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1.
Appl Microbiol Biotechnol ; 105(8): 3181-3194, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33791835

RESUMO

Thermoplasma trehalase Tvn1315 is predicted to be composed of a ß-sandwich domain (BD) and a catalytic domain (CD) based on the structure of the bacterial GH15 family glucoamylase (GA). Tvn1315 as well as Tvn1315 (Δ5), in which the 5 N-terminal amino acids are deleted, could be expressed in Escherichia coli as active enzymes, but deletion of 10 residues (Δ10) led to inclusion body formation. To further investigate the role of the N-terminal region of BD, we constructed five mutants of Δ5, in which each of the 5th to 10th residues of the N-terminus of Tvn1315 was mutated to Ala. Every mutant protein could be recovered in soluble form, but only a small fraction of the Y9A mutant was recovered in the soluble fraction. The Y9A mutant recovered in soluble form had similar specific activity to the other proteins. Subsequent mutation analysis at the 9th position of Tvn1315 in Δ5 revealed that aromatic as well as bulky hydrophobic residues could function properly, but residues with hydroxy groups impaired the solubility. Similar results were obtained with mutants based on untruncated Tvn1315. When the predicted BD, Δ5BD, Δ10BD, and BD mutants were expressed, the Δ10BD protein formed inclusion bodies, and the BD mutants behaved similarly to the Δ5 and full-length enzyme mutants. These results suggest that the hydrophobic region is involved in the solubilization of BD during the folding process. Taken together, these results indicate that the solubility of CD depends on BD folding. KEY POINTS: • N-terminal hydrophobic region of the BD is involved in the protein folding. • The N-terminal hydrophobic region of the BD is also involved in the BD folding. • BD is able to weakly interact with the insoluble ß-glucan.


Assuntos
Archaea , Trealase , Sequência de Aminoácidos , Archaea/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Dobramento de Proteína , Trealase/metabolismo
2.
Ecotoxicol Environ Saf ; 217: 112274, 2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-33930771

RESUMO

Canonical ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) and complete-nitrifying bacteria (comammox) exist in a variety of ecosystems. However, little is known about AOA, AOB and comammox or their contributions to nitrification in the soils of heavily degraded and acidic mine regions. In the present study, the activity, richness, diversity and distribution patterns of AOA, AOB and comammox in the Siding mine area were investigated. Nemerow's multifactor pollution index (PN) values indicated that the soil in all three areas in the Siding mine area was highly contaminated by Cd, Pb, Zn, Mn and Cu. The AOA, AOB and comammox amoA gene copy numbers exhibited significant positive correlations with Pb and Zn levels and PN values, which indicated that the populations of AOA, AOB and comammox underwent adaptation and reproduction in response to pollution from multiple metals in the Siding mine area. Among them, the abundance of AOA was the highest, and AOA may survive better than AOB and comammox under such severely pollution-stressed and ammonia-limited conditions. The phyla Thaumarchaeota and Crenarchaeota may play vital roles in the soil ammonia oxidation process. Unlike AOA, AOB may use soil available phosphorus to help them compete for NH3 and other limiting nutrients with AOA and heterotrophs. Moreover, soil organic matter was the main factor influencing the species diversity of AOB, the ß-diversity of AOB and comammox, and the community composition of AOA, AOB and comammox. Our research will help to explain the role and importance of AOA, AOB and comammox in the different ecological restoration regions in the Siding mine area.


Assuntos
Amônia/metabolismo , Biodegradação Ambiental , Mineração , Microbiologia do Solo , Archaea/metabolismo , Bactérias/metabolismo , Betaproteobacteria/metabolismo , Biodiversidade , Ecossistema , Nitrificação , Oxirredução , Fósforo/metabolismo , Filogenia , Solo , Poluentes do Solo
3.
Biochemistry (Mosc) ; 86(Suppl 1): S38-S49, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33827399

