scholarly journals Molecular characterization of bacterial diversity in New Zealand groundwater

2021 ◽  
Author(s):  
◽  
Katugampalage Kosala Ayantha Sirisena
Keyword(s):  
Community Structure ◽  
New Zealand ◽  
Bacterial Diversity ◽  
Groundwater Monitoring ◽  
Genetic Material ◽  
Illumina Miseq ◽  
Abundant Species ◽  
Diverse Range ◽  
Pseudomonas Spp ◽  
Groundwater Ecosystems

<p>Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and availability of groundwater are both extensively monitored in New Zealand and globally, under State-of-the-Environment (SOE) monitoring programmes. SOE groundwater monitoring in New Zealand mainly evaluates hydrochemistry and until this thesis has largely overlooked the biotic component. Microbes including bacteria play a crucial role in ecosystem functioning by mediating biogeochemical processes in subsurface environments. Therefore, analysis of microbiological content will enable better evaluation of the health of groundwater ecosystems that is not fully reflected by chemical data alone. This project characterizes the bacterial diversity in New Zealand groundwater at national and regional scales using molecular methods and explores the underlying factors that shape the bacterial community structure. A simple molecular profiling tool, Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine community structure at local and national scales. The results revealed considerable diversity that was driven by groundwater chemistry. Roche 454-pyrosequencing was then used to obtain a deeper insight into New Zealand groundwater ecosystems, and showed that bacterial communities have many low abundance taxa and relatively few highly abundant species. In addition, microbial diversity is mainly related to the redox potential of the groundwater. But, despite this relationship, Pseudomonas spp. were the dominant genus at many sites even those with diverse chemistries and environmental factors. The final phase of the project set the platform to test whether these Pseudomonas spp. have acquired genetic material from other species via horizontal gene transfer (HGT) enabling them to adapt into a diverse range of habitats. A whole-genome sequencing approach (Illumina MiSeq platform) was used to develop six metagenomic databases as a resource to test this hypothesis. Initial results show some evidence for HGT and further investigations are underway. Overall, the knowledge generated across all phases of this project provides novel insights into New Zealand groundwater ecosystems and creates a scientific basis for the future inclusion of microbial status assessment criteria into regional and national groundwater monitoring programmes and related policies in New Zealand.</p>

scholarly journals Molecular characterization of bacterial diversity in New Zealand groundwater

2021 ◽  
Author(s):  
◽  
Katugampalage Kosala Ayantha Sirisena
Keyword(s):  
Community Structure ◽  
New Zealand ◽  
Bacterial Diversity ◽  
Groundwater Monitoring ◽  
Genetic Material ◽  
Illumina Miseq ◽  
Abundant Species ◽  
Diverse Range ◽  
Pseudomonas Spp ◽  
Groundwater Ecosystems

<p>Groundwater is a globally important natural resource and an integral part of the water supply in New Zealand. Due to high demand, the quality and availability of groundwater are both extensively monitored in New Zealand and globally, under State-of-the-Environment (SOE) monitoring programmes. SOE groundwater monitoring in New Zealand mainly evaluates hydrochemistry and until this thesis has largely overlooked the biotic component. Microbes including bacteria play a crucial role in ecosystem functioning by mediating biogeochemical processes in subsurface environments. Therefore, analysis of microbiological content will enable better evaluation of the health of groundwater ecosystems that is not fully reflected by chemical data alone. This project characterizes the bacterial diversity in New Zealand groundwater at national and regional scales using molecular methods and explores the underlying factors that shape the bacterial community structure. A simple molecular profiling tool, Terminal Restriction Fragment Length Polymorphism (T-RFLP) was used to determine community structure at local and national scales. The results revealed considerable diversity that was driven by groundwater chemistry. Roche 454-pyrosequencing was then used to obtain a deeper insight into New Zealand groundwater ecosystems, and showed that bacterial communities have many low abundance taxa and relatively few highly abundant species. In addition, microbial diversity is mainly related to the redox potential of the groundwater. But, despite this relationship, Pseudomonas spp. were the dominant genus at many sites even those with diverse chemistries and environmental factors. The final phase of the project set the platform to test whether these Pseudomonas spp. have acquired genetic material from other species via horizontal gene transfer (HGT) enabling them to adapt into a diverse range of habitats. A whole-genome sequencing approach (Illumina MiSeq platform) was used to develop six metagenomic databases as a resource to test this hypothesis. Initial results show some evidence for HGT and further investigations are underway. Overall, the knowledge generated across all phases of this project provides novel insights into New Zealand groundwater ecosystems and creates a scientific basis for the future inclusion of microbial status assessment criteria into regional and national groundwater monitoring programmes and related policies in New Zealand.</p>

scholarly journals The Aromatic Plant Clary Sage Shaped Bacterial Communities in the Roots and in the Trace Element-Contaminated Soil More Than Mycorrhizal Inoculation – A Two-Year Monitoring Field Trial

2020 ◽  
Vol 11 ◽  
Author(s):  
Robin Raveau ◽  
Joël Fontaine ