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1.
Appl Environ Microbiol ; 87(9)2021 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-33674432

RESUMO

Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus, three groups of Synechococcus, photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (µ) for Prochlorococcus, all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45 µ day-1, respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h-1 and 387 ng h-1, depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus, coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs.IMPORTANCE We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down.


Assuntos
Antozoários/fisiologia , Bactérias/crescimento & desenvolvimento , Recifes de Corais , Eucariotos/crescimento & desenvolvimento , Microbiota , Animais , Região do Caribe , Água do Mar/microbiologia , Microbiologia da Água
2.
Nat Commun ; 12(1): 641, 2021 01 28.
Artigo em Inglês | MEDLINE | ID: mdl-33510166

RESUMO

The colonization of land by fungi had a significant impact on the terrestrial ecosystem and biogeochemical cycles on Earth surface systems. Although fungi may have diverged ~1500-900 million years ago (Ma) or even as early as 2400 Ma, it is uncertain when fungi first colonized the land. Here we report pyritized fungus-like microfossils preserved in the basal Ediacaran Doushantuo Formation (~635 Ma) in South China. These micro-organisms colonized and were preserved in cryptic karstic cavities formed via meteoric water dissolution related to deglacial isostatic rebound after the terminal Cryogenian snowball Earth event. They are interpreted as eukaryotes and probable fungi, thus providing direct fossil evidence for the colonization of land by fungi and offering a key constraint on fungal terrestrialization.


Assuntos
Ecossistema , Eucariotos/crescimento & desenvolvimento , Fósseis , Fungos/crescimento & desenvolvimento , Animais , Evolução Biológica , China , Planeta Terra , Fatores de Tempo
3.
NPJ Syst Biol Appl ; 6(1): 14, 2020 05 15.
Artigo em Inglês | MEDLINE | ID: mdl-32415097

RESUMO

Cells can sense changes in their extracellular environment and subsequently adapt their biomass composition. Nutrient abundance defines the capability of the cell to produce biomass components. Under nutrient-limited conditions, resource allocation dramatically shifts to carbon-rich molecules. Here, we used dynamic biomass composition data to predict changes in growth and reaction flux distributions using the available genome-scale metabolic models of five eukaryotic organisms (three heterotrophs and two phototrophs). We identified temporal profiles of metabolic fluxes that indicate long-term trends in pathway and organelle function in response to nitrogen depletion. Surprisingly, our calculations of model sensitivity and biosynthetic cost showed that free energy of biomass metabolites is the main driver of biosynthetic cost and not molecular weight, thus explaining the high costs of arginine and histidine. We demonstrated how metabolic models can accurately predict the complexity of interwoven mechanisms in response to stress over the course of growth.


Assuntos
Eucariotos/crescimento & desenvolvimento , Eucariotos/metabolismo , Nitrogênio/metabolismo , Animais , Bacteroidetes/metabolismo , Biomassa , Células CHO/metabolismo , Carbono/metabolismo , Isótopos de Carbono , Chlorella vulgaris/metabolismo , Cricetulus , Genoma , Saccharomyces cerevisiae/metabolismo , Inanição , Yarrowia/metabolismo
4.
Eur J Protistol ; 73: 125686, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32109646

RESUMO

The life cycle of the centrohelid heliozoan Raphidiophrys heterophryoidea Zlatogursky, 2012 was studied with light and electron microscopy in clonal cultures from the type locality. The alternation of two types of trophozoites, having contrastingly different morphology, was observed. Type 1 trophozoites morphology matched the original description. Type 2 trophozoites tended to form colonies usually of 6-8 individuals, connected with cytoplasmic bridges and their cell size was noticeably bigger, namely 43-45 µm compared to 24.5 µm on average in type 1 trophozoites. Some colonies were forming stalks composed of three or four axopodia covered with scales. Spicules were lacking completely, while plate-scales differed from those of type 1 trophozoites: they had oblong-elliptical shape, larger (5.9-14.1 × 2.4-5.8 µm) size, non-branching septa always reaching scale centre, solid upper plate. The conspecificity of the two trophozoite types was confirmed with the comparison of SSU rDNA gene sequence data. Both types of trophozoites were capable of encystment and excysted individuals always were type 1 trophozoites. A new type of cyst-scales (cup-scales) was described. Transitions between cysts and the two trophozoites types were documented. The diagnosis of R. heterophryoidea was improved accordingly. The possible functions, driving forces, and taxonomic consequences of the polymorphism were discussed.


