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1.
Int J Mol Sci ; 20(18)2019 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-31505830

RESUMO

Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.


Assuntos
Adaptação Fisiológica , Archaea/fisiologia , Membrana Celular/metabolismo , Lipídeos de Membrana/metabolismo
2.
Sci Total Environ ; 693: 133507, 2019 Nov 25.
Artigo em Inglês | MEDLINE | ID: mdl-31377366

RESUMO

Systems with strong horizontal and vertical gradients, such as fjords, are useful models for studying environmental forcing. Here we examine microbial (prokaryotic and eukaryotic) community changes associated with the surface low salinity layer (LSL) and underlying seawater in multiple fjords in Fiordland National Park (New Zealand). High rainfall (1200-8000 mm annually) and linked runoff from native forested catchments results in surface LSLs with high tannin concentrations within each fjord. These gradients are expected to drive changes in microbial communities. We used amplicon sequencing (16S and 18S) to assess the impact of these gradients on microbial communities and identified depth linked changes in diversity and community structure. With increasing depth, we observed significant increases in Proteobacteria (15%) and SAR (37%), decreases in Opisthokonta (35%), and transiently increased Bacteroidetes (3% increase from 0 to 40 m, decreasing by 8% at 200 m). Community structure differences were observed along a transect from the head to the mouth, specifically 25% mean relative abundance decreases in Opisthokonta and Bacteroidetes, and increases in SAR (25%) and Proteobacteria (>5%) at the surface, indicating changes based on distance from the ocean. This provides the first in-depth view into the ecological drivers of microbial communities within New Zealand fjords.


Assuntos
Microbiota/fisiologia , Fitoplâncton/fisiologia , Água do Mar/química , Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Estuários , Eucariotos , Nova Zelândia , Salinidade
3.
Environ Sci Pollut Res Int ; 26(28): 29127-29137, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31392608

RESUMO

Archaea play a vital role in Earth's geochemical cycles, but the factors that drive their distribution between sediments and water-level-fluctuating zones in the East Dongting Lake (EDL) wetland are poorly understood. Here, we used Illumina MiSeq to investigate the variation in the soil archaeal community structure and diversity among sediments and four water-level-fluctuating zones (mudflat, sedge, sedge-Phragmites, and Phragmites) in the EDL wetland. Diverse archaeal assemblages were found in our study, Crenarchaeota, Euryarchaeota, and ammonia-oxidizing and methanogenic subset were the dominant groups, and all their abundances shifted from sediment to water-level-fluctuating zones. The principal coordinates analysis and cluster analysis showed that the overall archaeal community structure was separated into two clusters: cluster I contained nine samples from sediment, mudflat, and sedge zones, whereas cluster II contained six samples from sedge-Phragmites and Phragmites zones. Archaeal diversity was significantly highest in sediment and lowest in Phragmites zone soils. The Mantel test showed that the variation in archaeal community structure was significantly positively correlated with soil water content and pH. The relative abundances of Crenarchaeota and Nitrososphaerales decreased with soil water content, while Euryarchaeota and Methanomicrobiales increased with soil water content. The relative abundance of Methanomicrobiales significantly decreased with pH (R2 = 0.34-0.48). Chao 1, observed operational taxonomic units, Shannon index, and Simpson index all correlated significantly positively with water content (R2 = 0.40-0.60), while Shannon and Simpson indexes both correlated significantly negatively with pH (R2 = 0.20-0.37). Our results demonstrated that the variations in the archaeal community structure were markedly driven by soil water content and pH in the EDL wetland. Our findings suggested that archaeal communities shifted among sediment and four water-level-fluctuating zones, highlighting that the spatiotemporal heterogeneity of greenhouse gas flux in small scale should be taken into account for accurate prediction of greenhouse gas emissions in the Dongting Lake area, especially on the background of climate change and human activities.


