Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 3.758
Filtrar
1.
Bioresour Technol ; 391(Pt A): 129966, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37918493

RESUMO

Different gradients of dissolved oxygen (DO) regulate the microbial community and nitrogen removal pathways of denitrifying anaerobic methane oxidation (DAMO) and anaerobic ammonium oxidation (Anammox) coupled process in a batch biofilm reactor. Under completely anaerobic condition, approximately 72 mg NO3--N/L was removed at a daily rate of 6.55 mg N/L, whereas a peak accumulation of 95 mg NO3--N/L was observed during DO reached 0.5 mg/L. There is a decrease in the abundance of Candidatus Methylomirabilis (24.1%), Candidatus Methanoperedens (23.3%), and Candidatus Kuenenia (22.6%) to below 5% when DO levels reached 0.2 mg/L. Moreover, key genes associated with the reverse methanogenesis (mcrA) and anaerobic ammonium oxidase (hzo) decreased. These findings indicate that during oxygen shock, methanotrophs and denitrifiers replace Anammox bacteria on the outer sphere of the biofilm, whereas DAMO bacteria and archaea are protected from external oxygen shock due to the microbial stratification of biofilm.


Assuntos
Compostos de Amônio , Archaea , Archaea/genética , Archaea/metabolismo , Anaerobiose , Metano/metabolismo , Bactérias/genética , Bactérias/metabolismo , Oxirredução , Biofilmes , Methanobacteriaceae/metabolismo , Compostos de Amônio/metabolismo , Reatores Biológicos/microbiologia , Desnitrificação
2.
Results Probl Cell Differ ; 71: 185-212, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-37996679

RESUMO

The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.


Assuntos
Bactérias , Microbiota , Humanos , Filogenia , Bactérias/genética , Bactérias/metabolismo , Archaea/genética , Archaea/metabolismo , Cloreto de Sódio/metabolismo , Microbiota/genética , Metagenômica
3.
Bioresour Technol ; 391(Pt B): 129988, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37949149

RESUMO

Elevated temperatures favor bioleaching processes through faster kinetics, more favorable mineral chemistry, lower cooling requirements, and less surface passivation. Extremely thermoacidophilic archaea from the order Sulfolobales exhibit novel mechanisms for bioleaching metals from ores and have great potential. Genome sequences of many extreme thermoacidophiles are now available and provide new insights into their biochemistry, metabolism, physiology and ecology as these relate to metal mobilization from ores. Although there are some molecular genetic tools available for extreme thermoacidophiles, further development of these is sorely needed to advance the study and application of these archaea for bioleaching applications. The evolving landscape for bioleaching technologies at high temperatures merits a closer look through a genomic lens at what is currently possible and what lies ahead in terms of new developments and emerging opportunities. The need for critical metals and the diminishing primary deposits for copper should provide incentives for high temperature bioleaching.


Assuntos
Archaea , Metais , Archaea/genética , Archaea/metabolismo , Oxirredução , Metais/metabolismo , Cobre/metabolismo , Minerais
4.
Sci Total Environ ; 908: 168530, 2024 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-37963541

RESUMO

Nitrification is a major pathway of N2O production, especially in aerobic soils. The amendment of soils with biochar has been suggested as a promising solution to regulate soil N cycle and reduce N2O emissions. However, there is a lack of comprehensive and quantitative understanding of biochar impacts on soil nitrification and nitrification-induced N2O emissions. In this study, a meta-analysis was conducted using data compiled across 95 peer-reviewed studies. Results showed that biochar in general significantly increased soil nitrification rate by 56 %, with overall no significant effect on nitrification-induced N2O emissions, suggesting that biochar likely restricted the fraction of nitrified N emitted as N2O emissions. The abundance of ammonia-oxidizing bacteria (AOB) was significantly increased by 37 % following biochar addition, but that of ammonia-oxidizing archaea (AOA) did not change significantly, indicating that the impact of biochar on AOB rather than AOA may play an important role in soil nitrification. The impacts of biochar on soil nitrification processes were heterogeneous depending on soil properties. Biochar increased soil nitrification rate and AOB abundance to a larger extent in poorly pH-buffered soils such as those with acidic pH (<5), low organic carbon (<10 g kg-1), or poor texture (rich in either sand or clay), which may be attributed to the liming and structural effects of biochar that regulate soil pH and water-air status. The overall no significant effect of biochar on nitrification-induced N2O emissions was due to a positive effect in acidic soils, a negative effect in alkaline soils, and little effect in neutral soils. This study provides a comprehensive insight into how different factors mediate the response of soil nitrification processes to biochar amendment, which contributes to a new understanding of biochar function in regulating soil N2O emissions, and can assist in designing biochar projects that would benefit soil N cycle while minimizing undesirable side effects.


