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1.
Ecotoxicol Environ Saf ; 195: 110481, 2020 Jun 01.
Artigo em Inglês | MEDLINE | ID: mdl-32203775

RESUMO

Archaea remain important players in global biogeochemical cycles worldwide, including in the highly productive mangrove estuarine ecosystems. In the present study, we have explored the diversity, distribution, and function of the metabolically active fraction of the resident archaeal community of the Sundarban mangrove ecosystem, using both culture-independent and culture-dependent approaches. To evaluate the diversity and distribution pattern of the active archaeal communities, RNA based analysis of the 16S rRNA gene was performed on an Illumina platform. The active Crenarchaeal community was observed to remain constant while active Euryarchaeal community underwent considerable change across the sampling sites depending on varying anthropogenic factors. Haloarchaea were the predominant group in hydrocarbon polluted sediments, leading us to successfully isolate eleven p-hydroxybenzoic acid degrading haloarchaeal species. The isolates could also survive in benzoic acid, naphthalene, and o-phthalate. Quantitative estimation of p-hydroxybenzoic acid degradation was studied on select isolates, and their ability to reduce COD of polluted saline waters of Sundarban was also evaluated. To our knowledge, this is the first ever study combining culture-independent (Next Generation sequencing and metatranscriptome) and culture-dependent analyses for an assessment of archaeal function in the sediment of Sundarban.


Assuntos
Archaea/metabolismo , Sedimentos Geológicos/microbiologia , Hidrocarbonetos/metabolismo , Poluentes Químicos da Água/metabolismo , Archaea/genética , Archaea/isolamento & purificação , Biodegradação Ambiental , Crenarchaeota/isolamento & purificação , Euryarchaeota/isolamento & purificação , Parabenos/metabolismo , RNA Ribossômico 16S/genética , Áreas Alagadas
2.
FEMS Microbiol Ecol ; 94(11)2018 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-30124835

RESUMO

Green-coloured sediments in low-temperature geothermal surface features are typically indicative of photosynthetic activity. A near-boiling (89-93°C), alkali-chloride spring in the Taupo Volcanic Zone, New Zealand, was observed to have dark green sediments despite being too hot to support any known photosynthetic organisms. Analysis of aqueous and sediment microbial communities via 16S rRNA amplicon sequencing revealed them to be dominated by Aquifex spp., a genus of known hyperthermophilic hydrogen-oxidisers (69%-91% of operational taxonomic units (OTUs)), followed by groups within the Crenarchaeota (3%-20%), including the known iron-reducing genus Pyrobaculum. Cultivation experiments suggest that the green colouration of clay sediments in this spring may be due in part to ferruginous clays and associated compounds serving as substrates for the iron-reducing activity of low-abundance Pyrobaculum spp. These findings demonstrate the dynamic nature of microbe-mineral interactions in geothermal environments, and the potential ability of the rarer biosphere (1%-2% of observed sequences, cell densities of 450-33 000 g-1 sediment) to influence mineral formation at a macro-scale.


Assuntos
Argila , Sedimentos Geológicos/microbiologia , Fontes Termais/microbiologia , Ferro/metabolismo , Pyrobaculum/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Crenarchaeota/classificação , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Sedimentos Geológicos/química , Microbiota , Nova Zelândia , Filogenia , Pyrobaculum/isolamento & purificação , RNA Ribossômico 16S/genética
3.
Nucleic Acids Res ; 46(14): 7085-7096, 2018 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-29618058

RESUMO

Previously it was shown that UV irradiation induces a strong upregulation of tfb3 coding for a paralog of the archaeal transcriptional factor B (TFB) in Sulfolobus solfataricus, a crenarchaea. To investigate the function of this gene in DNA damage response (DDR), tfb3 was inactivated by gene deletion in Sulfolobus islandicus and the resulting Δtfb3 was more sensitive to DNA damage agents than the original strain. Transcriptome analysis revealed that a large set of genes show TFB3-dependent activation, including genes of the ups operon and ced system. Furthermore, the TFB3 protein was found to be associated with DDR gene promoters and functional dissection of TFB3 showed that the conserved Zn-ribbon and coiled-coil motif are essential for the activation. Together, the results indicated that TFB3 activates the expression of DDR genes by interaction with other transcriptional factors at the promoter regions of DDR genes to facilitate the formation of transcription initiation complex. Strikingly, TFB3 and Ced systems are present in a wide range of crenarchaea, suggesting that the Ced system function as a primary DNA damage repair mechanism in Crenarchaeota. Our findings further suggest that TFB3 and the concurrent TFB1 form a TFB3-dependent DNA damage-responsive circuit with their target genes, which is evolutionarily conserved in the major lineage of Archaea.


