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1.
Chemosphere ; 254: 126881, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32957288

RESUMO

Application of biochar (BC) derived from rice straw has generated increasing interest in long-term storage of soil organic carbon (SOC), however its carbon (C) sequestration potential vary widely among agricultural soils despite the same BC dose used. These discrepancies in the ability of soils to sequester C after BC application are poorly understood. Metabolic quotient (qCO2) is a reflection of "microbial efficiency" and linked to SOC turnover across ecosystems. Therefore, we investigated the SOC sequestration and qCO2 in a Yellow River alluvium paddy soil (YP) and a quaternary red clay paddy soil (QP) under rice-wheat annual rotation following 4-year of BC application rate of 11.3 Mg ha-1 per cropping season. BC application consistently brought 65.3 Mg C ha-1 into the soils over 4-year experimental period but increased SOC by 57.6 Mg C ha-1 in YP and 64.5 Mg C ha-1 in QP. Calculating SOC mass balance showed 11.7% of BC-C losses from YP and only 1.16% from QP. BC application stimulated the G+ bacterial, fungi, and actinomycetes by increasing O-alkyl C content in YP, while decreased the same microorganisms by decreasing anomeric C-H content in QP. Importantly, higher clay and amorphous Fe (Feo) contents in QP after BC application protected SOC from further decomposition, which in turn decreased microorganisms and resulted in higher SOC sequestration than YP. Our results indicated that soil properties controlled the extent of SOC sequestration after BC application and site-specific soil properties must be carefully considered to maximize long-term SOC sequestration after BC application.


Assuntos
Agricultura/métodos , Sequestro de Carbono , Carvão Vegetal/química , Carbono/metabolismo , Argila , Ecossistema , Oryza/metabolismo , Solo/química
2.
Nat Commun ; 11(1): 4241, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32901006

RESUMO

Land vegetation is currently taking up large amounts of atmospheric CO2, possibly due to tree growth stimulation. Extant models predict that this growth stimulation will continue to cause a net carbon uptake this century. However, there are indications that increased growth rates may shorten trees' lifespan and thus recent increases in forest carbon stocks may be transient due to lagged increases in mortality. Here we show that growth-lifespan trade-offs are indeed near universal, occurring across almost all species and climates. This trade-off is directly linked to faster growth reducing tree lifespan, and not due to covariance with climate or environment. Thus, current tree growth stimulation will, inevitably, result in a lagged increase in canopy tree mortality, as is indeed widely observed, and eventually neutralise carbon gains due to growth stimulation. Results from a strongly data-based forest simulator confirm these expectations. Extant Earth system model projections of global forest carbon sink persistence are likely too optimistic, increasing the need to curb greenhouse gas emissions.


Assuntos
Sequestro de Carbono , Carbono/metabolismo , Árvores/crescimento & desenvolvimento , Mudança Climática , Simulação por Computador , Longevidade , Mortalidade , Árvores/metabolismo
3.
Bull Environ Contam Toxicol ; 105(3): 481-489, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32914331

RESUMO

The purpose of this study is to enhance the biodegradability of atrazine with FH-1 and NJ-1 alone by selecting the mixing ratio, optimizing the culture medium and conditions. The results showed that FH-1 and NJ-1 have the best biodegradation effect on atrazine being mixed in a volume ratio of 3:2. In a single factor experiment, sucrose and NH4Cl provided carbon and nitrogen sources for the mixed bacteria. Subsequently, composition of fermentation medium was further optimized using Box-Behnken design of response surface methodology. Based on the results, growth of mixed bacteria and biodegradation of atrazine performed best effects with a biodegradation rate of 85.6% when sucrose and NH4Cl amounts were 35.30 g/L and 10.28 g/L. The optimal medium condition was 10% inoculum of mixed bacteria, with initial atrazine concentration of 50 mg/L, neutral or weakly alkaline pH value, 30°C. The biodegradation rate reached 97.4%, 11.8% higher than the unoptimized condition.


