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1.
Nat Commun ; 11(1): 1710, 2020 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-32249765

RESUMO

The discovery of eukaryotic giant viruses has transformed our understanding of the limits of viral complexity, but the extent of their encoded metabolic diversity remains unclear. Here we generate 501 metagenome-assembled genomes of Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from environments around the globe, and analyze their encoded functional capacity. We report a remarkable diversity of metabolic genes in widespread giant viruses, including many involved in nutrient uptake, light harvesting, and nitrogen metabolism. Surprisingly, numerous NCLDV encode the components of glycolysis and the TCA cycle, suggesting that they can re-program fundamental aspects of their host's central carbon metabolism. Our phylogenetic analysis of NCLDV metabolic genes and their cellular homologs reveals distinct clustering of viral sequences into divergent clades, indicating that these genes are virus-specific and were acquired in the distant past. Overall our findings reveal that giant viruses encode complex metabolic capabilities with evolutionary histories largely independent of cellular life, strongly implicating them as important drivers of global biogeochemical cycles.


Assuntos
Carbono/metabolismo , Genoma Viral , Vírus Gigantes/genética , Asfarviridae/genética , Ciclo do Ácido Cítrico/genética , Citoplasma/virologia , Eucariotos/virologia , Evolução Molecular , Vírus Gigantes/enzimologia , Vírus Gigantes/metabolismo , Glicólise/genética , Família Multigênica , Nitrogênio/metabolismo , Processos Fototróficos/genética , Processos Fototróficos/efeitos da radiação , Filogenia , Poxviridae/genética
2.
J Agric Food Chem ; 68(6): 1654-1665, 2020 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-31935099

RESUMO

Microalgae accumulate bioavailable selenium-containing amino acids (Se-AAs), and these are useful as a food supplement. While this accumulation has been studied in phototrophic algal cultures, little data exists for heterotrophic cultures. We have determined the Se-AAs content, selenium/sulfur (Se/S) substitution rates, and overall Se accumulation balance in photo- and heterotrophic Chlorella cultures. Laboratory trials revealed that heterotrophic cultures tolerate Se doses ∼8-fold higher compared to phototrophic cultures, resulting in a ∼2-3-fold higher Se-AAs content. In large-scale experiments, both cultivation regimes provided comparable Se-AAs content. Outdoor phototrophic cultures accumulated up to 400 µg g-1 of total Se-AAs and exhibited a high level of Se/S substitution (5-10%) with 30-60% organic/total Se embedded in the biomass. A slightly higher content of Se-AAs and ratio of Se/S substitution was obtained for a heterotrophic culture in pilot-scale fermentors. The data presented here shows that heterotrophic Chlorella cultures provide an alternative for Se-enriched biomass production and provides information on Se-AAs content and speciation in different cultivation regimes.


Assuntos
Aminoácidos/metabolismo , Chlorella/metabolismo , Chlorella/efeitos da radiação , Selênio/metabolismo , Aminoácidos/análise , Biomassa , Chlorella/classificação , Chlorella/crescimento & desenvolvimento , Processos Heterotróficos , Microalgas/química , Microalgas/crescimento & desenvolvimento , Microalgas/metabolismo , Microalgas/efeitos da radiação , Processos Fototróficos , Selênio/análise
3.
Proc Natl Acad Sci U S A ; 117(5): 2704-2709, 2020 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-31941711

RESUMO

Nitrous oxide (N2O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N2O production by photosynthetic organisms are poorly described. Here we show that the green microalga Chlamydomonas reinhardtii reduces NO into N2O using the photosynthetic electron transport. Through the study of C. reinhardtii mutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Both pathways are active when NO is produced in vivo during the reduction of nitrites and participate in NO homeostasis. Furthermore, NO reduction by both pathways is restricted to chlorophytes, organisms particularly abundant in ocean N2O-producing hot spots. Our results provide a mechanistic understanding of N2O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.


