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1.
J Hazard Mater ; 390: 122144, 2020 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-32006845

RESUMO

Many studies have examined changes in soil microbial community structure and composition by carbon nanomaterials (CNMs). Few, however, have investigated their impact on microbial community functions. This study explored how fullerene (C60) and multi-walled carbon nanotubes (M50) altered functionality of an agricultural soil microbial community (Archaea, Bacteria and Eukarya), using microcosm experiments combined with GeoChip microarray. M50 had a stronger effect than C60 on alpha diversity of microbial functional genes; both CNMs increased beta diversity, resulting in functional profiles distinct from the control. M50 exerted a broader, severer impact on microbially mediated nutrient cycles. Together, these two CNMs affected CO2 fixation pathways, microbial degradation of diverse carbohydrates, secondary plant metabolites, lipids and phospholipids, proteins, as well as methanogenesis and methane oxidation. They also suppressed nitrogen fixation, nitrification, dissimilatory nitrogen reduction, eukaryotic assimilatory nitrogen reduction, and anaerobic ammonium oxidation (anammox). Phosphorus and sulfur cycles were less vulnerable; only phytic acid hydrolysis and sulfite reduction were inhibited by M50 but not C60. Network analysis suggested decoupling of nutrient cycles by CNMs, manifesting closer and more hierarchical gene networks. This work reinforces profound impact of CNMs on soil microbial community functions and ecosystem services, laying a path for future investigation in this direction.

2.
Environ Microbiol ; 22(3): 1052-1065, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31599105

RESUMO

The factors determining stochastic and deterministic processes that drive microbial community structure, specifically the balance of abundant and rare bacterial taxa, remain underexplored. Here we examined biogeographic patterns of abundant and rare bacterial taxa and explored environmental factors influencing their community assembly processes in agricultural fields across eastern China. More phylogenetic turnover correlating with spatial distance was observed in abundant than rare sub-communities. Homogeneous selection was the main assembly process for both the abundant and rare sub-communities; however, the abundant sub-community was more tightly clustered phylogenetically and was more sensitive to dispersal limitations than the rare sub-community. Rare sub-community of rice fields and abundant sub-community of maize fields were more governed by stochastic assembly processes, which showed higher operational taxonomic unit richness. We propose a conceptual paradigm wherein soil pH and mean annual temperature mediate the assembly of the abundant and rare sub-communities respectively. A higher soil pH leads to deterministic assembly of the abundant sub-community. For the rare sub-community, the dominance of stochasticity in low-temperature regions indicates weaker niche-based exclusion and the arrival of more evolutionary lineages. These findings suggest that the community assembly processes for abundant and rare bacterial taxa are dependent on distinct environmental variables in agro-ecosystems.

3.
ISME J ; 14(1): 202-216, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31611655

RESUMO

Revealing the linkages between community assembly and species coexistence, which is crucial for the understanding of ecosystem diversity and functioning, is a fundamental but rarely investigated subject in microbial ecology. Here we examined archaeal, bacterial, and fungal community assembly in adjacent pairs of maize (water-unsaturated) and rice (water-saturated) fields across different habitats and regions throughout Eastern China. The high-throughput sequencing dataset was analyzed by variation partitioning, null model, and neutral community model analyses. We demonstrated that microbial community assembly was governed more by species sorting than by dispersal limitation in maize fields, and to a lesser extent in rice fields. The relative importance of species sorting in maize soils was greater at low latitudes than at high latitudes, while rice soils exhibited an opposite trend. Microbial co-occurrence associations tended to be higher when communities were primarily driven by dispersal limitation relative to species sorting. There were greater community dissimilarities between maize and rice soils in low-latitude regions, which was consistent with the higher proportion of negative edges in the correlation networks. The results indicate that a balance between species sorting and dispersal limitation mediates species coexistence in soil microbiomes. This study enhances our understanding of contemporary coexistence theory in microbial ecosystems.