RESUMO

Members of the Lsm protein family are found in all three domains of life: bacteria, archaea, and eukarya. They are involved in numerous processes associated with RNA processing and gene expression regulation. A common structural feature of all Lsm family proteins is the presence of the Sm fold consisting of a five-stranded ß-sheet and an α-helix at the N-terminus. Heteroheptameric eukaryotic Sm and Lsm proteins participate in the formation of spliceosomes and mRNA decapping. Homohexameric bacterial Lsm protein, Hfq, is involved in the regulation of transcription of different mRNAs by facilitating their interactions with small regulatory RNAs. Furthermore, recently obtained data indicate a new role of Hfq as a ribosome biogenesis factor, as it mediates formation of the productive structure of the 17S rRNA 3'- and 5'-sequences, facilitating their further processing by RNases. Lsm archaeal proteins (SmAPs) form homoheptamers and likely interact with single-stranded uridine-rich RNA elements, although the role of these proteins in archaea is still poorly understood. In this review, we discuss the structural features of the Lsm family proteins from different life domains and their structure-function relationships.


Assuntos
Proteínas de Ligação a RNA/metabolismo , Ribossomos/metabolismo , Archaea/metabolismo , Bactérias/metabolismo , Eucariotos/metabolismo , Conformação Proteica , RNA Mensageiro/metabolismo
4.
Mar Drugs ; 19(3)2021 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-33803653

RESUMO

Plastic pollution is a worldwide concern causing the death of animals (mainly aquatic fauna) and environmental deterioration. Plastic recycling is, in most cases, difficult or even impossible. For this reason, new research lines are emerging to identify highly biodegradable bioplastics or plastic formulations that are more environmentally friendly than current ones. In this context, microbes, capable of synthesizing bioplastics, were revealed to be good models to design strategies in which microorganisms can be used as cell factories. Recently, special interest has been paid to haloarchaea due to the capability of some species to produce significant concentrations of polyhydroxyalkanoate (PHA), polyhydroxybutyrate (PHB), and polyhydroxyvalerate (PHV) when growing under a specific nutritional status. The growth of those microorganisms at the pilot or industrial scale offers several advantages compared to that of other microbes that are bioplastic producers. This review summarizes the state of the art of bioplastic production and the most recent findings regarding the production of bioplastics by halophilic microorganisms with special emphasis on haloarchaea. Some protocols to produce/analyze bioplastics are highlighted here to shed light on the potential use of haloarchaea at the industrial scale to produce valuable products, thus minimizing environmental pollution by plastics made from petroleum.


Assuntos
Archaea/metabolismo , Plásticos Biodegradáveis/metabolismo , Biopolímeros/biossíntese , Biotecnologia , Química Verde
5.
Int J Mol Sci ; 22(5)2021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33806708

RESUMO

Small heat shock proteins (sHsps) are widely distributed among various types of organisms and function in preventing the irreversible aggregation of thermal denaturing proteins. Here, we report that Hsp17.6 from Methanolobus psychrophilus exhibited protection of proteins from oxidation inactivation. The overexpression of Hsp17.6 in Escherichia coli markedly increased the stationary phase cell density and survivability in HClO and H2O2. Treatments with 0.2 mM HClO or 10 mM H2O2 reduced malate dehydrogenase (MDH) activity to 57% and 77%, whereas the addition of Hsp17.6 recovered the activity to 70-90% and 86-100%, respectively. A similar effect for superoxide dismutase oxidation was determined for Hsp17.6. Non-reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis assays determined that the Hsp17.6 addition decreased H2O2-caused disulfide-linking protein contents and HClO-induced degradation of MDH; meanwhile, Hsp17.6 protein appeared to be oxidized with increased molecular weights. Mass spectrometry identified oxygen atoms introduced into the larger Hsp17.6 molecules, mainly at the aspartate and methionine residues. Substitution of some aspartate residues reduced Hsp17.6 in alleviating H2O2- and HClO-caused MDH inactivation and in enhancing the E. coli survivability in H2O2 and HClO, suggesting that the archaeal Hsp17.6 oxidation protection might depend on an "oxidant sink" effect, i.e., to consume the oxidants in environments via aspartate oxidation.