Assuntos
Proteínas Arqueais/metabolismo , Reparo do DNA , Sulfolobus/genética , Fatores de Transcrição/metabolismo , 4-Nitroquinolina-1-Óxido/farmacologia , Proteínas Arqueais/biossíntese , Proteínas Arqueais/química , Proteínas Arqueais/genética , Crenarchaeota/genética , Dano ao DNA , Evolução Molecular , Deleção de Genes , Regiões Promotoras Genéticas , Domínios Proteicos , Sulfolobus/citologia , Sulfolobus/efeitos dos fármacos , Sulfolobus/metabolismo , Fatores de Transcrição/biossíntese , Fatores de Transcrição/química , Fatores de Transcrição/genética , Ativação Transcricional
4.
Appl Microbiol Biotechnol ; 102(1): 499-507, 2018 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29079864

RESUMO

Spent mushroom substrate (SMS) is the residue of edible mushroom production occurring in huge amounts. The SMS residue can be digested for biogas production in the mesophilic anaerobic digestion. In the present study, performance of batch thermophilic anaerobic digestion (TAD) of SMS was investigated as well as the interconnected microbial population structure changes. The analyzed batch TAD process lasted for 12 days with the cumulative methane yields of 177.69 mL/g volatile solid (VS). Hydrolytic activities of soluble sugar, crude protein, and crude fat in SMS were conducted mainly in the initial phase, accompanied by the excessive accumulation of volatile fatty acids and low methane yield. Biogas production increased dramatically from days 4 to 6. The degradation rates of cellulose and hemicellulose were 47.53 and 55.08%, respectively. The high-throughput sequencing of 16S rRNA gene amplicons revealed that Proteobacteria (56.7%-62.8%) was the dominant phylum in different fermentative stages, which was highly specific compared with other anaerobic processes of lignocellulosic materials reported in the literature. Crenarchaeota was abundant in the archaea. The most dominant genera of archaea were retrieved as Methanothermobacter and Methanobacterium, but the latter decreased sharply with time. This study shows that TAD is a feasible method to handle the waste SMS.


Assuntos
Agaricales/metabolismo , Bactérias/metabolismo , Biocombustíveis , Consórcios Microbianos/fisiologia , Anaerobiose , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biomassa , Reatores Biológicos/microbiologia , Crenarchaeota/metabolismo , Ácidos Graxos Voláteis , Hidrólise , Lignina/metabolismo , Metano/análise , Metano/biossíntese , Metano/metabolismo , Methanobacteriaceae/metabolismo , Consórcios Microbianos/genética , Proteobactérias/metabolismo , RNA Ribossômico 16S/metabolismo , Esgotos/microbiologia
5.
FEMS Microbiol Ecol ; 93(10)2017 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-28961955

RESUMO

Aridisols are the dominant soil type in drylands, which occupy one-third of Earth's terrestrial surface. We examined controls on biogeographical patterns of Aridisol prokaryotic (bacterial and archaeal) communities at a regional scale by comparing communities from 100 Aridisols throughout the southwestern United States using high-throughput sequencing of the 16S rRNA gene. We found that microbial communities differed among global biomes and deserts of the Southwest. Differences among biomes were driven by differences in taxonomic identities, whereas differences among deserts of the Southwest were driven by differences in relative sequence abundance. Desert communities were dominated by Actinobacteria, Proteobacteria and Crenarchaeota, supporting the notion of a core set of abundant taxa in desert soils. Our findings contrast with studies showing little taxonomic overlap at the OTU level (97% sequence similarity) across large spatial scales, as we found ∼90% of taxa in at least two of the three deserts. Geographic distance structured prokaryotic communities indirectly through the influence of climate and soil properties. Structural equation modeling suggests that climate exerts a stronger influence than soil properties in shaping the composition of Aridisol microbial communities, with annual heat moisture index (an aridity metric) being the strongest climate driver. Annual heat moisture index was associated with decreased microbial diversity and richness. If the Desert Southwest becomes hotter and drier as predicted, these findings suggest that prokaryotic diversity and richness in Aridisols will decline.


