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1.
Nat Commun ; 11(1): 4453, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32901025

RESUMO

Archaea have evolved to survive in some of the most extreme environments on earth. Life in extreme, nutrient-poor conditions gives the opportunity to probe fundamental energy limitations on movement and response to stimuli, two essential markers of living systems. Here we use three-dimensional holographic microscopy and computer simulations to reveal that halophilic archaea achieve chemotaxis with power requirements one hundred-fold lower than common eubacterial model systems. Their swimming direction is stabilised by their flagella (archaella), enhancing directional persistence in a manner similar to that displayed by eubacteria, albeit with a different motility apparatus. Our experiments and simulations reveal that the cells are capable of slow but deterministic chemotaxis up a chemical gradient, in a biased random walk at the thermodynamic limit.


Assuntos
Archaea/fisiologia , Quimiotaxia/fisiologia , Modelos Biológicos , Simulação por Computador , Extremófilos/fisiologia , Haloarcula/fisiologia , Haloferax/fisiologia , Holografia , Imageamento Tridimensional , Microscopia de Vídeo , Movimento/fisiologia , Nutrientes/fisiologia
2.
Proc Biol Sci ; 287(1931): 20201134, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32693727

RESUMO

Antarctica is estimated to contain as much as a quarter of earth's marine methane, however we have not discovered an active Antarctic methane seep limiting our understanding of the methane cycle. In 2011, an expansive (70 m × 1 m) microbial mat formed at 10 m water depth in the Ross Sea, Antarctica which we identify here to be a high latitude hydrogen sulfide and methane seep. Through 16S rRNA gene analysis on samples collected 1 year and 5 years after the methane seep formed, we identify the taxa involved in the Antarctic methane cycle and quantify the response rate of the microbial community to a novel input of methane. One year after the seep formed, ANaerobic MEthane oxidizing archaea (ANME), the dominant sink of methane globally, were absent. Five years later, ANME were found to make up to 4% of the microbial community, however the dominant member of this group observed (ANME-1) were unexpected considering the cold temperature (-1.8°C) and high sulfate concentrations (greater than 24 mM) present at this site. Additionally, the microbial community had not yet formed a sufficient filter to mitigate the release of methane from the sediment; methane flux from the sediment was still significant at 3.1 mmol CH4 m-2 d-1. We hypothesize that this 5 year time point represents an early successional stage of the microbiota in response to methane input. This study provides the first report of the evolution of a seep system from a non-seep environment, and reveals that the rate of microbial succession may have an unrealized impact on greenhouse gas emission from marine methane reservoirs.


Assuntos
Metano , Regiões Antárticas , Archaea/fisiologia , Temperatura Baixa , Fenômenos Ecológicos e Ambientais , Sedimentos Geológicos , Microbiota , Filogenia , Água do Mar , Análise de Sequência de DNA , Sulfatos
3.
Appl Environ Microbiol ; 86(17)2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32561585

RESUMO

Hydrogen-entangled electron transfer has been verified as an important extracellular pathway of sharing reducing equivalents to regulate biofilm activities within a diversely anaerobic environment, especially in microbial electrosynthesis systems. However, with a lack of useful methods for in situ hydrogen detection in cathodic biofilms, the role of hydrogen involvement in electron transfer is still debatable. Here, a cathodic biofilm was constructed in CH4-produced microbial electrosynthesis reactors, in which the hydrogen evolution dynamic was analyzed to confirm the presence of hydrogen-associated electron transfer near the cathode within a micrometer scale. Fluorescent in situ hybridization images indicated that a colocalized community of archaea and bacteria developed within a 58.10-µm-thick biofilm at the cathode, suggesting that the hydrogen gradient detected by the microsensor was consumed by the collaboration of bacteria and archaea. Coupling of a microsensor and cyclic voltammetry test further provided semiquantitative results of the hydrogen-associated contribution to methane generation (around 21.20% ± 1.57% at a potential of -0.5 V to -0.69 V). This finding provides deep insight into the mechanism of electron transfer in biofilm on conductive materials.IMPORTANCE Electron transfer from an electrode to biofilm is of great interest to the fields of microbial electrochemical technology, bioremediation, and methanogenesis. It has a promising potential application to boost more value-added products or pollutant degradation. Importantly, the ability of microbes to obtain electrons from electrodes and utilize them brings new insight into direct interspecies electron transfer during methanogenesis. Previous studies verified the direct pathway of electron transfer from the electrode to a pure-culture bacterium, but it was rarely reported how the methanogenic biofilm of mixed cultures shares electrons by a hydrogen-associated or hydrogen-free pathway. In the current study, a combination method of microsensor and cyclic voltammetry successfully semiquantified the role of hydrogen in electron transfer from an electrode to methanogenic biofilm.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Biofilmes , Hidrogênio/metabolismo , Metano/metabolismo , Archaea/metabolismo , Bactérias/metabolismo , Transporte de Elétrons
4.
Int J Mol Sci ; 21(5)2020 Mar 06.
Artigo em Inglês | MEDLINE | ID: mdl-32155764