Assuntos
Atrazina/metabolismo , Biodegradação Ambiental , Herbicidas/metabolismo , Klebsiella/metabolismo , Arthrobacter/metabolismo , Atrazina/análise , Carbono/metabolismo , Herbicidas/análise , Nitrogênio/metabolismo , Microbiologia do Solo
4.
Nat Commun ; 11(1): 4897, 2020 09 29.
Artigo em Inglês | MEDLINE | ID: mdl-32994415

RESUMO

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. However, its feedbacks to climate warming and underlying microbial mechanisms are still poorly understood. Here we show that the temperature sensitivity of soil microbial respiration (Q10) in a temperate grassland ecosystem persistently decreases by 12.0 ± 3.7% across 7 years of warming. Also, the shifts of microbial communities play critical roles in regulating thermal adaptation of soil respiration. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improves the modeling performance of soil microbial respiration by 5-19%, and reduces model parametric uncertainty by 55-71%. In addition, modeling analyses show that the microbial thermal adaptation can lead to considerably less heterotrophic respiration (11.6 ± 7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.


Assuntos
Carbono/análise , Metagenoma/genética , Microbiota/fisiologia , Microbiologia do Solo , Solo/química , Aclimatação/genética , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Carbono/metabolismo , Ciclo do Carbono , Celulose/metabolismo , DNA Ambiental/genética , DNA Ambiental/isolamento & purificação , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Aquecimento Global , Pradaria , Temperatura Alta/efeitos adversos , Metagenômica , Modelos Genéticos , Raízes de Plantas/química , Poaceae/química
5.
Aquat Toxicol ; 226: 105585, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32763644

RESUMO

Although excess ammoniacal-nitrogen (NH4+-N) results in the disturbance of various important biochemical and physiological processes, a detailed study on the effects of NH4+-N stress on the photosynthesis and global changes in protein levels in submerged macrophytes is still lacking. Here, the changes of excess NH4+-N on physiological parameters in Hydrilla verticillata (L.f.) Royle, a submerged macrophyte were investigated, including the contents of photosynthetic pigments, soluble sugars, net photosynthesis and respiration, glutamine synthetase (GS) and glutamate synthase (GOGAT) activities, chloroplast ultrastructure, chloroplast reactive oxygen species (ROS) accumulation and protein levels. Our results showed that the net photosynthetic rate and pigment content reached maximum values when the plants were treated with 1 and 2 mg L-1 NH4+-N, respectively, and decreased at NH4+-N concentrations at 5, 10, 15 and 20 mg L-1. This decrease might be caused by ROS accumulation. Compared that in 0.02 mg L-1 NH4+-N as a control, ROS generation in chloroplasts significantly increased in the presence of more than 2 mg L-1 NH4+-N. Consistently, the damages caused by over-accumulated ROS were observed in chloroplast ultrastructure, showing a loose thylakoid membranes and swollen grana/stroma lamellae. Furthermore, through proteomic analysis, we identified 91 differentially expressed protein spots. Among them, six proteins involved in photosynthesis decreased in abundance in response to excess NH4+-N. Surprisingly, the abundance of all the identified proteins that were involved in nitrogen assimilation and amino acid metabolism tended to increase under excess NH4+-N compared with the control, suggestive of the imbalanced carbon and nitrogen (C-N) metabolisms. In support, activated GS and GOGAT cycle was observed, evidenced by higher activities of GS and GOGAT enzymes. To our knowledge, this work is the first description that excess NH4+-N results in chloroplast ultrastructural damages and the first proteomic evidence to support that excess NH4+-N can lead to a decline in photosynthesis and imbalance of C-N metabolism in submerged macrophytes.