Assuntos
Archaea/metabolismo , Proteínas de Choque Térmico Pequenas/metabolismo , Escherichia coli/metabolismo , Peróxido de Hidrogênio/metabolismo , Oxirredução , Estresse Oxidativo/fisiologia , Oxigênio/metabolismo
6.
Biochemistry (Mosc) ; 86(3): 319-337, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33838632

RESUMO

Bacteriophages or phages are viruses that infect bacterial cells (for the scope of this review we will also consider viruses that infect Archaea). Constant threat of phage infection is a major force that shapes evolution of the microbial genomes. To withstand infection, bacteria had evolved numerous strategies to avoid recognition by phages or to directly interfere with phage propagation inside the cell. Classical molecular biology and genetic engineering have been deeply intertwined with the study of phages and host defenses. Nowadays, owing to the rise of phage therapy, broad application of CRISPR-Cas technologies, and development of bioinformatics approaches that facilitate discovery of new systems, phage biology experiences a revival. This review describes variety of strategies employed by microbes to counter phage infection, with a focus on novel systems discovered in recent years. First chapter covers defense associated with cell surface, role of small molecules, and innate immunity systems relying on DNA modification.


Assuntos
Archaea/virologia , Bactérias/virologia , Bacteriófagos , Archaea/genética , Archaea/metabolismo , Archaea/fisiologia , Bactérias/genética , Bactérias/metabolismo , Fenômenos Fisiológicos Bacterianos , Sistemas CRISPR-Cas , Interações entre Hospedeiro e Microrganismos
7.
Nat Commun ; 12(1): 2404, 2021 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-33893309

RESUMO

Geothermal environments, such as hot springs and hydrothermal vents, are hotspots for carbon cycling and contain many poorly described microbial taxa. Here, we reconstructed 15 archaeal metagenome-assembled genomes (MAGs) from terrestrial hot spring sediments in China and deep-sea hydrothermal vent sediments in Guaymas Basin, Gulf of California. Phylogenetic analyses of these MAGs indicate that they form a distinct group within the TACK superphylum, and thus we propose their classification as a new phylum, 'Brockarchaeota', named after Thomas Brock for his seminal research in hot springs. Based on the MAG sequence information, we infer that some Brockarchaeota are uniquely capable of mediating non-methanogenic anaerobic methylotrophy, via the tetrahydrofolate methyl branch of the Wood-Ljungdahl pathway and reductive glycine pathway. The hydrothermal vent genotypes appear to be obligate fermenters of plant-derived polysaccharides that rely mostly on substrate-level phosphorylation, as they seem to lack most respiratory complexes. In contrast, hot spring lineages have alternate pathways to increase their ATP yield, including anaerobic methylotrophy of methanol and trimethylamine, and potentially use geothermally derived mercury, arsenic, or hydrogen. Their broad distribution and their apparent anaerobic metabolic versatility indicate that Brockarchaeota may occupy previously overlooked roles in anaerobic carbon cycling.


Assuntos
Archaea/genética , Ciclo do Carbono/genética , Genoma Arqueal/genética , Metagenoma/genética , Filogenia , Archaea/classificação , Archaea/metabolismo , Carbono/metabolismo , China , Geografia , Sedimentos Geológicos/microbiologia , Fontes Termais/microbiologia , Fontes Hidrotermais/microbiologia , Metano/metabolismo , RNA Ribossômico 16S/genética , Especificidade da Espécie
8.
Nat Commun ; 12(1): 2069, 2021 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-33824308

RESUMO

The oxygenation of early Earth's atmosphere during the Great Oxidation Event, is generally accepted to have been caused by oceanic Cyanobacterial oxygenic photosynthesis. Recent studies suggest that Fe(II) toxicity delayed the Cyanobacterial expansion necessary for the GOE. This study investigates the effects of Fe(II) on two Cyanobacteria, Pseudanabaena sp. PCC7367 and Synechococcus sp. PCC7336, in a simulated shallow-water marine Archean environment. A similar Fe(II) toxicity response was observed as reported for closed batch cultures. This toxicity was not observed in cultures provided with continuous gaseous exchange that showed significantly shorter doubling times than the closed-culture system, even with repeated nocturnal addition of Fe(II) for 12 days. The green rust (GR) formed under high Fe(II) conditions, was not found to be directly toxic to Pseudanabaena sp. PCC7367. In summary, we present evidence of diurnal Fe cycling in a simulated shallow-water marine environment for two ancestral strains of Cyanobacteria, with increased O2 production under anoxic conditions.


