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1.
Environ Microbiol ; 26(1): e16553, 2024 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-38062568

RESUMEN

Interspecific interactions in biofilms have been shown to cause the emergence of community-level properties. To understand the impact of interspecific competition on evolution, we deep-sequenced the dispersal population of mono- and co-culture biofilms of two antagonistic marine bacteria (Phaeobacter inhibens 2.10 and Pseudoalteromononas tunicata D2). Enhanced phenotypic and genomic diversification was observed in the P. tunicata D2 populations under both mono- and co-culture biofilms in comparison to P. inhibens 2.10. The genetic variation was exclusively due to single nucleotide variants and small deletions, and showed high variability between replicates, indicating their random emergence. Interspecific competition exerted an apparent strong positive selection on a subset of P. inhibens 2.10 genes (e.g., luxR, cobC, argH, and sinR) that could facilitate competition, while the P. tunicata D2 population was genetically constrained under competition conditions. In the absence of interspecific competition, the P. tunicata D2 replicate populations displayed high levels of mutations affecting the same genes involved in cell motility and biofilm formation. Our results show that interspecific biofilm competition has a complex impact on genomic diversification, which likely depends on the nature of the competing strains and their ability to generate genetic variants due to their genomic constraints.


Asunto(s)
Pseudoalteromonas , Rhodobacteraceae , Biopelículas , Rhodobacteraceae/genética , Pseudoalteromonas/genética , Genómica , Ecología , Evolución Molecular
2.
BMC Genomics ; 24(1): 508, 2023 Aug 31.
Artículo en Inglés | MEDLINE | ID: mdl-37653415

RESUMEN

BACKGROUND: Cold-adapted archaea have diverse ecological roles in a wide range of low-temperature environments. Improving our knowledge of the genomic features that enable psychrophiles to grow in cold environments helps us to understand their adaptive responses. However, samples from typical cold regions such as the remote Arctic and Antarctic are rare, and the limited number of high-quality genomes available leaves us with little data on genomic traits that are statistically associated with cold environmental conditions. RESULTS: In this study, we examined the haloarchaeal genus Halorubrum and defined a new clade that represents six isolates from polar and deep earth environments ('PD group' hereafter). The genomic G + C content and amino acid composition of this group distinguishes it from other Halorubrum and the trends are consistent with the established genomic optimization of psychrophiles. The cold adaptation of the PD group was further supported by observations of increased flexibility of proteins encoded across the genome and the findings of a growth test. CONCLUSIONS: The PD group Halorubrum exhibited denser genome packing, which confers higher metabolic potential with constant genome size, relative to the reference group, resulting in significant differences in carbon, nitrogen and sulfur metabolic patterns. The most marked feature was the enrichment of genes involved in sulfur cycling, especially the production of sulfite from organic sulfur-containing compounds. Our study provides an updated view of the genomic traits and metabolic potential of Halorubrum and expands the range of sources of cold-adapted haloarchaea.


Asunto(s)
Halorubrum , Temperatura , Genómica , Tamaño del Genoma , Aminoácidos
3.
Bioinformatics ; 38(15): 3684-3688, 2022 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-35713513

RESUMEN

MOTIVATION: Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads. RESULTS: Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrate 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG databases with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function and phylogeny. AVAILABILITY AND IMPLEMENTATION: MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Metagenoma , Metagenómica , ARN Ribosómico 16S/genética , Filogenia , Bases de Datos Factuales
4.
J Environ Manage ; 345: 118737, 2023 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-37657296

RESUMEN

Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.


Asunto(s)
Agua Potable , Metagenoma , Filogenia , Antibacterianos , Gestión de Riesgos
5.
Nanotechnology ; 33(2)2021 Oct 22.
Artículo en Inglés | MEDLINE | ID: mdl-34614481

RESUMEN

Biofuel cell (BFC) is a kind of bio-cell based on biological enzymes. The enzyme as a catalyst can interconvert renewable and sustainable energy into each other more rapidly, such as the biochemical energy in glucose and ethanol into electrical energy. In this work, artificial blood vessel and fuel cell are based on polyaniline/thermoplastic polyurethane (PANI/TPU) fiber membrane with an average fiber diameter of 1300 nm, a film thickness of 167µm, and a permeability of 18.4 mm s-1. The PANI/TPU fiber membrane was prepared by electrospinning and followedin situpolymerization. The membrane has good flexibility and mechanical properties, and can be stretched up to 200%. The advantages of good hydrophilicity, biocompatibility and high porosity make it possible to efficiently load glucose oxidase and laccase. The prepared BFC can stably output a voltage of 50 mV in simulated blood, and the output electrical signal changes significantly with the change of glucose concentration, which may be used in implantable devices or blood glucose monitoring.

