Endophytic root bacteria associated with the natural vegetation growing at the hydrocarbon-contaminated Bitumount Provincial Historic site

2017 ◽  
Vol 63 (6) ◽  
pp. 502-515 ◽  
Author(s):  
Natalie P. Blain ◽  
Bobbi L. Helgason ◽  
James J. Germida
Keyword(s):  
Plant Species ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Growth Promotion ◽  
Plant Root ◽  
Gene Copy ◽  
Sampling Location ◽  
Historic Site ◽  
Copy Numbers

The Bitumount Provincial Historic site is the location of 2 of the world’s first oil-extracting and -refining operations. Despite hydrocarbon levels ranging from 330 to 24 700 mg·(kg soil)−1, plants have been able to recolonize the site through means of natural revegetation. This study was designed to achieve a better understanding of the plant-root-associated bacterial partnerships occurring within naturally revegetated hydrocarbon-contaminated soils. Root endophytic bacterial communities were characterized from representative plant species throughout the site by both high-throughput sequencing and culturing techniques. Population abundance of rhizosphere and root endosphere bacteria was significantly influenced (p < 0.05) by plant species and sampling location. In general, members of the Actinomycetales, Rhizobiales, Pseudomonadales, Burkholderiales, and Sphingomonadales orders were the most commonly identified orders. Community structure of root-associated bacteria was influenced by both plant species and sampling location. Quantitative real-time polymerase chain reaction was used to determine the potential functional diversity of the root endophytic bacteria. The gene copy numbers of 16S rRNA and 2 hydrocarbon-degrading genes (CYP153 and alkB) were significantly affected (p < 0.05) by the interaction of plant species and sampling location. Our findings suggest that some of the bacterial communities detected are known to exhibit plant growth promotion characteristics.

The recruitment of bacterial communities by the plant root system changed by acid mine drainage pollution in soils

2020 ◽  
Vol 367 (15) ◽  
Author(s):  
Yang Li ◽  
Liang Yuan ◽  
Sheng Xue ◽  
Bingjun Liu ◽  
Gang Jin
Keyword(s):  
Acid Mine Drainage ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Mine Drainage ◽  
Plant Root ◽  
Bacterial Community Composition ◽  
Cellular Processes ◽  
Acid Mine ◽  
Functional Bacteria ◽  
Plant Root System

ABSTRACT This study aims to better understand the relationship between the response to acid mine drainage (AMD) stress of tolerant plants and changes in root-related bacterial communities. In this study, reed stems were planted in AMD-polluted and unpolluted soils, and high-throughput sequencing was conducted to analyze the bacterial community composition in the soil, rhizosphere, rhizoplane and endosphere. The results showed that the effect of AMD pollution on root-associated bacterial communities was greater than that of rhizo-compartments. Proteobacteria were dominant across the rhizo-compartments between treatments. The microbiomes of unpolluted treatments were enriched by Alphaproteobacteria and Betaproteobacteria and depleted in Gammaproteobacteria ranging from the rhizoplane into the endosphere. However, the opposite trend was observed in the AMD pollution treatment, namely, Gammaproteobacteria were enriched, and Alphaproteobacteria and Deltaproteobacteria were mostly depleted. In addition, endophytic microbiomes were dominated by Comamonadaceae and Rhodocyclaceae in the unpolluted treatment and by Enterobacteriaceae in the AMD-polluted soils. PICRUSt showed that functional categories associated with membrane transport, metabolism and cellular processes and signaling processes were overrepresented in the endosphere of the AMD-polluted treatment. In conclusion, our study reveals significant variation in bacterial communities colonizing rhizo-compartments in two soils, indicating that plants can recruit functional bacteria to the roots in response to AMD pollution.

scholarly journals Influence of Heat Events on the Composition of Airborne Bacterial Communities in Urban Ecosystems

2018 ◽  
Vol 15 (10) ◽  
pp. 2295 ◽  
Author(s):  
Zhiguo Fang ◽  
Weijun Guo ◽  
Junwen Zhang ◽  
Xiuqin Lou
Keyword(s):  
High Temperature ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Urban Ecosystems ◽  
Gene Copy ◽  
Airborne Bacteria ◽  
Rrna Gene ◽  
Before And After ◽  
Hot Weather ◽  
Heat Events