Assuntos
Eucariotos/classificação , Eucariotos/crescimento & desenvolvimento , Estágios do Ciclo de Vida , Eucariotos/genética , Eucariotos/ultraestrutura , Encistamento de Parasitas/fisiologia , RNA Ribossômico 18S/genética , Especificidade da Espécie , Trofozoítos/fisiologia
5.
Development ; 147(1)2020 01 02.
Artigo em Inglês | MEDLINE | ID: mdl-31898583

RESUMO

Snails, earthworms and flatworms are remarkably different animals, but they all exhibit a very similar mode of early embryogenesis: spiral cleavage. This is one of the most widespread developmental programs in animals, probably ancestral to almost half of the animal phyla, and therefore its study is essential for understanding animal development and evolution. However, our knowledge of spiral cleavage is still in its infancy. Recent technical and conceptual advances, such as the establishment of genome editing and improved phylogenetic resolution, are paving the way for a fresher and deeper look into this fascinating early cleavage mode.


Assuntos
Evolução Biológica , Padronização Corporal , Eucariotos/crescimento & desenvolvimento , Animais , Linhagem da Célula , Desenvolvimento Embrionário , Invertebrados/embriologia , Filogenia
6.
J Microbiol ; 58(4): 268-278, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31989545

RESUMO

We measured the grazing and growth response of the mixotrophic chrysomonad flagellate Poterioochromonas malhamensis on four closely related picocyanobacterial strains isolated from subalpine lakes in central Europe. The picocyanobacteria represented different pigment types (phycoerythrin-rich, PE, and phycocyanin-rich, PC) and phylogenetic clusters. The grazing experiments were conducted with laboratory cultures acclimated to 10 µmol photon/m2/sec (low light, LL) and 100 µmol photon/m2/sec (moderate light, ML), either in the dark or at four different irradiances ranging from low (6 µmol photon/m2/sec) to high (1,500 µmol photon/m2/sec) light intensity. Poterioochromonas malhamensis preferred the larger, green PC-rich picocyanobacteria to the smaller, red PE-rich picocyanobacterial, and heterotrophic bacteria. The feeding and growth rates of P. malhamensis were sensitive to the actual light conditions during the experiments; the flagellate performed relatively better in the dark and at LL conditions than at high light intensity. In summary, our results found strain-specific ingestion and growth rates of the flagellate; an effect of the preculturing conditions, and, unexpectedly, a direct adverse effect of high light levels. We conclude that this flagellate may avoid exposure to high surface light intensities commonly encountered in temperate lakes during the summer.


Assuntos
Eucariotos/crescimento & desenvolvimento , Eucariotos/efeitos da radiação , Lagos/microbiologia , Luz , Adaptação Fisiológica , Cianobactérias , Europa (Continente) , Processos Heterotróficos
7.
Environ Microbiol ; 22(1): 369-380, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31713276

RESUMO

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (TA ) and September (TS ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before TA and the bloom of prokaryotic phytoplankton before TS . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.


Assuntos
Bactérias , Fitoplâncton/classificação , Água do Mar/microbiologia , Alphaproteobacteria/isolamento & purificação , Oceano Atlântico , Bactérias/classificação , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Bacteroidetes/isolamento & purificação , Ecossistema , Eucariotos/classificação , Eucariotos/crescimento & desenvolvimento , Eucariotos/metabolismo , França , Microbiota/fisiologia , Filogenia , Estações do Ano , Espanha
8.
Biomolecules ; 9(11)2019 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-31690058