Assuntos
Archaea/fisiologia , Sedimentos Geológicos/microbiologia , Microbiologia do Solo , Solo/química , Áreas Alagadas , Amônia/metabolismo , Archaea/genética , Biodiversidade , China , Análise por Conglomerados , Concentração de Íons de Hidrogênio , Lagos , Filogenia , RNA Ribossômico 16S , Água
4.
Ecotoxicol Environ Saf ; 182: 109431, 2019 Oct 30.
Artigo em Inglês | MEDLINE | ID: mdl-31301593

RESUMO

The objective of this study was to examine the response of soil archaeal communities to saline stress in different types of Cd-contaminated soils from the North China Plain. Increased soil salinity by addition of 0.5% sodium salts (NaCl: Na2SO4: NaHCO3: Na2CO3 = 1:9:9:1) increased available Cd concentration, resulting in decreased ratios of Cd2+/CdT and CdSO4/CdT and increased ratios of CdCln2-n/CdT in soil solution. Soil saline stress decreased archaeal abundance and diversity and changed major soil archaeal taxa. For example, increased saline stress enriched taxa in the archaeal phyla Thaumarchaeota and Euryarchaeota, and these enriched tolerant taxa had much stronger correlations with soil properties, such as soil pH, EC or Na+. In addition, some microbes with low abundances like Bathyarchaeia (no rank) and Candidatus Nitrosotenuis were found to closely correlate with soil pH, EC, Na+, and Cl-, indicating they might play disproportionate roles in regulating ecological functions in stressed habitats. These results suggest that saline stress modified the effect of Cd toxicity on soil archaeal communities in different types of Cd-contaminated soils.


Assuntos
Archaea/efeitos dos fármacos , Cádmio/toxicidade , Estresse Salino , Microbiologia do Solo , Poluentes do Solo/toxicidade , Archaea/fisiologia , Cádmio/química , China , Solução Salina , Salinidade , Cloreto de Sódio , Solo/química , Poluentes do Solo/química
5.
Sci Total Environ ; 684: 629-640, 2019 Sep 20.
Artigo em Inglês | MEDLINE | ID: mdl-31170597

RESUMO

Ammonia-oxidizing archaea (AOA) microorganisms have been increasingly found in aquatic and terrestrial environments. These microorganisms make vital contributions to ammonia oxidation in such systems. However, their community succession characteristics in man-made wetland ecosystems have scarcely been reported. We assessed the AOA's spatiotemporal shifts in the sediments of a constructed wetland (CW) - the Shijiuyang constructed wetland (SJY-CW) - in China from the third year (2011) to the fifth year (2013) of the CW operation. The SJY-CW is composed of a pretreatment pond, a multiple plant-bed/ditch system, and a post-treatment pond. Results showed that AOA abundance in the pre- and post-treatment ponds remained invariant through 2011-2012 and decreased in 2013, while the abundance in the plant-bed/ditch system decreased gradually with wetland operation. The AOA abundance in 2013 was one order of magnitude lower than that through 2011-2012, and the AOA abundance in the plant-bed/ditch system was generally higher than that in the pre- and post-treatment ponds from 2011 to 2013. AOA diversity showed little temporal differentiation with a slightly decreasing trend for community richness index Chao1 and diversity index Shannon H' from 2011 to 2013. The AOA community was dominated by the Nitrososphaera cluster accompanied by an increasing Nitrosopumilus cluster and Nitrososphaera sister cluster within the wetland operation. Hierarchical clustering and redundancy analysis verified the horizontal shifts of AOA communities. The shifts occurred preferentially in the central plant-bed/ditch system. The operational duration of the wetland became a key factor influencing AOA abundance and community shift in SJY-CW sediments.


Assuntos
Archaea/fisiologia , Conservação dos Recursos Naturais , Microbiota , Áreas Alagadas , Amônia/metabolismo , Archaea/classificação , Oxirredução , Dinâmica Populacional , Análise Espaço-Temporal
6.
BMC Biol ; 17(1): 48, 2019 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-31189463

RESUMO

Metagenomics allows exploration of aspects of a microbial community that were inaccessible by cultivation-based approaches targeting single microbes. Many new microbial taxa and genes have been discovered using metagenomics, but different kinds of "unknowns" still remain in a microbiome experiment. We discuss here whether and how it is possible to deal with them.