Assuntos
Organismos Aquáticos/metabolismo , Archaea/metabolismo , Ritmo Circadiano , Ferro/metabolismo , Oxigênio/metabolismo , Organismos Aquáticos/efeitos dos fármacos , Organismos Aquáticos/crescimento & desenvolvimento , Archaea/efeitos dos fármacos , Archaea/crescimento & desenvolvimento , Atmosfera , Clorofila A/metabolismo , Ferro/toxicidade , Modelos Biológicos , Água do Mar
9.
Dtsch Med Wochenschr ; 146(7): 441-445, 2021 04.
Artigo em Alemão | MEDLINE | ID: mdl-33780988

RESUMO

The functional gastrointestinal disorders (FGIDs) have a high prevalence and are associated with high healthcare costs. The diagnosis of these diseases could be difficult and require func-tional tests such as high-resolution manometry (HRM) of the esophagus, anorectal manometry and H2-Breathtests. Due to the COVID-19 Pandemic and the fear of infections there was a marked reduction in the number of performed exams in the last months - nevertheless some exams are necessary, in order to exclude or to diagnose important and dangerous diseases like Achalasia. Goal of this article is to present some new and relevant developments in the field. The HRM of the esophagus is the diagnostic standard for Achalasia, a rare clinical condi-tion associated to dysphagia - new European guidelines suggests a safe strategy in perform-ing the pneumatic dilatation.The intestinal methanogen overgrowth (IMO) is a clinical condition caused by a high production of methane in the small intestine due to overgrowth of Methanobrevibacter smithii, this condition could be in some patients associated with irritable bowel syndrome.


Assuntos
/complicações , Gastroenteropatias/diagnóstico , Archaea/metabolismo , Testes Respiratórios , Acalasia Esofágica/diagnóstico , Esôfago/fisiopatologia , Gastroenteropatias/economia , Gastroenteropatias/epidemiologia , Humanos , Intestino Delgado/microbiologia , Manometria , Metano/biossíntese , Guias de Prática Clínica como Assunto , Reto/fisiopatologia
10.
Int J Mol Sci ; 22(4)2021 Feb 18.
Artigo em Inglês | MEDLINE | ID: mdl-33670786

RESUMO

The DING proteins are ubiquitous in the three domains of life, from mesophiles to thermo- and hyperthermophiles. They belong to a family of more than sixty members and have a characteristic N-terminus, DINGGG, which is considered a "signature" of these proteins. Structurally, they share a highly conserved phosphate binding site, and a three dimensional organization resembling the "Venus Flytrap", both reminding the ones of PstS proteins. They have unusually high sequence conservation, even between distantly related species. Nevertheless despite that the genomes of most of these species have been sequenced, the DING gene has not been reported for all the relative characterized DING proteins. Identity of known DING proteins has been confirmed immunologically and, in some cases, by N-terminal sequence analysis. Only a few of the DING proteins have been purified and biochemically characterized. DING proteins are heterogeneous for their wide range of biological activities and some show different activities not always correlated with each other. Most of them have been originally identified for different biological properties, or rather for binding to phosphate and also to other ligands. Their involvement in pathologies is described. This review is an update of the most recent findings on old and new DING proteins.


Assuntos
Extremófilos/metabolismo , Proteínas de Ligação a Fosfato/metabolismo , Sequência de Aminoácidos , Archaea/metabolismo , Eucariotos/metabolismo , Proteínas de Ligação a Fosfato/química , Proteínas de Ligação a Fosfato/genética
11.
Appl Environ Microbiol ; 87(9)2021 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-33608286