Airborne bacteria are significantly affected by meteorological and environmental conditions. However, there is little quantitative data available on the effects of these factors on airborne bacteria in urban ecosystems. In the present study, we analyzed weather-dependent changes in the composition of airborne bacterial communities using high throughput sequencing. Samples were collected before and after a period of constant hot weather at four selected sampling sites (YRBS, ZJGUSJC, TJCR, and BLQG) in Hangzhou. Our results show that the average amount of bacterial 16S rRNA gene copy numbers per m3 of air decreased significantly after constant high temperature. In addition, the number of operational taxonomic units and the Shannon–Wiener diversity indexes of the samples at all four selected sampling sites were significantly decreased after the heat event, showing notable impact on bacterial diversity. We also detected a significant increase in the abundances of spore-forming bacteria. Firmicutes increased from 3.7% to 9.9%, Bacillales increased from 2.6% to 7.6%, and Bacillaceae increased from 1.5% to 5.9%. In addition, we observed an increase in beta-Proteobacteria (18.2% to 50.3%), Rhodocyclaceae (6.9% to 29.9%), and Burkholderiaceae (8.1% to 15.2%). On the other hand, the abundance of alpha-Proteobacteria (39.6% to 9.8%), Caulobacteraceae (17.9% to 0.5%), Sphingomonadaceae (7.2% to 3.3%), and Xanthomonadaceae (3.0% to 0.5%) was significantly lower. Taken together, our data suggest that the composition of airborne bacterial communities varies greatly dependent on heat events, and that such communities include several species that are highly susceptible to high-temperature related stressors such as high air temperature, low relative humidity, and high intensity of solar radiation.

scholarly journals Ammonia-oxidizing Archaea (AOA) are Winners to Survive in Oxygen-limited Habitat Compared to Ammonia-oxidizing Bacteria (AOB)

2021 ◽  
Author(s):  
Peigang Dai ◽  
Wenjing Song ◽  
Zhao Che ◽  
Lili Zhang ◽  
Zhaorong Dong
Keyword(s):  
Intertidal Zone ◽  
High Throughput Sequencing ◽  
Ammonia Oxidation ◽  
Illumina Miseq ◽  
Gene Copy ◽  
Ammonia Oxidizing Bacteria ◽  
Niche Specialization ◽  
Ammonia Oxidizing Archaea ◽  
Copy Numbers ◽  
Oxidation Reduction

Abstract Purpose: Both ammonia oxidizing archaea (AOA) and bacteria (AOB) perform the ammonia oxidation together. These two kinds of microbes present a convenient model for studying niche specialization. To date, few surveys concentrated on the influence of oxygen concentration on niche specialization of AOA and AOB in intertidal zones. Methods: Here, high-throughput sequencing by Illumina MiSeq and qPCR were applied to detect the change of abundance, diversity as well as community structure of both AOA and AOB with 0-60 cm sediments depth in the intertidal zone in Qingdao.Results and Conclusion: The AOA/AOB amoA gene copy numbers and AOA/AOB OTU numbers were all increased as sediment depth went deeper, which indicated that AOA were more adaptive to oxygen-limited niches compared to AOB and oxygen indeed led to the niche specialization of AOA and AOB in intertidal sediments. The dominant AOA and AOB were the Nitrosopumilus and Nitrosospira clusters, respectively, which indicated an ecological success in intertidal zone. Oxidation-reduction potential (ORP) was significantly positively correlated with AOB abundance and AOB OTU numbers (P < 0.01). In addition, both TN (P < 0.01) and pH (P < 0.05) were significantly and negatively correlated with AOB abundance. TN was also significantly and negatively correlated with AOB OTU numbers (P < 0.05).

scholarly journals Cadmium Exposure-Sedum alfrediiPlanting Interactions Shape the Bacterial Community in the Hyperaccumulator Plant Rhizosphere