Assuntos
Nitrificação , Solo , Solo/química , Amônia/metabolismo , Microbiologia do Solo , Archaea/metabolismo , Óxido Nitroso/análise
5.
Cell Host Microbe ; 31(11): 1837-1849.e5, 2023 11 08.
Artigo em Inglês | MEDLINE | ID: mdl-37909049

RESUMO

Despite a wide presence of type III clustered regularly interspaced short palindromic repeats, CRISPR-associated (CRISPR-Cas) in archaea and bacteria, very few anti-CRISPR (Acr) proteins inhibiting type III immunity have been identified, and even less is known about their inhibition mechanism. Here, we present the discovery of a type III CRISPR-Cas inhibitor, AcrIIIB2, encoded by Sulfolobus virus S. islandicus rod-shaped virus 3 (SIRV3). AcrIIIB2 inhibits type III-B CRISPR-Cas immune response to protospacers encoded in middle/late-expressed viral genes. Investigation of the interactions between S. islandicus type III-B CRISPR-Cas Cmr-α-related proteins and AcrIIIB2 reveals that the Acr does not bind to Csx1 but rather interacts with the Cmr-α effector complex. Furthermore, in vitro assays demonstrate that AcrIIIB2 can block the dissociation of cleaved target RNA from the Cmr-α complex, thereby inhibiting the Cmr-α turnover, thus preventing host cellular dormancy and further viral genome degradation by the type III-B CRISPR-Cas immunity.


Assuntos
Vírus de Archaea , Proteínas Associadas a CRISPR , Vírus de Archaea/metabolismo , Proteínas Virais/genética , Sistemas CRISPR-Cas , Archaea/metabolismo , Proteínas Associadas a CRISPR/genética
6.
Microbiome ; 11(1): 238, 2023 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-37924150

RESUMO

BACKGROUND: Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle. RESULTS: The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1ß, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host. CONCLUSIONS: This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.


Assuntos
Dieta , Microbiota , Bovinos , Animais , Dieta/veterinária , Rúmen/microbiologia , Bactérias/genética , Bactérias/metabolismo , Archaea/metabolismo , Inflamação/metabolismo , Metano/metabolismo , Ornitina/metabolismo , Poliaminas/metabolismo , Ração Animal/análise , Fermentação
7.
Nat Commun ; 14(1): 7597, 2023 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-37989750

RESUMO

NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.


Assuntos
NAD , RNA , NAD/metabolismo , Adenosina Difosfato Ribose/metabolismo , Archaea/metabolismo , Cromatografia Líquida , Espectrometria de Massas em Tandem
8.
Nat Commun ; 14(1): 7305, 2023 11 11.
Artigo em Inglês | MEDLINE | ID: mdl-37951938

RESUMO

Knowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.


Assuntos
Ecossistema , Solo , Filogenia , Archaea/metabolismo , Genômica , Microbiologia do Solo , Oxirredução , Amônia/metabolismo
9.
Protein Sci ; 32(12): e4829, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37921047

RESUMO

Cyclic di-adenosine monophosphate (c-di-AMP) is a newly identified prokaryotic cyclic dinucleotide second messenger well elucidated in bacteria, while less studied in archaea. Here, we describe the enzymes involved in c-di-AMP metabolism in the hyperthermophilic archaeon Pyrococcus yayanosii. Our results demonstrate that c-di-AMP is synthesized from two molecules of ATP by diadenylate cyclase (DAC) and degraded into pApA and then to AMP by a DHH family phosphodiesterase (PDE). DAC can be activated by a wider variety of ions, using two conserved residues, D188 and E244, to coordinate divalent metal ions, which is different from bacterial CdaA and DisA. PDE possesses a broad substrate spectrum like bacterial DHH family PDEs but shows a stricter base selection between A and G in cyclic dinucleotides hydrolysis. PDE shows differences in substrate binding patches from bacterial counterparts. C-di-AMP was confirmed to exist in Thermococcus kodakarensis cells, and the deletion of the dac or pde gene supports that the synthesis and degradation of c-di-AMP are catalyzed by DAC and PDE, respectively. Our results provide a further understanding of the metabolism of c-di-AMP in archaea.


