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1.
J Environ Sci (China) ; 99: 1-9, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33183685

RESUMO

Freshwater cyanobacterial blooms have drawn public attention because they threaten the safety of water resources and human health worldwide. Heavy cyanobacterial blooms outbreak in Lake Taihu in summer annually and vanish in other months. To find out the factors impacting the cyanobacterial blooms, the present study measured the physicochemical parameters of water and investigated the composition of microbial community using the 16S rRNA gene and internal transcribed spacer amplicon sequencing in the months with or without bloom. The most interesting finding is that two major cyanobacteria, Planktothrix and Microcystis, dramatically alternated during a cyanobacterial bloom in 2016, which is less mentioned in previous studies. When the temperature of the water began increasing in July, Planktothrix appeared first and showed as a superior competitor for M. aeruginosa in NO3--rich conditions. Microcystis became the dominant genus when the water temperature increased further in August. Laboratory experiments confirmed the influence of temperature and the total dissolved nitrogen (TDN) form on the growth of Planktothrix and Microcystis in a co-culture system. Besides, species interactions between cyanobacteria and non-cyanobacterial microorganisms, especially the prokaryotes, also played a key role in the alteration of Planktothrix and Microcystis. The present study exhibited the alteration of two dominant cyanobacteria in the different bloom periods caused by the temperature, TDN forms as well as the species interactions. These results helped the better understanding of cyanobacterial blooms and the factors which contribute to them.


Assuntos
Cianobactérias , Microbiota , Microcystis , Cianobactérias/genética , Lagos , Microcystis/genética , RNA Ribossômico 16S/genética
2.
Water Res ; 185: 116292, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33086464

RESUMO

The current study reports the community succession of different toxin and non-toxin producing cyanobacteria at different stages of cyanobacterial harmful algal blooms (CyanoHABs) and their connectivity with nitrogen and phosphorus cycles in a freshwater lake using an ecogenomics framework. Comprehensive high throughput DNA sequencing, water quality parameter measurements, and functional gene expressions over temporal and spatial scales were employed. Among the cyanobacterial community, the lake was initially dominated by Cyanobium during the months of May, June, and early July, and later primarily by Aphanizomenon and Dolichospermum depicting functional redundancy. Finally, Planktothrix appeared in late August and then the dominance switched to Planktothrix in September. Microcystis aeruginosa and Microcystis panniformis; two species responsible for cyanotoxin production, were also present in August and September, but in significantly smaller relative abundance. MC-LR (0.06-1.32 µg/L) and MC-RR (0.01-0.26 µg/L) were two major types of cyanotoxins detected. The presence of MC-LR and MC-RR were significantly correlated with the Microcystis-related genes (16SMic/mcyA/mcyG) and their expressions (r = 0.33 to 0.8, p < 0.05). The metabolic analyses further linked the presence of different cyanobacterial groups with distinct functions. The nitrogen metabolisms detected a relatively higher abundance of nitrite/nitrate reductase in early summer, indicating significant denitrification activity and the activation of N-fixation in the blooms dominated by Aphanizomenon/Dolichospermum (community richness) during nutrient-limited conditions. The phosphorus and carbohydrate metabolisms detected a trend to initiate a nutrient starvation alert and store nutrients from early summer, while utilizing the stored polyphosphate and carbohydrate (PPX and F6PPK) during the extreme ortho-P scarcity period, mostly in August or September. Specifically, the abundance of Aphanizomenon and Dolichospermum was positively correlated with the nitrogen-fixing nif gene and (p < 0.001) and the PPX enzyme for the stored polyphosphate utilization (r = 0.77, p < 0.001). Interestingly, the lake experienced a longer N-fixing period (2-3 months) before non-fixing cyanobacteria (Planktothrix) dominated the entire lake in late summer. The Provo Bay site, which is known to be nutrient-rich historically, had early episodes of filamentous cyanobacteria blooms compared to the rest of the lake.