Assuntos
Actinobacteria/genética , Crenarchaeota/genética , Clima Desértico , Proteobactérias/genética , Microbiologia do Solo , Solo/química , Actinobacteria/classificação , Actinobacteria/isolamento & purificação , Biodiversidade , Crenarchaeota/classificação , Crenarchaeota/isolamento & purificação , Ecossistema , Temperatura Alta , Microbiota/genética , Proteobactérias/classificação , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Sudoeste dos Estados Unidos
6.
PLoS One ; 12(6): e0178467, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28594863

RESUMO

Throughout the Baltic Sea redoxcline, virus production and the frequency of lytically-infected prokaryotic cells were estimated from parallel incubations of undiluted seawater and seawater that contained prokaryotes with substantially reduced numbers of viruses (virus dilution approach), effectively preventing viral reinfection during the incubation period. Undiluted seawater incubations resulted in much higher estimates of virus production (6-35×104 mL-1 h-1) and the frequency of infected cells (5-84%) than the virus dilution approach (virus production: 1-3×104 mL-1 h-1; frequency of infected cells: 1-11%). Viral production and the frequency of infected cells from both approaches, however, cannot be directly compared, as data obtained from undiluted incubations were biased by viral reinfection and other uncontrollable processes during the incubation period. High in situ viral abundance (1-2×107 mL-1) together with low virus production rates based on the virus dilution approach resulted in some of the longest viral turnover times (24-84 d) ever reported for the epipelagial. Throughout a wide range of environmental conditions, viral turnover time and burst size were negatively correlated. Given that viral decay estimated in ultra-filtered water was below the detection limit and the burst size was low (1-17), we conclude that prokaryotic viruses in the Baltic Sea redoxcline are investing most of their resources into stress defense (strong capsids) rather than proliferation (high burst size). In summary, the Baltic Sea redoxcline constitutes an environment where low virus production is found in combination with low viral decay, resulting in high viral abundance.


Assuntos
Água do Mar/virologia , Vírus/crescimento & desenvolvimento , Bactérias/crescimento & desenvolvimento , Biodiversidade , Crenarchaeota/crescimento & desenvolvimento , Euryarchaeota/crescimento & desenvolvimento , Temperatura
7.
FEMS Microbiol Ecol ; 93(8)2017 08 01.
Artigo em Inglês | MEDLINE | ID: mdl-28645185

RESUMO

After the Chernobyl nuclear power plant accident in 1986, contaminated soils, vegetation from the Red Forest and other radioactive debris were buried within trenches. In this area, trench T22 has long been a pilot site for the study of radionuclide migration in soil. Here, we used 454 pyrosequencing of 16S rRNA genes to obtain a comprehensive view of the bacterial and archaeal diversity in soils collected inside and in the vicinity of the trench T22 and to investigate the impact of radioactive waste disposal on prokaryotic communities. A remarkably high abundance of Chloroflexi and AD3 was detected in all soil samples from this area. Our statistical analysis revealed profound changes in community composition at the phylum and OTUs levels and higher diversity in the trench soils as compared to the outside. Our results demonstrate that the total absorbed dose rate by cell and, to a lesser extent the organic matter content of the trench, are the principal variables influencing prokaryotic assemblages. We identified specific phylotypes affiliated to the phyla Crenarchaeota, Acidobacteria, AD3, Chloroflexi, Proteobacteria, Verrucomicrobia and WPS-2, which were unique for the trench soils.


Assuntos
Acidobacteria/isolamento & purificação , Acidente Nuclear de Chernobyl , Chloroflexi/isolamento & purificação , Crenarchaeota/isolamento & purificação , Proteobactérias/isolamento & purificação , Resíduos Sólidos/análise , Verrucomicrobia/isolamento & purificação , Acidobacteria/classificação , Acidobacteria/genética , Sequência de Bases , Chloroflexi/classificação , Chloroflexi/genética , Crenarchaeota/classificação , Crenarchaeota/genética , Proteobactérias/classificação , Proteobactérias/genética , RNA Ribossômico 16S/genética , Resíduos Radioativos/análise , Radioisótopos/análise , Eliminação de Resíduos , Análise de Sequência de DNA , Solo , Microbiologia do Solo , Poluentes Radioativos do Solo/análise , Ucrânia , Verrucomicrobia/classificação , Verrucomicrobia/genética
8.
Biochem J ; 474(10): 1727-1739, 2017 05 09.
Artigo em Inglês | MEDLINE | ID: mdl-28377493

