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1.
Nat Commun ; 11(1): 3831, 2020 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-32737305

RESUMO

Long-term time series have provided evidence that anthropogenic pressures can threaten lakes. Yet it remains unclear how and the extent to which lake biodiversity has changed during the Anthropocene, in particular for microbes. Here, we used DNA preserved in sediments to compare modern micro-eukaryotic communities with those from the end of the 19th century, i.e., before acceleration of the human imprint on ecosystems. Our results obtained for 48 lakes indicate drastic changes in the composition of microbial communities, coupled with a homogenization of their diversity between lakes. Remote high elevation lakes were globally less impacted than lowland lakes affected by local human activity. All functional groups (micro-algae, parasites, saprotrophs and consumers) underwent significant changes in diversity. However, we show that the effects of anthropogenic changes have benefited in particular phototrophic and mixotrophic species, which is consistent with the hypothesis of a global increase of primary productivity in lakes.


Assuntos
DNA/genética , Eucariotos/genética , Sedimentos Geológicos/análise , Lagos/análise , Alveolados/classificação , Alveolados/genética , Alveolados/isolamento & purificação , Biodiversidade , Evolução Biológica , Ecossistema , Eucariotos/classificação , Eucariotos/isolamento & purificação , História do Século XIX , História do Século XX , História do Século XXI , Atividades Humanas/história , Humanos , Microalgas/classificação , Microalgas/genética , Microalgas/isolamento & purificação , Microbiota/genética , Processos Fototróficos/fisiologia , Rhizaria/classificação , Rhizaria/genética , Rhizaria/isolamento & purificação , Estramenópilas/classificação , Estramenópilas/genética , Estramenópilas/isolamento & purificação
2.
Science ; 369(6499)2020 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-32631870

RESUMO

Microbial communities are essential to fundamental processes on Earth. Underlying the compositions and functions of these communities are nutritional interdependencies among individual species. One class of nutrients, cobamides (the family of enzyme cofactors that includes vitamin B12), is widely used for a variety of microbial metabolic functions, but these structurally diverse cofactors are synthesized by only a subset of bacteria and archaea. Advances at different scales of study-from individual isolates, to synthetic consortia, to complex communities-have led to an improved understanding of cobamide sharing. Here, we discuss how cobamides affect microbes at each of these three scales and how integrating different approaches leads to a more complete understanding of microbial interactions.


Assuntos
Cobamidas/metabolismo , Meio Ambiente , Interações Microbianas , Microbiota , Complexo Vitamínico B/metabolismo , Animais , Archaea/metabolismo , Bactérias/metabolismo , Cobamidas/química , Planeta Terra , Eucariotos/metabolismo , Modelos Biológicos , Complexo Vitamínico B/química
3.
PLoS Comput Biol ; 16(7): e1007553, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32697802

RESUMO

Phylogenetic profiling is a computational method to predict genes involved in the same biological process by identifying protein families which tend to be jointly lost or retained across the tree of life. Phylogenetic profiling has customarily been more widely used with prokaryotes than eukaryotes, because the method is thought to require many diverse genomes. There are now many eukaryotic genomes available, but these are considerably larger, and typical phylogenetic profiling methods require at least quadratic time as a function of the number of genes. We introduce a fast, scalable phylogenetic profiling approach entitled HogProf, which leverages hierarchical orthologous groups for the construction of large profiles and locality-sensitive hashing for efficient retrieval of similar profiles. We show that the approach outperforms Enhanced Phylogenetic Tree, a phylogeny-based method, and use the tool to reconstruct networks and query for interactors of the kinetochore complex as well as conserved proteins involved in sexual reproduction: Hap2, Spo11 and Gex1. HogProf enables large-scale phylogenetic profiling across the three domains of life, and will be useful to predict biological pathways among the hundreds of thousands of eukaryotic species that will become available in the coming few years. HogProf is available at https://github.com/DessimozLab/HogProf.


