-over scavengers' nutritional model and highlight these protists as a significant component of the marine microbial loop. The higher average abundance and phylogenetic diversity in the nearshore compared with those in the offshore reveal their predominant role in the terrigenous matter decomposition. Furthermore, the differential relationship of the protist genera to environmental conditions together with their co-occurrence network suggests their unique substrate preferences and niche partitioning. With few subnetworks and possible keystone species, their network topology indicates community resilience and high connectance level of few operational taxonomic units (OTUs). We demonstrate the significant contribution of these protists to the secondary production and nutrient cycling in the coastal waters. As secondary producers, their role will become more important with increasingly coastal eutrophication.


Assuntos
Eucariotos/classificação , Eucariotos/isolamento & purificação , Água do Mar/parasitologia , Biodiversidade , Biomassa , Eucariotos/genética , Eucariotos/crescimento & desenvolvimento , Oceanos e Mares , Filogenia
10.
FEMS Microbiol Lett ; 365(10)2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29788084

RESUMO

Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2.5 mg m-3 in March, together with a decrease in nutrients; however, nutrients were never depleted. The microbial community composition remained similar throughout both sampling periods; however, microbial abundance and activity changed with Chla levels. An increased biomass of Bacillariophyta, Haptophyceae and Cryptophyceae was observed along with night-grazing activity of Dinophyceae and ciliates (Alveolates). During high Chla conditions, HCO3- uptake rates during daytime incubations increased 5-fold (>2516 nmol C L-1 d-1), and increased photosynthetic transcript numbers that were mainly associated with cryptophytes; meanwhile night time NO3- (>706 nmol N L-1 d-1) and NH4+ (41.7 nmol N L-1 d-1) uptake rates were 2- and 3-fold higher, respectively, due to activity from Alpha-/Gammaproteobacteria and Bacteroidetes (Flavobacteriia). Due to a projected acceleration in climate change in the WAP, this information is valuable for predicting the composition and functional changes in Antarctic microbial communities.


Assuntos
Bactérias/metabolismo , Microbiota , Fitoplâncton/metabolismo , Água do Mar/microbiologia , Regiões Antárticas , Bactérias/classificação , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Ecossistema , Eucariotos/classificação , Eucariotos/genética , Eucariotos/crescimento & desenvolvimento , Eucariotos/metabolismo , Fotossíntese , Fitoplâncton/classificação , Fitoplâncton/genética , Fitoplâncton/crescimento & desenvolvimento , Estações do Ano , Água do Mar/química
11.
Microbiology ; 164(5): 727-739, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29620506

RESUMO

Not long ago, protists were considered one of four eukaryote kingdoms, but recent gene-based phylogenies show that they contribute to all nine eukaryote subdomains. The former kingdoms of animals, plants and fungi are now relegated to lower ranks within subdomains. Most unicellular protists respond to adverse conditions by differentiating into dormant walled cysts. As cysts, they survive long periods of starvation, drought and other environmental threats, only to re-emerge when conditions improve. For protists pathogens, the resilience of their cysts can prevent successful treatment or eradication of the disease. In this context, effort has been directed towards understanding the molecular mechanisms that control encystation. We here firstly summarize the prevalence of encystation across protists and next focus on Amoebozoa, where most of the health-related issues occur. We review current data on processes and genes involved in encystation of the obligate parasite Entamoeba histolytica and the opportunistic pathogen Acanthamoeba. We show how the cAMP-mediated signalling pathway that controls spore and stalk cell encapsulation in Dictyostelium fruiting bodies could be retraced to a stress-induced pathway controlling encystation in solitary Amoebozoa. We highlight the conservation and prevalence of cAMP signalling genes in Amoebozoan genomes and the suprisingly large and varied repertoire of proteins for sensing and processing environmental signals in individual species.


Assuntos
Amebozoários/crescimento & desenvolvimento , AMP Cíclico/metabolismo , Eucariotos/crescimento & desenvolvimento , Encistamento de Parasitas , Transdução de Sinais , Amebozoários/classificação , Proteínas Quinases Dependentes de AMP Cíclico/metabolismo , Encistamento de Parasitas/genética , Filogenia , Proteínas de Protozoários/metabolismo , Esporos de Protozoários/genética , Esporos de Protozoários/crescimento & desenvolvimento , Estresse Fisiológico
12.
Geobiology ; 16(4): 369-377, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29527802

RESUMO

The Cryogenian (~717-636 Ma) is characterized by widespread glaciation and dramatic fluctuations in biogeochemical cycling during the Sturtian and Marinoan glaciations. The Snowball Earth hypothesis posits that during this period, ice-covered oceans of more or less global extent shut down or greatly diminished photosynthesis in the marine realm. However, rather than suffering a catastrophic loss of biodiversity, fossil evidence suggests that major eukaryotic lineages survived and, indeed, the end of the Cryogenian marks the onset of a rapid diversification of eukaryotic life. Persistence of diverse life forms through glaciations is thought to have occurred in supraglacial refugia although the exact nature and full extent of such habitats remain uncertain. We present further evidence for the diversity and characteristics of supraglacial ecosystems on the McMurdo Ice Shelf in Antarctica and suggest that refugia analogous to "dirty ice," that is debris-covered ice shelf ecosystems, potentially provided nutrient-rich and long-lasting biological Cryogenian oases. We also discuss how features of the McMurdo Ice Shelf indicate that mechanisms exist whereby material can be exchanged between the shallow sea floor and the surfaces of ice shelves along continental margins, providing vectors whereby ice shelf ecosystems can nourish underlying seafloor communities and vice versa.