Assuntos
Agricultura , Microbiota , Microbiologia do Solo , Archaea/genética , Archaea/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , China , Ecossistema , Fungos/genética , Fungos/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Oryza , Zea mays
4.
Microorganisms ; 7(9)2019 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-31505744

RESUMO

Pennisetum sinese is a good forage grass with high biomass production and crude proteins. However, little is known about the endophytic fungi diversity of P. sinese, which might play an important role in the plant's growth and biomass production. Here, we used high throughput sequencing of the Internal Transcribed Spacer (ITS) sequences based on primers ITS5-1737 and ITS2-2043R to investigate the endophytic fungi diversity of P. sinese roots at the maturity stage, as collected from four provinces (Shaanxi province, SX; Fujian province, FJ; the Xinjiang Uyghur autonomous prefecture, XJ and Inner Mongolia, including sand (NS) and saline-alkali land (NY), China). The ITS sequences were processed using QIIME and R software. A total of 374,875 effective tags were obtained, and 708 operational taxonomic units (OTUs) were yielded with 97% identity in the five samples. Ascomycota and Basidiomycota were the two dominant phyla in the five samples, and the genera Khuskia and Heydenia were the most abundant in the FJ and XJ samples, respectively, while the most abundant tags in the other three samples could not be annotated at the genus level. In addition, our study revealed that the FJ sample possessed the highest OTU numbers (242) and the NS sample had the lowest (86). Moreover, only 22 OTUs were present in all samples simultaneously. The beta diversity analysis suggested a division of two endophytic fungi groups: the FJ sample from the south of China and the other four samples from north or northwest China. Correlation analysis between the environmental factors and endophytic fungi at the class level revealed that Sordariomycetes and Pucciniomycetes had extremely significant positive correlations with the total carbon, annual average precipitation, and annual average temperature, while Leotiomycetes showed an extremely significant negative correlation with quick acting potassium. The results revealed significant differences in the root endophytic fungi diversity of P. sinese in different provinces and might be useful for growth promotion and biomass production in the future.

5.
Chemosphere ; 235: 248-259, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31260865

RESUMO

Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.


Assuntos
Bactérias/classificação , Biodiversidade , Microbiota , Plantas/microbiologia , Microbiologia do Solo , Solo/química , Bactérias/genética , DNA Bacteriano/genética
6.
Genome Biol Evol ; 11(7): 1736-1750, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-31192354

RESUMO

Nitrogen fixation in legumes occurs via symbiosis with rhizobia. This process involves packages of symbiotic genes on mobile genetic elements that are readily transferred within or between rhizobial species, furnishing the recipient with the ability to interact with plant hosts. However, it remains elusive whether plant host migration has played a role in shaping the current distribution of genetic variation in symbiotic genes. Herein, we examined the genetic structure and phylogeographic pattern of symbiotic genes in 286 symbiotic strains of Mesorhizobium nodulating black locust (Robinia pseudoacacia), a cross-continental invasive legume species that is native to North America. We conducted detailed phylogeographic analysis and approximate Bayesian computation to unravel the complex demographic history of five key symbiotic genes. The sequencing results indicate an origin of symbiotic genes in Germany rather than North America. Our findings provide strong evidence of prehistoric lineage splitting and spatial expansion events resulting in multiple radiations of descendent clones from founding sequence types worldwide. Estimates of the timescale of divergence in North American and Chinese subclades suggest that black locust-specific symbiotic genes have been present in these continent many thousands of years before recent migration of plant host. Although numerous crop plants, including legumes, have found their centers of origin as centers of evolution and diversity, the number of legume-specific symbiotic genes with a known geographic origin is limited. This work sheds light on the coevolution of legumes and rhizobia.


Assuntos
Rhizobium/fisiologia , Robinia/microbiologia , Nódulos Radiculares de Plantas/microbiologia , Teorema de Bayes , Filogenia , Simbiose/genética , Simbiose/fisiologia
7.
Sci Rep ; 9(1): 7987, 2019 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-31118425

RESUMO

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

8.
mSystems ; 4(2)2019.
Artigo em Inglês | MEDLINE | ID: mdl-30944882

RESUMO

Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and ß-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services-the ultimate goal of microbial ecology.

