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1.
Nat Commun ; 11(1): 4708, 2020 09 18.
Artigo em Inglês | MEDLINE | ID: mdl-32948758

RESUMO

While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 102-104 for bacterial populations and 103-105 for an archaeon, which is more comparable to Eukaryotic representatives' humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.


Assuntos
Microbiota/genética , Microbiota/fisiologia , Proteínas/genética , Proteínas/metabolismo , RNA/genética , RNA/metabolismo , Archaea/genética , Archaea/metabolismo , Bactérias/genética , Bactérias/metabolismo , DNA , Perfilação da Expressão Gênica , Genoma Microbiano , Humanos , Metabolômica , Fenótipo , Proteoma , Proteômica , Transcriptoma , Leveduras
2.
Nat Commun ; 11(1): 4580, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917864

RESUMO

Proteasomal machinery performs essential regulated protein degradation in eukaryotes. Classic proteasomes are symmetric, with a regulatory ATPase docked at each end of the cylindrical 20S. Asymmetric complexes are also present in cells, either with a single ATPase or with an ATPase and non-ATPase at two opposite ends. The mechanism that populates these different proteasomal complexes is unknown. Using archaea homologs, we construct asymmetric forms of proteasomes. We demonstrate that the gate conformation of the two opposite ends of 20S are coupled: binding one ATPase opens a gate locally, and also opens the opposite gate allosterically. Such allosteric coupling leads to cooperative binding of proteasomal ATPases to 20S and promotes formation of proteasomes symmetrically configured with two identical ATPases. It may also promote formation of asymmetric complexes with an ATPase and a non-ATPase at opposite ends. We propose that in eukaryotes a similar mechanism regulates the composition of the proteasomal population.


Assuntos
Archaea/metabolismo , Complexo de Endopeptidases do Proteassoma/química , Complexo de Endopeptidases do Proteassoma/metabolismo , Adenosina Trifosfatases/metabolismo , Archaea/genética , Microscopia Crioeletrônica , Cinética , Modelos Moleculares , Complexo de Endopeptidases do Proteassoma/genética , Conformação Proteica , Thermoplasma/genética , Thermoplasma/metabolismo
3.
Nat Commun ; 11(1): 4897, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994415

RESUMO

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.


Assuntos
Carbono/análise , Metagenoma/genética , Microbiota/fisiologia , Microbiologia do Solo , Solo/química , Aclimatação/genética , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Carbono/metabolismo , Ciclo do Carbono , Celulose/metabolismo , DNA Ambiental/genética , DNA Ambiental/isolamento & purificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Aquecimento Global , Pradaria , Temperatura Alta/efeitos adversos , Metagenômica , Modelos Genéticos , Raízes de Plantas/química , Poaceae/química
4.
PLoS One ; 15(8): e0236932, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32745120

RESUMO

Humanity's reliance on clean water and the ecosystem services provided makes identifying efficient and effective ways to assess the ecological condition of streams ever more important. We used high throughput sequencing of the 16S rRNA region to explore relationships between stream microbial communities, environmental attributes, and assessments of stream ecological condition. Bacteria and archaea in microbial community samples collected from the water column and from stream sediments during spring and summer were used to replicate standard assessments of ecological condition performed with benthic macroinvertebrate collections via the Benthic Index of Biotic Integrity (BIBI). Microbe-based condition assessments were generated at different levels of taxonomic resolution from phylum to OTU (Operational Taxonomic Units) in order to understand appropriate levels of taxonomic aggregation. Stream sediment microbial communities from both spring and summer were much better than the water column at replicating BIBI condition assessment results. Accuracies were as high as 100% on training data used to build the models and up to 80% on validation data used to assess predictions. Assessments using all OTUs usually had the highest accuracy on training data, but were lower on validation data due to overfitting. In contrast, assessments at the order-level had similar performance accuracy for validation data, and a reduced subset of orders also performed well, suggesting the method could be generalized to other watersheds. Subsets of the important orders responded similarly to environmental gradients compared to the entire community, where strong shifts in community structure occurred for known aquatic stressors such as pH, dissolved organic carbon, and nitrate nitrogen. The results suggest the stream microbes may be useful for assessing the ecological condition of streams and especially useful for stream restorations where many eukaryotic taxa have been eliminated due to prior degradation and are unable to recolonize.


Assuntos
Monitorização de Parâmetros Ecológicos/métodos , Microbiota/genética , Rios/microbiologia , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Ecossistema , Monitoramento Ambiental/métodos , Sedimentos Geológicos/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Metagenômica , RNA Ribossômico 16S/genética
5.
Nat Commun ; 11(1): 3941, 2020 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-32770005

RESUMO

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.