Assuntos
Metagenoma , Metagenômica , Microbiota , Archaea/classificação , Archaea/fisiologia , Bactérias/classificação , Fenômenos Fisiológicos Bacterianos , Microbiota/genética
7.
Sci Total Environ ; 670: 1068-1074, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31018422

RESUMO

Copper nanoparticles (NCu) may co-exist with other pollutants in agricultural soils, such as pesticides. However, this has been little evaluated yet. Thus, possible effects of the simultaneous applications of pesticides and NCu on biogeochemical cycles are expected, for example on the nitrogen cycle. Therefore, the aim of this work was to evaluate the effect of simultaneous application of the herbicide atrazine (ATZ) and NCu on the abundance of total bacteria and nitrifying communities: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Moreover, the ATZ dissipation was evaluated. A soil-plant system containing ATZ at field dose (3 mg a.i. kg-1) was mixed with two doses of NCu (0.05% or 0.15% w/w). Changes in the abundance of 16S rRNA and ammonia monooxygenase (amoA) genes of AOA and AOB were evaluated by real-time quantitative PCR (qPCR) at three sampling times (1, 15 and 30 days). The residual ATZ and nitrate production were also measured. The results showed significant differences in microbial composition and abundance over the 30 days of the experiment. Particularly, an initial decrease was observed in total bacterial abundance due to the presence of ATZ and NCu respect to ATZ alone (~60%). The abundance of AOA was also remarkably reduced (~85%), but these communities gradually recovered towards the end of the experiment. Conversely, AOB abundance initially increased (>100%) and remained mainly unaltered in soil exposed to ATZ and NCu 0.15% w/w, where nitrate formation was also constant. Moreover, NCu decreased the ATZ dissipation, which was translated in a 2-fold increase on the ATZ half-life values (T1/2). This study demonstrates that the simultaneous presence of NCu and ATZ may represent a risk for the total bacteria present in soil and sensitive microorganisms such as nitrifying communities, and changes in the dissipation of the pesticide could influence this process.


Assuntos
Archaea/fisiologia , Atrazina/efeitos adversos , Fenômenos Fisiológicos Bacterianos , Cobre/efeitos adversos , Herbicidas/efeitos adversos , Nanopartículas Metálicas/efeitos adversos , Poluentes do Solo/efeitos adversos , Genes Bacterianos , Ciclo do Nitrogênio , RNA Bacteriano/análise , RNA Ribossômico 16S/análise , Microbiologia do Solo
8.
Sci Total Environ ; 670: 993-1000, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31018441

RESUMO

A laboratory scale anaerobic membrane bioreactor was operated for 11 months treating synthetic wastewater that mimicked the concentrate from a forward osmosis process treating municipal wastewater with 80% water recovery. The effect of temperature variation on reactor performance was assessed. The reactor operated during 4 months at 34 °C and then temperature was decreased to 23 °C, 17 °C and 15 °C mimicking the typical temperature seasonal variations of the sewage. Average COD removal efficiencies were 95, 87, 76 and 67% at 34, 23, 17 and 15 °C respectively, obtaining lower biogas production and lower COD removal at lower temperatures. Dissolved methane in the permeate averaged 8.2 mg CH4/L and did not significantly change with temperature. After 2 months operating at 15 °C, temperature was progressively increased, resulting in an immediate increase of methane production and COD removal efficiencies. Microbial analysis showed important changes in the archaeal community when temperature was changed from 34 to 23 °C.


Assuntos
Biocombustíveis/análise , Reatores Biológicos , Esgotos/análise , Eliminação de Resíduos Líquidos/métodos , Águas Residuárias/análise , Anaerobiose , Archaea/fisiologia , Membranas Artificiais , Microbiota , Esgotos/microbiologia , Águas Residuárias/microbiologia
9.
Biochimie ; 164: 3-16, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-30995539

RESUMO

Prokaryotes encounter constant and often brutal modifications to their environment. In order to survive, they need to maintain fitness, which includes adapting their protein expression patterns. Many factors control gene expression but this review focuses on just one, namely antisense RNAs (asRNAs), a class of non-coding RNAs (ncRNAs) characterized by their location in cis and their perfect complementarity with their targets. asRNAs were considered for a long time to be trivial and only to be found on mobile genetic elements. However, recent advances in methodology have revealed that their abundance and potential activities have been underestimated. This review aims to illustrate the role of asRNA in various physiologically crucial functions in both archaea and bacteria, which can be regrouped in three categories: cell maintenance, horizontal gene transfer and virulence. A literature survey of asRNAs demonstrates the difficulties to characterize and assign a role to asRNAs. With the aim of facilitating this task, we describe recent technological advances that could be of interest to identify new asRNAs and to discover their function.