Assuntos
Ecossistema , Eucariotos/crescimento & desenvolvimento , Gelo , Água do Mar , Regiões Antárticas , Fósseis
14.
Environ Microbiol ; 20(3): 1185-1203, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29417706

RESUMO

Although previous studies, mostly based on microscopy analyses of a few groups of protists, have suggested that protists are abundant and diverse in litter and moss habitats, the overall diversity of moss and litter associated protists remains elusive. Here, high-throughput environmental sequencing was used to characterize the diversity and community structure of litter- and moss-associated protists along a gradient of soil drainage and forest primary productivity in a temperate rainforest in British Columbia. We identified 3262 distinct protist OTUs from 36 sites. Protists were strongly structured along the landscape gradient, with a significant increase in alpha diversity from the blanket bog ecosystem to the zonal forest ecosystem. Among all investigated environmental variables, calcium content was the most strongly associated with the community composition of protists, but substrate composition, plant cover and other edaphic factors were also significantly correlated with these communities. Furthermore, a detailed phylogenetic analysis of unicellular opisthokonts identified OTUs covering most lineages, including novel OTUs branching with Discicristoidea, the sister group of Fungi, and with Filasterea, one of the closest unicellular relatives to animals. Altogether, this study provides unprecedented insight into the community composition of moss- and litter-associated protists.


Assuntos
Biodiversidade , Briófitas/parasitologia , Eucariotos/classificação , Eucariotos/isolamento & purificação , Solo/parasitologia , Animais , Ecossistema , Eucariotos/crescimento & desenvolvimento , Resíduos de Alimentos , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Floresta Úmida , Solo/química
15.
J Biol Dyn ; 12(1): 242-270, 2018 12.
Artigo em Inglês | MEDLINE | ID: mdl-29461937

RESUMO

A stochastic control model for finding an ecologically sound, fit-for-purpose dam operation policy to suppress bloom of attached algae in its downstream is presented. A singular exactly solvable and a more realistic regular-singular cases are analysed in terms of a Hamilton-Jacobi-Bellman equation. Regularity and consistency of the value function are analysed and its classical verification theorem is established. Practical implications of the mathematical analysis results are discussed focusing on parameter dependence of the optimal controls. An asymptotic analysis with a numerical computation reveals solution behaviour of the Hamilton-Jacobi-Bellman equation near the origin, namely at the early stage of algae growth.


Assuntos
Eucariotos/crescimento & desenvolvimento , Modelos Biológicos , Rios , Processos Estocásticos , Viscosidade
16.
Environ Microbiol ; 20(3): 1095-1111, 2018 03.
Artigo em Inglês | MEDLINE | ID: mdl-29349913

RESUMO

Over the span of a year, we investigated the interactions between biotic and abiotic factors within the eutrophic Neuse River Estuary (NRE). Through metatranscriptomic sequencing in combination with water quality measurements, we show that there are different metabolic strategies deployed along the NRE. In the upper estuary, taxonomically resolved phytoplankton groups express more transcripts of genes for synthesis of cellular components and carbon metabolism whereas in the lower estuary, transcripts allocated to nutrient metabolism and transport were more highly expressed. Metabolisms for polysaccharide synthesis and transportation were elevated in the lower estuary and could be reflective of unbalanced growth and/or interactions with their surrounding microbial consortia. Our results indicate phytoplankton have high metabolic activity, suggestive of increased growth rates in the upper estuary and display patterns reflective of nutrient limitation in the lower estuary. Among all the environmental parameters varying along the NRE, nitrogen availability is found to be the main driving factor for the observed spatial divergence.


Assuntos
Monitoramento Ambiental , Eutrofização/fisiologia , Regulação da Expressão Gênica/genética , Fitoplâncton/crescimento & desenvolvimento , Fitoplâncton/metabolismo , Estuários , Eucariotos/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Consórcios Microbianos/fisiologia , Nitrogênio/análise , Fitoplâncton/genética , Rios/química , Rios/microbiologia , Estações do Ano
17.
Curr Opin Microbiol ; 43: 108-116, 2018 06.
Artigo em Inglês | MEDLINE | ID: mdl-29331767

RESUMO

Molecular cues from environmental bacteria influence important developmental decisions in diverse marine eukaryotes. Yet, relatively little is understood about the mechanisms underlying these interactions, in part because marine ecosystems are dynamic and complex. With the help of simple model systems, including the choanoflagellate Salpingoeca rosetta, we have begun to uncover the bacterial cues that shape eukaryotic development in the ocean. Here, we review how diverse bacterial cues-from lipids to macromolecules-regulate development in marine eukaryotes. It is becoming clear that there are networks of chemical information circulating in the ocean, with both eukaryotes and bacteria acting as nodes; one eukaryote can precisely respond to cues from several diverse environmental bacteria, and a single environmental bacterium can regulate the development of different eukaryotes.