Assuntos
Acetatos/metabolismo , Archaea/enzimologia , Proteínas de Bactérias/metabolismo , Coenzima A Ligases/metabolismo , Metano/metabolismo , Anaerobiose , Archaea/genética , Proteínas de Bactérias/genética , Ciclo do Carbono/fisiologia , Coenzima A Ligases/genética , Genoma Arqueal , Sedimentos Geológicos/microbiologia , Redes e Vias Metabólicas/genética , Oxirredução , Água do Mar/microbiologia
6.
Nat Commun ; 11(1): 3939, 2020 08 07.
Artigo em Inglês | MEDLINE | ID: mdl-32770105

RESUMO

The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.


Assuntos
Archaea/genética , Evolução Molecular , Transferência Genética Horizontal , Genoma Arqueal , Simbiose/genética , Filogenia
7.
Arch Virol ; 165(10): 2177-2191, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32748179

RESUMO

The canonical frameworks of viral evolution describe viruses as cellular predecessors, reduced forms of cells, or entities that escaped cellular control. The discovery of giant viruses has changed these standard paradigms. Their genetic, proteomic and structural complexities resemble those of cells, prompting a redefinition and reclassification of viruses. In a previous genome-wide analysis of the evolution of structural domains in proteomes, with domains defined at the fold superfamily level, we found the origins of viruses intertwined with those of ancient cells. Here, we extend these data-driven analyses to the study of fold families confirming the co-evolution of viruses and ancient cells and the genetic ability of viruses to foster molecular innovation. The results support our suggestion that viruses arose by genomic reduction from ancient cells and validate a co-evolutionary 'symbiogenic' model of viral origins.


Assuntos
Evolução Biológica , DNA Viral/genética , Genoma Viral , Vírus Gigantes/genética , Filogenia , Proteínas Virais/genética , Archaea/genética , Archaea/virologia , Bactérias/genética , Bactérias/virologia , DNA Viral/química , Eucariotos/genética , Eucariotos/virologia , Tamanho do Genoma , Vírus Gigantes/classificação , Proteogenômica/métodos , Proteoma/genética , Proteínas Virais/química
8.
PLoS One ; 15(8): e0237135, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32822422

RESUMO

DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.


Assuntos
Archaea/genética , Proteínas Arqueais/genética , Proteínas de Bactérias/genética , Proteínas de Ligação a DNA/genética , Escherichia coli K12/genética , Fatores de Transcrição/genética , Archaea/patogenicidade , Proteínas Arqueais/metabolismo , Proteínas de Bactérias/metabolismo , Sítios de Ligação , DNA Arqueal/metabolismo , DNA Bacteriano/metabolismo , Proteínas de Ligação a DNA/metabolismo , Escherichia coli K12/patogenicidade , Regulação da Expressão Gênica em Archaea , Regulação Bacteriana da Expressão Gênica , Genoma Arqueal , Genoma Bacteriano , Ligação Proteica , Fatores de Transcrição/metabolismo , Virulência/genética
9.
Sci Total Environ ; 746: 141139, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32745858

RESUMO

Human activities have largely modified nitrogen (N) sources supply, cycling and export from land to ocean. Nitrification and denitrification are vital processes alleviating N pollution in aquatic ecosystems but the diverse responses and niche of microbial N retention to human disturbance are still understudied. Here we investigated the changes in N species and functional genes in the urban, agriculture and reservoir river sections of the Jiulong River (southeast China). Our results show that ammonia-oxidizing bacteria (AOB) (Nitrosomonas) were dominant in the urban river section receiving ammonium-rich sewage that enhanced nitrification and subsequent denitrification, while ammonia-oxidizing archaea (AOA) was more abundant than AOB in the river section flowing through areas of pomelo (Citrus maxima) agriculture with low pH, low ammonium and very high nitrate input. Warm temperatures and large total suspended matter (TSM) in the wet season promoted growth of nitrifiers and denitrifiers, which were mostly particle-attached. The potential river N retention through gaseous N removal (PRN2O and PRN2) in the agriculture section with huge N loading was among the lowest. Strong nitrification and denitrification were suspected to occur in the agricultural acid soil system rather than in the river network. In addition, the decreased TSM and N concentration promoted free-living microbes in the reservoir. The highest PRN2 and N2 production observed in the reservoir in the dry season implied that denitrification and anammox occurring in sediments was likely to increase N retention. This study suggests the diverse factors involved in processing of N pollution among diverse landscapes.