Assuntos
Chlamydomonas reinhardtii/metabolismo , Óxido Nítrico/metabolismo , Óxido Nitroso/metabolismo , Chlamydomonas reinhardtii/genética , Sistema Enzimático do Citocromo P-450/genética , Sistema Enzimático do Citocromo P-450/metabolismo , Fotossíntese , Processos Fototróficos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
4.
Int J Syst Evol Microbiol ; 70(1): 327-333, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31592760

RESUMO

An oval- to rod-shaped, motile, Gram-stain-negative, oxidase-positive, catalase-negative, pink-coloured phototrophic bacterium (designated as strain JA968T) was isolated from an estuary near Pata, Gujarat, India. Cells had an intracytoplasmic membrane architecture as lamellae and divided by budding. Strain JA968T had bacteriochlorophyll-a and spirilloxanthin series carotenoids as photosynthetic pigments. The strain exhibited photolithoautotrophic, photoorganoheterotrophic and chemoorganoheterotrophic growth modes and required thiamine as a growth factor. Strain JA968T had C18 : 1ω7c/C18  : 1ω6c as the predominant fatty acid with ubiquinone-10 (Q-10) and menaquinone-10 (MK-10) forming the quinone composition. The genomic DNA G+C content of the strain was 63.5 mol%. Pairwise comparison of 16S rRNA gene sequences showed that strain JA968T was highly similar to Afifella marina DSM 2698T (99.9 %) and Afifella pfennigii DSM 17143T (98.4 %). The average nucleotide identity values were 92 % between strain JA968T and A. marina DSM 2698T, and 78 % between strain JA968T and A. pfennigii DSM 17143T. The digital DNA-DNA hybridization values between strain JA968T and A. marina and A. pfennigii were 49 and 19 %, respectively. The genomic distinction was also supported by differences in phenotypic and chemotaxonomic characteristics. We propose that strain JA968T represents a new species of the genus Afifella with the name Afifella aestuarii sp. nov. The type strain is JA968T (=KCTC 15634T=NBRC 113338T).


Assuntos
Alphaproteobacteria/classificação , Estuários , Filogenia , Alphaproteobacteria/isolamento & purificação , Técnicas de Tipagem Bacteriana , Bacterioclorofila A/química , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Índia , Hibridização de Ácido Nucleico , Fotossíntese , Processos Fototróficos , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Ubiquinona/química , Vitamina K 2/química , Xantofilas/química
5.
Syst Appl Microbiol ; 43(1): 126024, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31708159

RESUMO

Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium able to carry out photoautotrophic metabolism when grown under anaerobic conditions. The results suggested that this bacterium, which is able to fix carbon dioxide, could be considered for use in transparent biogas fermenters in order to contribute to the production of optimized biogas with a higher CH4:CO2 ratio than the biogas produced in regular, opaque digesters. To the best of our knowledge, this is the first study characterising the phototrophic biofilm associated with illuminated bioreactors.


Assuntos
Biofilmes , Biocombustíveis/microbiologia , Microbiota/fisiologia , Processos Fototróficos , Anaerobiose , Archaea/classificação , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biofilmes/crescimento & desenvolvimento , Reatores Biológicos/microbiologia , Metagenoma , Microbiota/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Esgotos/microbiologia
6.
Commun Biol ; 2: 388, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31667362

RESUMO

Microalgae are promising biocatalysts for applications in sustainable fuel, food, and chemical production. Here, we describe culture collection screening, down-selection, and development of a high-productivity, halophilic, thermotolerant microalga, Picochlorum renovo. This microalga displays a rapid growth rate and high diel biomass productivity (34 g m-2 day-1), with a composition well-suited for downstream processing. P. renovo exhibits broad salinity tolerance (growth at 107.5 g L-1 salinity) and thermotolerance (growth up to 40 °C), beneficial traits for outdoor cultivation. We report complete genome sequencing and analysis, and genetic tool development suitable for expression of transgenes inserted into the nuclear or chloroplast genomes. We further evaluate mechanisms of halotolerance via comparative transcriptomics, identifying novel genes differentially regulated in response to high salinity cultivation. These findings will enable basic science inquiries into control mechanisms governing Picochlorum biology and lay the foundation for development of a microalga with industrially relevant traits as a model photobiology platform.