Assuntos
Amônia/toxicidade , Cloroplastos/ultraestrutura , Hydrocharitaceae/efeitos dos fármacos , Nitrogênio/toxicidade , Fotossíntese/efeitos dos fármacos , Espécies Reativas de Oxigênio/metabolismo , Poluentes Químicos da Água/toxicidade , Amônia/metabolismo , Carbono/metabolismo , Cloroplastos/efeitos dos fármacos , Hydrocharitaceae/metabolismo , Nitrogênio/metabolismo , Proteômica , Poluentes Químicos da Água/metabolismo
6.
Ecotoxicol Environ Saf ; 204: 111073, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32755736

RESUMO

The high pH and salinity of textile wastewater is a major hindrance to azo dye decolorization. In this study, a mixed bacterial consortium ZW1 was enriched under saline (10% salinity) and alkaline (pH 10.0) conditions to decolorize Methanil Yellow G (MY-G). Consortium ZW1 was mainly composed of Halomonas (49.8%), Marinobacter (30.7%) and Clostridiisalibacter (19.2%). The effects of physicochemical factors were systematically investigated, along with the degradation pathway and metagenome analysis. The co-carbon source was found to be necessary, and the addition of yeast extract led to 93.3% decolorization of 100 mg/L MY-G within 16 h (compared with 1.12% for control). The optimum pH, salinity, temperature and initial dye concentration were 8.0, 5-10%, 40 °C and 100 mg/L, respectively. The typical dye-related degradation enzymes were most effective at 10% salinity. Consortium ZW1 was also able to differentially decolorize five other direct and acidic dyes in a short period. Phototoxicity tests revealed the detoxification of MY-G degradation products. Combining UV-vis, FTIR and GC-MS detection, the MY-G degradation pathway by consortium ZW1 was proposed. Furthermore, metagenomic approach was used to elucidate the functional potential of genes in MY-G biodegradation. These results signify the broad potential application of halo-alkaliphilic consortia in the bioremediation of dyeing wastewater.


Assuntos
Compostos Azo/toxicidade , Corantes/toxicidade , Metagenoma , Microbiota/efeitos dos fármacos , Águas Residuárias , Poluentes Químicos da Água/toxicidade , Purificação da Água/métodos , Compostos Azo/metabolismo , Biodegradação Ambiental , Carbono/metabolismo , Corantes/metabolismo , Microbiota/genética , Salinidade , Temperatura , Indústria Têxtil , Águas Residuárias/química , Águas Residuárias/microbiologia , Poluentes Químicos da Água/metabolismo
7.
Nat Commun ; 11(1): 4028, 2020 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-32788591

RESUMO

Changes in atmospheric CO2 concentration have played a central role in algal and plant adaptation and evolution. The commercially important red algal genus, Pyropia (Bangiales) appears to have responded to inorganic carbon (Ci) availability by evolving alternating heteromorphic generations that occupy distinct habitats. The leafy gametophyte inhabits the intertidal zone that undergoes frequent emersion, whereas the sporophyte conchocelis bores into mollusk shells. Here, we analyze a high-quality genome assembly of Pyropia yezoensis to elucidate the interplay between Ci availability and life cycle evolution. We find horizontal gene transfers from bacteria and expansion of gene families (e.g. carbonic anhydrase, anti-oxidative related genes), many of which show gametophyte-specific expression or significant up-regulation in gametophyte in response to dehydration. In conchocelis, the release of HCO3- from shell promoted by carbonic anhydrase provides a source of Ci. This hypothesis is supported by the incorporation of 13C isotope by conchocelis when co-cultured with 13C-labeled CaCO3.


Assuntos
Carbono/metabolismo , Genoma , Rodófitas/genética , Rodófitas/metabolismo , Movimentos da Água , Exoesqueleto/química , Animais , Antioxidantes/farmacologia , Composição de Bases/genética , Evolução Biológica , Carbonato de Cálcio/metabolismo , Anidrases Carbônicas/genética , Anidrases Carbônicas/metabolismo , Núcleo Celular/genética , Dosagem de Genes , Perfilação da Expressão Gênica , Transferência Genética Horizontal/genética , Moluscos , Fotossíntese/efeitos dos fármacos , Ploidias , Rodófitas/efeitos dos fármacos , Superóxido Dismutase/genética , Transcrição Genética/efeitos dos fármacos
8.
Science ; 369(6500): 198-202, 2020 07 10.
Artigo em Inglês | MEDLINE | ID: mdl-32647002

RESUMO

Historically, sea ice loss in the Arctic Ocean has promoted increased phytoplankton primary production because of the greater open water area and a longer growing season. However, debate remains about whether primary production will continue to rise should sea ice decline further. Using an ocean color algorithm parameterized for the Arctic Ocean, we show that primary production increased by 57% between 1998 and 2018. Surprisingly, whereas increases were due to widespread sea ice loss during the first decade, the subsequent rise in primary production was driven primarily by increased phytoplankton biomass, which was likely sustained by an influx of new nutrients. This suggests a future Arctic Ocean that can support higher trophic-level production and additional carbon export.