9.
Microbiome ; 7(1): 15, 2019 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-30709414

RESUMO

BACKGROUND: Understanding the spatial distributions and ecological diversity of soil archaeal communities in agricultural ecosystems is crucial for improvements in crop productivity. Here, we conducted a comprehensive, continental-scale survey of soil archaeal communities in adjacent pairs of maize (dryland) and rice (wetland) fields in eastern China. RESULTS: We revealed the consequential roles of environmental filtering in driving archaeal community assembly for both maize and rice fields. Rice fields, abundant with Euryarchaeota, had higher archaeal diversity and steeper distance-decay slopes than maize fields dominated by Thaumarchaeota. Dominant soil archaea showed distinct continental atlases and niche differentiation between dryland and wetland habitats, where they were associated with soil pH and mean annual temperature, respectively. After identifying their environmental preferences, we grouped the dominant archaeal taxa into different ecological clusters and determined the unique co-occurrence patterns within each cluster. Using this empirical dataset, we built a continental atlas of soil archaeal communities to provide reliable estimates of their spatial distributions in agricultural ecosystems. CONCLUSIONS: Environmental filtering plays a crucial role in driving the distinct continental atlases of dominant soil archaeal communities between dryland and wetland, with contrasting strategies of archaeal-driven nutrient cycling within these two agricultural ecosystems. These findings improve our ability to predict how soil archaeal communities respond to environmental changes and to manage soil archaeal communities for provisioning of agricultural ecosystem services.


Assuntos
Archaea/classificação , Produtos Agrícolas/microbiologia , Oryza/microbiologia , Microbiologia do Solo , Zea mays/microbiologia , Agricultura , Archaea/genética , Meio Ambiente , RNA Ribossômico 16S/genética , Solo/química , Áreas Alagadas
10.
Appl Environ Microbiol ; 85(6)2019 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-30658982

RESUMO

A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.


Assuntos
Bactérias/isolamento & purificação , Fabaceae/crescimento & desenvolvimento , Fabaceae/microbiologia , Microbiota , Poluentes do Solo/metabolismo , Bactérias/classificação , Bactérias/genética , Bactérias/metabolismo , Biodiversidade , Metagenômica , Metais/análise , Metais/metabolismo , Filogenia , Solo/química , Microbiologia do Solo , Poluentes do Solo/análise
11.
Sci Total Environ ; 651(Pt 1): 281-290, 2019 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-30243161

RESUMO

Large variation of CH4 emissions from paddy and wetland ecosystems exists across different geographical locations in China. To obtain mechanistic understanding of this variation, we investigated the dynamics of methanogenesis over the course of glucose degradation in fourteen paddy field soils and five wetland soils collected from different regions of China. The results revealed that the maximal rate (2-3 mM per day) and the total amount (25-30 mM) of CH4 produced were similar across soil samples. The lag phase of methanogenesis, however, differed substantially with the shortest lag phase of 4 days in a paddy soil from north China and the longest of 32 days in a soil from south China, and this difference reflected a general geographical trend among all soils tested. Nitrate was reduced completely within 4 days in all soils. The reduction of Fe(III) and sulfate was completed after 21 days and 29 days, respectively. The depletion time of Fe(III) and sulfate were positively correlated with the lag phase of methanogenesis. Competition for common substrates between methanogens and iron and sulfate reducers, however, does not explain this coincidence because a slow production of CH4 was detected at the very beginning. It appears that the geographical variations in methanogenesis and the reduction of ferric iron and sulfate are related to the variation in soil pH but not to temperature, soil organic C and nutrient conditions in paddy and wetland soils across eastern China.


Assuntos
Metano/metabolismo , Oryza/crescimento & desenvolvimento , Microbiologia do Solo , Solo/química , Áreas Alagadas , Agricultura , China , Compostos Férricos/análise , Íons/análise , Nitratos/análise , Sulfatos/análise
12.
Sci Rep ; 8(1): 15634, 2018 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-30353073

RESUMO

Agrilus mali (Coleoptera: Buprestidae) is an invasive wood borer pest that has caused considerable damage to the Xinjiang wild fruit forest. In this study, we investigated the bacterial and fungal intestinal microbial communities of A. mali during different developmental stages, including larvae, pupae and newly eclosed adults or fed different diets (leaves of Malus halliana and Malus pumila) using Illumina MiSeq high-throughput sequencing technology. The results showed that microbial alpha diversity first increased and then decreased during the developmental stages, with the most dominant bacteria and fungi exhibiting the dynamic patterns "Decrease", "Increase" and "Fluctuation". With respect to the different diets, the bacterial communities were similar between the newly eclosed adults and adults fed M. pumila leaves, while the structure of the fungal communities showed great differences between newly eclosed adults and adults fed different diets. Through a co-correlation network analysis, we observed complex microbial interactions among bacterial and fungal taxa that were associated with potential diverse functions and intricate biological processes in the intestinal microbiota of A. mali. Overall, the results of this study demonstrated that the invasive insect A. mali harbours diverse, dynamic, and presumably multifunctional microbial communities, an understanding of which could improve our ability to develop more effective management approaches to control A. mali.