Assuntos
Ecossistema , Rios , Amônia , Archaea/genética , China , Humanos , Nitrificação , Nitrogênio/análise , Ciclo do Nitrogênio , Oxirredução
10.
Sci Total Environ ; 746: 141086, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32750579

RESUMO

In order to evaluate microbial community structure dominated metabolic function profiles in large-scale food waste (FW) biotreatment systems, bacterial, archaeal and fungal community associated with metabolic function in high-temperature aerobic fermentation (AF) and anaerobic co-digestion (AcoD) processes were comprehensively investigated in this study. The qPCR results showed the higher gene copies of bacteria and fungi in initial and AF-treated FW compared with AcoD-treated FW, as well as bacteria and archaea in AcoD-treated FW were highly abundant among detected samples. Furthermore, the total abundances of archaea ((1.18-4.88) × 106 copies/ng DNA) in AcoD system were 2-3 orders of magnitude higher than that in other samples (P < 0.01), indicating active archaeal activity in AcoD system. Correlation analysis of microbial community and metabolic function indicated that the higher abundances of Kazachstania, Pyrobaculum, Sulfophobococcus, Lactobacillus and Candida in initial FW had close linkages with lipid metabolism (P < 0.05). Abundant Aspergillus, Staphylococcus, Pelomonas, Corynebacterium, Faecalibacterium, Methanobacterium and Xeromyces in AF system were positively and significantly correlated with high metabolic activities of energy metabolism, carbohydrate metabolism, amino acid metabolism, fatty acid metabolism, glycosaminoglycan degradation, sulfur metabolism and nitrogen metabolism. As for AcoD system, dominant genera Methanosaeta, Methanoculleus, Methanobacterium, Fastidiosipila, Rikenellaceae RC9, Bifidobacterium and Xeromyces had close relationships with metabolism of cofactors and vitamins, energy metabolism, methane metabolism, carbohydrate metabolism and glycosaminoglycan degradation (P < 0.05). These results are expected to improve the metabolic efficiency by functional microorganism in different large-scale FW treatment systems.


Assuntos
Microbiota , Eliminação de Resíduos , Anaerobiose , Archaea/genética , Reatores Biológicos , Alimentos , Metano , Esgotos
11.
Sci Total Environ ; 743: 140699, 2020 Nov 15.
Artigo em Inglês | MEDLINE | ID: mdl-32679495

RESUMO

Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.


Assuntos
Archaea/genética , Metagenoma , Bactérias/genética , Sedimentos Geológicos , Índia , Filogenia , RNA Ribossômico 16S
12.
PLoS One ; 15(7): e0235508, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32614917

RESUMO

This study examined the influence of bioaugmentation on metal concentrations (aluminum, cadmium, chromium, cobalt, copper, iron, lead, manganese, molybdenum, nickel and zinc) in anaerobically digested sewage sludge. To improve the digestion efficiency, bioaugmentation with a mixture of wild-living Archaea and Bacteria (MAB) from Yellowstone National Park, USA, was used. The total concentration of all metals was higher in the digestate than in the feedstock. During anaerobic digestion, the percent increase in the concentration of most of metals was slightly higher in the bioaugmented runs than in the un-augmented runs, but these differences were not statistically significant. However, the percent increase in cadmium and cobalt concentration was significantly higher in the bioaugmented runs than in the un-augmented runs. At MAB doses of 9 and 13% v/v, cadmium concentration in the digestate was 211 and 308% higher than in the feedstock, respectively, and cobalt concentration was 138 and 165%, respectively. Bioaugmentation increased over 4 times the percentage of Pseudomonas sp. in the biomass that are able to efficiently accumulate metals by both extracellular adsorption and intracellular uptake. Biogas production was not affected by the increased metal concentrations. In conclusion, bioaugmentation increased the concentration of metals in dry sludge, which means that it could potentially have negative effects on the environment.