Assuntos
Clorófitas/metabolismo , Microalgas/metabolismo , Biocatálise , Biomassa , Biotecnologia , Clorófitas/genética , Clorófitas/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Engenharia Genética , Genoma de Cloroplastos , Genoma Microbiano , Microbiologia Industrial/métodos , Microalgas/genética , Microalgas/crescimento & desenvolvimento , Processos Fototróficos , Tolerância ao Sal/genética , Termotolerância/genética
7.
Microbes Environ ; 34(4): 374-387, 2019 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-31685759

RESUMO

Phototrophic microbial mats are assemblages of vertically layered microbial populations dominated by photosynthetic microorganisms. In order to elucidate the vertical distribution and diversity of phototrophic microorganisms in a hot spring-associated microbial mat in Nakabusa (Japan), we analyzed the 16S rRNA gene amplicon sequences of the microbial mat separated into five depth horizons, and correlated them with microsensor measurements of O2 and spectral scalar irradiance. A stable core community and high diversity of phototrophic organisms dominated by the filamentous anoxygenic phototrophs, Roseiflexus castenholzii and Chloroflexus aggregans were identified together with the spectral signatures of bacteriochlorophylls (BChls) a and c absorption in all mat layers. In the upper mat layers, a high abundance of cyanobacteria (Thermosynechococcus sp.) correlated with strong spectral signatures of chlorophyll a and phycobiliprotein absorption near the surface in a zone of high O2 concentrations during the day. Deeper mat layers were dominated by uncultured chemotrophic Chlorobi such as the novel putatively sulfate-reducing "Ca. Thermonerobacter sp.", which showed increasing abundance with depth correlating with low O2 in these layers enabling anaerobic metabolism. Oxygen tolerance and requirements for the novel phototroph "Ca. Chloroanaerofilum sp." and the uncultured chemotrophic Armatimonadetes member type OS-L detected in Nakabusa hot springs, Japan appeared to differ from previously suggested lifestyles for close relatives identified in hot springs in Yellowstone National Park, USA. The present study identified various microenvironmental gradients and niche differentiation enabling the co-existence of diverse chlorophototrophs in metabolically diverse communities in hot springs.


Assuntos
Bactérias/classificação , Biodiversidade , Fontes Termais/microbiologia , Bactérias/genética , Bactérias/isolamento & purificação , Bacterioclorofilas/metabolismo , DNA Bacteriano/genética , Fontes Termais/química , Japão , Luz , Microbiota/genética , Oxigênio/análise , Oxigênio/metabolismo , Fotossíntese , Processos Fototróficos , Ficobiliproteínas/metabolismo , Filogenia , RNA Ribossômico 16S/genética
8.
Phys Rev Lett ; 123(15): 158101, 2019 Oct 11.
Artigo em Inglês | MEDLINE | ID: mdl-31702314

RESUMO

Microorganismal motility is often characterized by complex responses to environmental physico-chemical stimuli. Although the biological basis of these responses is often not well understood, their exploitation already promises novel avenues to directly control the motion of living active matter at both the individual and collective level. Here we leverage the phototactic ability of the model microalga Chlamydomonas reinhardtii to precisely control the timing and position of localized cell photoaccumulation, leading to the controlled development of isolated bioconvective plumes. This novel form of photobioconvection allows a precise, fast, and reconfigurable control of the spatiotemporal dynamics of the instability and the ensuing global recirculation, which can be activated and stopped in real time. A simple continuum model accounts for the phototactic response of the suspension and demonstrates how the spatiotemporal dynamics of the illumination field can be used as a simple external switch to produce efficient bio mixing.