Assuntos
Besouros/microbiologia , Microbioma Gastrointestinal , Fenômenos Fisiológicos da Nutrição Animal , Animais , Bactérias/genética , Bactérias/isolamento & purificação , Besouros/crescimento & desenvolvimento , Besouros/fisiologia , Dieta , Fungos/genética , Fungos/isolamento & purificação , Micobioma , Filogenia
13.
Microbiome ; 6(1): 146, 2018 08 21.
Artigo em Inglês | MEDLINE | ID: mdl-30131068

RESUMO

BACKGROUND: Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0-300 cm) and horizontal (i.e., distance from trees of 30-90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration. RESULTS: In the superficial layers (0-80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers. CONCLUSIONS: Taken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.


Assuntos
Archaea/classificação , Bactérias/classificação , Fungos/classificação , Árvores/crescimento & desenvolvimento , Archaea/genética , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/genética , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biodiversidade , Fungos/genética , Fungos/isolamento & purificação , Fungos/metabolismo , Metagenômica , Nutrientes/metabolismo , Filogenia , Raízes de Plantas/microbiologia , Análise de Sequência de DNA , Solo/química , Microbiologia do Solo , Árvores/microbiologia
14.
Sci Total Environ ; 622-623: 664-675, 2018 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-29223893

RESUMO

Natural wetlands and anthropogenic paddy fields are the dominant biogenic sources of atmospheric methane emission which have been speculated as the most probable sources for the increase of post-2006 atmospheric methane. Regional differences in CH4 emission is possibly due to microbial biogeographic distribution. Here we collected soils from 19 wetlands from different regions in China. The methane production capacity (MPC) was measured for each soil samples and varied from 1.11 to 841.94mg/kg dry soil. High throughput sequencing was employed to investigate the diversity and composition of bacterial, archaeal and methanogenic communities. Similar biogeographic patterns for bacterial, archaeal and methanogenic communities along the latitudinal gradient were observed, and the biogeographic assemblies of different microbial groups were driven by concurrent factors, including edaphic variables (total organic carbon, total phosphorus and pH) and climatic variables (annual frost days, mean annual temperature, direct solar radiation and mean annual precipitation). MPC was significantly correlated with TOC concentration, and in addition, various functional taxa were positively correlated with MPC (P<0.05), for example, Sphingomonas, Syntrophomonas, Methanospirillum and Methanoregula, indicating their potential contributions in the methanogenic process, and many of them were fermentative bacteria and methanogens. Network analysis showed that some syntrophs, sulfate-reducers and methanogens were tightly co-occurred in one module, suggesting their involvements in cross-linked functional processes. Our study implicated both temperature and substrate availability altered the biogeographic patterns of microbial community as well as methane production potential in Chinese wetlands.


Assuntos
Archaea/classificação , Bactérias/classificação , Metano/metabolismo , Microbiologia do Solo , Áreas Alagadas , China , RNA Ribossômico 16S/genética
15.
Appl Environ Microbiol ; 83(20)2017 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-28778889