Assuntos
Camada de Gelo , Fitoplâncton/crescimento & desenvolvimento , Regiões Árticas , Biomassa , Carbono/metabolismo , Oceanos e Mares , Estações do Ano
9.
PLoS One ; 15(6): e0230222, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603332

RESUMO

Conservation efforts are increasingly being challenged by a rapidly changing environment, and for some aquatic species the use of captive rearing or selective breeding is an attractive option. However, captivity itself can impose unintended artificial selection known as domestication selection (adaptation to culture conditions) and is relatively understudied for most marine species. To test for domestication selection in marine bivalves, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection. Using larvae produced from a wild population of Crassostrea virginica and a selectively bred, disease-resistant line we measured growth and survival during starvation versus standard algal diet conditions. Larvae from both lineages showed a remarkable resilience to food limitation, possibly mediated by an ability to utilize dissolved organic matter for somatic maintenance. Water chemistry analysis showed dissolved organic carbon in filtered tank water to be at concentrations similar to natural river water. We observed that survival in larvae produced from the aquaculture line was significantly lower compared to larvae produced from wild broodstock (8 ± 3% and 21 ± 2%, respectively) near the end of a 10-day period with no food (phytoplankton). All larval cohorts had arrested growth and depressed respiration during the starvation period and took at least two days to recover once food was reintroduced before resuming growth. Respiration rate recovered rapidly and final shell length was similar between the two treatments Phenotypic differences between the wild and aquaculture lines suggest potential differences in the capacity to sustain extended food limitation, but this work requires replication with multiple selection lines and wild populations to make more general inferences about domestication selection. With this contribution we explore the potential for domestication selection in bivalves, discuss the physiological and fitness implications of reduced starvation tolerance, and aim to inspire further research on the topic.


Assuntos
Crassostrea/fisiologia , Domesticação , Larva/fisiologia , Inanição/fisiopatologia , Animais , Carbono/metabolismo , Crassostrea/metabolismo , Larva/metabolismo , Nitrogênio/metabolismo , Respiração , Inanição/metabolismo
10.
Proc Natl Acad Sci U S A ; 117(29): 17418-17428, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32636267

RESUMO

Carboxysomes are membrane-free organelles for carbon assimilation in cyanobacteria. The carboxysome consists of a proteinaceous shell that structurally resembles virus capsids and internal enzymes including ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), the primary carbon-fixing enzyme in photosynthesis. The formation of carboxysomes requires hierarchical self-assembly of thousands of protein subunits, initiated from Rubisco assembly and packaging to shell encapsulation. Here we study the role of Rubisco assembly factor 1 (Raf1) in Rubisco assembly and carboxysome formation in a model cyanobacterium, Synechococcus elongatus PCC7942 (Syn7942). Cryo-electron microscopy reveals that Raf1 facilitates Rubisco assembly by mediating RbcL dimer formation and dimer-dimer interactions. Syn7942 cells lacking Raf1 are unable to form canonical intact carboxysomes but generate a large number of intermediate assemblies comprising Rubisco, CcaA, CcmM, and CcmN without shell encapsulation and a low abundance of carboxysome-like structures with reduced dimensions and irregular shell shapes and internal organization. As a consequence, the Raf1-depleted cells exhibit reduced Rubisco content, CO2-fixing activity, and cell growth. Our results provide mechanistic insight into the chaperone-assisted Rubisco assembly and biogenesis of carboxysomes. Advanced understanding of the biogenesis and stepwise formation process of the biogeochemically important organelle may inform strategies for heterologous engineering of functional CO2-fixing modules to improve photosynthesis.