Assuntos
Cianobactérias , Microbiota , Cianobactérias/genética , Proliferação Nociva de Algas , Lagos , Microcystis
3.
Artigo em Inglês | MEDLINE | ID: mdl-32882819

RESUMO

Harmful cyanobacterial blooms pose a risk to human health worldwide. To enhance understanding on the bloom-forming mechanism, the spatiotemporal changes in cyanobacterial diversity and composition in two eutrophic lakes (Erhai Lake and Lushui Reservoir) of China were investigated from 2010 to 2011 by high-throughput sequencing of environmental DNA. For each sample, 118 to 260 cpcBA-IGS operational taxonomic units (OTUs) were obtained. Fifty-two abundant OTUs were identified, which made up 95.2% of the total sequences and were clustered into nine cyanobacterial groups. Although the cyanobacterial communities of both lakes were mainly dominated by Microcystis, Erhai Lake had a higher cyanobacterial diversity. The abundance of mixed Nostocales species was lower than that of Microcystis, whereas Phormidium and Synechococcus were opportunistically dominant. The correlation between the occurrence frequency and relative abundance of OTUs was poorly fitted by the Sloan neutral model. Deterministic processes such as phosphorus availability were shown to have significant effects on the cyanobacterial community structure in Erhai Lake. In summary, the Microcystis-dominated cyanobacterial community was mainly affected by the deterministic process. Opportunistically dominant species have the potential to replace Microcystis and form blooms in eutrophic lakes, indicating the necessity to monitor these species for drinking water safety.


Assuntos
Cianobactérias , Eutrofização , Microcystis , Análise de Sequência de DNA , China , Cianobactérias/genética , DNA Bacteriano , Lagos , Microcystis/genética , Fósforo
4.
Proc Natl Acad Sci U S A ; 117(34): 20926-20931, 2020 08 25.
Artigo em Inglês | MEDLINE | ID: mdl-32747571

RESUMO

The circadian clock of cyanobacteria consists of only three clock proteins, KaiA, KaiB, and KaiC, which generate a circadian rhythm of KaiC phosphorylation in vitro. The adenosine triphosphatase (ATPase) activity of KaiC is the source of the 24-h period and temperature compensation. Although numerous circadian mutants of KaiC have been identified, the tuning mechanism of the 24-h period remains unclear. Here, we show that the circadian period of in vitro phosphorylation rhythm of mutants at position 402 of KaiC changed dramatically, from 15 h (0.6 d) to 158 h (6.6 d). The ATPase activities of mutants at position 402 of KaiC, without KaiA and KaiB, correlated with the frequencies (1/period), indicating that KaiC structure was the source of extra period change. Despite the wide-range tunability, temperature compensation of both the circadian period and the KaiC ATPase activity of mutants at position 402 of KaiC were nearly intact. We also found that in vivo and in vitro circadian periods and the KaiC ATPase activity of mutants at position 402 of KaiC showed a correlation with the side-chain volume of the amino acid at position 402 of KaiC. Our results indicate that residue 402 is a key position of determining the circadian period of cyanobacteria, and it is possible to dramatically alter the period of KaiC while maintaining temperature compensation.


Assuntos
Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Peptídeos e Proteínas de Sinalização do Ritmo Circadiano/genética , Peptídeos e Proteínas de Sinalização do Ritmo Circadiano/metabolismo , Ritmo Circadiano/genética , Adenosina Trifosfatases/metabolismo , Substituição de Aminoácidos/genética , Relógios Circadianos/genética , Cianobactérias/genética , Cianobactérias/metabolismo , Regulação Bacteriana da Expressão Gênica/genética , Mutação/genética , Fosforilação , Synechococcus/genética , Synechococcus/metabolismo
5.
Proc Natl Acad Sci U S A ; 117(33): 19705-19712, 2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32747579

RESUMO

Photosystem II (PS II) captures solar energy and directs charge separation (CS) across the thylakoid membrane during photosynthesis. The highly oxidizing, charge-separated state generated within its reaction center (RC) drives water oxidation. Spectroscopic studies on PS II RCs are difficult to interpret due to large spectral congestion, necessitating modeling to elucidate key spectral features. Herein, we present results from time-dependent density functional theory (TDDFT) calculations on the largest PS II RC model reported to date. This model explicitly includes six RC chromophores and both the chlorin phytol chains and the amino acid residues <6 Å from the pigments' porphyrin ring centers. Comparing our wild-type model results with calculations on mutant D1-His-198-Ala and D2-His-197-Ala RCs, our simulated absorption-difference spectra reproduce experimentally observed shifts in known chlorophyll absorption bands, demonstrating the predictive capabilities of this model. We find that inclusion of both nearby residues and phytol chains is necessary to reproduce this behavior. Our calculations provide a unique opportunity to observe the molecular orbitals that contribute to the excited states that are precursors to CS. Strikingly, we observe two high oscillator strength, low-lying states, in which molecular orbitals are delocalized over ChlD1 and PheD1 as well as one weaker oscillator strength state with molecular orbitals delocalized over the P chlorophylls. Both these configurations are a match for previously identified exciton-charge transfer states (ChlD1 +PheD1 -)* and (PD2 +PD1 -)*. Our results demonstrate the power of TDDFT as a tool, for studies of natural photosynthesis, or indeed future studies of artificial photosynthetic complexes.