RESUMO

Crenarchaeal chromatin protein Cren7 binds double-stranded DNA in the minor groove, introducing a sharp single-step DNA kink. The side chain of Leu28, a residue conserved among all Cren7 homologs, intercalates into the kinked DNA step. In the present study, we replaced Leu28 with a residue containing a hydrophobic side chain of different sizes (i.e. L28A, L28V, L28I, L28M and L28F). Both the stability of the Cren7-DNA complex and the ability of Cren7 to constrain DNA supercoils correlated well with the size of the intercalated side chain. Structural analysis shows that L28A induces a kink (∼43°), nearly as sharp as that produced by wild-type Cren7 (∼48°), in the bound DNA fragment despite the lack of side chain intercalation. In another duplex DNA fragment, L28F inserts a large hydrophobic side chain deep into the DNA step, but introduces a smaller kink (∼39°) than that formed by the wild-type protein (∼50°). Mutation of Leu28 into methionine yields two protein conformers differing in loop ß3-ß4 orientation, DNA-binding surface and DNA geometry in the protein-DNA structure. Our results indicate that side chain intercalation is not directly responsible for DNA kinking or bending by Cren7, but plays a critical role in the stabilization of the Cren7-DNA complex. In addition, the flexibility of loop ß3-ß4 in Cren7, as revealed in the crystal structure of L28M-DNA, may serve a role in the modulation of chromosomal organization and function in the cell.


Assuntos
Proteínas Arqueais/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Crenarchaeota/metabolismo , DNA Arqueal/metabolismo , DNA Super-Helicoidal/metabolismo , Leucina/química , Modelos Moleculares , Substituição de Aminoácidos , Proteínas Arqueais/química , Proteínas Arqueais/genética , Proteínas Cromossômicas não Histona/química , Proteínas Cromossômicas não Histona/genética , Cristalografia por Raios X , DNA Arqueal/química , DNA Super-Helicoidal/química , Interações Hidrofóbicas e Hidrofílicas , Cinética , Mutagênese Sítio-Dirigida , Mutação , Conformação de Ácido Nucleico , Conformação Proteica , Estabilidade Proteica , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Ressonância de Plasmônio de Superfície
9.
FEMS Microbiol Ecol ; 93(2)2017 02.
Artigo em Inglês | MEDLINE | ID: mdl-27940645

RESUMO

Although Thaumarchaeota are important contributors to ammonia oxidation in terrestrial habitats, distributions of ammonia oxidizers along soil depth profiles are poorly understood, especially in relation to distinct land usages. Leveraging the close proximity of forest, field and agricultural plots at the RARE: Charitable Research Reserve, we examined soil thaumarchaeotal biogeography at three different depths (0-15, 15-30 and 30-45 cm) from plots within areas of contrasting land usage. Data from high-throughput sequencing of thaumarchaeotal 16S rRNA gene sequences demonstrated that OTU richness was affected significantly by depth and land-use type. Specifically, thaumarchaeotal diversity was higher in soils from forest sites than from field sites, and lower within 0-15 cm soils than either 15-30 cm or 30-45 cm soils. Soil land-use type influenced the relative abundance of the Soil Crenarchaeota Group (SCG), with a lower relative abundance of SCG in forest sites compared to field sites. At the OTU level, thaumarchaeotal communities changed with increasing soil depth for agricultural soils, in contrast to homogeneous depth profiles generated from forest site samples. Soil pH was the strongest factor impacting thaumarchaeotal community composition and, importantly, the evenness of archaeal taxa. Nitrogen, carbon and soil texture shaped thaumarchaeotal community composition among field site samples.


Assuntos
Archaea/genética , Filogeografia , Microbiologia do Solo , Agricultura , Amônia/metabolismo , Archaea/fisiologia , Crenarchaeota/genética , Ecossistema , Florestas , Nitrogênio , Oxirredução , RNA Ribossômico 16S/genética , Solo/química
10.
J Genet ; 95(3): 537-49, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-27659324

RESUMO

The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the HEG was found to be less in comparison to the genome G+C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea. The analysis revealed prevalence of Uending codons even within theWWY(nucleotide ambiguity code) families in Crenarchaea vis-à-vis Euryarchaea, bacteria and Eukarya. No plausible interpretation of the observed disparity could be made either in the context of tRNA gene composition or genome G+C%. The results in this study attested that the preferential biasness for codons in HEG of Crenarchaea might be different from Euryarchaea. The main highlights are (i) varied CUB in the HEG and in the whole genomes in Euryarchaea and Crenarchaea. (ii) Crenarchaea was found to have some unusual optimal codons (OCs) compared to other organisms. (iii) G+C% (and GC3) of the HEG were different from the genome G+C% in the two phyla. (iv) Genome G+C% and tRNA gene number failed to explain CUB in Crenarchaea. (v) Translational selection is possibly responsible for A+T rich OCs in Crenarchaea.