6.
Environ Microbiol ; 22(4): 1409-1420, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-32090405

RESUMEN

The link between guanine-cytosine (GC) content and thermal adaptation is controversial. Here, we compared maximum growth temperature (TMGT ) and genomics of 78 Cryobacterium strains to avoid unreliable conclusions resulting from distantly phylogenetic groups. Phylogenomic analysis revealed this taxon had much higher diversification than we knew. Interestingly, these strains showed thermotolerance divergence with phylogenetic cohesion. A significant difference was found between TMGT ≤ 20°C strains and TMGT > 20°C strains in genomic GC content which mainly caused by variation of GC3. TMGT ≤ 20°C strains tended to use synonymous codons ended with A/U, but TMGT > 20°C strains tended to use G/C. Lower GC content at synonymous sites (≈GC3) of TMGT ≤ 20°C strains could provide lower intrinsic DNA flexibility which strongly associated with optimal molecular dynamics, and then guarantee DNA function at lower growth temperatures. This analysis of codon bias revealed close relationships for thermal adaptation, GC content at synonymous sites (≈GC3), intrinsic DNA flexibility and optimal DNA dynamics. Natural selection was main force driving this codon bias; strains with lower TMGT endured stronger natural selection. Therefore, this study provided molecular basis for bacterial adaptive evolution from moderate temperature to low temperature.


Asunto(s)
Actinomycetales/fisiología , Evolución Biológica , ADN Bacteriano/fisiología , Termotolerancia/fisiología , Actinomycetales/genética , Composición de Base , Uso de Codones , Cubierta de Hielo , Fenotipo , Filogenia , Termotolerancia/genética
7.
Bioinformatics ; 33(12): 1873-1875, 2017 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-28186226

RESUMEN

SUMMARY: Microbial genomes have recently been reconstructed from metagenomic datasets using binning approaches. Inconsistent binning results are however often observed between different binning programs, likely due to the different algorithms or statistical models used. We present Binning_refiner, a pipeline that merges the results of different binning programs. Our results demonstrated that Binning_refiner can significantly reduce the contamination level of genome bins and increase the total size of contamination-free and 'good-quality' genome bins. Binning_refiner is thus an useful tool to improve the quality of genome bins derived from metagenomic data. AVAILABILITY AND IMPLEMENTATION: Binning_refiner is implemented in Python3 and is freely available at: https://github.com/songweizhi/Binning_refiner . CONTACT: songwz03@gmail.com or t.thomas@unsw.edu.au. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Genoma Microbiano , Metagenómica/métodos , Análisis de Secuencia de ADN/métodos , Programas Informáticos , Algoritmos , Modelos Estadísticos
8.
Extremophiles ; 21(3): 581-589, 2017 May.
Artículo en Inglés | MEDLINE | ID: mdl-28314921

RESUMEN

Psychrobacter has been regarded as an important genus for bacterial cold adaptation studies. However, members of this genus are highly varied in terms of both cold adaptability and genome content. To get an understanding of the diversity of members of this genus, five Psychrobacter strains (G, K5, 273-4, PAMC21119 and PRwf-1), with publicly available complete/draft genome, were selected and comprehensive comparative genomics analyses were performed among them. The closest phylogenetic relationship, highest average nucleotide identity (96.78%) and best sequence synteny were identified between strains G and K5. These findings suggest they belong to the same species, despite the long geographic distance between them (Antarctic and Siberia). 4542 gene clusters in total were identified from the five genomes, and of which 1424 were shared by all of them. The number of genes unique to strains G, K5, 273-4, PAMC21119 and PRwf-1 are 183, 188, 300, 637 and 665, respectively. COG assignment revealed their differences in gene content related to stress response. The extensive sequence rearrangements and the large number of genes unique to strain PAMC21119 and PRwf-1 suggest they may have experienced a high level of gene exchanges in the permafrost soil and the surface of fish skin.