Assuntos
Archaea , Proteínas de Bactérias , Archaea/metabolismo , Proteínas de Bactérias/química , Bactérias/metabolismo , Diester Fosfórico Hidrolases/química , Diester Fosfórico Hidrolases/genética , Diester Fosfórico Hidrolases/metabolismo , Íons
10.
Proc Natl Acad Sci U S A ; 120(49): e2316668120, 2023 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-38011558

RESUMO

Type IV pili (T4P) are ubiquitous in both bacteria and archaea. They are polymers of the major pilin protein, which has an extended and protruding N-terminal helix, α1, and a globular C-terminal domain. Cryo-EM structures have revealed key differences between the bacterial and archaeal T4P in their C-terminal domain structure and in the packing and continuity of α1. This segment forms a continuous α-helix in archaeal T4P but is partially melted in all published bacterial T4P structures due to a conserved helix breaking proline at position 22. The tad (tight adhesion) T4P are found in both bacteria and archaea and are thought to have been acquired by bacteria through horizontal transfer from archaea. Tad pilins are unique among the T4 pilins, being only 40 to 60 residues in length and entirely lacking a C-terminal domain. They also lack the Pro22 found in all high-resolution bacterial T4P structures. We show using cryo-EM that the bacterial tad pilus from Caulobacter crescentus is composed of continuous helical subunits that, like the archaeal pilins, lack the melted portion seen in other bacterial T4P and share the packing arrangement of the archaeal T4P. We further show that a bacterial T4P, the Vibrio cholerae toxin coregulated pilus, which lacks Pro22 but is not in the tad family, has a continuous N-terminal α-helix, yet its α1 s are arranged similar to those in other bacterial T4P. Our results highlight the role of Pro22 in helix melting and support an evolutionary relationship between tad and archaeal T4P.


Assuntos
Proteínas de Fímbrias , Fímbrias Bacterianas , Proteínas de Fímbrias/genética , Proteínas de Fímbrias/química , Fímbrias Bacterianas/metabolismo , Archaea/genética , Archaea/metabolismo , Bactérias/metabolismo
11.
J Biosci ; 482023.
Artigo em Inglês | MEDLINE | ID: mdl-38018541

RESUMO

The symbiotic evolution between the two prokaryotic domains of life (bacteria and archaea) is believed to have given rise to the third domain of life, the eukaryotes. Common to all three domains of life, is an ancient mechanism of ribosome-mediated protein synthesis (translation). Can the evolutionary history of the protein translation apparatus shed light on the evolutionary history of life forms? This commentary addresses this broad question with the spotlight on a specific component of the translation apparatus.


Assuntos
Eucariotos , Evolução Molecular , Eucariotos/genética , Bactérias/genética , Bactérias/metabolismo , Archaea/genética , Archaea/metabolismo , Filogenia
12.
Proc Natl Acad Sci U S A ; 120(48): e2308224120, 2023 Nov 28.
Artigo em Inglês | MEDLINE | ID: mdl-37983496

RESUMO

The TnpB proteins are transposon-associated RNA-guided nucleases that are among the most abundant proteins encoded in bacterial and archaeal genomes, but whose functions in the transposon life cycle remain unknown. TnpB appears to be the evolutionary ancestor of Cas12, the effector nuclease of type V CRISPR-Cas systems. We performed a comprehensive census of TnpBs in archaeal and bacterial genomes and constructed a phylogenetic tree on which we mapped various features of these proteins. In multiple branches of the tree, the catalytic site of the TnpB nuclease is rearranged, demonstrating structural and probably biochemical malleability of this enzyme. We identified numerous cases of apparent recruitment of TnpB for other functions of which the most common is the evolution of type V CRISPR-Cas effectors on about 50 independent occasions. In many other cases of more radical exaptation, the catalytic site of the TnpB nuclease is apparently inactivated, suggesting a regulatory function, whereas in others, the activity appears to be retained, indicating that the recruited TnpB functions as a nuclease, for example, as a toxin. These findings demonstrate remarkable evolutionary malleability of the TnpB scaffold and provide extensive opportunities for further exploration of RNA-guided biological systems as well as multiple applications.