Assuntos
Proteínas de Bactérias/química , Cianobactérias/metabolismo , Complexo de Proteína do Fotossistema II/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Clorofila/química , Clorofila/metabolismo , Cianobactérias/química , Cianobactérias/genética , Cinética , Modelos Moleculares , Fotossíntese , Complexo de Proteína do Fotossistema II/genética , Complexo de Proteína do Fotossistema II/metabolismo
6.
Proc Natl Acad Sci U S A ; 117(33): 19731-19736, 2020 08 18.
Artigo em Inglês | MEDLINE | ID: mdl-32759207

RESUMO

Cyanobacteriochromes are photoreceptors in cyanobacteria that exhibit a wide spectral coverage and unique photophysical properties from the photoinduced isomerization of a linear tetrapyrrole chromophore. Here, we integrate femtosecond-resolved fluorescence and transient-absorption methods and unambiguously showed the significant solvation dynamics occurring at the active site from a few to hundreds of picoseconds. These motions of local water molecules and polar side chains are continuously convoluted with the isomerization reaction, leading to a nonequilibrium processes with continuous active-site motions. By mutations of critical residues at the active site, the modified local structures become looser, resulting in faster solvation relaxations and isomerization reaction. The observation of solvation dynamics is significant and critical to the correct interpretation of often-observed multiphasic dynamic behaviors, and thus the previously invoked ground-state heterogeneity may not be relevant to the excited-state isomerization reaction.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Cianobactérias/metabolismo , Fotorreceptores Microbianos/química , Proteínas de Bactérias/genética , Domínio Catalítico , Cianobactérias/química , Cianobactérias/genética , Isomerismo , Cinética , Fotorreceptores Microbianos/genética , Fotorreceptores Microbianos/metabolismo
7.
Artigo em Inglês | MEDLINE | ID: mdl-32784524

RESUMO

To better understand the characteristics of soil bacterial diversity in different environments, the Laiwu Qilongwan experimental site was selected as it is of great significance for the study of geochemical cycles. The soil CO2, mineral composition and bacterial community were analyzed by an EGM-4 portable environmental gas detector, an X-ray diffractometer and 16S rDNA high-throughput sequencing, and soil bacterial diversity and the relationship between soil bacterial diversity and environmental factors were studied. The results showed that with increasing soil depth, the CO2 content increased, the feldspar and amphibole contents increased, the quartz content decreased, the richness of the soil bacterial community increased, the relative richness of Nitrospirae increased, and Chloroflexi decreased. The dominant bacteria were Proteobacteria, Actinobacteria and Acidobacteria. There were slight differences in soil CO2, mineral composition and dominant bacterial flora at the same depth. Actinobacteria, Proteobacteria and Firmicutes were the dominant phyla of L02. The CO2 was lowest in bare land, and the quartz and K-feldspar contents were the highest. Soil CO2 mainly affected the deep bacterial diversity, while shallow soil bacteria were mainly affected by mineral components (quartz and K-feldspar). At the same depth, amphibole and clay minerals had obvious effects on the bacterial community, while CO2 had obvious effects on subdominant bacteria.