Assuntos
Organelas/metabolismo , Ribulose-Bifosfato Carboxilase/metabolismo , Synechococcus/metabolismo , Carbono/metabolismo , Ciclo do Carbono , Microscopia Crioeletrônica , Regulação Bacteriana da Expressão Gênica , Genes Bacterianos/genética , Modelos Moleculares , Chaperonas Moleculares/metabolismo , Fotossíntese , Subunidades Proteicas/metabolismo , Ribulose-Bifosfato Carboxilase/química , Ribulose-Bifosfato Carboxilase/genética , Synechococcus/genética , Transcriptoma
11.
PLoS One ; 15(7): e0234611, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32649667

RESUMO

Perennial vegetables are a neglected and underutilized class of crops with potential to address 21st century challenges. They represent 33-56% of cultivated vegetable species, and occupy 6% of world vegetable cropland. Despite their distinct relevance to climate change mitigation and nutritional security, perennial vegetables receive little attention in the scientific literature. Compared to widely grown and marketed vegetable crops, many perennial vegetables show higher levels of key nutrients needed to address deficiencies. Trees with edible leaves are the group of vegetables with the highest levels of these key nutrients. Individual "multi-nutrient" species are identified with very high levels of multiple nutrients for addressing deficiencies. This paper reports on the synthesis and meta-analysis of a heretofore fragmented global literature on 613 cultivated perennial vegetables, representing 107 botanical families from every inhabited continent, in order to characterize the extent and potential of this class of crops. Carbon sequestration potential from new adoption of perennial vegetables is estimated at 22.7-280.6 MMT CO2-eq/yr on 4.6-26.4 Mha by 2050.


Assuntos
Agricultura/métodos , Sequestro de Carbono/fisiologia , Verduras/metabolismo , Biodiversidade , Carbono/metabolismo , Mudança Climática , Produtos Agrícolas/química , Produtos Agrícolas/metabolismo , Abastecimento de Alimentos , Nutrientes/análise , Nutrientes/metabolismo , Estado Nutricional/fisiologia
12.
PLoS One ; 15(7): e0236739, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32730333

RESUMO

Rhodopseudomonas palustris PS3 is one of the purple phototrophic non-sulfur bacteria (PNSB), which have plant growth-promoting effects on various plants. To expand the scale of PS3 fermentation in a time- and cost-effective fashion, the purpose of this work was to evaluate the use of low-cost materials as culture media and to optimize the culture conditions via response surface methodology. Corn steep liquor (CSL) and molasses were identified as potential materials to replace the nitrogen and carbon sources, respectively, in the conventional growth medium. The optimum culture conditions identified through central composite design were CSL, 39.41 mL/L; molasses, 32.35 g/L; temperature, 37.9°C; pH, 7.0; and DO 30%. Under the optimized conditions, the biomass yield reached 2.18 ± 0.01 g/L at 24 hours, which was 7.8-fold higher than that under the original medium (0.28 ± 0.01 g/L). The correlation between the predicted and experimental values of the model was over 98%, which verified the validity of the response models. Furthermore, we verified the effectiveness of the R. palustris PS3 inoculant grown under the newly developed culture conditions for plant growth promotion. This study provides a potential strategy for improving the fermentation of R. palustris PS3 in low-cost media for large-scale industrial production.


Assuntos
Carbono/metabolismo , Meios de Cultura/química , Meios de Cultura/economia , Nitrogênio/metabolismo , Desenvolvimento Vegetal , Rodopseudomonas/crescimento & desenvolvimento , Meios de Cultura/metabolismo , Fermentação , Microbiologia Industrial , Rodopseudomonas/metabolismo
13.
Chemosphere ; 257: 127165, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32480088