Assuntos
Bactérias , Ribonucleases , Ribonucleases/metabolismo , Filogenia , Bactérias/metabolismo , Archaea/metabolismo , Endonucleases/metabolismo , Sistemas CRISPR-Cas , RNA
13.
Proc Natl Acad Sci U S A ; 120(42): e2305837120, 2023 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-37819981

RESUMO

Bacteria possess various receptors that sense different signals and transmit information to enable an optimal adaptation to the environment. A major limitation in microbiology is the lack of information on the signal molecules that activate receptors. Signals recognized by sensor domains are poorly reflected in overall sequence identity, and therefore, the identification of signals from the amino acid sequence of the sensor alone presents a challenge. Biogenic amines are of great physiological importance for microorganisms and humans. They serve as substrates for aerobic and anaerobic growth and play a role of neurotransmitters and osmoprotectants. Here, we report the identification of a sequence motif that is specific for amine-sensing sensor domains that belong to the Cache superfamily of the most abundant extracellular sensors in prokaryotes. We identified approximately 13,000 sensor histidine kinases, chemoreceptors, receptors involved in second messenger homeostasis and Ser/Thr phosphatases from 8,000 bacterial and archaeal species that contain the amine-recognizing motif. The screening of compound libraries and microcalorimetric titrations of selected sensor domains confirmed their ability to specifically bind biogenic amines. Mutants in the amine-binding motif or domains that contain a single mismatch in the binding motif had either no or a largely reduced affinity for amines. We demonstrate that the amine-recognizing domain originated from the universal amino acid-sensing Cache domain, thus providing insight into receptor evolution. Our approach enables precise "wet"-lab experiments to define the function of regulatory systems and therefore holds a strong promise to enable the identification of signals stimulating numerous receptors.


Assuntos
Aminoácidos , Archaea , Humanos , Archaea/genética , Archaea/metabolismo , Aminoácidos/metabolismo , Proteínas de Bactérias/metabolismo , Bactérias/genética , Bactérias/metabolismo , Aminas Biogênicas/metabolismo
14.
FEMS Microbiol Rev ; 47(5)2023 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-37796897

RESUMO

Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.


Assuntos
Archaea , Bactérias , Oxirredução , Bactérias/metabolismo , Archaea/metabolismo , Sulfatos/metabolismo , Sulfitos/metabolismo , Enxofre/metabolismo , Filogenia
15.
Biotechnol Adv ; 69: 108268, 2023 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-37793598

RESUMO

Ruminants are responsible for enteric methane production contributing significantly to the anthropogenic greenhouse gases in the atmosphere. Moreover, dietary energy is lost as methane gas without being available for animal use. Therefore, many mitigation strategies aiming at interventions at animals, diet, and microbiota have been explored by researchers. Specific chemical analogues targeting the enzymes of the methanogenic pathway appear to be more effective in specifically inhibiting the growth of methane-producing archaea without hampering another microbiome, particularly, cellulolytic microbiota. The targets of methanogenesis reactions that have been mainly investigated in ruminal fluid include methyl coenzyme M reductase (halogenated sulfonate and nitrooxy compounds), corrinoid enzymes (halogenated aliphatic compounds), formate dehydrogenase (nitro compounds, e.g., nitroethane and 2-nitroethanol), and deazaflavin (F420) (pterin and statin compounds). Many other potential metabolic reaction targets in methanogenic archaea have not been evaluated properly. The analogues are specifically effective inhibitors of methanogens, but their efficacy to lower methanogenesis over time reduces due to the metabolism of the compounds by other microbiota or the development of resistance mechanisms by methanogens. In this short review, methanogen populations inhabited in the rumen, methanogenesis pathways and methane analogues, and other chemical compounds specifically targeting the metabolic reactions in the pathways and methane production in ruminants have been discussed. Although many methane inhibitors have been evaluated in lowering methane emission in ruminants, advancement in unravelling the molecular mechanisms of specific methane inhibitors targeting the metabolic pathways in methanogens is very limited.