Assuntos
Dióxido de Carbono , Microbiologia do Solo , Solo , Bactérias/genética , Biodiversidade , Cianobactérias/classificação , Cianobactérias/genética , Cianobactérias/isolamento & purificação , Humanos , Minerais , Proteobactérias/classificação , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética
8.
PLoS One ; 15(7): e0232383, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32701963

RESUMO

HetR and PatS/PatX-derived peptides are the activator and diffusible inhibitor for cell differentiation and patterning in heterocyst-forming cyanobacteria. HetR regulates target genes via HetR-recognition sites. However, some genes (such as patS/patX) upregulated at the early stage of heterocyst differentiation possess DIF1 (or DIF+) motif (TCCGGA) promoters rather than HetR-recognition sites; hetR possesses both predicted regulatory elements. How HetR controls heterocyst-specific expression from DIF1 motif promoters remains to be answered. This study presents evidence that the expression from DIF1 motif promoters of hetR, patS and patX is more directly dependent on hetZ, a gene regulated by HetR via a HetR-recognition site. The HetR-binding site upstream of hetR is not required for the autoregulation of hetR. PatU3 (3' portion of PatU) that interacts with HetZ may modulate the expression of hetR, hetZ and patS. These findings contribute to understanding of the mutual regulation of hetR, hetZ-patU and patS/patX in a large group of multicellular cyanobacteria.


Assuntos
Proteínas de Bactérias/metabolismo , Diferenciação Celular , Cianobactérias/citologia , Cianobactérias/metabolismo , Motivos de Nucleotídeos/genética , Regiões Promotoras Genéticas/genética , Sequência de Bases , Cianobactérias/genética , Regulação para Cima
9.
Water Res ; 183: 116077, 2020 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-32693300

RESUMO

Harmful cyanobacterial blooms consisting of toxic taxa can produce a wide variety of toxins to threaten water quality, ecosystem functions and services. Of greater concern was the changing patterns of cyanobacterial assemblage were not well understood due to the lack of long-term monitoring data over the temporal scale. Biodiversity change in cyanobacterial community and paleoenvironmental variables over the past 170 years in Lake Chenghai were investigated based on sedimentary ancient DNA metabarcoding and traditional paleolimnological analysis. The results showed species richness and homogenization of cyanobacterial assemblage increased in the most recent decades, which were synchronized with the growth of artificial fertilization and decline in precipitation. Cyanobacterial co-occurrence network analysis revealed more complex interactions and weak community stability after the change point of ∼1987, while the rare cyanobacterial genera such as Anabaena, Planktothrix, Oscillatoria and Microcystis were identified to be keystone taxa affecting cyanobacterial assemblage. Furthermore, an increase of toxin-producing cyanobacterial taxa was significantly and positively associated with TN and TP, as well as TN/IP and TN/TP, which was verified by quantitative real-time PCR of mcyA and rpoC1 genes. Threshold in total nitrogen (TN) concentration should be targeted no more than 0.60 mg/L to alleviate nuisance cyanobacterial blooms in Lake Chenghai. These findings reinforce the comprehensive understanding for the long-term dynamics of cyanobacterial assemblage responding to environmental change, which could contribute to proactively regulate environmental conditions for avoiding undesirable ecological consequences.


Assuntos
Cianobactérias/genética , Lagos , Código de Barras de DNA Taxonômico , DNA Antigo , Ecossistema
10.
Nat Commun ; 11(1): 2991, 2020 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-32532989

RESUMO

Biocatalysts that perform C-H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes.


Assuntos
Variação Genética , Proteínas com Ferro-Enxofre/genética , Oxigenases de Função Mista/genética , Oxigenases/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Sítios de Ligação/genética , Biocatálise , Domínio Catalítico , Cianobactérias/enzimologia , Cianobactérias/genética , Hidroxilação , Proteínas com Ferro-Enxofre/química , Proteínas com Ferro-Enxofre/metabolismo , Cinética , Oxigenases de Função Mista/química , Oxigenases de Função Mista/metabolismo , Modelos Moleculares , Oxigenases/química , Oxigenases/metabolismo , Conformação Proteica , Multimerização Proteica , Especificidade por Substrato
11.
Proc Natl Acad Sci U S A ; 117(27): 15573-15580, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32571944