Assuntos
Composição de Bases , Códon/química , Crenarchaeota/genética , Euryarchaeota/genética , Genoma Arqueal , Códon/metabolismo , Crenarchaeota/classificação , Crenarchaeota/metabolismo , Euryarchaeota/classificação , Euryarchaeota/metabolismo , Filogenia , Biossíntese de Proteínas , RNA de Transferência/genética , RNA de Transferência/metabolismo
11.
FEMS Microbiol Ecol ; 92(12)2016 12.
Artigo em Inglês | MEDLINE | ID: mdl-27612495

RESUMO

Impacts of long-term CO2 exposure on environmental processes and microbial populations of near-surface soils are poorly understood. This near-surface long-term CO2 injection study demonstrated that soil microbiology and geochemistry is influenced more by seasonal parameters than elevated CO2 Soil samples were taken during a 3-year field experiment including sampling campaigns before, during and after 24 months of continuous CO2 injection. CO2 concentrations within CO2-injected plots increased up to 23% during the injection period. No CO2 impacts on geochemistry were detected over time. In addition, CO2-exposed samples did not show significant changes in microbial CO2 and CH4 turnover rates compared to reference samples. Likewise, no significant CO2-induced variations were detected for the abundance of Bacteria, Archaea (16S rDNA) and gene copy numbers of the mcrA gene, Crenarchaeota and amoA gene. The majority (75%-95%) of the bacterial sequences were assigned to five phyla: Firmicutes, Proteobacteria, Actinobacteria, Acidobacteria and Bacteroidetes The majority of the archaeal sequences (85%-100%) were assigned to the thaumarchaeotal cluster I.1b (soil group). Univariate and multivariate statistical as well as principal component analyses showed no significant CO2-induced variation. Instead, seasonal impacts especially temperature and precipitation were detected.


Assuntos
Bactérias/classificação , Dióxido de Carbono/química , Dióxido de Carbono/farmacologia , Crenarchaeota/classificação , Microbiologia do Solo , Solo/química , Bactérias/efeitos dos fármacos , Bactérias/genética , Crenarchaeota/efeitos dos fármacos , Crenarchaeota/genética , DNA Ribossômico/genética , Efeito Estufa , Filogenia , RNA Ribossômico 16S/genética , Reino Unido
12.
FEMS Microbiol Rev ; 40(5): 625-47, 2016 09.
Artigo em Inglês | MEDLINE | ID: mdl-27476079

RESUMO

Reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. However, whereas signal transduction is well studied in Eukaryotes and Bacteria, the knowledge in Archaea is still rather scarce. Archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the Euryarchaeota and Crenarchaeaota, seem to exhibit fundamental differences in regulatory systems. Euryarchaeota (e.g. halophiles, methanogens, thermophiles), like Bacteria and Eukaryotes, rely on bacterial-type two-component signal transduction systems (phosphorylation on His and Asp), as well as on the protein phosphorylation on Ser, Thr and Tyr by Hanks-type protein kinases. Instead, Crenarchaeota (e.g. acidophiles and (hyper)thermophiles) only depend on Hanks-type protein phosphorylation. In this review, the current knowledge of reversible protein phosphorylation in Archaea is presented. It combines results from identified phosphoproteins, biochemical characterization of protein kinases and protein phosphatases as well as target enzymes and first insights into archaeal signal transduction by biochemical, genetic and polyomic studies.