Assuntos
Chlamydomonas reinhardtii/fisiologia , Modelos Biológicos , Fotobiologia , Processos Fototróficos
9.
Microb Cell Fact ; 18(1): 165, 2019 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-31601201

RESUMO

BACKGROUND: Cyanobacteria and other phototrophic microorganisms allow to couple the light-driven assimilation of atmospheric [Formula: see text] directly to the synthesis of carbon-based products, and are therefore attractive platforms for microbial cell factories. While most current engineering efforts are performed using small-scale laboratory cultivation, the economic viability of phototrophic cultivation also crucially depends on photobioreactor design and culture parameters, such as the maximal areal and volumetric productivities. Based on recent insights into the cyanobacterial cell physiology and the resulting computational models of cyanobacterial growth, the aim of this study is to investigate the limits of cyanobacterial productivity in continuous culture with light as the limiting nutrient. RESULTS: We integrate a coarse-grained model of cyanobacterial growth into a light-limited chemostat and its heterogeneous light gradient induced by self-shading of cells. We show that phototrophic growth in the light-limited chemostat can be described using the concept of an average light intensity. Different from previous models based on phenomenological growth equations, our model provides a mechanistic link between intracellular protein allocation, population growth and the resulting reactor productivity. Our computational framework thereby provides a novel approach to investigate and predict the maximal productivity of phototrophic cultivation, and identifies optimal proteome allocation strategies for developing maximally productive strains. CONCLUSIONS: Our results have implications for efficient phototrophic cultivation and the design of maximally productive phototrophic cell factories. The model predicts that the use of dense cultures in well-mixed photobioreactors with short light-paths acts as an effective light dilution mechanism and alleviates the detrimental effects of photoinhibition even under very high light intensities. We recover the well-known trade-offs between a reduced light-harvesting apparatus and increased population density. Our results are discussed in the context of recent experimental efforts to increase the yield of phototrophic cultivation.


Assuntos
Cianobactérias/crescimento & desenvolvimento , Microalgas/crescimento & desenvolvimento , Fotobiorreatores , Luz , Modelos Biológicos , Processos Fototróficos
10.
Genome Biol Evol ; 11(10): 2895-2908, 2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31626703

RESUMO

Phyllosphere is a habitat to a variety of viruses, bacteria, fungi, and other microorganisms, which play a fundamental role in maintaining the health of plants and mediating the interaction between plants and ambient environments. A recent addition to this catalogue of microbial diversity was the aerobic anoxygenic phototrophs (AAPs), a group of widespread bacteria that absorb light through bacteriochlorophyll α (BChl a) to produce energy without fixing carbon or producing molecular oxygen. However, culture representatives of AAPs from phyllosphere and their genome information are lacking, limiting our capability to assess their potential ecological roles in this unique niche. In this study, we investigated the presence of AAPs in the phyllosphere of a winter wheat (Triticum aestivum L.) in Denmark by employing bacterial colony based infrared imaging and MALDI-TOF mass spectrometry (MS) techniques. A total of ∼4,480 colonies were screened for the presence of cellular BChl a, resulting in 129 AAP isolates that were further clustered into 21 groups based on MALDI-TOF MS profiling, representatives of which were sequenced using the Illumina NextSeq and Oxford Nanopore MinION platforms. Seventeen draft and four complete genomes of AAPs were assembled belonging in Methylobacterium, Rhizobium, Roseomonas, and a novel Alsobacter. We observed a diverging pattern in the evolutionary rates of photosynthesis genes among the highly homogenous AAP strains of Methylobacterium (Alphaproteobacteria), highlighting an ongoing genomic innovation at the gene cluster level.


Assuntos
Evolução Molecular , Methylobacterium/genética , Fotossíntese/genética , Triticum/microbiologia , Genômica , Processos Heterotróficos , Methylobacterium/classificação , Methylobacterium/isolamento & purificação , Processos Fototróficos , Filogenia
11.
Nat Commun ; 10(1): 4230, 2019 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-31530813

RESUMO

In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how microbial phototrophs and autotrophs contribute to this exceptional productivity. Amplicon and shotgun DNA sequencing data of microbial mats from four Canadian soda lakes indicate the presence of > 2,000 species of Bacteria and Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome of < 100 abundant bacteria, present in all four lakes. Most of these are related to microbes previously detected in sediments of Asian alkaline lakes, showing that common selection principles drive community assembly from a globally distributed reservoir of alkaliphile biodiversity. Detection of > 7,000 proteins show how phototrophic populations allocate resources to specific processes and occupy complementary niches. Carbon fixation proceeds by the Calvin-Benson-Bassham cycle, in Cyanobacteria, Gammaproteobacteria, and, surprisingly, Gemmatimonadetes. Our study provides insight into soda lake ecology, as well as a template to guide efforts to engineer biotechnology for carbon dioxide conversion.