RESUMO

Archaea, the most extremophilic domain of life, contain ether and branched lipids which provide extraordinary bilayer properties. We determined the structural characteristics of diether archaeal-like phospholipids as functions of hydration and temperature by neutron diffraction. Hydration and temperature are both crucial parameters for the self-assembly and physicochemical properties of lipid bilayers. In this study, we detected non-lamellar phases of archaeal-like lipids at low hydration levels, and lamellar phases at levels of 90% relative humidity or more exclusively. Moreover, at 90% relative humidity, a phase transition between two lamellar phases was discernible. At full hydration, lamellar phases were present up to 70ᵒC and no phase transition was observed within the temperature range studied (from 25 °C to 70 °C). In addition, we determined the neutron scattering length density and the bilayer's structural parameters from different hydration and temperature conditions. At the highest levels of hydration, the system exhibited rearrangements on its corresponding hydrophobic region. Furthermore, the water uptake of the lipids examined was remarkably high. We discuss the effect of ether linkages and branched lipids on the exceptional characteristics of archaeal phospholipids.


Assuntos
Archaea/fisiologia , Bicamadas Lipídicas/química , Transição de Fase , Fosfolipídeos/química , Temperatura , Água/metabolismo , Difração de Nêutrons
5.
Proc Natl Acad Sci U S A ; 117(13): 7263-7270, 2020 03 31.
Artigo em Inglês | MEDLINE | ID: mdl-32165545

RESUMO

Spatial heterogeneity in composition and function enables ecosystems to supply diverse services. For soil microbes and the ecosystem functions they catalyze, whether such heterogeneity can be maintained in the face of altered resource inputs is uncertain. In a 50-ha northern California grassland with a mosaic of plant communities generated by different soil types, we tested how spatial variability in microbial composition and function changed in response to nutrient and water addition. Fungal composition lost some of its spatial variability in response to nutrient addition, driven by decreases in mutualistic fungi and increases in antagonistic fungi that were strongest on the least fertile soils, where mutualists were initially most frequent and antagonists initially least frequent. Bacterial and archaeal community composition showed little change in their spatial variability with resource addition. Microbial functions related to nitrogen cycling showed increased spatial variability under nutrient, and sometimes water, additions, driven in part by accelerated nitrification on the initially more-fertile soils. Under anthropogenic changes such as eutrophication and altered rainfall, these findings illustrate the potential for significant changes in ecosystem-level spatial heterogeneity of microbial functions and communities.


Assuntos
Conservação dos Recursos Naturais/métodos , Microbiota/fisiologia , Microbiologia do Solo , Archaea/fisiologia , Bactérias , Demografia/métodos , Ecossistema , Fungos/fisiologia , Nitrificação , Nitrogênio/análise , Chuva , Solo , Simbiose , Água
6.
Cell ; 180(4): 818-818.e1, 2020 02 20.
Artigo em Inglês | MEDLINE | ID: mdl-32084345

RESUMO

Extremophiles are remarkable examples of life's resilience, thriving in hot springs at boiling temperatures, in brine lakes saturated with salt, and in the driest deserts. We review the biogeography, currently known limits of life, and molecular adaptations to extremes. See the online interactive map for additional detail on biogeography, environmental microbiology, and exemplary species. To view this SnapShot, open or download the PDF.