Assuntos
Archaea , Bactérias , Fenômenos Fisiológicos Bacterianos/genética , Transferência Genética Horizontal/genética , RNA Antissenso , Virulência/genética , Archaea/genética , Archaea/patogenicidade , Archaea/fisiologia , Bactérias/genética , Bactérias/patogenicidade , Regulação da Expressão Gênica em Archaea , Regulação Bacteriana da Expressão Gênica , RNA Antissenso/genética , RNA Antissenso/fisiologia , RNA Arqueal/genética , RNA Arqueal/fisiologia , RNA Bacteriano/genética , RNA Bacteriano/fisiologia
10.
Nat Commun ; 10(1): 1688, 2019 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-30975999

RESUMO

Archaea and Bacteria have evolved different defence strategies that target virtually all steps of the viral life cycle. The diversified virion morphotypes and genome contents of archaeal viruses result in a highly complex array of archaea-virus interactions. However, our understanding of archaeal antiviral activities lags far behind our knowledges of those in bacteria. Here we report a new archaeal defence system that involves DndCDEA-specific DNA phosphorothioate (PT) modification and the PbeABCD-mediated halt of virus propagation via inhibition of DNA replication. In contrast to the breakage of invasive DNA by DndFGH in bacteria, DndCDEA-PbeABCD does not degrade or cleave viral DNA. The PbeABCD-mediated PT defence system is widespread and exhibits extensive interdomain and intradomain gene transfer events. Our results suggest that DndCDEA-PbeABCD is a new type of PT-based virus resistance system, expanding the known arsenal of defence systems as well as our understanding of host-virus interactions.


Assuntos
Archaea/fisiologia , Proteínas Arqueais/metabolismo , Vírus de Archaea/genética , DNA Viral/metabolismo , Interações entre Hospedeiro e Microrganismos/genética , Archaea/virologia , Proteínas Arqueais/genética , Proteínas Arqueais/imunologia , Vírus de Archaea/patogenicidade , Replicação do DNA/imunologia , Transferência Genética Horizontal/imunologia , Imunidade Inata/genética , Imunidade Inata/imunologia , Oligonucleotídeos Fosforotioatos/metabolismo , RNA Arqueal/genética , RNA Arqueal/isolamento & purificação , Análise de Sequência de DNA
11.
Sci Total Environ ; 666: 1106-1113, 2019 May 20.
Artigo em Inglês | MEDLINE | ID: mdl-30970476

RESUMO

The primary challenge of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) surviving in wetlands are the rapid and unpredictable environmental changes. To adapt to a fluctuant environment, ammonia oxidizers have to communicate with each other via acyl-homoserine lactones (AHLs). In this study, AOA and AOB in the soil samples taken from Zhalong wetland were incubated. Dynamics of AHLs during the incubation of ammonia oxidizers were measured. Then, the specific AHLs of AOA and AOB were identified, respectively. The results showed that AOA secreted N-butyryl-dl-homoserine lactone (C4-HSL) and N-octanoyl-l-homoserine lactone (C8-HSL) to cope with nitrite accumulation, while they secreted N-(3-oxododecanoyl)-dl-homoserine lactone (OXOC12-HSL) to regulate their ammonium metabolism activity. AOB secreted N-hexanoyl-dl-homoserine lactone (C6-HSL), N-dodecanoyl-l-homoserine lactone (C12-HSL), N-tetradecanoyl-dl-homoserine lactone (C14-HSL) and N-(3-oxododecanoyl)-tetradecanoyl-dl-homoserine lactone (OXOC14-HSL) only to enhance the metabolism activity. The dominant AOA belonged to the Nitrososphaera lineage, while the dominant AOB grouped into the Nitrosomonas lineage. The AHLs receptor homologs were identified in both AOA and AOB, which confirmed that AOA and AOB had the QS system. The present work was the first study that elucidated the QS system of AOA and AOB in multidimensional, and confirmed the role of QS system in ammonia oxidizers' metabolism.