Assuntos
Proteínas Arqueais/metabolismo , Crenarchaeota/metabolismo , Euryarchaeota/metabolismo , Fosfoproteínas Fosfatases/metabolismo , Fosforilação/genética , Proteínas Quinases/metabolismo , Crenarchaeota/genética , Euryarchaeota/genética , Domínios Proteicos/genética , Processamento de Proteína Pós-Traducional/genética , Processamento de Proteína Pós-Traducional/fisiologia , Transdução de Sinais/fisiologia
13.
Nat Commun ; 7: 12115, 2016 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-27378076

RESUMO

Biological features can be inferred, based on genomic data, for many microbial lineages that remain uncultured. However, cultivation is important for characterizing an organism's physiology and testing its genome-encoded potential. Here we use single-cell genomics to infer cultivation conditions for the isolation of an ectosymbiotic Nanoarchaeota ('Nanopusillus acidilobi') and its host (Acidilobus, a crenarchaeote) from a terrestrial geothermal environment. The cells of 'Nanopusillus' are among the smallest known cellular organisms (100-300 nm). They appear to have a complete genetic information processing machinery, but lack almost all primary biosynthetic functions as well as respiration and ATP synthesis. Genomic and proteomic comparison with its distant relative, the marine Nanoarchaeum equitans illustrate an ancient, common evolutionary history of adaptation of the Nanoarchaeota to ectosymbiosis, so far unique among the Archaea.


Assuntos
Proteínas Arqueais/genética , Crenarchaeota/genética , Genoma Arqueal , Nanoarchaeota/genética , Simbiose/genética , Proteínas Arqueais/metabolismo , Evolução Biológica , Mapeamento Cromossômico , Crenarchaeota/classificação , Crenarchaeota/metabolismo , Crenarchaeota/ultraestrutura , Expressão Gênica , Genômica/métodos , Fontes Termais , Nanoarchaeota/classificação , Nanoarchaeota/metabolismo , Nanoarchaeota/ultraestrutura , Filogenia
14.
PLoS One ; 11(5): e0154354, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27135948

RESUMO

Rumen microbial communities play important roles in feed conversion and the physiological development of the ruminants. Despite its significance, little is known about the rumen microbial communities at different life stages after birth. In this study, we characterized the rumen bacterial and the archaeal communities in 11 different age groups (7, 15, 30, 60, 90, 120, 150, 180, 360, 540 and 720 days old) of a crossbred F1 goats (n = 5 for each group) by using an Illumina MiSeq platform targeting the V3-V4 region of the 16S rRNA gene. We found that the bacterial communities were mainly composed of Bacteroidetes, Firmicutes, and Proteobacteria across all age groups. The relative abundance of Firmicutes was stable across all age groups. While changes in relative abundance were observed in Bacteroidetes and Proteobacteria, these two phyla reached a stable stage after weaning (day 90). Euryarchaeota (82%) and Thaumarchaeota (15%) were the dominant phyla of Archaea. Crenarchaeota was also observed, although at a very low relative abundance (0.68% at most). A clear age-related pattern was observed in the diversity of bacterial community with 59 OTUs associated with age. In contrast, no age-related OTU was observed in archaea. In conclusion, our results suggested that from 7 days to 2 years, the ruminal microbial community of our experimental goats underwent significant changes in response to the shift in age and diet.


Assuntos
Microbiota/genética , Animais , Archaea/genética , Archaea/isolamento & purificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Euryarchaeota/genética , Euryarchaeota/isolamento & purificação , Firmicutes/genética , Firmicutes/isolamento & purificação , Cabras , Microbiota/fisiologia , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Rúmen/microbiologia , Fatores de Tempo
15.
J Microbiol Biotechnol ; 26(5): 867-75, 2016 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-26869602

RESUMO

Archaea substantially contribute to global geochemical cycling and energy cycling and are impacted by land-use change. However, the response of archaeal communities to a change from upland field to paddy field has been poorly characterized. Here, soil samples were collected at two depths (0-20 cm and 20-40 cm) from one upland field and six paddy fields that were established on former upland fields at different times (1, 5, 10, 20, 30, and 40 years before the study). Barcoded pyrosequencing was employed to assess the archaeal communities from the samples at taxonomic resolutions from phylum to genus levels. The total archaeal operational taxonomic unit (OTU) richness showed a significant positive correlation with the land-use change duration. Two phyla, Euryarchaeota and Crenarchaeota, were recorded throughout the study. Both the relative abundance and OTU richness of Euryarchaeota increased at both depths but increased more steadily at the subsurface rather than at the surface. However, these data of Crenarchaeota were the opposite. Additionally, the archaeal composition exhibited a significant relationship with C/N ratios, total phosphorus, soil pH, Olsen phosphorus, and the land-use change duration at several taxonomic resolutions. Our results emphasize that after a change from upland fields to paddy fields, the archaeal diversity and composition changed, and the duration is an important factor in addition to the soil chemical properties.