Assuntos
Biologia Computacional/métodos , Eucariotos , Filogenia , Reprodução/genética , Análise por Conglomerados , Eucariotos/classificação , Eucariotos/genética , Cinetocoros/metabolismo , Modelos Estatísticos
4.
Nat Commun ; 11(1): 3690, 2020 07 23.
Artigo em Inglês | MEDLINE | ID: mdl-32704140

RESUMO

Mechanosensitive ion channels transduce physical force into electrochemical signaling that underlies an array of fundamental physiological processes, including hearing, touch, proprioception, osmoregulation, and morphogenesis. The mechanosensitive channels of small conductance (MscS) constitute a remarkably diverse superfamily of channels critical for management of osmotic pressure. Here, we present cryo-electron microscopy structures of a MscS homolog from Arabidopsis thaliana, MSL1, presumably in both the closed and open states. The heptameric MSL1 channel contains an unusual bowl-shaped transmembrane region, which is reminiscent of the evolutionarily and architecturally unrelated mechanosensitive Piezo channels. Upon channel opening, the curved transmembrane domain of MSL1 flattens and expands. Our structures, in combination with functional analyses, delineate a structural mechanism by which mechanosensitive channels open under increased membrane tension. Further, the shared structural feature between unrelated channels suggests the possibility of a unified mechanical gating mechanism stemming from membrane deformation induced by a non-planar transmembrane domain.


Assuntos
Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Eucariotos/metabolismo , Ativação do Canal Iônico , Mecanotransdução Celular , Proteínas de Arabidopsis/ultraestrutura , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Canais Iônicos/química , Canais Iônicos/metabolismo , Modelos Moleculares , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Domínios Proteicos , Estrutura Secundária de Proteína
5.
PLoS Genet ; 16(7): e1008964, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32716939

RESUMO

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.


Assuntos
Arabidopsis/genética , Cromatina/genética , Evolução Molecular , Histonas/genética , Arabidopsis/classificação , Eucariotos , Genoma de Planta/genética , Histonas/classificação , Família Multigênica/genética
6.
Eur J Protistol ; 75: 125721, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32575029

RESUMO

The dark ocean and the underlying deep seafloor together represent the largest environment on this planet, comprising about 80% of the oceanic volume and covering more than two-thirds of the Earth's surface, as well as hosting a major part of the total biosphere. Emerging evidence suggests that these vast pelagic and benthic habitats play a major role in ocean biogeochemistry and represent an "untapped reservoir" of high genetic and metabolic microbial diversity. Due to its huge volume, the water column of the dark ocean is the largest reservoir of organic carbon in the biosphere and likely plays a major role in the global carbon budget. The dark ocean and the seafloor beneath it are also home to a largely enigmatic food web comprising little-known and sometimes spectacular organisms, mainly prokaryotes and protists. This review considers the globally important role of pelagic and benthic protists across all protistan size classes in the deep-sea realm, with a focus on their taxonomy, diversity, and physiological properties, including their role in deep microbial food webs. We argue that, given the important contribution that protists must make to deep-sea biodiversity and ecosystem processes, they should not be overlooked in biological studies of the deep ocean.


Assuntos
Organismos Aquáticos/classificação , Eucariotos/classificação , Foraminíferos/classificação , Animais , Organismos Aquáticos/fisiologia , Eucariotos/fisiologia , Foraminíferos/fisiologia , Oceanos e Mares
7.
Eur J Protistol ; 75: 125720, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32569992

RESUMO

For hundreds of years, mankind has benefited from the natural metabolic processes of microorganisms to obtain basic products such as fermented foods and alcoholic beverages. More recently, microorganisms have been exploited for the production of antibiotics, vitamins and enzymes to be used in medicine and chemical industries. Additionally, several modern drugs, including those for cancer therapy, are natural products or their derivatives. Protists are a still underexplored source of natural products potentially of interest for biotechnological and biomedical applications. This paper focuses on some examples of bioactive molecules from protists and associated bacteria and their possible use in biotechnology.