RESUMO

The Asgard superphylum is a deeply branching monophyletic group of Archaea, recently described as some of the closest relatives of the eukaryotic ancestor. The wide application of genomic analyses from metagenome sequencing has established six distinct phyla, whose genomes encode diverse metabolic capacities and which play important biogeochemical and ecological roles in marine sediments. Here, we describe two metagenome-assembled genomes (MAGs) recovered from deep marine sediments off the Costa Rica margin, defining a novel lineage phylogenetically married to "Candidatus Thorarchaeota"; as such, we propose the name "Sifarchaeota" for this phylum. The two Sifarchaeota MAGs encode an anaerobic pathway for methylotrophy enabling the utilization of C1 to C3 compounds (methanol and methylamines) to synthesize acetyl coenzyme A (acetyl-CoA). The MAGs showed a remarkable saccharolytic capabilities compared to other Asgard lineages and encoded diverse classes of carbohydrate active enzymes (CAZymes) targeting different mono-, di-, and oligosaccharides. Comparative genomic analysis based on the full metabolic profiles of different Asgard lineages revealed the close relation between Sifarchaeota and "Candidatus Odinarchaeota" MAGs, which suggested similar metabolic potentials and ecological roles. Furthermore, we identified multiple HGT events from different bacterial donors within Sifarchaeota MAGs, which hypothetically expanded Sifarchaeota capacities for substrate utilization, energy production, and niche adaptation.IMPORTANCE The exploration of deep marine sediments has unearthed many new lineages of microbes. The finding of this novel phylum of Asgard archaea is important, since understanding the diversity and evolution of Asgard archaea may inform also about the evolution of eukaryotic cells. The comparison of metabolic potentials of the Asgard archaea can help inform about selective pressures the lineages have faced during evolution.


Assuntos
Archaea , Genoma Arqueal , Sedimentos Geológicos/microbiologia , Metagenoma , Polissacarídeos/metabolismo , Anaerobiose , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Biodegradação Ambiental , Costa Rica , Filogenia
12.
Appl Environ Microbiol ; 87(9)2021 04 13.
Artigo em Inglês | MEDLINE | ID: mdl-33608296

RESUMO

Due to their unique metabolism and important ecological roles, deep-sea hydrothermal archaea have attracted great scientific interest. Among these archaea, DPANN superphylum archaea are widely distributed in hydrothermal vent environments. However, DPANN metabolism and ecology remain largely unknown. In this study, we assembled 20 DPANN genomes among 43 reconstructed genomes obtained from deep-sea hydrothermal vent sediments. Phylogenetic analysis suggests 6 phyla, comprised of Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum we have designated Kexuearchaeota These are included in the 20 DPANN archaeal members, indicating their broad diversity in this special environment. Analyses of their metabolism reveal deficiencies due to their reduced genome size, including gluconeogenesis and de novo nucleotide and amino acid biosynthesis. However, DPANN archaea possess alternate strategies to address these deficiencies. DPANN archaea also have the potential to assimilate nitrogen and sulfur compounds, indicating an important ecological role in the hydrothermal vent system.IMPORTANCE DPANN archaea show high distribution in the hydrothermal system, although they display small genome size and some incomplete biological processes. Exploring their metabolism is helpful to understand how such small forms of life adapt to this unique environment and what ecological roles they play. In this study, we obtained 20 high-quality metagenome-assembled genomes (MAGs) corresponding to 6 phyla of the DPANN group (Aenigmarchaeota, Diapherotrites, Nanoarchaeota, Pacearchaeota, Woesearchaeota, and a new candidate phylum designated Kexuearchaeota). Further metagenomic analyses provided insights on the metabolism and ecological functions of DPANN archaea to adapt to deep-sea hydrothermal environments. Our study contributes to a deeper understanding of their special lifestyles and should provide clues to cultivate this important archaeal group in the future.


Assuntos
Archaea/genética , Fontes Hidrotermais/microbiologia , Aminoácidos/biossíntese , Archaea/metabolismo , Genoma Arqueal , Glucose/metabolismo , Metagenoma , Nucleotídeos/biossíntese , Filogenia
13.
PLoS One ; 16(1): e0243363, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33406114

RESUMO

Globally, wetlands are in decline due to anthropogenic modification and climate change. Knowledge about the spatial distribution of biodiversity and biological processes within wetlands provides essential baseline data for predicting and mitigating the effects of present and future environmental change on these critical ecosystems. To explore the potential for environmental DNA (eDNA) to provide such insights, we used 16S rRNA metabarcoding to characterise prokaryote communities and predict the distribution of prokaryote metabolic pathways in peats and sediments up to 4m below the surface across seven New Zealand wetlands. Our results reveal distinct vertical structuring of prokaryote communities and metabolic pathways in these wetlands. We also find evidence for differences in the relative abundance of certain metabolic pathways that may correspond to the degree of anthropogenic modification the wetlands have experienced. These patterns, specifically those for pathways related to aerobic respiration and the carbon cycle, can be explained predominantly by the expected effects of wetland drainage. Our study demonstrates that eDNA has the potential to be an important new tool for the assessment and monitoring of wetland health.