Assuntos
Agricultura/métodos , Archaea/classificação , Microbiologia do Solo , Solo/química , Archaea/química , Archaea/genética , Archaea/metabolismo , Crenarchaeota/química , Crenarchaeota/classificação , Crenarchaeota/genética , Monitoramento Ambiental , Euryarchaeota/química , Euryarchaeota/classificação , Euryarchaeota/genética , Fenômenos Geológicos , Compostos Orgânicos/análise , Oryza/crescimento & desenvolvimento , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
16.
FEMS Microbiol Ecol ; 92(4): fnw038, 2016 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26902803

RESUMO

Microbial communities in the glacier forefield of Styggedalsbreen, Norway, were investigated along a chronosequence from newly exposed soil to vegetated soils using next-generation sequencing of the 16S rRNA gene. In order to monitor the short-term effect of temperature on community successions along the soil gradient, the soil samples were incubated at three different temperatures (5°C, 10°C and 22°C). The microbial community composition along the chronosequence differed according to distance from the glacial terminus and incubation temperature. Samples close to the glacier terminus were dominated by Proteobacteria at 5°C and 10°C, while at 22°C members of Chloroflexi, Acidobacteria and Verrucomicrobia in addition to Proteobacteria accounted for most of the diversity, indicating that sites close to the glacier terminus are more closely related to former subglacial environments. Within the Archaea domain, members of the phylum Euryarchaeota dominated in samples closer to the glacier terminus with a shift to members of the phyla Thaumarchaeota-Crenarchaeota with increased soil age. Our data indicate that composition and diversity of the microbial communities along the glacier forefield depend not only on exposure time but are also to a large degree influenced by soil surface temperature and soil maturation.


Assuntos
DNA Arqueal/genética , DNA Bacteriano/genética , Aquecimento Global , Camada de Gelo/microbiologia , Microbiota/genética , Acidobacteria/genética , Acidobacteria/isolamento & purificação , Regiões Árticas , Sequência de Bases , Chloroflexi/genética , Chloroflexi/isolamento & purificação , Crenarchaeota/classificação , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Meio Ambiente , Sequenciamento de Nucleotídeos em Larga Escala , Líquens/classificação , Noruega , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Solo/química , Microbiologia do Solo , Temperatura , Verrucomicrobia/genética , Verrucomicrobia/isolamento & purificação
17.
Mikrobiologiia ; 85(4): 446-457, 2016 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28853776

RESUMO

Thermoacidophilic sulfate reduction remains a poorly studied process, which was investigated in the present work. Radioisotope analysis with 35S-Iabeled sulfate was used to determine the rates of dissimilatory sulfate reduction in acidic thermal springs of Kamchatka, Russia. Sulfate reduction rates were found to vary from 0.054 to 12.9 nmol S04/(cm3 day). The Neftyanaya ploshchadka spring (Uzon caldera, 60'C, pH 4.2) and Oreshek spring (Mutnovskii volcano, 91'C, pH 3.5) exhibited the highest activity of sulfate-reducing prokaryotes. Stable enrich- ment'cultures reducing sulfate at pH and temperature values close to'the environmental ones were obtained from these springs. Analysis of the 16S rRNA gene sequences revealed that'a chemolithoautotrophic bacterium Ther- modesufobium sp. 3127-1 was responsible for sulfate reduction in the enrichment from the Oil Site spring. A chemoorganoheterotrophic archaeon Vulcanisaeta sp. 3102-1 (phylum Crenarchaeota) was identified in the en- richment from Oreshek spring. Thus, dissimilatory sulfate reduction under thermoacidophilic conditions was demonstrated and the agents responsible for this process were revealed.