RESUMO

In the current study, corn steep liquor (CSL) is evaluated as an ideal raw agro-material for efficient lipid and docosahexaenoic acid DHA production by Aurantiochytrium sp. Low CSL level in medium (nitrogen deficiency) stimulated the biosynthesis of lipids and DHA while inhibiting cellular growth. The transcriptomic profiles of the Aurantiochytrium sp. cells are analyzed and compared when cultured under high (H group), normal (N group), and low (L group) levels of CSL in the medium. The discriminated transcriptomic profiles from the three groups indicates that changes in CSL level in medium result in a global change in transcriptome of Aurantiochytrium sp. The overall de novo assembly of cDNA sequence data generated 61,163 unigenes, and 18,129 of them were annotated in at least one database. A total of 5105 differently expressed (DE) genes were found in the N group versus the H group, with 2218 downregulated and 2887 upregulated. A total of 3625 DE genes were found in the N group versus the L group, with 1904 downregulated and 1721 upregulated. The analysis and categorization of the DE genes indicates that the regulation mechanism of CSL involved in the perception and transduction of the limited nitrogen signal, the interactions between the transcription factors (TFs) and multiple downstream genes, and the variations in downstream genes and metabolites, in sequence, are illuminated for the first time in the current study.


Assuntos
Ácidos Docosa-Hexaenoicos/biossíntese , Eucariotos/genética , Eucariotos/metabolismo , Lipídeos/biossíntese , Nitrogênio/metabolismo , Meios de Cultura/química , Meios de Cultura/metabolismo , Eucariotos/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma , Zea mays/metabolismo
9.
Genome Biol Evol ; 11(11): 3159-3178, 2019 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-31589292

RESUMO

Homopolymeric amino acid repeats (AARs) like polyalanine (polyA) and polyglutamine (polyQ) in some developmental proteins (DPs) regulate certain aspects of organismal morphology and behavior, suggesting an evolutionary role for AARs as developmental "tuning knobs." It is still unclear, however, whether these are occasional protein-specific phenomena or hints at the existence of a whole AAR-based regulatory system in DPs. Using novel approaches to trace their functional and evolutionary history, we find quantitative evidence supporting a generalized, combinatorial role of AARs in developmental processes with evolutionary implications. We observe nonrandom AAR distributions and combinations in HOX and other DPs, as well as in their interactomes, defining elements of a proteome-wide combinatorial functional code whereby different AARs and their combinations appear preferentially in proteins involved in the development of specific organs/systems. Such functional associations can be either static or display detectable evolutionary dynamics. These findings suggest that progressive changes in AAR occurrence/combination, by altering embryonic development, may have contributed to taxonomic divergence, leaving detectable traces in the evolutionary history of proteomes. Consistent with this hypothesis, we find that the evolutionary trajectories of the 20 AARs in eukaryotic proteomes are highly interrelated and their individual or compound dynamics can sharply mark taxonomic boundaries, or display clock-like trends, carrying overall a strong phylogenetic signal. These findings provide quantitative evidence and an interpretive framework outlining a combinatorial system of AARs whose compound dynamics mark at the same time DP functions and evolutionary transitions.


Assuntos
Eucariotos/genética , Evolução Molecular , Genes Controladores do Desenvolvimento/genética , Filogenia , Sequências Repetitivas de Aminoácidos/genética , Animais , Eucariotos/crescimento & desenvolvimento , Genes Homeobox , Genoma , Humanos , Proteoma
10.
Sci Rep ; 9(1): 12783, 2019 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-31484981

RESUMO

Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.


Assuntos
Reatores Biológicos , Eucariotos , Células Eucarióticas/metabolismo , RNA Ribossômico 18S , Esgotos/microbiologia , Anaerobiose , Eucariotos/genética , Eucariotos/crescimento & desenvolvimento , RNA Ribossômico 18S/genética , RNA Ribossômico 18S/metabolismo , Análise de Sequência de RNA , Purificação da Água
11.
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
12.
Philos Trans R Soc Lond B Biol Sci ; 374(1778): 20190035, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31203753

RESUMO

Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results also highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.


Assuntos
Eucariotos/crescimento & desenvolvimento , Eucariotos/fisiologia , Tamanho do Genoma , Animais , Tamanho Corporal , Mudança Climática , Ecossistema , Eucariotos/classificação , Eucariotos/genética , Aquecimento Global , Filogenia , Respiração , Termotolerância
13.
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
14.
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
15.
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
16.
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
17.
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
18.
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
19.
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
20.
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
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