RESUMO

Phytoplankton and bacterioplankton are the key components of the organic matter cycle in aquatic ecosystems, and their interactions can impact the transfer of carbon and ecosystem functioning. The aim of this work was to assess the consequences of chemical contamination on the coupling between phytoplankton and bacterioplankton in two contrasting marine coastal ecosystems: lagoon waters and offshore waters. Bacterial carbon demand was sustained by primary carbon production in the offshore situation, suggesting a tight coupling between both compartments. In contrast, in lagoon waters, due to a higher nutrient and organic matter availability, bacteria could rely on allochthonous carbon sources to sustain their carbon requirements, decreasing so the coupling between both compartments. Exposure to chemical contaminants, pesticides and metal trace elements, resulted in a significant inhibition of the metabolic activities (primary production and bacterial carbon demand) involved in the carbon cycle, especially in offshore waters during spring and fall, inducing a significant decrease of the coupling between primary producers and heterotrophs. This coupling loss was even more evident upon sediment resuspension for both ecosystems due to the important release of nutrients and organic matter. Resulting enrichment alleviated the toxic effects of contaminants as indicated by the stimulation of phytoplankton biomass and carbon production, and modified the composition of the phytoplankton community, impacting so the interactions between phytoplankton and bacterioplankton.


Assuntos
Fitoplâncton/fisiologia , Poluentes Químicos da Água/toxicidade , Bactérias/metabolismo , Biomassa , Carbono/metabolismo , Ecossistema , Praguicidas/metabolismo , Estações do Ano , Água do Mar/química , Oligoelementos/metabolismo
14.
Proc Biol Sci ; 287(1929): 20200620, 2020 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-32546098

RESUMO

The symbiotic planktonic foraminifera Orbulina universa inhabits open ocean oligotrophic ecosystems where dissolved nutrients are scarce and often limit biological productivity. It has previously been proposed that O. universa meets its nitrogen (N) requirements by preying on zooplankton, and that its symbiotic dinoflagellates recycle metabolic 'waste ammonium' for their N pool. However, these conclusions were derived from bulk 15N-enrichment experiments and model calculations, and our understanding of N assimilation and exchange between the foraminifer host cell and its symbiotic dinoflagellates remains poorly constrained. Here, we present data from pulse-chase experiments with 13C-enriched inorganic carbon, 15N-nitrate, and 15N-ammonium, as well as a 13C- and 15N- enriched heterotrophic food source, followed by TEM (transmission electron microscopy) coupled to NanoSIMS (nanoscale secondary ion mass spectrometry) isotopic imaging to visualize and quantify C and N assimilation and translocation in the symbiotic system. High levels of 15N-labelling were observed in the dinoflagellates and in foraminiferal organelles and cytoplasm after incubation with 15N-ammonium, indicating efficient ammonium assimilation. Only weak 15N-assimilation was observed after incubation with 15N-nitrate. Feeding foraminifers with 13C- and 15N-labelled food resulted in dinoflagellates that were labelled with 15N, thereby confirming the transfer of 15N-compounds from the digestive vacuoles of the foraminifer to the symbiotic dinoflagellates, likely through recycling of ammonium. These observations are important for N isotope-based palaeoceanographic reconstructions, as they show that δ15N values recorded in the organic matrix in symbiotic species likely reflect ammonium recycling rather than alternative N sources, such as nitrates.


Assuntos
Compostos de Amônio/metabolismo , Dinoflagelados/fisiologia , Foraminíferos/fisiologia , Animais , Carbono/metabolismo , Ecossistema , Nitrogênio/metabolismo , Plâncton , Simbiose
15.
PLoS One ; 15(6): e0235066, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32584859

RESUMO

Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.


Assuntos
Carbono/metabolismo , Infecções por Escherichia coli , Genótipo , Filogenia , Sorogrupo , Escherichia coli Shiga Toxigênica , Animais , Infecções por Escherichia coli/epidemiologia , Infecções por Escherichia coli/genética , Infecções por Escherichia coli/metabolismo , Humanos , Malatos/metabolismo , Nova Zelândia/epidemiologia , Serina/genética , Serina/metabolismo , Escherichia coli Shiga Toxigênica/genética , Escherichia coli Shiga Toxigênica/isolamento & purificação , Escherichia coli Shiga Toxigênica/metabolismo
16.
PLoS One ; 15(6): e0234315, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32516353