Assuntos
Bactérias/isolamento & purificação , Lagos/microbiologia , Microbiota , Filogenia , Álcalis/análise , Processos Autotróficos , Bactérias/classificação , Bactérias/genética , Bactérias/efeitos da radiação , Biodiversidade , Canadá , Ciclo do Carbono , Lagos/química , Luz , Processos Fototróficos , Enxofre/metabolismo
12.
Int J Mol Sci ; 20(18)2019 Sep 05.
Artigo em Inglês | MEDLINE | ID: mdl-31491935

RESUMO

Palmitoleic acid, one scarce omega-7 monounsaturated fatty acid, has important applications in the fields of medicine and health products. Tribonema has been considered as a promising candidate for the production of palmitoleic acid due to its high lipid and palmitoleic acid content and remarkable heterotrophic ability. The high-density heterotrophic cultivation of Tribonema minus was conducted in this work, and the highest biomass of 42.9 g L-1 and a relatively low lipid content of 28.7% were observed. To further enhance the lipid and palmitoleic acid accumulation, induction strategies under two regimes of phototrophy and heterotrophy with different conditions were investigated and compared. Results demonstrated encouraging promotions both by heterotrophic and phototrophic ways, and the final lipid contents reached 41.9% and 49.0%, respectively. In consideration of the time cost, however, the induction under heterotrophic conditions was much more advantageous, by which the highest lipid and palmitoleic acid productivities of 1.77 g L-1 d-1 and 924 mg L-1 d-1 were obtained respectively, with the lipid yield on glucose of 0.26 g g-1.


Assuntos
Clorófitas/metabolismo , Ácidos Graxos Monoinsaturados/metabolismo , Fermentação , Lipídeos/biossíntese , Sementes/metabolismo , Metabolismo dos Lipídeos , Processos Fototróficos
13.
Annu Rev Microbiol ; 73: 435-456, 2019 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-31500535

RESUMO

Cyanobacteria are common in symbiotic relationships with diverse multicellular organisms (animals, plants, fungi) in terrestrial environments and with single-celled heterotrophic, mixotrophic, and autotrophic protists in aquatic environments. In the sunlit zones of aquatic environments, diverse cyanobacterial symbioses exist with autotrophic taxa in phytoplankton, including dinoflagellates, diatoms, and haptophytes (prymnesiophytes). Phototrophic unicellular cyanobacteria related to Synechococcus and Prochlorococcus are associated with a number of groups. N2-fixing cyanobacteria are symbiotic with diatoms and haptophytes. Extensive genome reduction is involved in the N2-fixing endosymbionts, most dramatically in the unicellular cyanobacteria associated with haptophytes, which have lost most of the photosynthetic apparatus, the ability to fix C, and the tricarboxylic acid cycle. The mechanisms involved in N2-fixing symbioses may involve more interactions beyond simple exchange of fixed C for N. N2-fixing cyanobacterial symbioses are widespread in the oceans, even more widely distributed than the best-known free-living N2-fixing cyanobacteria, suggesting they may be equally or more important in the global ocean biogeochemical cycle of N.Despite their ubiquitous nature and significance in biogeochemical cycles, cyanobacterium-phytoplankton symbioses remain understudied and poorly understood.