Assuntos
Metais/metabolismo , Esgotos/química , Adsorção , Anaerobiose , Archaea/genética , Archaea/crescimento & desenvolvimento , Archaea/metabolismo , Bactérias/genética , Bactérias/crescimento & desenvolvimento , Bactérias/metabolismo , Biomassa , Cádmio/análise , Cádmio/metabolismo , Cobalto/análise , Cobalto/metabolismo , Metais/química , Pseudomonas/genética , Pseudomonas/crescimento & desenvolvimento , Pseudomonas/metabolismo , Esgotos/microbiologia , Eliminação de Resíduos Líquidos
13.
Nat Commun ; 11(1): 3784, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32728052

RESUMO

The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including diverse anti-CRISPR proteins (Acrs) that specifically inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small and highly variable proteins which makes their bioinformatic prediction a formidable task. We present a machine-learning approach for comprehensive Acr prediction. The model shows high predictive power when tested against an unseen test set and was employed to predict 2,500 candidate Acr families. Experimental validation of top candidates revealed two unknown Acrs (AcrIC9, IC10) and three other top candidates were coincidentally identified and found to possess anti-CRISPR activity. These results substantially expand the repertoire of predicted Acrs and provide a resource for experimental Acr discovery.


Assuntos
Bacteriófagos/genética , Proteína 9 Associada à CRISPR/antagonistas & inibidores , Aprendizado de Máquina , Análise de Sequência de Proteína/métodos , Proteínas Virais/genética , Archaea/genética , Archaea/virologia , Bactérias/genética , Bactérias/virologia , Proteína 9 Associada à CRISPR/genética , Sistemas CRISPR-Cas/genética , Biologia Computacional/métodos , Conjuntos de Dados como Assunto , Edição de Genes/métodos , Interações Hospedeiro-Parasita/genética , Homologia de Sequência de Aminoácidos
14.
Huan Jing Ke Xue ; 41(5): 2468-2475, 2020 May 08.
Artigo em Chinês | MEDLINE | ID: mdl-32608866

RESUMO

The application of exogenous organic matter is considered the main method of increasing the organic matter content of acidic red soils. Nitrogen is an important limiting factor for soil fertility. Changes to the soil ecosystem under organic matter promotion can affect soil nitrogen cycling and related functional microorganisms; however, there have been no studies on this aspect. Acidic upland red soils, with or without long-term organic fertilizer application, were chosen as the research materials in this study. Based on metagenomic sequencing and alignment in the nitrogen-cycling gene database, the present study aimed to investigate the effect of organic matter promotion on nitrogen-cycling genes and functional microorganisms in acidic red soils, which had been amended with exogenous organic matter for 32 years. The results showed that organic matter promotion in acidic soils increased the total organic carbon and total nitrogen content, and alleviated soil acidification. Organic matter promotion increased the soil net nitrification activity and potential for ammoxidation. Organic matter promotion increased the abundance of amoA genes (encoding ammonia monooxygenase) and nar, nap, nir, nor, and nos genes (encoding denitrification reductase); decreased the abundance of hao genes (encoding hydroxylamine oxidase) and nrf genes related to the dissimilatory nitrate reduction to ammonia; increased the abundance of glnA, gdh, glsA, ansB, and nao genes related to organic nitrogen metabolism; altered the abundance of functional genes related to assimilatory nitrate reduction; and changed the community composition of nitrogen-cycling microorganisms. After organic matter promotion, alleviation of soil acidification and enhancement of total organic carbon were the most important factors that affected the abundance of nitrogen-cycling genes and the community composition of functional microorganisms. Our results comprehensively investigated the inorganic and organic nitrogen-cycling genes, and correlated the functional genes, microbial populations, and functional activities in the ammonia oxidizing process, which provided supporting data to understand the nitrogen-cycling characteristics of acidic red soils and provided ideas for acidic soil improvement.


Assuntos
Genes Bacterianos , Ciclo do Nitrogênio , Microbiologia do Solo , Solo , Amônia , Archaea/genética , Ecossistema , Nitrificação , Nitrogênio , Oxirredução
15.
Proc Natl Acad Sci U S A ; 117(27): 15911-15922, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32576690

RESUMO

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O2 introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources.


Assuntos
Sedimentos Geológicos/química , Sedimentos Geológicos/microbiologia , Microbiota/fisiologia , Archaea/classificação , Archaea/genética , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Carbono/metabolismo , Nitrogênio/metabolismo , Oxigênio/metabolismo , Filogenia , Água do Mar/química , Água do Mar/microbiologia
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.
Arch Microbiol ; 202(7): 2005-2012, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32436040