Assuntos
DNA Ambiental/análise , Redes e Vias Metabólicas , Células Procarióticas/metabolismo , Áreas Alagadas , Archaea/classificação , Archaea/metabolismo , Bactérias/classificação , Bactérias/metabolismo , Biodiversidade , Ciclo do Carbono , Nova Zelândia , Análise de Componente Principal , RNA Ribossômico 16S/genética
14.
Ecotoxicol Environ Saf ; 208: 111669, 2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33396179

RESUMO

In this study, one lab-scale EGSB reactor (1.47 L volume) was designed to treat the antibiotic wastewater under different environmental factors, including the addition of cephalexin (CFX), Temperature (T) and Hydraulic Retention Time (HRT). The microbial community structure in EGSB reactor was analyzed with high-throughput sequencing technology to investigate their response to environmental factors changes, and then the random-matrix-theory (RMT)-based network analysis was used to investigate the microbial community's molecular ecological network in EGSB systems treating antibiotics wastewater. Moreover, the explanatory value of each environmental factor on the change of microbial community structure was obtained through the result of redundancy analysis (RDA). The results showed that the addition of cephalexin (CFX), decline of T and decline of HRT (8 h) would decrease the removal efficiency of COD decreasing. And the removal efficiency of CFX would not be affected by decline of T and HRT, except the producing and degrading process of CFX by-products was changed obviously. The result of RDA analysis suggested the environmental factors mainly affected bacterial and fungal microbial community structure but not archaeal ones. The result of high-throughput sequencing showed the relative abundance (RA) of Firmicutes had been obviously affected by T and HRT, which might be main reason leading to the decrease of COD removal efficiency. In addition, molecular ecological network analysis showed the growth of Bacteroidetes occupied the niche of functional microorganism and led to the unstable operation of EGSB when T declined. What's more, the molecular ecological network analysis revealed that Exophiala which belonged to fungi Ascomycota phylum was the hub genus to degrade complex refractory organic pollutants, and Aceticlastic methanogens Methanosaeta was the core functional archaea genus.


Assuntos
Antibacterianos/isolamento & purificação , Reatores Biológicos/microbiologia , Microbiota , Poluentes Químicos da Água/isolamento & purificação , Purificação da Água/métodos , Antibacterianos/metabolismo , Archaea/classificação , Archaea/genética , Archaea/crescimento & desenvolvimento , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Fungos/classificação , Fungos/genética , Fungos/crescimento & desenvolvimento , Fungos/metabolismo , Temperatura , Águas Residuárias/química , Poluentes Químicos da Água/metabolismo
15.
Ecotoxicol Environ Saf ; 207: 111246, 2021 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-32927157

RESUMO

Soilless revegetation is a cost-effective and eco-friendly method for the ecological restoration of gold mine tailings. However, due to gold mine tailings are high-salty, alkaline and low-nutrient, little research has been done on soilless revegetation of gold mine tailings. The aim of study was to apply soilless revegetation to gold mine tailings, and investigate the changes of physicochemical properties and microbial communities of tailings after soilless revegetation. Six selected herbaceous plants (Melilotus officinalis, Xanthium sibiricum, Festuca elata, Zoysia japonica, Amaranthus tricolor L., Artemisia desertorum) grew well on the bare tailings, and their heights reached as high as 16.28 cm after 90 days. After soilless revegetation, tailings salinity dramatically dropped from 547.15 to 129.24 µS cm-1, and pH went down from 8.68 to 7.59 at most. The content of available phosphorus (AP), available nitrogen (AN) and organic matter (OM) in tailings gradually improved, especially the content of AP and OM increased 53.36% and 52.58%, respectively. Furthermore, microbial metabolic activity and diversity in tailings obviously increased 70.33-264.70% and 1.64-13.97% respectively. The relative abundance of potential plant growth-promoting bacteria increased 1.40-3.05%, while the relative abundance of opportunistic pathogens and halophilic bacteria decreased 10.58-17.03% and 2.98-6.52% respectively. Such variations of microbial communities were beneficial for tailings restoration. This study provided insight into soilless revegetation and its impact on tailings microorganisms, which could be a new strategy for ecological restoration of gold mine tailings.