Assuntos
Acil-Butirolactonas/metabolismo , Amônia/metabolismo , Compostos de Amônio/metabolismo , Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Percepção de Quorum , Áreas Alagadas , China , Oxirredução , Microbiologia do Solo
12.
Res Vet Sci ; 124: 129-136, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-30897395

RESUMO

The interest in antimicrobial compounds as feed additives is currently increasing. Among different options, tannins seem to have several beneficial effects when employed in animals diet. The present study aimed at investigating the influence on caecal microbial communities of the supplementation of a chestnut and quebracho tannins mix in meat rabbit's diet, also considering animals live performances. Four groups of rabbits were fed with a different diet: a control diet (C); a control diet with coccidiostat (CC), and two experimental diets with 0.3% (T0.3) and 0.6% (T0.6) chestnut and quebracho tannins mix. For microbial analysis, culture-dependent and culture-independent methods were employed. Live performances were not significantly affected by tannins mix supplementations, as well as culturable microbial loads of E. coli, Enterobacteriaceae, Bacteroides spp. and Bifidobacterium spp. C. perfringens was always under the detection limit. A consistent result was obtained by qPCR. As for PCR-DGGE analysis, the Richness and evenness (Shannon-Weiner index) of bacterial communities in caecum resulted significantly higher in control samples (C and CC) than in those from rabbit fed with tannin-containing diets. Sequencing analysis revealed that the phylum Firmicutes was less represented in samples from control groups. As for the methanogen archaeal DGGE, no significant differences were found in richness and diversity among different groups, all dominated by Methanobrevibacter spp.. This work highlights the potential antimicrobial effect of chestnut and quebracho tannins mix in an in vivo system revealed by molecular analysis.


Assuntos
Anacardiaceae/química , Ceco/microbiologia , Fagaceae/química , Coelhos/crescimento & desenvolvimento , Coelhos/microbiologia , Taninos/metabolismo , Ração Animal/análise , Animais , Archaea/efeitos dos fármacos , Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos/efeitos dos fármacos , Dieta/veterinária , Suplementos Nutricionais/análise , Relação Dose-Resposta a Droga , Microbioma Gastrointestinal/fisiologia , Distribuição Aleatória , Taninos/administração & dosagem
13.
Nat Rev Microbiol ; 17(5): 307-319, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30846876

RESUMO

A vast array of microorganisms from all three domains of life can produce electrical current and transfer electrons to the anodes of different types of bioelectrochemical systems. These exoelectrogens are typically iron-reducing bacteria, such as Geobacter sulfurreducens, that produce high power densities at moderate temperatures. With the right media and growth conditions, many other microorganisms ranging from common yeasts to extremophiles such as hyperthermophilic archaea can also generate high current densities. Electrotrophic microorganisms that grow by using electrons derived from the cathode are less diverse and have no common or prototypical traits, and current densities are usually well below those reported for model exoelectrogens. However, electrotrophic microorganisms can use diverse terminal electron acceptors for cell respiration, including carbon dioxide, enabling a variety of novel cathode-driven reactions. The impressive diversity of electroactive microorganisms and the conditions in which they function provide new opportunities for electrochemical devices, such as microbial fuel cells that generate electricity or microbial electrolysis cells that produce hydrogen or methane.