RESUMO

Cyanobacteriochromes (CBCRs) are small, bistable linear tetrapyrrole (bilin)-binding light sensors which are typically found as modular components in multidomain cyanobacterial signaling proteins. The CBCR family has been categorized into many lineages that roughly correlate with their spectral diversity, but CBCRs possessing a conserved DXCF motif are found in multiple lineages. DXCF CBCRs typically possess two conserved Cys residues: a first Cys that remains ligated to the bilin chromophore and a second Cys found in the DXCF motif. The second Cys often forms a second thioether linkage, providing a mechanism to sense blue and violet light. DXCF CBCRs have been described with blue/green, blue/orange, blue/teal, and green/teal photocycles, and the molecular basis for some of this spectral diversity has been well established. We here characterize AM1_1499g1, an atypical DXCF CBCR that lacks the second cysteine residue and exhibits an orange/green photocycle. Based on prior studies of CBCR spectral tuning, we have successfully engineered seven AM1_1499g1 variants that exhibit robust yellow/teal, green/teal, blue/teal, orange/yellow, yellow/green, green/green, and blue/green photocycles. The remarkable spectral diversity generated by modification of a single CBCR provides a good template for multiplexing synthetic photobiology systems within the same cellular context, thereby bypassing the time-consuming empirical optimization process needed for multiple probes with different protein scaffolds.


Assuntos
Proteínas de Bactérias/metabolismo , Evolução Molecular , Luz , Fotorreceptores Microbianos/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/efeitos da radiação , Cor , Cianobactérias/genética , Cianobactérias/metabolismo , Cianobactérias/efeitos da radiação , Mutagênese Sítio-Dirigida , Nostoc/genética , Nostoc/metabolismo , Nostoc/efeitos da radiação , Fotobiologia/métodos , Fotorreceptores Microbianos/efeitos da radiação , Biologia Sintética/métodos , Tetrapirróis/metabolismo
12.
PLoS One ; 15(6): e0234440, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32530971

RESUMO

Research for biotechnological applications of cyanobacteria focuses on synthetic pathways and bioreactor design, while little effort is devoted to introduce new, promising organisms in the field. Applications are most often based on recombinant work, and the establishment of transformation can be a risky, time-consuming procedure. In this work we demonstrate the natural transformation of the filamentous cyanobacterium Phormidium lacuna and insertion of a selection marker into the genome by homologous recombination. This is the first example for natural transformation filamentous non-heterocystous cyanobacterium. We found that Phormidium lacuna is polyploid, each cell has about 20-90 chromosomes. Transformed filaments were resistant against up to 14 mg/ml of kanamycin. Formerly, natural transformation in cyanobacteria has been considered a rare and exclusive feature of a few unicellular species. Our finding suggests that natural competence is more distributed among cyanobacteria than previously thought. This is supported by bioinformatic analyses which show that all protein factors for natural transformation are present in the majority of the analyzed cyanobacteria.


Assuntos
Cianobactérias/genética , Farmacorresistência Bacteriana/genética , Genoma Bacteriano/genética , Recombinação Homóloga , Transformação Bacteriana , Cromossomos Bacterianos/genética , Biologia Computacional , Canamicina/farmacologia , Poliploidia
13.
Harmful Algae ; 93: 101800, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32307064

RESUMO

Microcystins (MCs) are secondary metabolites produced by cyanobacteria and have been well-documented in temperate and tropical regions. However, knowledge of the production of MCs in extremely cold environments is still in its infancy. Recently, examination of 100-year-old Antarctic cyanobacterial mats collected from Ross Island and the McMurdo Ice Shelf during Captain R.F. Scott's Discovery Expedition revealed that the presence of MCs in Antarctica is not a new phenomenon. Here, morphological and molecular phylogenetic analyses are used to identify a new microcystin-producing freshwater cyanobacterium, Anagnostidinema pseudacutissimum. The strain was isolated from a deep-frozen (-15 °C) sample collected from a red-brown cyanobacterial mat in a frozen pond at Cape Crozier (Ross Island, continental Antarctica) in 1984-1985. Amplification of the mcyE gene fragment involved in microcystin biosynthesis from A. pseudacutissimum confirmed that it is identical to the sequence from other known microcystin-producing cyanobacteria. Analysis of extracts from this A. pseudacutissimum strain by HPLC-MS/MS confirmed the presence of MC-LR and -YR at concentrations of 0.60 µg/L and MC-RR at concentrations of 0.20 µg/L. This is the first report of microcystin production from a species of Anagnostidinema from Antarctica.