Assuntos
Archaea , Microbiota , Animais , Archaea/metabolismo , Metano/metabolismo , Ruminantes/metabolismo , Fermentação
16.
World J Microbiol Biotechnol ; 39(11): 322, 2023 Sep 27.
Artigo em Inglês | MEDLINE | ID: mdl-37755613

RESUMO

Proteases and lipases are significant groups of enzymes for commercialization at the global level. Earlier, the industries depended on mesophilic proteases and lipases, which remain nonfunctional under extreme conditions. The discovery of extremophilic microorganisms, especially those belonging to haloarchaea, paved a new reserve of industrially competent extremozymes. Haloarchaea or halophilic archaea are polyextremophiles of domain Archaea that grow at high salinity, elevated temperature, pH range (pH 6-12), and low aw. Interestingly, haloarchaeal proteolytic and lipolytic enzymes also perform their catalytic function in the presence of 4-5 M NaCl in vivo and in vitro. Also, they are of great interest to study due to their capacity to function and are active at elevated temperatures, tolerance to pH extremes, and in non-aqueous media. In recent years, advances have been achieved in various aspects of genomic/molecular expression methods involving homologous and heterologous processes for the overproduction of these extremozymes and their characterization from haloarchaea. A few protease and lipase extremozymes have been successfully expressed in prokaryotic systems, especially E.coli, and enzyme modification techniques have improved the catalytic properties of the recombinant enzymes. Further, in-silico methods are currently applied to elucidate the structural and functional features of salt-stable protease and lipase in haloarchaea. In this review, the production and purification methods, catalytic and biochemical properties and biotechnological applications of haloextremozymes proteases and lipases are summarized along with recent advancements in overproduction and characterization of these enzymes, concluding with the directions for further in-depth research on proteases and lipases from haloarchaea.


Assuntos
Lipase , Peptídeo Hidrolases , Lipase/metabolismo , Biotecnologia/métodos , Archaea/metabolismo , Endopeptidases , Cloreto de Sódio
17.
Appl Environ Microbiol ; 89(9): e0103323, 2023 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-37695043

RESUMO

All nitrogen-fixing bacteria and archaea (diazotrophs) use molybdenum (Mo) nitrogenase to reduce dinitrogen (N2) to ammonia, with some also containing vanadium (V) and iron-only (Fe) nitrogenases that lack Mo. Among diazotrophs, the regulation and usage of the alternative V-nitrogenase and Fe-nitrogenase in methanogens are largely unknown. Methanosarcina acetivorans contains nif, vnf, and anf gene clusters encoding putative Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase, respectively. This study investigated nitrogenase expression and growth by M. acetivorans in response to fixed nitrogen, Mo/V availability, and CRISPRi repression of the nif, vnf, and/or anf gene clusters. The availability of Mo and V significantly affected growth of M. acetivorans with N2 but not with NH4Cl. M. acetivorans exhibited the fastest growth rate and highest cell yield during growth with N2 in medium containing Mo, and the slowest growth in medium lacking Mo and V. qPCR analysis revealed the transcription of the nif operon is only moderately affected by depletion of fixed nitrogen and Mo, whereas vnf and anf transcription increased significantly when fixed nitrogen and Mo were depleted, with removal of Mo being key. Immunoblot analysis revealed Mo-nitrogenase is detected when fixed nitrogen is depleted regardless of Mo availability, while V-nitrogenase and Fe-nitrogenase are detected only in the absence of fixed nitrogen and Mo. CRISPRi repression studies revealed that V-nitrogenase and/or Fe-nitrogenase are required for Mo-independent diazotrophy, and unexpectedly that the expression of Mo-nitrogenase is also required. These results reveal that alternative nitrogenase production in M. acetivorans is tightly controlled and dependent on Mo-nitrogenase expression. IMPORTANCE Methanogens and closely related methanotrophs are the only archaea known or predicted to possess nitrogenase. Methanogens play critical roles in both the global biological nitrogen and carbon cycles. Moreover, methanogens are an ancient microbial lineage and nitrogenase likely originated in methanogens. An understanding of the usage and properties of nitrogenases in methanogens can provide new insight into the evolution of nitrogen fixation and aid in the development nitrogenase-based biotechnology. This study provides the first evidence that a methanogen can produce all three forms of nitrogenases, including simultaneously. The results reveal components of Mo-nitrogenase regulate or are needed to produce V-nitrogenase and Fe-nitrogenase in methanogens, a result not seen in bacteria. Overall, this study provides a foundation to understand the assembly, regulation, and activity of the alternative nitrogenases in methanogens.