Assuntos
Biodegradação Ambiental , Microbiota , Microbiologia do Solo , Poluentes do Solo/análise , Archaea/metabolismo , Bactérias/metabolismo , Ouro/metabolismo , Nitrogênio/metabolismo , Fósforo/metabolismo , Desenvolvimento Vegetal , Plantas/metabolismo , Poaceae/metabolismo , Solo/química
16.
J Mol Biol ; 433(6): 166791, 2021 03 19.
Artigo em Inglês | MEDLINE | ID: mdl-33383035

RESUMO

The three domains of life employ various strategies to organize their genomes. Archaea utilize features similar to those found in both eukaryotic and bacterial chromatin to organize their DNA. In this review, we discuss the current state of research regarding the structure-function relationships of several archaeal chromatin proteins (histones, Alba, Cren7, and Sul7d). We address individual structures as well as inferred models for higher-order chromatin formation. Each protein introduces a unique phenotype to chromatin organization, and these structures are put into the context of in vivo and in vitro data. We close by discussing the present gaps in knowledge that are preventing further studies of the organization of archaeal chromatin, on both the organismal and domain level.


Assuntos
Archaea/genética , Proteínas Arqueais/química , Cromatina/ultraestrutura , DNA Arqueal/química , Proteínas de Ligação a DNA/química , Histonas/química , Sequência de Aminoácidos , Archaea/classificação , Archaea/metabolismo , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Cromatina/química , Cromatina/metabolismo , Sequência Conservada , DNA Arqueal/genética , DNA Arqueal/metabolismo , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Histonas/genética , Histonas/metabolismo , Conformação de Ácido Nucleico , Filogenia , Ligação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Domínios e Motivos de Interação entre Proteínas , Multimerização Proteica
17.
Nat Chem Biol ; 17(1): 10-19, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33328654

RESUMO

Many bacterial and archaeal organisms use clustered regularly interspaced short palindromic repeats-CRISPR associated (CRISPR-Cas) systems to defend themselves from mobile genetic elements. These CRISPR-Cas systems are classified into six types based on their composition and mechanism. CRISPR-Cas enzymes are widely used for genome editing and offer immense therapeutic opportunity to treat genetic diseases. To realize their full potential, it is important to control the timing, duration, efficiency and specificity of CRISPR-Cas enzyme activities. In this Review we discuss the mechanisms of natural CRISPR-Cas regulatory biomolecules and engineering strategies that enhance or inhibit CRISPR-Cas immunity by altering enzyme function. We also discuss the potential applications of these CRISPR regulators and highlight unanswered questions about their evolution and purpose in nature.


Assuntos
Archaea/genética , Bactérias/genética , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Regulação da Expressão Gênica em Archaea , Regulação Bacteriana da Expressão Gênica , Antibiose/genética , Archaea/metabolismo , Archaea/virologia , Bactérias/metabolismo , Bactérias/virologia , Bacteriófagos/genética , Bacteriófagos/crescimento & desenvolvimento , Bacteriófagos/metabolismo , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/metabolismo , Edição de Genes/métodos , Engenharia Genética/métodos , Humanos , Sequências Repetitivas Dispersas , RNA Guia/genética , RNA Guia/metabolismo
18.
Chemosphere ; 262: 127932, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-32805662

RESUMO

Zeolite addition has been widely suggested for its ability to overcome ammonia stress occurring during anaerobic digestion. However little is known regarding the underlying mechanisms of mitigation and especially how zeolite influences the microbial structuration. The aim of this study was to bring new contributions on the effect of zeolite on the microbial community arrangement under a low ammonia stress. Replicated batch experiments were conducted. The microbial population was characterised with 16S sequencing. Methanogenic pathways were identified with methane isotopic fractionation. In presence of ammonia, zeolite mitigated the decrease of biogas production rate. Zeolite induced the development of Izimaplasmatales order and preserved Peptococcaceae family members, known as propionate degraders. Moreover methane isotopic fractionation showed that hydrogenotrophic methanogenesis was maintained in presence of zeolite under ammonia low stress. Our results put forward the benefit of zeolite to improve the bacteria-archaea syntrophy needed for propionate degradation and methane production under a low ammonia stress.