Assuntos
Cianobactérias , Microcistinas , Regiões Antárticas , Cianobactérias/genética , Filogenia , Espectrometria de Massas em Tandem
14.
Harmful Algae ; 93: 101767, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32307065

RESUMO

Reports of anatoxins poisoning of wildlife and domestic animals by toxigenic cyanobacteria in streams and rivers are increasing globally. Little is known about the taxonomy, morphology and genomics of anatoxins producing species, limiting our knowledge about their environmental preferences. We isolated three benthic non-heterocystous filamentous cyanobacterial strains from the Russian River in Northern California (USA), which produce anatoxin-a and dihydroanatoxin-a. Both 16S rRNA and protein sequence phylogenetic analyses showed that the strains represent a distinct new member of the cyanobacterial genus Microcoleus (Oscillatoriales). A novel species, Microcoleus anatoxicus is described and accompanied with light microscope photomicrographs, toxin profiles and the complete anatoxin-a gene cassette with the first description of the anaK gene in Microcoleus.


Assuntos
Toxinas Bacterianas , Cianobactérias , Animais , Toxinas Bacterianas/genética , California , Cianobactérias/genética , Filogenia , Prolina/análogos & derivados , RNA Ribossômico 16S/genética , Rios , Federação Russa
15.
Arch Microbiol ; 202(7): 1717-1728, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32313992

RESUMO

Paeonia ludlowii is indigenous to Tibet and has an important ecological and economic value in China. In Tibet, P. ludlowii has been used in folk medicine with relative success. Plant microbial endophytes play an important role in plant growth, health and ecological function. The diversity of endophytic bacteria associated with P. ludlowii remains poorly understood. In this study, the structure of the endophytic bacterial communities associated with different tissues, including fruits, flowers, leaves, stems, and roots, and rhizosphere soils was analyzed with Illumina MiSeq sequencing of bacterial 16S rDNA. A total of 426,240 sequences and 4847 operational taxonomic units (OTUs) were obtained. The OTUs abundance of roots was higher than that of other tissues; however, the OTUs abundance was similar among different deep soil samples. In the plant tissues, Cyanobacteria was the most abundant bacterial phylum, followed by Proteobacteria; however, the most abundant phyla were Proteobacteria and Acidobacteria in soil samples from three different layers. In addition, the diversity and richness of the microorganisms in the soil were very similar to those in roots but higher than those in other tissues of P. ludlowii. Predictive metagenome analysis revealed that endophytic bacteria play critical functional roles in P. ludlowii. This conclusion could facilitate the study of the ecological functions of endophytic bacteria and their interactions with P. ludlowii to analyze the reasons why this important medicinal plant is becoming endangered.


Assuntos
Biodiversidade , Espécies em Perigo de Extinção , Endófitos/classificação , Endófitos/fisiologia , Paeonia/microbiologia , Rizosfera , Microbiologia do Solo , Cianobactérias/genética , Cianobactérias/isolamento & purificação , DNA Ribossômico/genética , Endófitos/genética , Sequenciamento de Nucleotídeos em Larga Escala , Raízes de Plantas/microbiologia , Proteobactérias/genética , Proteobactérias/isolamento & purificação , RNA Ribossômico 16S/genética , Tibet
16.
PLoS One ; 15(3): e0230071, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32210450

RESUMO

Microbialites are highly diverse microbial communities that represent modern examples of the oldest life forms, stromatolites (dated >3.7 Ga). Bacalar Lagoon, in Mexico, harbors the largest freshwater microbialite occurrences of the world; yet diverse anthropogenic activities are changing the oligotrophic conditions of the lagoon. The objective of this work was to perform a spatial exploration of the microbialites of Bacalar Lagoon, analyze their prokaryote diversity, following a high throughput sequencing approach of the V4 region of the 16S rDNA, and correlate to the environmental parameters that influence the structure of these communities. The results indicate the presence of microbialites throughout the periphery of the lagoon. The microbiome of the microbialites is composed primarily of Proteobacteria (40-80%), Cyanobacteria (1-11%), Bacteroidetes (7-8%), Chloroflexi (8-14%), Firmicutes (1-23%), Planctomycetes (1-8%), and Verrucomicrobia (1-4%). Phylogenetic distance analyses suggests two distinct groups of microbialites associated with regions in the lagoon that have differences in their environmental parameters, including soluble reactive silicate (in the north), bicarbonates and available forms of nitrogen (ammonium, nitrates and nitrites) (in the south). These microbialite groups had differences in their microbiome composition associated to strong anthropogenic pressure on water quality (agriculture, landfill leachate, lack of water treatment infrastructure and intensive tourism), which were related to a loss of microbial diversity.