Assuntos
Molibdênio , Nitrogenase , Nitrogenase/genética , Nitrogenase/metabolismo , Molibdênio/metabolismo , Methanosarcina/genética , Methanosarcina/metabolismo , Nitrogênio/metabolismo , Fixação de Nitrogênio/genética , Archaea/metabolismo
18.
FEMS Microbiol Ecol ; 99(11)2023 10 17.
Artigo em Inglês | MEDLINE | ID: mdl-37766397

RESUMO

Large amounts of carbon sequestered in permafrost on the Tibetan Plateau (TP) are becoming vulnerable to microbial decomposition in a warming world. However, knowledge about how the responsible microbial community responds to warming-induced permafrost thaw on the TP is still limited. This study aimed to conduct a comprehensive comparison of the microbial communities and their functional potential in the active layer of thawing permafrost on the TP. We found that the microbial communities were diverse and varied across soil profiles. The microbial diversity declined and the relative abundance of Chloroflexi, Bacteroidetes, Euryarchaeota, and Bathyarchaeota significantly increased with permafrost thawing. Moreover, warming reduced the similarity and stability of active layer microbial communities. The high-throughput qPCR results showed that the abundance of functional genes involved in liable carbon degradation and methanogenesis increased with permafrost thawing. Notably, the significantly increased mcrA gene abundance and the higher methanogens to methanotrophs ratio implied enhanced methanogenic activities during permafrost thawing. Overall, the composition and functional potentials of the active layer microbial community in the Tibetan permafrost region are susceptible to warming. These changes in the responsible microbial community may accelerate carbon degradation, particularly in the methane releases from alpine permafrost ecosystems on the TP.


Assuntos
Euryarchaeota , Microbiota , Pergelissolo , Pergelissolo/química , Tibet , Microbiota/genética , Archaea/genética , Archaea/metabolismo , Solo/química , Euryarchaeota/genética , Euryarchaeota/metabolismo , Carbono/metabolismo
19.
Environ Res ; 238(Pt 1): 117144, 2023 12 01.
Artigo em Inglês | MEDLINE | ID: mdl-37716381

RESUMO

A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.


Assuntos
Fontes Termais , Fontes Termais/química , Fontes Termais/microbiologia , Metagenoma , Archaea/genética , Archaea/metabolismo , Bactérias/metabolismo , China , Carboidratos , Enxofre/metabolismo , Nitrogênio/metabolismo , Filogenia
20.
Sci Total Environ ; 905: 167397, 2023 Dec 20.
Artigo em Inglês | MEDLINE | ID: mdl-37758143

RESUMO

Municipal solid waste (MSW) landfills are significant sources of antibiotics. However, the effects of antibiotics on MSW decomposition process and methanogenesis during solid waste decomposition remain insufficiently characterized. This study investigated the effects of environmentally relevant concentrations (ERCs) of antibiotics (200 µg/kg for each antibiotic) on MSW decomposition and methanogenesis in bioreactors treated with and without eight antibiotics (three tetracyclines, three sulfonamides, and two macrolides). The key phases of MSW decomposition, namely the aerobic, anaerobic acid, and methanogenic phases, were determined by analyzing the key physiochemical parameters of the leachate, including pH, chemical oxygen demand, and biochemical oxygen demand. We assessed the bacterial and archaeal compositions, along with the abundance of the gene encoding the alpha subunit of methyl-coenzyme M reductase (mcrA), during MSW decomposition using high throughput 16S ribosomal RNA (rRNA) gene sequencing and quantitative polymerase chain reactions, respectively. Our results revealed that antibiotics significantly altered the compositions of bacteria and methanogens, leading to decreased mcrA abundance and methanogenesis. Specifically, antibiotics inhibited cellulose-degrading bacteria (Firmicutes) and archaea (E2) in the anaerobic acid phase and hydrolytic bacteria (Proteobacteria) in the methanogenic phase, resulting in lower degradation of biodegradable matter than that of the biodegradation without antibiotics treatment. However, the typical MSW decomposition process indicated by the key decomposition phases was successfully separated in both bioreactors, suggesting that antibiotics did not affect overall MSW decomposition process development or the associated individual decomposition phases establishment. These findings suggest that antibiotics at ERCs may inhibit methanogenesis during MSW decomposition, thereby providing fundamental information for methane management and climate change studies.


Assuntos
Eliminação de Resíduos , Resíduos Sólidos , Resíduos Sólidos/análise , Antibacterianos/metabolismo , Bactérias/metabolismo , Archaea/metabolismo , Firmicutes , Reatores Biológicos/microbiologia , Metano/metabolismo , Instalações de Eliminação de Resíduos , Eliminação de Resíduos/métodos
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...