Assuntos
Archaea/fisiologia , Bactérias/metabolismo , Fontes de Energia Bioelétrica , Eletricidade , Biofilmes , Eletrodos , Eletrólise , Transporte de Elétrons , Geobacter/fisiologia , Hidrogênio/metabolismo , Metano/metabolismo
14.
mSphere ; 4(1)2019 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-30787117

RESUMO

Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate the hypotheses that newly established aquaria show clear microbial successional patterns over time and that common marine aquarium-conditioning practices, such as the addition of ocean-derived "live rocks" (defined as any "dead coral skeleton covered with crustose coralline algae" transferred into an aquarium from open ocean habitats) impact the diversity of microbial populations as well as nitrogen cycling in aquaria. We collected water chemistry data alongside water and sediment samples from two independent and newly established saltwater aquaria over a 3-month period. Microbial communities in samples were assessed by DNA extraction, amplification of the 16S rRNA gene, and Illumina MiSeq sequencing. Our results showed clear and replicable patterns of community succession in both aquaria, with the existence of multiple stable states for aquarium microbial assemblages. Notably, our results show that changes in aquarium microbial communities do not always correlate with water chemistry measurements and that operational taxonomic unit (OTU)-level patterns relevant to nitrogen cycling were not reported as statistically significant. Overall, our results demonstrate that aquarium perturbations have a substantial impact on microbial community profiles of aquarium water and sediment and that the addition of live rocks improves nutrient cycling by shifting aquarium communities toward a more typical saltwater assemblage of microbial taxa.IMPORTANCE Saltwater aquaria are living systems that support a complex biological community of fish, invertebrates, and microbes. The health and maintenance of saltwater tanks are pressing concerns for home hobbyists, zoos, and professionals in the aquarium trade; however, we do not yet understand the underlying microbial species interactions and community dynamics which contribute to tank setup and conditioning. This report provides a detailed view of ecological succession and changes in microbial community assemblages in two saltwater aquaria which were sampled over a 3-month period, from initial tank setup and conditioning with "live rocks" through subsequent tank cleanings and water replacement. Our results showed that microbial succession appeared to be consistent and replicable across both aquaria. However, changes in microbial communities did not always correlate with water chemistry measurements, and aquarium microbial communities appear to have shifted among multiple stable states without any obvious buildup of undesirable nitrogen compounds in the tank environment.


Assuntos
Archaea/classificação , Bactérias/classificação , Ecossistema , Microbiota , Salinidade , Água/química , Compostos de Amônio/análise , Archaea/fisiologia , Código de Barras de DNA Taxonômico , DNA Arqueal , DNA Bacteriano/genética , Nitratos/análise , Nitritos/análise , Ciclo do Nitrogênio , Filogenia , RNA Ribossômico 16S/genética
15.
Nat Rev Microbiol ; 17(4): 247-260, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30760902

RESUMO

Biofilms are a form of collective life with emergent properties that confer many advantages on their inhabitants, and they represent a much higher level of organization than single cells do. However, to date, no global analysis on biofilm abundance exists. We offer a critical discussion of the definition of biofilms and compile current estimates of global cell numbers in major microbial habitats, mindful of the associated uncertainty. Most bacteria and archaea on Earth (1.2 × 1030 cells) exist in the 'big five' habitats: deep oceanic subsurface (4 × 1029), upper oceanic sediment (5 × 1028), deep continental subsurface (3 × 1029), soil (3 × 1029) and oceans (1 × 1029). The remaining habitats, including groundwater, the atmosphere, the ocean surface microlayer, humans, animals and the phyllosphere, account for fewer cells by orders of magnitude. Biofilms dominate in all habitats on the surface of the Earth, except in the oceans, accounting for ~80% of bacterial and archaeal cells. In the deep subsurface, however, they cannot always be distinguished from single sessile cells; we estimate that 20-80% of cells in the subsurface exist as biofilms. Hence, overall, 40-80% of cells on Earth reside in biofilms. We conclude that biofilms drive all biogeochemical processes and represent the main way of active bacterial and archaeal life.


Assuntos
Archaea/fisiologia , Bactérias , Biofilmes , Ecossistema , Sedimentos Geológicos/microbiologia , Filogenia
16.
Environ Sci Pollut Res Int ; 26(9): 9352-9364, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30721439