Assuntos
Bactérias/genética , Eucariotos/genética , Regulação da Expressão Gênica , Organismos Aquáticos/genética , Organismos Aquáticos/crescimento & desenvolvimento , Organismos Aquáticos/fisiologia , Meio Ambiente , Eucariotos/crescimento & desenvolvimento , Eucariotos/fisiologia , Lipídeos/fisiologia , Substâncias Macromoleculares/metabolismo
18.
Eur J Protistol ; 60: 87-101, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28675820

RESUMO

During the last decades, the planktonic cyanobacterium Planktothrix rubescens became a dominant primary producer in many deep pre-alpine lakes. While altered physiochemical conditions due to lake warming seem to favour this cyanobacterial species, its dominance is partly attributed to factors conferring grazing resistance. The rigid structure of the cyanobacterial filaments and toxic secondary metabolites (e.g. microcystins) protect against diverse grazers. Nonetheless, species of the protistan genus Nuclearia (Nucleariidae, Opisthokonta) are able to overcome this grazing protection. Time lapse video documentation served as tool to record slow feeding processes of N. thermophila and N. delicatula. Three different feeding strategies could be distinguished: (i) Phagocytosis of small fragments, (ii) serial break-ups of cyanobacterial cells and (iii) bending and breaking of filaments. While observations revealed mechanical manipulation to be important for the efficient breakdown of P. rubescens filaments, the toxin microcystin had no pronounced negative effects on nucleariid cells. Growth experiments with N. thermophila/N. delicatula and different accompanying bacterial assemblages pointed to a pivotal role of distinct prokaryotic species for toxin degradation and for the growth success of the protists. Thus, the synergistic effect of nucleariids and specific bacteria favours an efficient degradation of P. rubescens along with its toxin.


Assuntos
Cianobactérias/fisiologia , Eucariotos/metabolismo , Eucariotos/citologia , Eucariotos/efeitos dos fármacos , Eucariotos/crescimento & desenvolvimento , Comportamento Alimentar , Microcistinas/farmacologia , Atividade Motora , Imagem com Lapso de Tempo
19.
Microbiologyopen ; 6(4)2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-28318115

RESUMO

Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3-µm prefilter and 0.2-µm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES-5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES-5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free-living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low-salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical "hotspot," which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater-brackish water interface in the fast-flowing Columbia River estuary.


Assuntos
Bactérias/crescimento & desenvolvimento , Bacteriófagos/crescimento & desenvolvimento , Biota , Estuários , Eucariotos/crescimento & desenvolvimento , Microbiologia da Água , Metagenômica
20.
J Eukaryot Microbiol ; 64(2): 153-163, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27432754

RESUMO

The study of cultured strains has a long tradition in protistological research and has greatly contributed to establishing the morphology, taxonomy, and ecology of many protist species. However, cultivation-independent techniques, based on 18S rRNA gene sequences, have demonstrated that natural protistan assemblages mainly consist of hitherto uncultured protist lineages. This mismatch impedes the linkage of environmental diversity data with the biological features of cultured strains. Thus, novel taxa need to be obtained in culture to close this knowledge gap. In this study, traditional cultivation techniques were applied to samples from coastal surface waters and from deep oxygen-depleted waters of the Baltic Sea. Based on 18S rRNA gene sequencing, 126 monoclonal cultures of heterotrophic protists were identified. The majority of the isolated strains were affiliated with already cultured and described taxa, mainly chrysophytes and bodonids. This was likely due to "culturing bias" but also to the eutrophic nature of the Baltic Sea. Nonetheless, ~ 12% of the isolates in our culture collection showed highly divergent 18S rRNA gene sequences compared to those of known organisms and thus may represent novel taxa, either at the species level or at the genus level. Moreover, we also obtained evidence that some of the isolated taxa are ecologically relevant, under certain conditions, in the Baltic Sea.


Assuntos
Eucariotos/classificação , Eucariotos/crescimento & desenvolvimento , Filogenia , Água do Mar/parasitologia , Biodiversidade , Técnicas de Cultura de Células/métodos , DNA de Protozoário/genética , DNA Ribossômico/genética , Eucariotos/genética , Eucariotos/isolamento & purificação , Alemanha , Processos Heterotróficos , Biologia Marinha , Oxigênio/química , RNA de Protozoário/genética , RNA Ribossômico 18S/genética , Água do Mar/química , Análise de Sequência de DNA
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