Assuntos
Produtos Biológicos/química , Biotecnologia/tendências , Eucariotos/química , Animais
8.
PLoS One ; 15(6): e0234918, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32579605

RESUMO

ZapE/Afg1 is a component of the inner cell membrane of some eubacteria and the inner mitochondrial membrane of eukaryotes. This protein is involved in FtsZ-dependent division of eubacteria. In the yeast and human mitochondrion, ZapE/Afg1 likely interacts with Oxa1 and facilitates the degradation of mitochondrion-encoded subunits of respiratory complexes. Furthermore, the depletion of ZapE increases resistance to apoptosis, decreases oxidative stress tolerance, and impacts mitochondrial protein homeostasis. It remains unclear whether ZapE is a multifunctional protein, or whether some of the described effects are just secondary phenotypes. Here, we have analyzed the functions of ZapE in Trypanosoma brucei, a parasitic protist, and an important model organism. Using a newly developed proximity-dependent biotinylation approach (BioID2), we have identified the inner mitochondrial membrane insertase Oxa1 among three putative interacting partners of ZapE, which is present in two paralogs. RNAi-mediated depletion of both ZapE paralogs likely affected the function of respiratory complexes I and IV. Consistently, we show that the distribution of mitochondrial ZapE is restricted only to organisms with Oxa1, respiratory complexes, and a mitochondrial genome. We propose that the evolutionarily conserved interaction of ZapE with Oxa1, which is required for proper insertion of many inner mitochondrial membrane proteins, is behind the multifaceted phenotype caused by the ablation of ZapE.


Assuntos
Deleção de Genes , Proteínas de Protozoários/metabolismo , Trypanosoma brucei brucei/metabolismo , Biotinilação , Regulação para Baixo , Complexo I de Transporte de Elétrons/metabolismo , Complexo IV da Cadeia de Transporte de Elétrons/metabolismo , Eucariotos/genética , Genoma Mitocondrial , Mitocôndrias/metabolismo , Proteínas Mitocondriais/metabolismo , Fenótipo , Filogenia , Ligação Proteica
9.
PLoS One ; 15(6): e0233921, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32569285

RESUMO

In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak of Miracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.


Assuntos
Eucariotos/classificação , Microbiota , Fitoplâncton/classificação , Código de Barras de DNA Taxonômico , Eucariotos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Mar do Norte , Filogenia , Fitoplâncton/genética , Fitoplâncton/crescimento & desenvolvimento , RNA Ribossômico 18S/genética , Estações do Ano , Água do Mar
10.
Biosens Bioelectron ; 159: 112214, 2020 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-32364936

RESUMO

Recent advances in electrochemical biosensors for pathogen detection are reviewed. Electrochemical biosensors for pathogen detection are broadly reviewed in terms of transduction elements, biorecognition elements, electrochemical techniques, and biosensor performance. Transduction elements are discussed in terms of electrode material and form factor. Biorecognition elements for pathogen detection, including antibodies, aptamers, and imprinted polymers, are discussed in terms of availability, production, and immobilization approach. Emerging areas of electrochemical biosensor design are reviewed, including electrode modification and transducer integration. Measurement formats for pathogen detection are classified in terms of sample preparation and secondary binding steps. Applications of electrochemical biosensors for the detection of pathogens in food and water safety, medical diagnostics, environmental monitoring, and bio-threat applications are highlighted. Future directions and challenges of electrochemical biosensors for pathogen detection are discussed, including wearable and conformal biosensors, detection of plant pathogens, multiplexed detection, reusable biosensors for process monitoring applications, and low-cost, disposable biosensors.


Assuntos
Bactérias/isolamento & purificação , Técnicas Biossensoriais/instrumentação , Técnicas Eletroquímicas , Eucariotos/isolamento & purificação , Técnicas Microbiológicas/instrumentação , Vírus/isolamento & purificação , Animais , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Eletrodos , Humanos , Técnicas Microbiológicas/normas , Técnicas Microbiológicas/tendências , Pandemias , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia
11.
Biol Res ; 53(1): 24, 2020 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-32471519

RESUMO

BACKGROUND: BMPR-1B is part of the transforming growth factor ß super family and plays a pivotal role in ewe litter size. Functional loss of exon-8 mutations in the BMPR-1B gene (namely the FecB gene) can increase both the ewe ovulation rate and litter size. RESULTS: This study constructed a eukaryotic expression system, prepared a monoclonal antibody, and characterized BMPR-1B/FecB protein-protein interactions (PPIs). Using Co-immunoprecipitation coupled to mass spectrometry (Co-IP/MS), 23 proteins were identified that specifically interact with FecB in ovary extracts of ewes. Bioinformatics analysis of selected PPIs demonstrated that FecB associated with several other BMPs, primarily via signal transduction in the ovary. FecB and its associated interaction proteins enriched the reproduction process via BMP2 and BMP4 pathways. Signal transduction was identified via Smads proteins and TGF-beta signaling pathway by analyzing the biological processes and pathways. Moreover, other target proteins (GDF5, GDF9, RhoD, and HSP 10) that interact with FecB and that are related to ovulation and litter size in ewes were identified. CONCLUSIONS: In summary, this research identified a novel pathway and insight to explore the PPi network of BMPR-1B.