Asunto(s)
Genoma Bacteriano , Polimorfismo Genético , Psychrobacter/genética , Adaptación Fisiológica , Ecosistema , Hielos Perennes/microbiología , Filogenia , Psychrobacter/clasificación , Psychrobacter/aislamiento & purificación , Homología de Secuencia , Sintenía
9.
FEMS Microbes ; 5: xtad023, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38213395

RESUMEN

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

10.
ISME J ; 18(1)2024 Jan 08.
Artículo en Inglés | MEDLINE | ID: mdl-38365240

RESUMEN

Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.


Asunto(s)
Exiguobacterium , Extremófilos , Genómica , Filogenia , Proteínas
11.
Curr Microbiol ; 66(3): 259-65, 2013 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-23179079

RESUMEN

An OmpR gene, named OmpR503, was cloned from the Antarctic psychrotrophic bacterium Psychrobacter sp. G according to its genomic draft. The deduced amino acid sequences of OmpR503 were highly conserved with other known protein members of OmpR family. qRT-PCR analysis showed that the expression of OmpR503 gene was significantly enhanced by high salinity (90, 120). The expression of OmpR503 gene was also significantly increased at low temperature (0, 10 °C), whereas depressed at high temperature (30 °C). When the strain was subjected to combined stress (0 °C with a salinity of 90), the expression of OmpR503 gene was increased significantly, which was up to 3.0-fold. In Antarctica, freezing tolerance of psychrotrophic bacteria is often accompanied by tolerance to osmotic stress caused by a lack of free water, thus the cold inducibility of OmpR503 gene might help the strain adapt to the harsh environment more efficiently.


Asunto(s)
Proteínas Bacterianas/genética , Regulación Bacteriana de la Expresión Génica , Psychrobacter/genética , Secuencias Reguladoras de Ácidos Nucleicos , Estrés Fisiológico , Secuencia de Aminoácidos , Regiones Antárticas , Secuencia de Bases , Clonación Molecular , Datos de Secuencia Molecular , Concentración Osmolar , Psychrobacter/metabolismo , Alineación de Secuencia , Temperatura
12.
Curr Microbiol ; 67(5): 601-8, 2013 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-23783560

RESUMEN

Temperature and salinity fluctuations are two of the most important factors affecting the growth of polar bacteria. In an attempt to better understand the function of heat-shock proteins (HSPs) in the adaptive mechanisms of the Antarctic psychrotrophic bacterium Psychrobacter sp. G to such conditions, genes Hsp845, Hsp2538, Hsp2666, and Hsp2667 were cloned on the basis of the draft genome. The expression characteristics of these HSP genes under different stress conditions were analyzed by the qRT-PCR method. Expression of Hsp845 and Hsp2667 was inhibited significantly by low temperature (0 and 10 °C, respectively). There was no difference of expression when Hsp2538 and Hsp2666 were exposed to 0 °C but the expression of Hsp2666 was inhibited when exposed to 10 °C. Expression of Hsp2538 and Hsp2667 was not sensitive but expression of Hsp845 and Hsp2666 was increased at low salinity (0 and 15, respectively). Expression of the four HSP genes was enhanced at high salinity (90 and 120) and at high temperature independent of salinity. By contrast, low temperature had no significant effect independent of salinity.


Asunto(s)
Proteínas de Choque Térmico/genética , Psychrobacter/genética , Psychrobacter/metabolismo , Salinidad , Temperatura , Regiones Antárticas , Clonación Molecular , Biología Computacional , Regulación Bacteriana de la Expresión Génica , Proteínas de Choque Térmico/química , Datos de Secuencia Molecular , Filogenia , Psychrobacter/clasificación , Agua de Mar/microbiología , Análisis de Secuencia de ADN , Estrés Fisiológico , Microbiología del Agua
13.
Syst Appl Microbiol ; 46(4): 126426, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37141831

RESUMEN

Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.


Asunto(s)
Proteínas Hedgehog , Simbiosis , Filogenia , Proteínas Hedgehog/genética , Proteínas Hedgehog/metabolismo , ARN Ribosómico 16S/genética , Bacterias
14.
Syst Appl Microbiol ; 46(2): 126401, 2023 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-36774720

RESUMEN

Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.