Assuntos
Biodiversidade , Cianobactérias/classificação , Cianobactérias/crescimento & desenvolvimento , Fitoplâncton/microbiologia , Simbiose , Endófitos/classificação , Endófitos/crescimento & desenvolvimento , Interações entre Hospedeiro e Microrganismos , Fixação de Nitrogênio , Processos Fototróficos , Fitoplâncton/fisiologia
14.
Microbes Environ ; 34(3): 278-292, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31413226

RESUMO

Hydrothermal systems, including terrestrial hot springs, contain diverse geochemical conditions that vary over short spatial scales due to progressive interactions between reducing hydrothermal fluids, the oxygenated atmosphere, and, in some cases, seawater. At Jinata Onsen on Shikinejima Island, Japan, an intertidal, anoxic, iron-rich hot spring mixes with the oxygenated atmosphere and seawater over short spatial scales, creating diverse chemical potentials and redox pairs over a distance of ~10 m. We characterized geochemical conditions along the outflow of Jinata Onsen as well as the microbial communities present in biofilms, mats, and mineral crusts along its traverse using 16S rRNA gene amplicon and genome-resolved shotgun metagenomic sequencing. Microbial communities significantly changed downstream as temperatures and dissolved iron concentrations decreased and dissolved oxygen increased. Biomass was more limited near the spring source than downstream, and primary productivity appeared to be fueled by the oxidation of ferrous iron and molecular hydrogen by members of Zetaproteobacteria and Aquificae. The microbial community downstream was dominated by oxygenic Cyanobacteria. Cyanobacteria are abundant and active even at ferrous iron concentrations of ~150 µM, which challenges the idea that iron toxicity limited cyanobacterial expansion in Precambrian oceans. Several novel lineages of Bacteria are also present at Jinata Onsen, including previously uncharacterized members of the phyla Chloroflexi and Calditrichaeota, positioning Jinata Onsen as a valuable site for the future characterization of these clades.


Assuntos
Bactérias/metabolismo , Biodiversidade , Fontes Termais/química , Fontes Termais/microbiologia , Ferro/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biomassa , Crescimento Quimioautotrófico , Geografia , Ferro/análise , Metagenômica , Microbiota/genética , Oxigênio/análise , Oxigênio/metabolismo , Processos Fototróficos , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Temperatura
15.
Microbes Environ ; 34(3): 304-309, 2019 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-31391357

RESUMO

Chloroflexus aggregans is a thermophilic filamentous anoxygenic phototrophic bacterium frequently found in microbial mats in natural hot springs. C. aggregans often thrives with cyanobacteria that engage in photosynthesis to provide it with an organic substrate; however, it sometimes appears as the dominant phototroph in microbial mats without cyanobacteria. This suggests that C. aggregans has the ability to grow photoautotrophically. However, photoautotrophic growth has not been observed in any cultured strains of C. aggregans. We herein attempted to isolate a photoautotrophic strain from C. aggregansdominated microbial mats in Nakabusa hot spring in Japan. Using an inorganic medium, we succeeded in isolating a new strain that we designated "ACA-12". A phylogenetic analysis based on 16S rRNA gene and 16S-23S rRNA gene internal transcribed spacer (ITS) region sequences revealed that strain ACA-12 was closely related to known C. aggregans strains. Strain ACA-12 showed sulfide consumption along with autotrophic growth under anaerobic light conditions. The deposited elemental sulfur particles observed by microscopy indicated that sulfide oxidation occurred, similar to that in photoautotrophic strains in the related species, C. aurantiacus. Moreover, we found that other strains of C. aggregans, including the type strain, also exhibited a slight photoautotrophic growing ability, whereas strain ACA-12 showed the fastest growth rate. This is the first demonstration of photoautotrophic growth with sulfide in C. aggregans. The present results strongly indicate that C. aggregans is associated with inorganic carbon incorporation using sulfide as an electron donor in hot spring microbial mats.