Assuntos
Receptores de Proteínas Morfogenéticas Ósseas Tipo I/genética , Eucariotos/genética , Ovário/metabolismo , Mapas de Interação de Proteínas/genética , Animais , Receptores de Proteínas Morfogenéticas Ósseas Tipo I/metabolismo , Biologia Computacional , Eucariotos/metabolismo , Feminino , Genótipo , Espectrometria de Massas , Mutação , Reação em Cadeia da Polimerase , Polimorfismo de Fragmento de Restrição , Ovinos , Transdução de Sinais
12.
13.
PLoS One ; 15(4): e0232046, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32352996

RESUMO

Advancements in the field of synthetic biology have been possible due to the development of genetic tools that are able to regulate gene expression. However, the current toolbox of gene regulatory tools for eukaryotic systems have been outpaced by those developed for simple, single-celled systems. Here, we engineered a set of gene regulatory tools by combining self-cleaving ribozymes with various upstream competing sequences that were designed to disrupt ribozyme self-cleavage. As a proof-of-concept, we were able to modulate GFP expression in mammalian cells, and then showed the feasibility of these tools in Drosophila embryos. For each system, the fold-reduction of gene expression was influenced by the location of the self-cleaving ribozyme/upstream competing sequence (i.e. 5' vs. 3' untranslated region) and the competing sequence used. Together, this work provides a set of genetic tools that can be used to tune gene expression across various eukaryotic systems.


Assuntos
Engenharia Genética/métodos , RNA Catalítico/fisiologia , Biologia Sintética/métodos , Animais , Drosophila/genética , Eucariotos/genética , Eucariotos/metabolismo , Células Eucarióticas/metabolismo , Expressão Gênica/genética , Expressão Gênica/fisiologia , Regulação da Expressão Gênica/genética , Regulação da Expressão Gênica/fisiologia , Conformação de Ácido Nucleico , Estudo de Prova de Conceito , RNA Catalítico/genética , RNA Mensageiro/metabolismo
14.
Parasitol Res ; 119(7): 2005-2023, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32394001

RESUMO

The focus of this review is a group of structures/organelles collectively known as extracellular vesicles (EVs) that are secreted by most, if not all, cells, varying from mammalian cells to protozoa and even bacteria. They vary in size: some are small (100-200 nm) and others are larger (> 200 nm). In protozoa, however, most of them are small or medium in size (200-400 nm). These include vesicles from different origins. We briefly review the biogenesis of this distinct group that includes (a) exosome, which originates from the multivesicular bodies, an important component of the endocytic pathway; (b) ectosome, formed from a budding process that takes place in the plasma membrane of the cells; (c) vesicles released from the cell surface following a process of patching and capping of ligand/receptor complexes; (d) other processes where tubules secreted by the parasite subsequently originate exosome-like structures. Here, special emphasis is given to EVs secreted by parasitic protozoa such as Leishmania, Trypanosoma, Plasmodium, Toxoplasma, Cryptosporidium, Trichomonas, and Giardia. Most of them have been characterized as exosomes that were isolated using several approaches and characterized by electron microscopy, proteomic analysis, and RNA sequencing. The results obtained show clearly that they present several proteins and different types of RNAs. From the functional point of view, it is now clear that the secreted exosomes can be incorporated by the parasite itself as well as by mammalian cells with which they interact. As a consequence, there is interference both with the parasite (induction of differentiation, changes in infectivity, etc.) and with the host cell. Therefore, the EVs constitute a new system of transference of signals among cells. On the other hand, there are suggestions that exosomes may constitute potential biotechnology tools and are important players of what has been designated as nanobiotechnology. They may constitute an important delivery system for gene therapy and molecular-displaying cell regulation capabilities when incorporated into other cells and even by interfering with the exosomal membrane during its biogenesis, targeting the vesicles via specific ligands to different cell types. These vesicles may reach the bloodstream, overflow through intercellular junctions, and even pass through the central nervous system blood barrier. There is evidence that it is possible to interfere with the composition of the exosomes by interfering with multivesicular body biogenesis.