Assuntos
Clostridiales/metabolismo , Crenarchaeota/metabolismo , Fontes Termais/microbiologia , RNA Ribossômico 16S/genética , Bactérias Redutoras de Enxofre/metabolismo , Microbiologia da Água , Carbono/metabolismo , Radioisótopos de Carbono , Clostridiales/classificação , Clostridiales/genética , Clostridiales/isolamento & purificação , Crenarchaeota/classificação , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Concentração de Íons de Hidrogênio , Oxirredução , Filogenia , Federação Russa , Sulfatos/metabolismo , Bactérias Redutoras de Enxofre/classificação , Bactérias Redutoras de Enxofre/genética , Temperatura
18.
Mikrobiologiia ; 85(5): 522-530, 2016 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29364600

RESUMO

Bacterial mats formed by a colorless sulfur bacterium Thioploca sp. in the area of the Posolski Bank cold methane seep (southern Baikal) were -studied using electron microscopy and phylogenetic analysis. Morphologically the bacteria were identified as Thioploca ingrica.- Confocal microscopy of DAPI-stained samples revealed numerous rod-shaped, filamentous, and spiral microorganisms in the sheaths, as well as in- side and between the trichomes. Transmission electron microscopy revealed nonvacuolated bacteria and small cells-without cell envelopes within the sheath. Bacteria with pronounced intracytoplasmic membranes characteristic; of type I methanotrophs were observed at the outer side of the sheath. Based on analysis of the 16S rRNA gene sequences, the following phyla were idenified in the sheath community: Bacteroidetes, Nitro- spira, Chloroflexi, Planctomycetes, Verrucomicrobia,'y-, and 6-Proteobacteria, Euryarchaeota, Crenarchaeota, and Thaumarchaeota, as well as anammox bacteria. A hypothetical scheme of matter flows in the Lake Baikal bacterial mats was proposed based on the data on metabolism of the cultured homologues.


Assuntos
Água Subterrânea/microbiologia , Lagos/microbiologia , Consórcios Microbianos/fisiologia , RNA Ribossômico 16S/genética , Thiotrichaceae/genética , Bacteroidetes/classificação , Bacteroidetes/genética , Bacteroidetes/isolamento & purificação , Chloroflexi/classificação , Chloroflexi/genética , Chloroflexi/isolamento & purificação , Crenarchaeota/classificação , Crenarchaeota/genética , Crenarchaeota/isolamento & purificação , Ecossistema , Euryarchaeota/classificação , Euryarchaeota/genética , Euryarchaeota/isolamento & purificação , Metano/química , Metano/metabolismo , Filogenia , Planctomycetales/classificação , Planctomycetales/genética , Planctomycetales/isolamento & purificação , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , Sibéria , Thiotrichaceae/classificação , Thiotrichaceae/isolamento & purificação , Thiotrichaceae/ultraestrutura , Verrucomicrobia/classificação , Verrucomicrobia/genética , Verrucomicrobia/isolamento & purificação
19.
Archaea ; 2015: 978632, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26539062

RESUMO

We expressed a putative ß-galactosidase Asac_1390 from hyperthermophilic crenarchaeon Acidilobus saccharovorans in Escherichia coli and purified the recombinant enzyme. Asac_1390 is composed of 490 amino acid residues and showed high sequence similarity to family 1 glycoside hydrolases from various thermophilic Crenarchaeota. The maximum activity was observed at pH 6.0 and 93°C. The half-life of the enzyme at 90°C was about 7 hours. Asac_1390 displayed high tolerance to glucose and exhibits hydrolytic activity towards cellobiose and various aryl glucosides. The hydrolytic activity with p-nitrophenyl (pNP) substrates followed the order pNP-ß-D-galactopyranoside (328 U mg(-1)), pNP-ß-D-glucopyranoside (246 U mg(-1)), pNP-ß-D-xylopyranoside (72 U mg(-1)), and pNP-ß-D-mannopyranoside (28 U mg(-1)). Thus the enzyme was actually a multifunctional ß-glycosidase. Therefore, the utilization of Asac_1390 may contribute to facilitating the efficient degradation of lignocellulosic biomass and help enhance bioconversion processes.


Assuntos
Crenarchaeota/enzimologia , Estabilidade Enzimática , beta-Glucosidase/metabolismo , Crenarchaeota/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Expressão Gênica , Glucosídeos/metabolismo , Concentração de Íons de Hidrogênio , Hidrólise , Cinética , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Homologia de Sequência de Aminoácidos , Temperatura , Fatores de Tempo , beta-Glucosidase/química , beta-Glucosidase/genética , beta-Glucosidase/isolamento & purificação
20.
Ecology ; 96(8): 2300-10, 2015 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-26405754

RESUMO

Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.


Assuntos
Nitrogênio/metabolismo , Plantas/metabolismo , Rizosfera , Microbiologia do Solo , Bactérias/genética , Crenarchaeota/genética , RNA Arqueal/genética , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Solo/química
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