RESUMO

The symbiosis of the highly metal-resistant Sinorhizobium meliloti CCNWSX0020 and Medicago lupulina has been considered an efficient tool for bioremediation of heavy metal-polluted soils. However, the metal resistance mechanisms of S. meliloti CCNWSX00200 have not been elucidated in detail. Here we employed a comparative transcriptome approach to analyze the defense mechanisms of S. meliloti CCNWSX00200 against Cu or Zn exposure. Six highly upregulated transcripts involved in Cu and Zn resistance were identified through deletion mutagenesis, including genes encoding a multicopper oxidase (CueO), an outer membrane protein (Omp), sulfite oxidoreductases (YedYZ), and three hypothetical proteins (a CusA-like protein, a FixH-like protein, and an unknown protein), and the corresponding mutant strains showed various degrees of sensitivity to multiple metals. The Cu-sensitive mutant (ΔcueO) and three mutants that were both Cu and Zn sensitive (ΔyedYZ, ΔcusA-like, and ΔfixH-like) were selected for further study of the effects of these metal resistance determinants on bioremediation. The results showed that inoculation with the ΔcueO mutant severely inhibited infection establishment and nodulation of M. lupulina under Cu stress, while inoculation with the ΔyedYZ and ΔfixH-like mutants decreased just the early infection frequency and nodulation under Cu and Zn stresses. In contrast, inoculation with the ΔcusA-like mutant almost led to loss of the symbiotic capacity of M. lupulina to even grow in uncontaminated soil. Moreover, the antioxidant enzyme activity and metal accumulation in roots of M. lupulina inoculated with all mutants were lower than those with the wild-type strain. These results suggest that heavy metal resistance determinants may promote bioremediation by directly or indirectly influencing formation of the rhizobium-legume symbiosis.IMPORTANCE Rhizobium-legume symbiosis has been promoted as an appropriate tool for bioremediation of heavy metal-contaminated soils. Considering the plant-growth-promoting traits and survival advantage of metal-resistant rhizobia in contaminated environments, more heavy metal-resistant rhizobia and genetically manipulated strains were investigated. In view of the genetic diversity of metal resistance determinants in rhizobia, their effects on phytoremediation by the rhizobium-legume symbiosis must be different and depend on their specific assigned functions. Our work provides a better understanding of the mechanism of heavy metal resistance determinants involved in the rhizobium-legume symbiosis, and in further studies, genetically modified rhizobia harboring effective heavy metal resistance determinants may be engineered for the practical application of rhizobium-legume symbiosis for bioremediation in metal-contaminated soils.


Assuntos
Proteínas de Bactérias/genética , Cobre/metabolismo , Medicago/microbiologia , Sinorhizobium meliloti/genética , Sinorhizobium meliloti/metabolismo , Poluentes do Solo/metabolismo , Zinco/metabolismo , Proteínas de Bactérias/metabolismo , Biodegradação Ambiental , Medicago/metabolismo , Oxirredutases/genética , Oxirredutases/metabolismo , Raízes de Plantas/metabolismo , Raízes de Plantas/microbiologia , Transcriptoma
16.
Mol Ecol ; 26(19): 5305-5317, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28665016

RESUMO

Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long-term oil-contaminated soils at intervals of 46-360 km by performing high-throughput sequencing of 16S rRNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples. Both rare and abundant subcommunities showed significant distance-decay relationships, and their assemblies were driven by different factors. The rare subcommunity primarily exhibited a spatially structured distribution (i.e., stochastic processes), while edaphic factors (i.e., deterministic processes) largely contributed to the structure of the abundant subcommunity. A network analysis revealed closer relationships between abundant bacteria and their heightened influence on other co-occurrences in the community compared with rare species. In conclusion, rare microbial taxa may play potential roles in maintaining ecosystem diversity, although they do not appear to be central to microbial networks. Abundant microbes are vital for microbial co-occurrences in oil-contaminated soils, and high relative abundance and ubiquitous distribution suggest potential roles in the degradation of organic pollutants.


Assuntos
Bactérias/classificação , Biodiversidade , Microbiota , Poluição por Petróleo , Microbiologia do Solo , China , DNA Bacteriano/genética , Sequenciamento de Nucleotídeos em Larga Escala , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Poluentes do Solo
17.
Sci Rep ; 7(1): 3608, 2017 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-28620188