Assuntos
Membrana Celular/metabolismo , Eucariotos/metabolismo , Vesículas Extracelulares/metabolismo , Interações Hospedeiro-Parasita/fisiologia , Proteínas de Protozoários/metabolismo , Animais , Transporte Biológico , Exossomos/metabolismo , Vesículas Extracelulares/fisiologia , Humanos , Microscopia Eletrônica , Proteômica
15.
Nucleic Acids Res ; 48(12): 6685-6698, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32442316

RESUMO

Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.


Assuntos
Elementos de DNA Transponíveis/genética , Genoma/genética , RNA Polimerase II/genética , Transcrição Genética , Animais , Cromatina/genética , Drosophila melanogaster/genética , Eucariotos/genética , Regulação da Expressão Gênica/genética , Especificidade de Órgãos/genética , Oryza/genética
16.
BMC Bioinformatics ; 21(1): 220, 2020 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-32471343

RESUMO

BACKGROUND: The first step in understanding ecological community diversity and dynamics is quantifying community membership. An increasingly common method for doing so is through metagenomics. Because of the rapidly increasing popularity of this approach, a large number of computational tools and pipelines are available for analysing metagenomic data. However, the majority of these tools have been designed and benchmarked using highly accurate short read data (i.e. Illumina), with few studies benchmarking classification accuracy for long error-prone reads (PacBio or Oxford Nanopore). In addition, few tools have been benchmarked for non-microbial communities. RESULTS: Here we compare simulated long reads from Oxford Nanopore and Pacific Biosciences (PacBio) with high accuracy Illumina read sets to systematically investigate the effects of sequence length and taxon type on classification accuracy for metagenomic data from both microbial and non-microbial communities. We show that very generally, classification accuracy is far lower for non-microbial communities, even at low taxonomic resolution (e.g. family rather than genus). We then show that for two popular taxonomic classifiers, long reads can significantly increase classification accuracy, and this is most pronounced for non-microbial communities. CONCLUSIONS: This work provides insight on the expected accuracy for metagenomic analyses for different taxonomic groups, and establishes the point at which read length becomes more important than error rate for assigning the correct taxon.


Assuntos
Metagenômica/métodos , Simulação por Computador , Eucariotos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Sequenciamento por Nanoporos , Análise de Sequência de DNA
17.
Nat Commun ; 11(1): 2384, 2020 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-32404905

RESUMO

TATA-box binding protein (TBP) is required for every single transcription event in archaea and eukaryotes. It binds DNA and harbors two repeats with an internal structural symmetry that show sequence asymmetry. At various times in evolution, TBP has acquired multiple interaction partners and different organisms have evolved TBP paralogs with additional protein regions. Together, these observations raise questions of what molecular determinants (i.e. key residues) led to the ability of TBP to acquire new interactions, resulting in an increasingly complex transcriptional system in eukaryotes. We present a comprehensive study of the evolutionary history of TBP and its interaction partners across all domains of life, including viruses. Our analysis reveals the molecular determinants and suggests a unified and multi-stage evolutionary model for the functional innovations of TBP. These findings highlight how concerted chemical changes on a conserved structural scaffold allow for the emergence of complexity in a fundamental biological process.


Assuntos
Domínios Proteicos , TATA Box/genética , Proteína de Ligação a TATA-Box/genética , Transcrição Genética , Algoritmos , Sequência de Aminoácidos , Animais , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Sítios de Ligação/genética , Eucariotos/classificação , Eucariotos/genética , Eucariotos/metabolismo , Evolução Molecular , Humanos , Modelos Moleculares , Ligação Proteica , Homologia de Sequência de Aminoácidos , Proteína de Ligação a TATA-Box/química , Proteína de Ligação a TATA-Box/metabolismo , Vírus/classificação , Vírus/genética , Vírus/metabolismo
18.
PLoS One ; 15(5): e0233065, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32413056