Assuntos
Adaptação Fisiológica , Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Ambientes Extremos , Filogeografia
7.
Microb Ecol ; 80(1): 103-119, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31932882

RESUMO

In the present study, we assessed prokaryotic communities of demosponges, a calcareous sponge, octocorals, sediment and seawater in coral reef habitat of the central Red Sea, including endemic species and species new to science. Goals of the study were to compare the prokaryotic communities of demosponges with the calcareous sponge and octocorals and to assign preliminary high microbial abundance (HMA) or low microbial abundance (LMA) status to the sponge species based on compositional trait data. Based on the compositional data, we were able to assign preliminary LMA or HMA status to all sponge species. Certain species, however, had traits of both LMA and HMA species. For example, the sponge Ectyoplasia coccinea, which appeared to be a LMA species, had traits, including a relatively high abundance of Chloroflexi members, that were more typical of HMA species. This included dominant OTUs assigned to two different classes within the Chloroflexi. The calcareous sponge clustered together with seawater, the known LMA sponge Stylissa carteri and other presumable LMA species. The two dominant OTUs of this species were assigned to the Deltaproteobacteria and had no close relatives in the GenBank database. The octocoral species in the present study had prokaryotic communities that were distinct from sediment, seawater and all sponge species. These were characterised by OTUs assigned to the orders Rhodospirillales, Cellvibrionales, Spirochaetales and the genus Endozoicomonas, which were rare or absent in samples from other biotopes.


Assuntos
Antozoários/microbiologia , Archaea/fisiologia , Bactérias/isolamento & purificação , Sedimentos Geológicos/microbiologia , Poríferos/microbiologia , Água do Mar/microbiologia , Animais , Archaea/classificação , Archaea/isolamento & purificação , Bactérias/classificação , Fenômenos Fisiológicos Bacterianos , Oceano Índico , Microbiota , Arábia Saudita
8.
Antonie Van Leeuwenhoek ; 113(2): 185-195, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31535335

RESUMO

The Atacama Desert is one of the oldest and driest places on Earth. In the last decade, microbial richness and diversity has been acknowledged as an important biological resource of this region. Owing to the value of the microbial diversity apparent in potential biotechnology applications and conservation purposes, it is necessary to catalogue these microbial communities to promote research activities and help to preserve the wide range of ecological niches of the Atacama region. A prototype Atacama Database has been designed and it provides a description of the rich microbial diversity of the Atacama Desert, and helps to visualise available literature resources. Data has been collected, curated, and organised into several categories to generate a single record for each organism in the database that covers classification, isolation metadata, morphology, physiology, genome and metabolism information. The current version of Atacama Database contains 2302 microorganisms and includes cultured and uncultured organisms retrieved from different environments within the desert between 1984 and 2016. These organisms are distributed in bacterial, archaeal or eukaryotic domains, along with those that are unclassified taxonomically. The initial prototype of the Atacama Database includes a basic search and taxonomic and advanced search tools to allow identification and comparison of microbial populations, and space distribution within this biome. A geolocation search was implemented to visualise the microbial diversity of the ecological niches defined by sectors and extract general information of the sampling sites. This effort will aid understanding of the microbial ecology of the desert, microbial population dynamics, seasonal behaviour, impact of climate change over time, and reveal further biotechnological applications of these microorganisms. The Atacama Database is freely available at: https://www.atacamadb.cl.


Assuntos
Bases de Dados Factuais , Archaea/genética , Archaea/fisiologia , Bactérias/genética , Biotecnologia , Clima Desértico , Microbiota/fisiologia , Microbiologia do Solo
9.
Microb Ecol ; 79(3): 527-538, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31511911

RESUMO

This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Ecossistema , Microbiota , Rios/microbiologia , Archaea/classificação , Archaea/genética , Bactérias/classificação , Bactérias/genética , China , Modelos Biológicos , Filogenia , RNA Bacteriano/análise , RNA Ribossômico 16S/análise
10.
Microb Ecol ; 79(2): 342-356, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31428833

RESUMO

Current technologies could identify the abundance and functions of specific microbes, and evaluate their individual effects on microbial ecology. However, these microbes interact with each other, as well as environmental factors, in the form of complex network. Determination of their combined ecological influences remains a challenge. In this study, we developed a tripartite microbial-environment network (TMEN) analysis method that integrates microbial abundance, metabolic function, and environmental data as a tripartite network to investigate the combined ecological effects of microbes. Applying TMEN to analyzing the microbial-environment community structure in the sediments of Hangzhou Bay, one of the most seriously polluted coastal areas in China, we found that microbes were well-organized into 4 bacterial communities and 9 archaeal communities. The total organic carbon, sulfate, chemical oxygen demand, salinity, and nitrogen-related indexes were detected as crucial environmental factors in the microbial-environmental network. With close interactions with these environmental factors, Nitrospirales and Methanimicrococcu were identified as hub microbes with connection advantage. Our TMEN method could close the gap between lack of efficient statistical and computational approaches and the booming of large-scale microbial genomic and environmental data. Based on TMEN, we discovered a potential microbial ecological mechanism that crucial species with significant influence on the microbial community ecology would possess one or two of the community advantages for enhancing their ecological status and essentiality, including abundance advantage and connection advantage.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Baías/microbiologia , Sedimentos Geológicos/microbiologia , Consórcios Microbianos , Técnicas Microbiológicas/métodos , China
11.
Microb Ecol ; 79(1): 38-49, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31079197

RESUMO

To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.