2018 ◽  
Vol 84 (12) ◽  
pp. e02797-17 ◽  
Author(s):  
Dandi Hou ◽  
Zhi Lin ◽  
Runze Wang ◽  
Jun Ge ◽  
Shuai Wei ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Rrna Gene ◽  
Sedum Alfredii ◽  
Cd Stress ◽  
Metal Hyperaccumulation ◽  
Content Type

ABSTRACTRhizospheric bacteria play important roles in plant tolerance and activation of heavy metals. Understanding the bacterial rhizobiome of hyperaccumulators may contribute to the development of optimized phytoextraction for metal-polluted soils. We used 16S rRNA gene amplicon sequencing to investigate the rhizospheric bacterial communities of the cadmium (Cd) hyperaccumulating ecotype (HE)Sedum alfrediiin comparison to its nonhyperaccumulating ecotype (NHE). Both planting of two ecotypes ofS. alfrediiand elevated Cd levels significantly decreased bacterial alpha-diversity and altered bacterial community structure in soils. The HE rhizosphere harbored a unique bacterial community differing from those in its bulk soil and NHE counterparts. Several key taxa fromActinobacteria,Bacteroidetes, and TM7 were especially abundant in HE rhizospheres under high Cd stress. The actinobacterial genusStreptomyceswas responsible for the majority of the divergence of bacterial community composition between the HE rhizosphere and other soil samples. In the HE rhizosphere, the abundance ofStreptomyceswas 3.31- to 16.45-fold higher than that in other samples under high Cd stress. These results suggested that both the presence of the hyperaccumulatorS. alfrediiand Cd exposure select for a specialized rhizosphere bacterial community during phytoextraction of Cd-contaminated soils and that key taxa, such as the species affiliated with the genusStreptomyces, may play an important role in metal hyperaccumulation.IMPORTANCESedum alfrediiis a well-known Cd hyperaccumulator native to China. Its potential for extracting Cd relies not only on its powerful uptake, translocation, and tolerance for Cd but also on processes underground (especially rhizosphere microbes) that facilitate root uptake and tolerance of the metal. In this study, a high-throughput sequencing approach was applied to gain insight into the soil-plant-microbe interactions that may influence Cd accumulation in the hyperaccumulatorS. alfredii. Here, we report the investigation of rhizosphere bacterial communities ofS. alfrediiin phytoremediation of different levels of Cd contamination in soils. Moreover, some key taxa in its rhizosphere identified in the study, such as the species affiliated with genusStreptomyces, may shed new light on the involvement of bacteria in phytoextraction of contaminated soils and provide new materials for phytoremediation optimization.

scholarly journals MEKANISME FISIOLOGIS TUMBUHAN HIPERAKUMULATOR LOGAM BERAT = Heavy Metal Hyperaccumulator Plant Physiology Mechanism

2016 ◽  
Vol 14 (2) ◽  
pp. 75 ◽  
Author(s):  
Nuril Hidayanti
Keyword(s):  
Plant Species ◽  
Contaminated Soils ◽  
Plant Root ◽  
Toxic Metal ◽  
Transport Systems ◽  
Metal Hyperaccumulation ◽  
Long Distance ◽  
Hyperaccumulator Plants ◽  
Plant Root System ◽  
Distance Transport