RESUMO

In addition to geological, geochemical, and geophysical aspects, also, microbial aspects have to be taken into account when considering the final storage of high-level radioactive waste in a deep geological repository. Rock salt is a potential host rock formation for such a repository. One indigenous microorganism, that is, common in rock salt, is the halophilic archaeon Halobacterium noricense DSM15987T, which was used in our study to investigate its interactions with the trivalent actinide curium and its inactive analogue europium as a function of time and concentration. Time-resolved laser-induced fluorescence spectroscopy was applied to characterize formed species in the micromolar europium concentration range. An extended evaluation of the data with parallel factor analysis revealed the association of Eu(III) to a phosphate compound released by the cells (F2/F1 ratio, 2.50) and a solid phosphate species (F2/F1 ratio, 1.80). The association with an aqueous phosphate species and a solid phosphate species was proven with site-selective TRLFS. Experiments with Cm(III) in the nanomolar concentration range showed a time- and pCH+-dependent species distribution. These species were characterized by red-shifted emission maxima, 600-602 nm, in comparison to the free Cm(III) aqueous ion, 593.8 nm. After 24 h, 40% of the luminescence intensity was measured on the cells corresponding to 0.18 µg Cm(III)/gDBM. Our results demonstrate that Halobacterium noricense DSM15987T interacts with Eu(III) by the formation of phosphate species, whereas for Cm(III), a complexation with carboxylic functional groups was also observed.


Assuntos
Archaea/fisiologia , Cúrio/metabolismo , Európio/metabolismo , Resíduos Radioativos , Archaea/metabolismo , Európio/química , Lasers , Tolerância ao Sal , Espectrometria de Fluorescência/métodos
17.
Sci Total Environ ; 661: 178-186, 2019 Apr 15.
Artigo em Inglês | MEDLINE | ID: mdl-30669050

RESUMO

The underlying dynamics of microbial (bacteria and archaea) communities ecologically responding to an applied potential are critical to achieving the goal of enhancing bioenergy recovery but are not sufficiently understood. We built a MEC-AD mode that increased methane production rate by several times (max. 3.8 times) during the startup period compared to control AD, changed the absence or presence of external voltage to provide the pre-, dur-, and post- samples for microbial analysis. From a time and spatially dependent community analysis of electrode-respiring bacteria and methanogens, the corresponding Geobacter developed under the influence of external voltage, pairing with methanogens in the anodic and cathodic biofilm to generate methane. Additionally, at the cathode, the Alkaliphilus (basophilic bacteria) also correspondingly shifted alongside the change of external voltage. The mcrA sequencing confirmed a change in the dominant microbe from acetoclastic (mostly Methanosarcina mazei LYC) to hydrogenotrophic methanogens (mostly basophilic Methanobacterium alcaliphilum) at the cathode with 0.8 V voltage. Overall, the external voltage not only enriched the functional microbes including electrogens and methanogens but also indirectly shifted the composition of the bacterial and archaeal community via disturbing the pH condition. The predictive functional profiling indicated that the cathodic methanogenesis principally followed the metabolism pathway of the hydrogenotrophic methanogens, suggesting the F420 co-enzyme could be the key mediate for electron transfer. All data suggested that the electric stimulation would change and maintain the micro-environmental conditions to shift the bacterial/archaeal community.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Reatores Biológicos/microbiologia , Metano/metabolismo , Microbiota , Archaea/classificação , Archaea/enzimologia , Bactérias/classificação , Bactérias/enzimologia , Proteínas de Bactérias/análise , Enzimas de Restrição do DNA/análise , Eletrodos , RNA Arqueal/análise , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
18.
Sci Total Environ ; 658: 723-731, 2019 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-30583167

RESUMO

Archaea play crucial roles in geochemical cycles and influence the emission of greenhouse gases in acidic soils. However, little is known about the distribution pattern of total archaeal diversity and community composition with increasing elevation, especially in acidic agricultural ecosystems. Terraces, characterized by vertical climate changes and unique hydrological properties, are "natural experiments" to explore the spatial distribution of microorganisms along elevation in paddy soils. Here we investigated the diversity and structure of soil archaeal communities in nine increasingly elevated acidic paddy soils of the Yunhe terrace, China. Archaeal communities were dominated by Methanomicrobia of Euryarchaeota (38.5%), Group 1.1a-associated cluster (SAGSCG-1) of Thaumarchaeota (22.0%) and Subgroup-6 (previously described as crenarchaeotal group 1.3b) of Bathyarchaeota (17.8%). The archaeal phylotype richness decreased with increasing elevation. Both the species richness and phylogenetic diversity of the archaeal communities were significantly negatively correlated with soil available phosphorus (AP) content according to linear regression analyses. The archaeal communities differed greatly between soils of increasing elevation, and were roughly clustered into three groups, mostly in relation to AP contents. A variation partitioning analysis further confirmed that edaphic factors including the content of AP (17.1%), nitrate (7.83%), soil organic carbon (4.69%), dissolved organic carbon (4.22%) and soil pH (4.07%) shaped the archaeal community. The variation of soil properties were probably induced by elevation. The co-occurrence network indicated a modular structure of the archaeal community. Overall, our results emphasized that soil AP content was the best predictor of archaeal diversity and community structure, and the impacts of elevation on soil archaeal communities were not diminished by long-term rice cultivation, although minor compared with the effects of soil properties.