Asunto(s)
Bacterias , Microbiota , Filogenia , ARN Ribosómico 16S/genética , Metagenoma , Compuestos de Azufre/metabolismo
15.
RSC Adv ; 13(17): 11697-11705, 2023 Apr 11.
Artículo en Inglés | MEDLINE | ID: mdl-37063728

RESUMEN

The corrosion of materials severely limits the application scenarios of triboelectric nanogenerators (TENGs), especially in laboratories, chemical plants and other fields where leakage of chemically corrosive solutions is common. Here, we demonstrate a chemical-resistant triboelectric nanogenerator (CR-TENG) based on polysulfonamide (PSA) and polytetrafluoroethylene (PTFE) non-woven fabrics. The CR-TENG can stably harvest biological motion energy and perform intelligent safety protection monitoring in a strong corrosive environment. After treatment with strong acid and alkali solution for 7 days, the fabric morphology, diameter, tensile properties and output of CR-TENG are not affected, showing high reliability. CR-TENG integrated into protective equipment can detect the working status of protective equipment in real time, monitor whether it is damaged, and provide protection for wearers working in high-risk situations. In addition, the nonwoven-based CR-TENG has better wearing comfort and is promising for self-powered sensing in harsh environments.

16.
PNAS Nexus ; 1(5): pgac226, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-36712370

RESUMEN

Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes and discover carbon fixation pathways in 1,007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognized archaeal and bacterial phyla (i.e. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expand the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin-Benson-Bassham cycle. Finally, the genomic potential for carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation thus appears to be much more widespread than previously known, and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.

17.
Materials (Basel) ; 15(3)2022 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-35160847

RESUMEN

In this paper, the ballistic damage mechanism and residual bearing capacity of ceramic/backing plate armor were investigated. First, a series of lightweight armors were prepared, consisting of ceramic and ultra-high molecular weight polyethylene fiber-reinforced resin matrix composite (UHMWPE) plates, and were wrapped in a high-strength fabric. Then, the ceramic/UHMWPE armors were hit by one or two bullets, and finally subjected to compression testing. The results showed that the main failure mode of integral ceramic/UHMWPE armors was ceramic brittle fracture. Many zigzag patterns on the compression curve indicated that the specimens had undergone the stages of crack propagation, ceramic fragment reorganization, plastic deformation of UHMWPE backing plate, interlaminar tearing, and overall fracture. The failure of spliced ceramic/UHMWPE armors was mainly due to the dislocation between ceramic sheets; the smooth compression curves indicated that there was no recombination of ceramic fragments and obvious interlayer debonding during the compression. Under the maximum load, each ceramic/UHMWPE armor with ballistic damage did not suddenly break and fail. The structure and thickness of ceramic plates all had an impact on residual strength: under the same structure, the greater the thickness, the greater the residual strength, but the relationship between them was not linear; under the same thickness, the residual strength of the spliced ceramic/UHMWPE armor was higher. The residual strength was also related to the number of shots: after two bullets hit, its value was only one-third of that after one bullet hit.

18.
Microbiome ; 10(1): 22, 2022 02 01.
Artículo en Inglés | MEDLINE | ID: mdl-35105377

RESUMEN

BACKGROUND: Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species. RESULTS: Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms. CONCLUSIONS: This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.


Asunto(s)
Metabolómica , Espectrometría de Masas en Tándem , Cromatografía Liquida
19.
Microbiome ; 10(1): 75, 2022 05 10.
Artículo en Inglés | MEDLINE | ID: mdl-35538590

RESUMEN

BACKGROUND: The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean. RESULTS: In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition. CONCLUSION: This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.


Asunto(s)
Chloroflexi , Carbono/metabolismo , Chloroflexi/genética , Ecosistema , Océanos y Mares , Azufre/metabolismo
20.
Water Res ; 226: 119242, 2022 Nov 01.
Artículo en Inglés | MEDLINE | ID: mdl-36257156

RESUMEN

Under the limitation of the carrier yield and mobility of semiconductor photocatalysts and the reaction domain, it seems that the photocatalytic efficiency cannot be greatly improved. Here, an efficient contact-electro-catalysis (CEC) system based on droplet triboelectric nanogenerator (TENG) is developed. Instead of using traditional semiconductor catalysts, the electric charge transferred during the electrification process of the contact between water droplets and polytetrafluoroethylene (PTFE) is used to participate in catalysis, and the output electrical signal can also monitor the degree of catalysis. The important role of light in the circulation of this CEC system is studied and discussed for the first time. It is proved that the contact electrification at the liquid-solid interface is accompanied by the generation of a large number of strong oxidizing radicals. The efficient transport of charge carriers driven by mechanical force and the active oxygen species distributed in the whole domain greatly improve the degradation rate of dyes. The experimental data show that the degradation efficiency of crystal violet (CV) reaches 90% within 38 s, and the rate constant k is as high as 3.7 min-1. This is a breakthrough in the field of catalysis.

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