Assuntos
Alimentos , Eliminação de Resíduos , Zeolitas/química , Amônia/metabolismo , Anaerobiose , Archaea/metabolismo , Bactérias/metabolismo , Biocombustíveis , Reatores Biológicos , Metano/metabolismo , Microbiota , Propionatos/metabolismo
19.
Int J Food Microbiol ; 337: 108951, 2021 Jan 16.
Artigo em Inglês | MEDLINE | ID: mdl-33202299

RESUMO

Pit mud microbiota plays a key role in flavour production for Chinese strong-aroma type liquor. However, the pit mud microbiota cannot be cultured in laboratory. In this study, an oligotrophic medium with acetate as carbon source was used to enrich pit mud microbiota. The 16S rRNA gene amplicon sequencing was applied to examine the microbial dynamics of the enrichment consortia. Both methanogens and bacteria were simultaneously enriched. Euryarchaeota, Bacteroidetes and Firmicutes were the top 3 enriched phyla, and 31 genera were successfully enriched. More specifically, 11 genera (65%) out of the 17 dominant genera in pit mud were successfully enriched, including Petrimonas, Proteiniphilum, Anaerocella, Hydrogenispora, Methanosarcina, Fermentimonas, LNR_A2-18, Sedimentibacter, Lutispora, Syntrophomonas and Aminobacterium. Furthermore, 20 rare genera in the analyzed pit mud samples were also enriched. Aceticlastic Methanosaeta and Methanosarcina were found to be dominant methanogens in the enrichment consortia. Metagenomic sequencing was then applied to the enriched microbial consortia to explore the metabolic potentials of pit mud microbes. Aceticlastic methanogenesis pathway of Methanosaeta was reconstructed. Furthermore, 26 high-quality metagenome-assembled genomes (MAGs) were obtained based on the metagenomic binning analysis. Moreover, nutrients in pit mud were found to be crucial to sustain the methanogenesis of the enriched microbial consortia. These results suggested that the enrichment approach by using oligotrophic culturing can effectively cultivate the pit mud microbiota. Combined with metagenomics, the oligotrophic culturing will be greatly helpful to decipher the community composition and metabolic potentials of pit mud microbiota.


Assuntos
Bebidas Alcoólicas/microbiologia , Microbiota , Acetatos/análise , Acetatos/metabolismo , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , China , Meios de Cultura/química , Fermentação , Humanos , Microbiota/genética , RNA Ribossômico 16S/genética
20.
Nat Commun ; 11(1): 5494, 2020 10 30.
Artigo em Inglês | MEDLINE | ID: mdl-33127895

RESUMO

Ammonia-oxidising archaea of the phylum Thaumarchaeota are important organisms in the nitrogen cycle, but the mechanisms driving their radiation into diverse ecosystems remain underexplored. Here, existing thaumarchaeotal genomes are complemented with 12 genomes belonging to the previously under-sampled Nitrososphaerales to investigate the impact of lateral gene transfer (LGT), gene duplication and loss across thaumarchaeotal evolution. We reveal a major role for gene duplication in driving genome expansion subsequent to early LGT. In particular, two large LGT events are identified into Nitrososphaerales and the fate of these gene families is highly lineage-specific, being lost in some descendant lineages, but undergoing extensive duplication in others, suggesting niche-specific roles. Notably, some genes involved in carbohydrate transport or coenzyme metabolism were duplicated, likely facilitating niche specialisation in soils and sediments. Overall, our results suggest that LGT followed by gene duplication drives Nitrososphaerales evolution, highlighting a previously under-appreciated mechanism of genome expansion in archaea.


Assuntos
Archaea/classificação , Archaea/genética , Duplicação Gênica , Genoma Arqueal , Filogenia , Archaea/metabolismo , Ecossistema , Evolução Molecular , Transferência Genética Horizontal , Metagenômica , Proteoma
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