RESUMO

The hindgut protists of wood-feeding termites are usually colonized by prokaryotic symbionts. Many of the hurdles that have prevented a better understanding of these symbionts arise from variation among protist and termite host species and the inability to maintain prominent community members in culture. These issues have made it difficult to study the fidelity, acquisition, and differences in colonization of protists by bacterial symbionts. In this study, we use high throughput amplicon sequencing of the V4 region of 16S rRNA genes to determine the composition of bacterial communities associated with single protist cells of six protist species, from the genera Pyrsonympha, Dinenympha, and Trichonympha that are present in the hindgut of the termite Reticulitermes flavipes. By analyzing amplicon sequence variants (ASVs), the diversity and distribution of protist-associated bacteria was compared within and across these six different protist species. ASV analysis showed that, in general, each protist genus associated with a distinct community of bacterial symbionts which were conserved across different termite colonies. However, some ASVs corresponding to ectosymbionts (Spirochaetes) were shared between different Dinenympha species and to a lesser extent with Pyrsonympha and Trichonympha hosts. This suggested that certain bacterial symbionts may be cosmopolitan to some degree and perhaps acquired by horizontal transmission. Using a fluorescence-based cell assay, we could observe the horizontal acquisition of surface-bound bacteria. This acquisition was shown to be time-dependent, involve active processes, and was non-random with respect to binding locations on some protists.


Assuntos
Bactérias/genética , Eucariotos/genética , Isópteros/microbiologia , Simbiose/genética , Animais , Sistema Digestório/metabolismo , Sistema Digestório/microbiologia , Sistema Digestório/parasitologia , Sequenciamento de Nucleotídeos em Larga Escala , Interações entre Hospedeiro e Microrganismos/genética , Isópteros/genética , Isópteros/metabolismo , Microbiota/genética , Oximonadídeos/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de RNA
19.
Phytochemistry ; 175: 112370, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32289597

RESUMO

Peptidoglycan has been retained in chloroplasts that have evolved from cyanobacteria along some evolutionary tracks, but has seemingly been quickly eliminated during evolution of others. It has been eliminated in Rhodophyta, Chlorophyta, Pteridophyta and Spermatophyta, but has been retained in streptophyte algae, Glaukophyta, and Lycophyta. In this article questions emerging from this are raised, and for some of them answers are suggested.


Assuntos
Clorófitas , Eucariotos , Parede Celular , Cloroplastos , Peptidoglicano , Filogenia
20.
Chemosphere ; 254: 126810, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32334259

RESUMO

Anaerobic membrane bioreactor (AnMBR) is used for the treatment of organic solid waste. Clogging of filtration membrane pores, called membrane fouling, is one of the most serious issues for the sustainable operation of AnMBR. Although the physical and chemical mechanisms of the membrane fouling have been widely studied, the biological mechanisms are still unclear. The biofilm formation and development on the membrane might cause the membrane fouling. In this study, the prokaryotic and eukaryotic microbiomes of the membrane-attached biofilms in an AnMBR treating a model slurry of organic solid waste were investigated by non-destructive microscopy and high-throughput sequencing of 16S and 18S rRNA genes. The non-destructive visualization indicated that the biofilm was layered with different structures. The lowermost residual fouling layer was mesh-like and composed of filamentous microorganisms, while the upper cake layer was mainly the non-dense and non-cell region. The principal coordinate and phylogenetic analyses of the sequence data showed that the biofilm microbiomes were different from the sludge. The lowermost layer consisted of operational taxonomic units that were related to Leptolinea tardivitalis and Methanosaeta concilii (9.53-10.07% and 1.14-1.64% of the total prokaryotes, respectively) and Geotrichum candidum (30.22-82.31% of the total eukaryotes), all of which exhibited the filamentous morphology. Moreover, the upper layer was inhabited by the presumably cake-degrading bacteria and predatory eukaryotes. The biofilm microbiome features were consistent with the microscope-visualized structure. These results demonstrated that the biofilm structure and microbiome were the layer specific, which provides better understanding of biological mechanisms of membrane fouling in the AnMBR.


Assuntos
Reatores Biológicos/microbiologia , Eliminação de Resíduos Líquidos/métodos , Anaerobiose , Bactérias , Biofilmes/crescimento & desenvolvimento , Eucariotos , Sequenciamento de Nucleotídeos em Larga Escala , Membranas , Membranas Artificiais , Microbiota , Microscopia , Filogenia , Células Procarióticas , Esgotos , Resíduos Sólidos
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