Assuntos
Bacteroidetes/classificação , Biodiversidade , Cianobactérias/classificação , Água Doce/microbiologia , Sedimentos Geológicos/microbiologia , Microbiota , Proteobactérias/classificação , Bacteroidetes/genética , Bacteroidetes/crescimento & desenvolvimento , Cianobactérias/genética , Cianobactérias/crescimento & desenvolvimento , Sedimentos Geológicos/análise , Sequenciamento de Nucleotídeos em Larga Escala , México , Nutrientes , Filogenia , Proteobactérias/genética , Proteobactérias/crescimento & desenvolvimento , RNA Ribossômico 16S/genética
17.
Environ Monit Assess ; 192(4): 244, 2020 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-32198545

RESUMO

The information available on microalgae-sourced compounds, especially antibiotics and other bioactive compounds, and their potential commercial applications is still insufficient. In this study, antibacterial activity, metabolites, and molecular characterization of Phormidium autumnale, which was isolated from samples collected from different natural freshwater sources in Ankara, Turkey, were investigated. Sequencing results of 16s rDNA confirmed the molecular identification of P. autumnale by 99%. It was determined that the peak values of some phenolic compounds and cyclic peptides were consistent with the 1653-1389 cm-1 band regions in the FTIR spectra of the species. The antibacterial activities of P. autumnale cyanobacteria (CBA) extracts that were obtained by using different solvents were tested on Escherichia coli, Staphylococcus epidermidis, methicillin-resistant (MR) Staphylococcus aureus, Streptococcus agalactiae, and Enterococcus faecalis by using a disc diffusion method. Also, the minimum inhibition concentration (MIC) and antimicrobial indexes of all extracts were determined. It was found that P. autumnale methanol extracts showed antibacterial activity on all test bacteria, whereas acetone extracts showed effects only on E. coli. For the inhibition of MR S. aureus, the control methanol extract was found to give very similar results to those exhibited by the control antibiotics, and the antimicrobial index results were determined to be 58.7-67.5%. According to the results of the analysis of methanol extract, gentisic acid, vanillic acid, 4-hydroxybenzoic acid, p-coumaric acid, and catechin (especially phenolic compounds) were determined to be the active compounds. It can be concluded that P. autumnale is an alternative to current commercial applications as an antibacterial agent in phytotherapy.


Assuntos
Cianobactérias , Escherichia coli , Compostos Fitoquímicos , Staphylococcus aureus , Antibacterianos/isolamento & purificação , Antibacterianos/farmacologia , Cianobactérias/química , Cianobactérias/genética , Escherichia coli/efeitos dos fármacos , Água Doce , Testes de Sensibilidade Microbiana , Compostos Fitoquímicos/isolamento & purificação , Compostos Fitoquímicos/farmacologia , Fitoterapia , Staphylococcus aureus/efeitos dos fármacos , Turquia
18.
BMC Bioinformatics ; 21(Suppl 2): 83, 2020 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-32164552

RESUMO

BACKGROUND: Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes. RESULTS: Surprisingly, eight cluster structure has been found, for chloroplasts. The pattern observed for chloroplasts differs rather significantly, from bacterial one, and from that latter observed for cyanobacteria. The structure is provided by clustering of the fragments of equal length isolated within a genome so that each fragment is converted in triplet frequency dictionary with non-overlapping triplets with no gaps in frame tiling. The points in 63-dimensional space were clustered due to elastic map technique. The eight cluster found in chloroplasts comprises the fragments of a genome bearing tRNA genes and exhibiting excessively high GC-content, in comparison to the entire genome. CONCLUSION: Chloroplasts exhibit very specific symmetry type in distribution of coding and non-coding fragments of a genome in the space of triplet frequencies: this is mirror symmetry. Cyanobacteria may have both mirror symmetry, and the rotational symmetry typical for other bacteria.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos , Composição de Bases , Análise por Conglomerados , Cianobactérias/genética , RNA de Transferência/genética
19.
Biochem J ; 477(5): 971-983, 2020 03 13.
Artigo em Inglês | MEDLINE | ID: mdl-32142118