Assuntos
Chloroflexus/metabolismo , Processos Fototróficos , Sulfetos/metabolismo , Proteínas de Bactérias/genética , Chloroflexus/classificação , Chloroflexus/genética , Chloroflexus/efeitos da radiação , Meios de Cultura/química , DNA Bacteriano/genética , DNA Espaçador Ribossômico/genética , Fontes Termais/microbiologia , Japão , Luz , Oxirredução , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfetos/análise , Enxofre/metabolismo
16.
Folia Microbiol (Praha) ; 64(5): 705-710, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31346963

RESUMO

Aerobic anoxygenic phototrophic (AAP) bacteria are a common component of freshwater microbial communities. They harvest light energy using bacteriochlorophyll a-containing reaction centers to supplement their predominantly heterotrophic metabolism. We used epifluorescence microscopy, HPLC, and infrared fluorometry to examine the dynamics of AAP bacteria in the mesotrophic lake Vlkov during the seasonal cycle. The mortality of AAP bacteria was estimated from diel changes of bacteriochlorophyll a fluorescence. The AAP abundance correlated with water temperature and DOC concentration. Its maximum was registered during late summer, when AAP bacteria made up 20% of total bacteria. The novel element of this study is the seasonal measurements of AAP mortality rates. The rates ranged between 1.15 and 4.56 per day with the maxima registered in early summer coinciding with the peak of primary production, which documents that AAP bacteria are a highly active component of freshwater microbial loop.


Assuntos
Bactérias Aeróbias/isolamento & purificação , Bactérias Aeróbias/efeitos da radiação , Biodiversidade , Lagos/microbiologia , Bactérias Aeróbias/classificação , Bactérias Aeróbias/genética , Luz , Oxigênio/metabolismo , Processos Fototróficos , Estações do Ano
17.
PLoS One ; 14(6): e0218753, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31216335

RESUMO

Pigmented bacteria cells, including aerobic anoxygenic phototrophic (AAP) bacteria, contribute significantly to secondary production and aquatic carbon cycling but their distribution in the deep sea is still not well understood, especially in the South China Sea. In this study, microscopic, flow cytometric, and molecular analyses were carried out to investigate the abundance and diversity of AAP bacteria at seven stations in the South China Sea. The results revealed the existence of bacteriochlorophyll-containing bacteria below 500 m from two of seven stations. Flow cytometric analysis detected red and infra-red fluorescence under blue (488 nm) light excitation from fluorescent cells. Blue light-excited red fluorescence of these cells from the 1000 m depth at station E403 were verified using epifluorescence microscopy. Based on fluorescence and side scatter features, fluorescent cells were sorted and subjected to molecular analysis. DNA was extracted from these sorted cells from both stations for PCR amplification using 16S rDNA primers. Sequencing of the PCR products showed that the sorted cells from the 1000 m depth at station E403 belonged to the genus Porphyrobacter. The cell population sorted from 500 m at station E703 contained Sphingomonas and a Methylobacterium-like taxon. All these three taxa belong to aerobic anoxygenic phototrophic alpha-proteobacteria. Using flow cytometric analysis, we found that the abundance of Porphyrobacter sp. at 1000 m was 2.71-2.95×104 cells mL-1 whereas cell counts of Sphingomonas sp. and Methylobacterium at 500 m were about 3.75-4.12×105 cells mL-1. These results indicate that albeit not ubiquitous in deep water, bacteriochlorophyll-containing bacteria can be abundant in the deep-sea aphotic zone.


Assuntos
Bactérias/classificação , RNA Ribossômico 16S/genética , Água do Mar/microbiologia , Análise de Sequência de DNA/métodos , Bactérias/genética , Bactérias/metabolismo , Bacterioclorofilas/metabolismo , China , DNA Bacteriano/genética , DNA Ribossômico/genética , Citometria de Fluxo , Processos Fototróficos , Filogenia
18.
Mol Microbiol ; 112(2): 442-460, 2019 08.
Artigo em Inglês | MEDLINE | ID: mdl-31125464