RESUMO

Stable carbon and oxygen isotope ratios of raw pollen sampled from nine abundant tree species growing in natural habitats of central and northern Europe were investigated to understand the intra- and inter-specific variability of pollen-isotope values. All species yielded specific δ13Cpollen and δ18Opollen values and patterns, which can be ascribed to their physiology and habitat preferences. Broad-leaved trees flowering early in the year before leaf proliferation (Alnus glutinosa and Corylus avellana) exhibited on average 2.6‰ lower δ13Cpollen and 3.1‰ lower δ18Opollen values than broad-leaved and coniferous trees flowering during mid and late spring (Acer pseudoplatanus, Betula pendula, Carpinus betulus, Fagus sylvatica, Picea abies, Pinus sylvestris and Quercus robur). Mean species-specific δ13Cpollen values did not change markedly over time, whereas δ18Opollen values of two consecutive years were often statistically distinct. An intra-annual analysis of B. pendula and P. sylvestris pollen revealed increasing δ18Opollen values during the final weeks of pollen development. However, the δ13Cpollen values remained consistent throughout the pollen-maturation process. Detailed intra-individual analysis yielded circumferential and height-dependent variations within carbon and oxygen pollen-isotopes and the sampling position on a tree accounted for differences of up to 3.5‰ for δ13Cpollen and 2.1‰ for δ18Opollen. A comparison of isotope ranges from different geographic settings revealed gradients between maritime and continental as well as between high and low altitudinal study sites. The results of stepwise regression analysis demonstrated, that carbon and oxygen pollen-isotopes also reflect local non-climate environmental conditions. A detailed understanding of isotope patterns and ranges in modern pollen is necessary to enhance the accuracy of palaeoclimate investigations on δ13C and δ18O of fossil pollen. Furthermore, pollen-isotope values are species-specific and the analysis of species growing during different phenophases may be valuable for palaeoweather reconstructions of different seasons.


Assuntos
Carbono/metabolismo , Oxigênio/metabolismo , Pólen/metabolismo , Betulaceae/crescimento & desenvolvimento , Isótopos de Carbono/análise , Clima , Ecossistema , Fagaceae/crescimento & desenvolvimento , Isótopos de Oxigênio/análise , Pinaceae/crescimento & desenvolvimento , Pólen/genética , Sapindaceae/crescimento & desenvolvimento , Estações do Ano , Especificidade da Espécie , Árvores/genética , Árvores/crescimento & desenvolvimento , Árvores/metabolismo
17.
Nat Commun ; 11(1): 3135, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561713

RESUMO

It is commonly thought that when multiple carbon sources are available, bacteria metabolize them either sequentially (diauxic growth) or simultaneously (co-utilization). However, this view is mainly based on analyses in relatively simple laboratory settings. Here we show that a heterotrophic marine bacterium, Pseudoalteromonas haloplanktis, can use both strategies simultaneously when multiple possible nutrients are provided in the same growth experiment. The order of nutrient uptake is partially determined by the biomass yield that can be achieved when the same compounds are provided as single carbon sources. Using transcriptomics and time-resolved intracellular 1H-13C NMR, we reveal specific pathways for utilization of various amino acids. Finally, theoretical modelling indicates that this metabolic phenotype, combining diauxie and co-utilization of substrates, is compatible with a tight regulation that allows the modulation of assimilatory pathways.


Assuntos
Carbono/metabolismo , Processos Heterotróficos/fisiologia , Modelos Biológicos , Pseudoalteromonas/fisiologia , Biomassa , Espectroscopia de Ressonância Magnética Nuclear de Carbono-13 , Meios de Cultura/metabolismo , Cinética , Espectroscopia de Prótons por Ressonância Magnética
18.
PLoS Comput Biol ; 16(6): e1007533, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32542021

RESUMO

Metabolism underpins the pathogenic strategy of the causative agent of TB, Mycobacterium tuberculosis (Mtb), and therefore metabolic pathways have recently re-emerged as attractive drug targets. A powerful approach to study Mtb metabolism as a whole, rather than just individual enzymatic components, is to use a systems biology framework, such as a Genome-Scale Metabolic Network (GSMN) that allows the dynamic interactions of all the components of metabolism to be interrogated together. Several GSMNs networks have been constructed for Mtb and used to study the complex relationship between the Mtb genotype and its phenotype. However, the utility of this approach is hampered by the existence of multiple models, each with varying properties and performances. Here we systematically evaluate eight recently published metabolic models of Mtb-H37Rv to facilitate model choice. The best performing models, sMtb2018 and iEK1011, were refined and improved for use in future studies by the TB research community.