One approach to remediate toxic metal pollutants is phytoextraction using hyperaccumulator plants. These plant species are able to accumulate high concentrations of metal ions without suffering fromyield reduction as a result of metal toxicity. Physiological studies showed that metal hyperaccumulation in particular plant species is regulated by multiple pathways and genes controlling metal uptake,accumulation, and tolerance. Currently, research and development on hyperaccumulator plants are progressing in at least seven focus areas: (1) Improving plant root system for higher penetration capacity and more efficient pollutant extraction from heterogeneous contaminated soils, (2) Altering plant’s rhizosphere for secreting various enzymes to enhance extraction, (3) Improving short distance transport systems for nutrients and toxic elements in roots (4) Enhancing mobility of metalsfrom roots up to shoots. (5) Improving long-distance transport of metals, (6) Maximizing capacity of physical sinks such as subcellular vacuoles and epidermal cells and (7) hypertolerance mechanismsto resist the cytotoxic effects of the accumulated metals. Current trends in phytoremediation research are focus at genetic and molecular level. Research objectives in this area include: understanding bio-pathways involved in contaminant degradation and sequestration, identifying specific genes involved in phytoremediation processes, investigating cell signaling pathways that affect genetic expression of plant enzymes, analyzing and identifying root exudates components and chemical fingerprinting to assess phytoremediation effects at specific sites. Keywords: hyperaccumulator, phytoextraction, phytoremediation, heavy metalsAbstrakSalah satu pendekatan untuk memulihkan polutan logam beracun adalah phytoextraction menggunakan tanaman hiperakumulator . Jenis tanaman ini mampu mengakumulasi konsentrasitinggi ion logam tanpa mengalami penurunan hasil akibat keracunan logam. Studi fisiologis menunjukkan bahwa hyperaccumulator logam dalam spesies tanaman tertentu diatur oleh beberapajalur dan gen mengendalikan serapan, akumulasi , dan toleransi logam. Saat ini, penelitian dan pengembangan tanaman hiperakumulator mengalami kemajuan dalam setidaknya tujuh bidangfokus: (1) Meningkatkan sistem perakaran tanaman untuk kapasitas penetrasi yang lebih tinggi dan ekstraksi polutan lebih efisien dari tanah yang terkontaminasi, (2) Mengubah rizosfir tanaman untukmengekstrak berbagai enzim guna meningkatkan ekstraksi, (3) Meningkatkan sistem transportasi jarak pendek untuk nutrisi dan unsur-unsur beracun dalam akar, (4) Meningkatkan mobilitas logamdari akar hingga pucuk, (5) Meningkatkan transportasi jarak jauh dari logam, (6) Memaksimalkan kapasitas tenggelam fisik seperti vakuola subselular, sel-sel epidermis, dan (7) Mekanisme hypertolerance untuk melawan efek sitotoksik dari logam akumulasi . Saat ini kecenderungan dalam penelitian fitoremediasi adalah fokus pada tingkat genetik dan molekuler. Tujuan penelitian di bidangini meliputi: pemahaman bio - jalur yang terlibat dalam degradasi kontaminan dan penyerapan , mengidentifikasi gen tertentu yang terlibat dalam proses fitoremediasi , menyelidiki jalur sinyal selyang mempengaruhi ekspresi genetik dari enzim tanaman , menganalisis dan mengidentifikasi eksudat akar komponen dan sidik jari kimia untuk menilai fitoremediasi efek pada situs tertentuKata Kunci: hiperakumulator, phytoextraction, fitoremediasi, logam berat

scholarly journals Structure and variation of root-associated bacterial communities of Cyperus rotundus L. in the contaminated soils around Pb/Zn mine sites

2021 ◽  
Author(s):  
Pin Gao ◽  
Benru Song ◽  
Rui Xu ◽  
Xiaoxu Sun ◽  
Hanzhi Lin ◽  
...  
Keyword(s):  
Contaminated Soils ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Plant Root ◽  
Sampling Site ◽  
Cyperus Rotundus ◽  
Mining Pollution ◽  
Unpolluted Site ◽  
Mine Sites ◽  
Contamination Levels

Abstract Soil contamination due to mining activities is a great concern in China. Although the effects of mining pollution resulting in changes of soil characteristics and the microbiome have been documented, studies on the responses of plant root-associated microbial assemblages remain scarce. In this work, we collected bulk soil, rhizosphere soil, and root endosphere samples of Cyperus rotundus L (Cyp) plants from two Pb/Zn mines, of which, one was abandoned (SL) and the other was active (GD), to investigate the bacterial community responses across different site contamination levels and Cyp plant compartments. For comparison, one unpolluted site (SD) was included. Results revealed that soils from the SL and GD sites were seriously contaminated by metal(loid)s, including Pb, Zn, As, and Sb. Bacterial richness and diversity depended on the sampling site and plant compartment. All sample types from the SL site had the lowest bacterial diversities and their bacterial communities also exhibited distinct patterns compared to GD and SD samples. As for the specific sampling site, bacterial communities from the root endosphere exhibited different patterns from those in bulk and rhizosphere soil. Compared to the GD and SD sites, the root endosphere and the rhizosphere soil from the SL site shared core microbes, including Halomonas, Pelagibacterium, and Chelativorans, suggesting that they play key roles in Cyp plant survival in such harsh environments.