RESUMO

Extracytoplasmic function (ECF) sigma factors are environmentally responsive transcriptional regulators. In Alphaproteobacteria, σEcfG activates general stress response (GSR) transcription and protects cells from multiple stressors. A phosphorylation-dependent protein partner switching mechanism, involving HWE/HisKA_2-family histidine kinases, underlies σEcfG activation. The identity of these sensor kinases and the signals that regulate them remain largely uncharacterized. We have developed the aerobic anoxygenic photoheterotroph (AAP), Erythrobacter litoralis DSM 8509, as a comparative genetic model to investigate GSR. Using this system, we sought to define the role of visible light and a photosensory HWE kinase, LovK, in regulation of GSR transcription. We identified three HWE kinase genes that collectively control GSR: gsrK and lovK are activators, while gsrP is a repressor. In wild-type cells, GSR transcription is activated in the dark and nearly off in the light, and the opposing activities of gsrK and gsrP are sufficient to modulate GSR transcription in response to illumination. In the absence of gsrK and gsrP, lovK alone is sufficient to activate GSR transcription. lovK is a more robust activator in the dark, and light-dependent regulation by LovK requires that its N-terminal LOV domain be photochemically active. Our studies establish a role for visible light and an ensemble of HWE kinases in light-dependent regulation of GSR transcription in E. litoralis.


Assuntos
Proteínas de Bactérias/metabolismo , Proteínas Quinases/metabolismo , Sphingomonadaceae/enzimologia , Sphingomonadaceae/efeitos da radiação , Proteínas de Bactérias/genética , Regulação Bacteriana da Expressão Gênica/efeitos da radiação , Luz , Processos Fototróficos , Proteínas Quinases/genética , Fator sigma/genética , Fator sigma/metabolismo , Sphingomonadaceae/genética , Sphingomonadaceae/metabolismo , Estresse Fisiológico/efeitos da radiação
19.
Biol Rev Camb Philos Soc ; 94(5): 1701-1721, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31095885

RESUMO

Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (ß-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.


Assuntos
Evolução Biológica , Euglenozoários/classificação , Biologia Molecular , Trypanosomatina/genética , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Euglênidos/classificação , Euglênidos/genética , Euglenozoários/genética , Genoma/fisiologia , Íntrons/fisiologia , Mitocôndrias/genética , Processos Fototróficos , Filogenia , Interferência de RNA , RNA Ribossômico 28S/genética , Trypanosomatina/classificação , Trypanosomatina/enzimologia
20.
BMC Bioinformatics ; 20(1): 233, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072303

RESUMO

BACKGROUND: Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological trade-offs can provide invaluable information regarding the biophysical and biochemical bases behind observed cellular phenotypes. A quantitative knowledge of a cell system's critical objectives is also needed for engineering of cellular metabolism, where there is interest in mitigating the fitness costs that may result from human manipulation. RESULTS: To study metabolism in photoheterotrophs, we developed and validated a genome-scale model of metabolism in Rhodopseudomonas palustris, a metabolically versatile gram-negative purple non-sulfur bacterium capable of growing phototrophically on various carbon sources, including inorganic carbon and aromatic compounds. To quantitatively assess trade-offs among a set of important biological objectives during different metabolic growth modes, we used our new model to conduct an 8-dimensional multi-objective flux analysis of metabolism in R. palustris. Our results revealed that phototrophic metabolism in R. palustris is light-limited under anaerobic conditions, regardless of the available carbon source. Under photoheterotrophic conditions, R. palustris prioritizes the optimization of carbon efficiency, followed by ATP production and biomass production rate, in a Pareto-optimal manner. To achieve maximum carbon fixation, cells appear to divert limited energy resources away from growth and toward CO2 fixation, even in the presence of excess reduced carbon. We also found that to achieve the theoretical maximum rate of biomass production, anaerobic metabolism requires import of additional compounds (such as protons) to serve as electron acceptors. Finally, we found that production of hydrogen gas, of potential interest as a candidate biofuel, lowers the cellular growth rates under all circumstances. CONCLUSIONS: Photoheterotrophic metabolism of R. palustris is primarily regulated by the amount of light it can absorb and not the availability of carbon. However, despite carbon's secondary role as a regulating factor, R. palustris' metabolism strives for maximum carbon efficiency, even when this increased efficiency leads to slightly lower growth rates.


Assuntos
Processos Fototróficos/genética , Rodopseudomonas/genética
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