Assuntos
Genoma Bacteriano , Redes e Vias Metabólicas , Mycobacterium tuberculosis/genética , Teorema de Bayes , Biomassa , Carbono/metabolismo , Colesterol/metabolismo , Meios de Cultura , Reações Falso-Positivas , Genótipo , Glicerol/metabolismo , Modelos Biológicos , Mycobacterium tuberculosis/metabolismo , Fenótipo , Valor Preditivo dos Testes , Software , Biologia de Sistemas , Termodinâmica
19.
Int J Food Microbiol ; 328: 108687, 2020 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-32474227

RESUMO

Penicilium griseofulvum, the causal agent of apple blue mold, is able to produce in vitro and on apple a broad spectrum of secondary metabolites (SM), including patulin, roquefortine C and griseofulvin. Among them, griseofulvin is known for its antifungal and antiproliferative activity, and has received interest in many sectors, from medicine to agriculture. The biosynthesis of SM is finely regulated by filamentous fungi and can involve global regulators and pathway specific regulators, which are usually encoded by genes present in the same gene cluster as the backbone gene and tailoring enzymes. In the griseofulvin gene cluster, two putative transcription factors were previously identified, encoded by genes gsfR1 and gsfR2, and their role has been investigated in the present work. Analysis of P. griseofulvum knockout mutants lacking either gene suggest that gsfR2 forms part of a different pathway and gsfR1 exhibits many spectra of action, acting as regulator of griseofulvin and patulin biosynthesis and influencing conidia production and virulence on apple. The analysis of gsfR1 promoter revealed that the regulation of griseofulvin biosynthesis is also controlled by global regulators in response to many environmental stimuli, such as carbon and nitrogen. The influence of carbon and nitrogen on griseofulvin production was further investigated and verified, revealing a complex network of response and confirming the central role of gsfR1 in many processes in P. griseofulvum.


Assuntos
Griseofulvina/biossíntese , Patulina/biossíntese , Penicillium/metabolismo , Penicillium/patogenicidade , Esporos Fúngicos/crescimento & desenvolvimento , Carbono/metabolismo , Microbiologia de Alimentos , Griseofulvina/metabolismo , Malus/microbiologia , Família Multigênica , Nitrogênio/metabolismo , Patulina/metabolismo , Esporos Fúngicos/metabolismo , Fatores de Transcrição/genética , Virulência
20.
Artigo em Inglês | MEDLINE | ID: mdl-32545542

RESUMO

Increasing drought globally is a severe threat to fragile desert wetland ecosystem. It is of significance to study the effects of wetland drying on microbial regulation of soil carbon (C) in the desert. In this study, we examined the impacts of wetland drying on microbial biomass, microbial community (bacteria, fungi) and microbial activity [basal microbial respiration, microbial metabolic quotient (qCO2)]. Relationships of microbial properties with biotic factors [litter, soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP)], abiotic factors (soil moisture, pH and clay content) and biological processes (basal microbial respiration, qCO2) were also developed. Results showed that the drying of wetland led to a decrease of soil microbial biomass carbon (MBC) content, microbial biomass nitrogen (MBN) content and fungi and bacterial abundance, and an increase of the fungi:bacteria ratio. Wetland drying also led to increased soil basal respiration and increased qCO2, which was attributed to lower soil clay content and litter N concentration. The MBC:SOC ratios were higher under drier soil conditions than under virgin wetland, which was attributed to stronger C conserve ability of fungi than bacteria. The wetland drying process exacerbated soil C loss by strengthening heterotrophic respiration; however, the exact effects of soil microbial community structure on microbial C mineralization were not clear in this study and need further research.


Assuntos
Carbono , Microbiota , Microbiologia do Solo , Solo , Áreas Alagadas , Biomassa , Carbono/metabolismo , China , Nitrogênio/metabolismo , Areia
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