RESUMO

Switchgrass (Panicum virgatum L.) is a cellulosic biofuel feedstock and their effects on bacterial communities in deep soils remain poorly understood. To reveal the responses of bacterial communities to long-term switchgrass cultivation through the soil profile, we examined the shift of soil microbial communities with depth profiles of 0-60 cm in five-year switchgrass cultivation and fallow plots. The Illumina sequencing of the 16S rRNA gene showed that switchgrass cultivation significantly increased microbial OTU richness, rather than microbial Shannon diversity; however, there was no significant difference in the structure of microbial communities between switchgrass cultivation and fallow soils. Both switchgrass cultivation and fallow soils exhibited significant negative vertical spatial decay of microbial similarity, indicating that more vertical depth distant soils had more dissimilar communities. Specifically, switchgrass cultivation soils showed more beta-diversity variations across soil depth profile. Through network analysis, more connections and closer relationships of microbial taxa were observed in soils under switchgrass cultivation, suggesting that microbial co-occurrence patterns were substantially influenced by switchgrass cultivation. Overall, our study suggested that five-year switchgrass cultivation could generated more beta-diversity variations across soil depth and more complex inter-relationships of microbial taxa, although did not significantly shape the structure of soil microbial community.


Assuntos
Bactérias , Microbiota , Panicum , Microbiologia do Solo , Bactérias/classificação , Bactérias/genética , Biodiversidade , Biologia Computacional/métodos
18.
Environ Pollut ; 225: 497-505, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28336094

RESUMO

Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl2) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for ß-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants.


Assuntos
Bactérias/metabolismo , Microbiologia do Solo , Alcanos/metabolismo , Bactérias/classificação , Ecossistema , Hidrocarbonetos/metabolismo , Fenantrenos/metabolismo , Poluentes do Solo/metabolismo , Processos Estocásticos
19.
Mol Ecol ; 26(6): 1641-1651, 2017 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-28139080

RESUMO

The microbiomes of rhizocompartments (nodule endophytes, root endophytes, rhizosphere and root zone) in soya bean and alfalfa were analysed using high-throughput sequencing to investigate the interactions among legume species, microorganisms and soil types. A clear hierarchical filtration of microbiota by plants was observed in the four rhizocompartments - the nodule endosphere, root endosphere, rhizosphere and root zone - as demonstrated by significant variations in the composition of the microbial community in the different compartments. The rhizosphere and root zone microbial communities were largely influenced by soil type, and the nodule and root endophytes were primarily determined by plant species. Diverse microbes inhabited the root nodule endosphere, and the corresponding dominant symbiotic rhizobia belonged to Ensifer for alfalfa and Ensifer-Bradyrhizobium for soya bean. The nonsymbiotic nodule endophytes were mainly Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The variation in root microbial communities was also affected by the plant growth stage. In summary, this study demonstrated that the enrichment process of nodule endophytes follows a hierarchical filtration and that the bacterial communities in nodule endophytes vary according to the plant species.


Assuntos
Fabaceae/microbiologia , Microbiota , Rizosfera , Microbiologia do Solo , Bactérias/classificação , Endófitos/classificação , Medicago sativa/microbiologia , Nódulos Radiculares de Plantas/microbiologia , Soja/microbiologia
20.
Mol Ecol ; 26(3): 923-936, 2017 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-28012222

RESUMO

Elucidating the mechanisms underlying microbial succession is a major goal of microbial ecology research. Given the increasing human pressure on the environment and natural resources, responses to the repeated introduction of organic and inorganic pollutants are of particular interest. To investigate the temporal dynamics of microbial communities in response to pollutants, we analysed the microbial community structure in batch microcosms that were inoculated with soil bacteria following exposure to individual or combined pollutants (phenanthrene, n-octadecane, phenanthrene + n-octadecane and phenanthrene + n-octadecane + CdCl2 ). Subculturing was performed at 10-day intervals, followed by high-throughput sequencing of 16S rRNA genes. The dynamics of microbial communities in response to different pollutants alone and in combination displayed similar patterns during enrichment. Specifically, the repression and induction of microbial taxa were dominant, and the fluctuation was not significant. The rate of appearance for new taxa and the temporal turnover within microbial communities were higher than the rates reported in other studies of microbial communities in air, water and soil samples. In addition, conditionally rare taxa that were specific to the treatments exhibited higher betweenness centrality values in the co-occurrence network, indicating a strong influence on other interactions in the community. These results suggest that the repeated introduction of pollutants could accelerate microbial succession in microcosms, resulting in the rapid re-equilibration of microbial communities.


Assuntos
Bactérias/classificação , Microbiologia do Solo , Poluentes do Solo , RNA Ribossômico 16S/genética , Fatores de Tempo
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