scholarly journals Distribution of Bacterial Communities in Petroleum-Contaminated Soils from the Dagang Oilfield, China

2019 ◽  
Vol 26 (1) ◽  
pp. 22-32 ◽  
Author(s):  
Xueke Feng ◽  
Zhen Liu ◽  
Xiaoqiang Jia ◽  
Wenyu Lu
Keyword(s):  
Bacterial Community ◽  
Contaminated Soil ◽  
Contaminated Soils ◽  
Bacterial Communities ◽  
Petroleum Hydrocarbon ◽  
High Throughput Sequencing ◽  
Environmental Parameters ◽  
Significant Difference ◽  
Petroleum Contaminated Soil ◽  
Different Depths

AbstractDiversity in bacterial communities was investigated along a petroleum hydrocarbon content gradient (0–0.4043 g/g) in surface (5–10 cm) and subsurface (35–40 cm) petroleum-contaminated soil samples from the Dagang Oilfield, China. Using 16S rRNA Illumina high-throughput sequencing technology and several statistical methods, the bacterial diversity of the soil was studied. Subsequently, the environmental parameters were measured to analyze its relationship with the community variation. Nonmetric multidimensional scaling and analysis of similarities indicated a significant difference in the structure of the bacterial community between the nonpetroleum-contaminated surface and subsurface soils, but no differences were observed in different depths of petroleum-contaminated soil. Meanwhile, many significant correlations were obtained between diversity in soil bacterial community and physicochemical properties. Total petroleum hydrocarbon, total organic carbon, and total nitrogen were the three important factors that had the greatest impacts on the bacterial community distribution in the long-term petroleum-contaminated soils. Our research has provided references for the bacterial community distribution along a petroleum gradient in both surface and subsurface petroleum-contaminated soils of oilfield areas.

scholarly journals Structure of Bacterial Communities in Phosphorus-Enriched Rhizosphere Soils

2020 ◽  
Vol 10 (18) ◽  
pp. 6387
Author(s):  
Yuwei Hu ◽  
Changqun Duan ◽  
Denggao Fu ◽  
Xiaoni Wu ◽  
Kai Yan ◽  
...  
Keyword(s):  
Plant Species ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Nutrient Content ◽  
Illumina Miseq ◽  
Dianchi Lake ◽  
Lake Basin ◽  
Rhizosphere Soils ◽  
Abundance And Diversity ◽  
And Function

Although phytoremediation is the main method for P-removal and maintaining ecosystem balance in geological phosphorus-enriched soils (PES), little is known about the structure and function of microbial communities in PES. Interactions between plants and soil microorganisms mainly occur in the rhizosphere. The aim of this work was to investigate the composition and diversity of bacterial communities found in rhizosphere soils associated with the following three dominant plant species: Erianthus rufipilus, Coriaria nepalensis, and Pinus yunnanensis. In addition, we compared these rhizosphere bacterial communities with those derived from bulk soils and grassland plots in PES from the Dianchi Lake basin of southwestern China. The Illumina MiSeq platform for high-throughput sequencing of 16S rRNA was used for the taxonomy and the analysis of soil bacterial communities. The results showed higher bacterial diversity and nutrient content in rhizosphere soils as compared with bulk soils. Rhizosphere bacteria were predominantly comprised of Proteobacteria (24.43%) and Acidobacteria (21.09%), followed by Verrucomicrobia (19.48%) and Planctomycetes (9.20%). A comparison of rhizosphere soils of the selected plant species in our study and the grassland plots showed that Acidobacteria were the most abundant in the rhizosphere soil of E. rufipilus; Bradyrhizobiaceae and Rhizobiaceae in the order Rhizobiales from C. nepalensis were found to have the greatest abundance; and Verrucomicrobia and Planctomycetes were in higher abundance in P. yunnanensis rhizosphere soils and in grassland plots. A redundancy analysis revealed that bacterial abundance and diversity were mainly influenced by soil water content, soil organic matter, and total nitrogen.

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