RESUMO

The cyanobacterium Anabaena PCC 7120 shows the presence of Type I-D CRISPR system that can potentially confer adaptive immunity. The Cas7 protein (Alr1562), which forms the backbone of the type I-D surveillance complex, was characterized from Anabaena. Alr1562, showed the presence of the non-canonical RNA recognition motif and two intrinsically disordered regions (IDRs). When overexpressed in E. coli, the Alr1562 protein was soluble and could be purified by affinity chromatography, however, deletion of IDRs rendered Alr1562 completely insoluble. The purified Alr1562 was present in the dimeric or a RNA-associated higher oligomeric form, which appeared as spiral structures under electron microscope. With RNaseA and NaCl treatment, the higher oligomeric form converted to the lower oligomeric form, indicating that oligomerization occurred due to the association of Alr1562 with RNA. The secondary structure of both these forms was largely similar, resembling that of a partially folded protein. The dimeric Alr1562 was more prone to temperature-dependent aggregation than the higher oligomeric form. In vitro, the Alr1562 bound more specifically to a minimal CRISPR unit than to the non-specific RNA. Residues required for binding of Alr1562 to RNA, identified by protein modeling-based approaches, were mutated for functional validation. Interestingly, these mutant proteins, showing reduced ability to bind RNA were predominantly present in dimeric form. Alr1562 was detected with specific antiserum in Anabaena, suggesting that the type I-D system is expressed and may be functional in vivo. This is the first report that describes the characterization of a Cas protein from any photosynthetic organism.


Assuntos
Anabaena/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas Associadas a CRISPR/química , Proteínas Associadas a CRISPR/metabolismo , Sistemas CRISPR-Cas/fisiologia , Anabaena/genética , Proteínas de Bactérias/genética , Proteínas Associadas a CRISPR/genética , Cianobactérias/química , Cianobactérias/genética , Cianobactérias/metabolismo , Estrutura Secundária de Proteína
20.
Sci Rep ; 10(1): 1894, 2020 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-32024928

RESUMO

Filament-forming proteins in bacteria function in stabilization and localization of proteinaceous complexes and replicons; hence they are instrumental for myriad cellular processes such as cell division and growth. Here we present two novel filament-forming proteins in cyanobacteria. Surveying cyanobacterial genomes for coiled-coil-rich proteins (CCRPs) that are predicted as putative filament-forming proteins, we observed a higher proportion of CCRPs in filamentous cyanobacteria in comparison to unicellular cyanobacteria. Using our predictions, we identified nine protein families with putative intermediate filament (IF) properties. Polymerization assays revealed four proteins that formed polymers in vitro and three proteins that formed polymers in vivo. Fm7001 from Fischerella muscicola PCC 7414 polymerized in vitro and formed filaments in vivo in several organisms. Additionally, we identified a tetratricopeptide repeat protein - All4981 - in Anabaena sp. PCC 7120 that polymerized into filaments in vitro and in vivo. All4981 interacts with known cytoskeletal proteins and is indispensable for Anabaena viability. Although it did not form filaments in vitro, Syc2039 from Synechococcus elongatus PCC 7942 assembled into filaments in vivo and a Δsyc2039 mutant was characterized by an impaired cytokinesis. Our results expand the repertoire of known prokaryotic filament-forming CCRPs and demonstrate that cyanobacterial CCRPs are involved in cell morphology, motility, cytokinesis and colony integrity.


Assuntos
Anabaena/citologia , Proteínas de Bactérias/metabolismo , Cianobactérias/citologia , Proteínas do Citoesqueleto/metabolismo , Synechococcus/citologia , Motivos de Aminoácidos/genética , Anabaena/genética , Anabaena/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/isolamento & purificação , Cianobactérias/genética , Cianobactérias/metabolismo , Proteínas do Citoesqueleto/genética , Proteínas do Citoesqueleto/isolamento & purificação , Citoesqueleto/metabolismo , Genes Bacterianos/genética , Mutação , Conformação Proteica em alfa-Hélice/genética , Multimerização Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/isolamento & purificação , Proteínas Recombinantes/metabolismo , Synechococcus/genética , Synechococcus/metabolismo
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