RESUMO

Grasses of the Urochloa genus have been widely used in crop-livestock integration systems or as cover crops in no-till systems such as in rotation with maize. Some species of Urochloa have mechanisms to reduce nitrification. However, the responses of microbial functions in crop-rotation systems with grasses and its consequence on soil N dynamics are not well-understood. In this study, the soil nitrification potential and the abundance of ammonifying microorganisms, total bacteria and total archaea (16S rRNA gene), nitrogen-fixing bacteria (NFB, nifH), ammonia-oxidizing bacteria (AOB, amoA) and archaea (AOA, amoA) were assessed in soil cultivated with ruzigrass (Urochloa ruziziensis), palisade grass (Urochloa brizantha) and Guinea grass (Panicum maximum). The abundance of ammonifying microorganisms was not affected by ruzigrass. Ruzigrass increased the soil nitrification potential compared with palisade and Guinea grass. Ruzigrass increased the abundance of N-fixing microorganisms at the middle and late growth stages. The abundances of nitrifying microorganisms and N-fixers in soil were positively correlated with the soil N-NH4+ content. Thus, biological nitrogen fixation might be an important input of N in systems of rotational production of maize with forage grasses. The abundance of microorganisms related to ammonification, nitrification and nitrogen fixing and ammonia-oxidizing archea was related to the development stage of the forage grass.


Assuntos
Agricultura , Produtos Agrícolas/microbiologia , Ciclo do Nitrogênio/genética , Microbiologia do Solo , Amônia/metabolismo , Archaea/genética , Bactérias/genética , Nitrificação , Nitrogênio/metabolismo , Oxirredução , RNA Ribossômico 16S/genética , Solo/química , Zea mays
19.
Nucleic Acids Res ; 48(12): 6906-6918, 2020 07 09.
Artigo em Inglês | MEDLINE | ID: mdl-32459340

RESUMO

The universal L-shaped tertiary structure of tRNAs is maintained with the help of nucleotide modifications within the D- and T-loops, and these modifications are most extensive within hyperthermophilic species. The obligate-commensal Nanoarchaeum equitans and its phylogenetically-distinct host Ignicoccus hospitalis grow physically coupled under identical hyperthermic conditions. We report here two fundamentally different routes by which these archaea modify the key conserved nucleotide U54 within their tRNA T-loops. In N. equitans, this nucleotide is methylated by the S-adenosylmethionine-dependent enzyme NEQ053 to form m5U54, and a recombinant version of this enzyme maintains specificity for U54 in Escherichia coli. In N. equitans, m5U54 is subsequently thiolated to form m5s2U54. In contrast, I. hospitalis isomerizes U54 to pseudouridine prior to methylating its N1-position and thiolating the O4-position of the nucleobase to form the previously uncharacterized nucleotide m1s4Ψ. The methyl and thiol groups in m1s4Ψ and m5s2U are presented within the T-loop in a spatially identical manner that stabilizes the 3'-endo-anti conformation of nucleotide-54, facilitating stacking onto adjacent nucleotides and reverse-Hoogsteen pairing with nucleotide m1A58. Thus, two distinct structurally-equivalent solutions have evolved independently and convergently to maintain the tertiary fold of tRNAs under extreme hyperthermic conditions.


Assuntos
Desulfurococcaceae/genética , Nanoarchaeota/genética , Conformação de Ácido Nucleico , RNA de Transferência/ultraestrutura , Archaea/genética , Archaea/ultraestrutura , Escherichia coli/genética , Metilação , Filogenia , RNA de Transferência/genética , tRNA Metiltransferases/genética , tRNA Metiltransferases/ultraestrutura
20.
J Biosci Bioeng ; 130(3): 247-252, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32451245

RESUMO

A gene encoding a dye-linked d-amino acid dehydrogenase (Dye-DADH) homologue was found in a hyperthermophilic archaeon, Sulfurisphaera tokodaii. The predicted amino acid sequence suggested that the gene product is a membrane-bound type enzyme. The gene was overexpressed in Escherichia coli, but the recombinant protein was exclusively produced as an inclusion body. In order to avoid production of the inclusion body, an expression system using the thermoacidophilic archaeon Sulfolobus acidocaldarius instead of E. coli as the host cell was constructed. The gene was successfully expressed in Sulfolobus acidocaldarius, and its product was purified to homogeneity and characterized. The purified enzyme catalyzed the dehydrogenation of various d-amino acids, with d-phenylalanine being the most preferred substrate. The enzyme retained its full activity after incubation at 90 °C for 30 min and after incubation at pH 4.0-11.0 for 30 min at 50 °C. This is the first report on membrane-bound Dye-DADH from thermophilic archaea that was successfully expressed in an archaeal host.


Assuntos
Archaea/genética , D-Aminoácido Oxidase/metabolismo , Proteínas Recombinantes/metabolismo , Sulfolobus/enzimologia , Sequência de Aminoácidos , Clonagem Molecular , D-Aminoácido Oxidase/química , Expressão Gênica , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Sulfolobus/genética
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