Assuntos
Archaea/fisiologia , Microbiota , Fósforo/análise , Microbiologia do Solo , Solo/química , Altitude , Archaea/química , China , Oryza/crescimento & desenvolvimento , Análise Espacial
19.
Microb Ecol ; 77(1): 25-36, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-29766224

RESUMO

Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.


Assuntos
Archaea/classificação , Betaproteobacteria/classificação , Haliclona/microbiologia , Microbiota , Água do Mar/microbiologia , Simbiose , Animais , Archaea/genética , Archaea/isolamento & purificação , Archaea/fisiologia , Bactérias , Betaproteobacteria/genética , Betaproteobacteria/isolamento & purificação , Betaproteobacteria/fisiologia , DNA Arqueal/análise , DNA Bacteriano/análise , França , Mar Mediterrâneo , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Especificidade da Espécie , Microbiologia da Água
20.
ISME J ; 13(4): 885-901, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30514872

RESUMO

Marine Benthic Group D (MBG-D) archaea, discovered by 16S rRNA gene survey decades ago, are ecologically important, yet understudied and uncultured sedimentary archaea. In this study, a comprehensive meta-analysis based on the 16S rRNA genes of MBG-D archaea showed that MBG-D archaea are one of the most frequently found archaeal lineages in global sediment with widespread distribution and high abundance, including 16 subgroups in total. Interestingly, some subgroups show significant segregations toward salinity and methane seeps. Co-occurrence analyses indicate significant non-random association of MBG-D archaea with Lokiarchaeota (in both saline and freshwater sediments) and Hadesarchaea, suggesting potential interactions among these archaeal groups. Meanwhile, based on four nearly complete metagenome-assembled genomes (MAGs) and corresponding metatranscriptomes reconstructed from mangrove and intertidal mudflat sediments, we provide insights on metabolic potentials and ecological functions of MBG-D archaea. MBG-D archaea appear to be capable of transporting and assimilating peptides and generating acetate and ethanol through fermentation. Metatranscriptomic analysis suggests high expression of genes for acetate and amino acid utilization and for peptidases, especially the M09B-type extracellular peptidase (collagenase) showing high expression levels in all four mangrove MAGs. Beyond heterotrophic central carbon metabolism, the MBG-D genomes include genes that might encode two autotrophic pathways: Wood-Ljundahl (WL) pathways using both H4MPT and H4folate as C1 carriers, and an incomplete dicarboxylate/4-hydroxybutyrate cycle with alternative bypasses from pyruvate to malate/oxaloacetate during dicarboxylation. These findings reveal MBG-D archaea as an important ubiquitous benthic sedimentary archaeal group with specific mixotrophic metabolisms, so we proposed the name Thermoprofundales as a new Order within the Class Thermoplasmata. Globally, Thermoprofundales and other benthic archaea might synergistically transform benthic organic matter, possibly playing a vital role in sedimentary carbon cycle.


Assuntos
Archaea/classificação , Archaea/fisiologia , Sedimentos Geológicos/microbiologia , Microbiologia da Água , Archaea/genética , Ciclo do Carbono , Ecologia , Genômica , Sedimentos Geológicos/química , Metagenoma , Metano/metabolismo , Filogenia , RNA Arqueal/genética , RNA Ribossômico 16S/genética , Transcriptoma
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