Assuntos
Archaea/química , Archaea/fisiologia , Fontes Hidrotermais/microbiologia , Acetatos/metabolismo , Archaea/classificação , Archaea/genética , Biofilmes , Eletricidade , Eletrodos/microbiologia , Fermentação , Hidrogênio/metabolismo , Oxirredução , Ácido Pirúvico/metabolismo
12.
Microb Ecol ; 79(2): 357-366, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31342100

RESUMO

Rice root-associated microbial community play an important role in plant nutrient acquisition, biomass production, and stress tolerance. Herein, root-associated community assembly was investigated under different phosphate input levels in phosphorus (P)-deficient paddy soil. Rice was grown in a long-term P-depleted paddy soil with 0 (P0), 50 (PL), or 200 (PH) mg P2O5 kg-1 application. DNA from root endophytes was isolated after 46 days, and PCR amplicons from archaea, bacteria, and fungi were sequenced by an Illumina Miseq PE300 platform, respectively. P application had no significant effect on rice root endophytic archaea, which were dominated by ammonia-oxidizing Candidatus Nitrososphaera. By contrast, rice root endophytic community structure of the bacteria and fungi was affected by soil P. Low P input increased endophytic bacterial diversity, whereas high P input increased rhizosphere fungi diversity. Bacillus and Pleosporales, associated with phosphate solubilization and P uptake, dominated in P0 and PH treatments, and Pseudomonas were more abundant in the PL treatment than in the P0 and PH treatments. Co-occurrence network analysis revealed a close interaction between endophytic bacteria and fungi. Soil P application affected both the rice root endosphere and soil rhizosphere microbial community and interaction between rice root endophytic bacteria, and fungi, especially species related to P cycling.


Assuntos
Microbiota/efeitos dos fármacos , Oryza/microbiologia , Fósforo/metabolismo , Raízes de Plantas/microbiologia , Microbiologia do Solo , Archaea/efeitos dos fármacos , Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos/efeitos dos fármacos , Relação Dose-Resposta a Droga , Fungos/efeitos dos fármacos , Fungos/fisiologia , Fósforo/administração & dosagem , Rizosfera
13.
Chemosphere ; 245: 125615, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31864063

RESUMO

Understanding environmental factors driving ecological processes of archaeal communities in heavily contaminated rivers is crucial for improvements in river ecological monitoring and indication. However, succession mechanisms underlying vertical and horizontal archaeal community assemblages in contaminated rivers remains largely unstudied. Here, to investigate ecological processes controlling archaeal community succession in a contaminated urban river, multivariate statistics approaches were applied to fields samples collected from locations representing vertical and horizontal assemblages of archaeal community. Our results revealed that archaeal community in the river showed distinct vertical and horizontal distribution patterns and the differences between water and sediment samples were most significant. Beta-diversity patterns in the vertical and horizontal assemblages are both almost completely caused by species replacement between sampling points (horizontal ßSIM = 0.60 ± 0.09, ßNES = 0.09 ± 0.05; vertical ßSIM = 0.40 ± 0.07, ßNES = 0.10 ± 0.06). Considering phylogenetic turnover deviation, homogenizing dispersal was the most crucial process dominating archaeal community assemblages in water samples while main ecological process in sediment samples was variable selection. Euryarchaeota and Thaumarchaeota were found to prefer high-nutrients and low-nutrients environments, respectively. Analysis of environmental drivers of archaeal phyla distribution and community assemblages indicated that nutrients played a decisive role in driving the sediment archaeal community. Dissolved oxygen (DO) explained the most variation in phylogenetic turnover deviation within all water archaeal community while oxidation reduction potential (ORP) contributed most for horizontal sediment archaeal community assemblages. These findings help to indicate the pollution situation of the river and provide information to predict how archaeal communities would respond to different environmental variations.


Assuntos
Archaea/fisiologia , Ecologia , Sedimentos Geológicos/microbiologia , Microbiota , Filogenia , Rios/química , Archaea/genética , Oxirredução , Oxigênio , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genética , Poluição da Água
14.
Biochem Soc Trans ; 47(6): 1895-1907, 2019 12 20.
Artigo em Inglês | MEDLINE | ID: mdl-31819955

RESUMO

Research on methanogenic Archaea has experienced a revival, with many novel lineages of methanogens recently being found through cultivation and suggested via metagenomics approaches, respectively. Most of these lineages comprise Archaea (potentially) capable of methanogenesis from methylated compounds, a pathway that had previously received comparably little attention. In this review, we provide an overview of these new lineages with a focus on the Methanomassiliicoccales. These lack the Wood-Ljungdahl pathway and employ a hydrogen-dependent methylotrophic methanogenesis pathway fundamentally different from traditional methylotrophic methanogens. Several archaeal candidate lineages identified through metagenomics, such as the Ca. Verstraetearchaeota and Ca. Methanofastidiosa, encode genes for a methylotrophic methanogenesis pathway similar to the Methanomassiliicoccales. Thus, the latter are emerging as a model system for physiological, biochemical and ecological studies of hydrogen-dependent methylotrophic methanogens. Methanomassiliicoccales occur in a large variety of anoxic habitats including wetlands and animal intestinal tracts, i.e. in the major natural and anthropogenic sources of methane emissions, respectively. Especially in ruminant animals, they likely are among the major methane producers. Taken together, (hydrogen-dependent) methylotrophic methanogens are much more diverse and widespread than previously thought. Considering the role of methane as potent greenhouse gas, resolving the methanogenic nature of a broad range of putative novel methylotrophic methanogens and assessing their role in methane emitting environments are pressing issues for future research on methanogens.


Assuntos
Archaea/fisiologia , Metano/metabolismo , Animais , Archaea/genética , Archaea/metabolismo , Ciclo do Carbono , Genes Arqueais , Hidrogênio/metabolismo , Ruminantes , Áreas Alagadas
15.
EBioMedicine ; 49: 354-363, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31685443

RESUMO

BACKGROUND: Mothers are the primary source of bacteria for newborns, but it is unclear whether mother-to-newborn transmission occurs prior to, during or after birth. Similarly, the effect of the delivery mode on neonatal microorganisms has been the focus of controversy. METHODS: Healthy maternal and neonatal pairs that underwent vaginal birth and caesarean section were enrolled in this study. Meconium, placenta, membrane and amniotic fluid samples for newborns and vaginal, rectal and oral samples for mothers were collected. All samples were amplified and sequenced by a 16S rRNA gene primer set targeting bacteria and archaea. FINDINGS: A total of 550 samples from 36 mother-neonate pairs with vaginal births and 42 mother-neonate pairs with caesarean sections were included in this study. The negative controls showed that the data analysis in this study was not affected by contamination. There was a high diversity of microbial communities in the pregnancy environment of the foetus. Meconium samples could be divided into three distinct types that were not influenced by the delivery method. INTERPRETATION: The distribution patterns of bacterial communities in the meconium, placenta, and foetal membranes were highly similar and had nothing to do with the mode of delivery. For approximately half of the placental microorganisms, the same sequence could be found in the vaginal, rectal, and oral samples of the mother.


Assuntos
Parto Obstétrico , Mecônio/microbiologia , Microbiota , Adulto , Líquido Amniótico/microbiologia , Archaea/fisiologia , Feminino , Humanos , Recém-Nascido , Filogenia , Placenta/microbiologia , Gravidez
16.
Philos Trans R Soc Lond B Biol Sci ; 374(1786): 20190076, 2019 11 25.
Artigo em Inglês | MEDLINE | ID: mdl-31587644

RESUMO

Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue 'Single cell ecology'.


Assuntos
Archaea/fisiologia , Fenômenos Fisiológicos Bacterianos , Fungos/fisiologia , Análise de Célula Única
17.
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
18.
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
19.
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
20.
Microbiol Mol Biol Rev ; 83(3)2019 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-31366606

RESUMO

In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.


Assuntos
Archaea/fisiologia , Metano/metabolismo , Oxirredução , Sulfatos/metabolismo , Anaerobiose , Sedimentos Geológicos/microbiologia , Fontes Hidrotermais/microbiologia , Filogenia , RNA Ribossômico 16S , Água do Mar/microbiologia
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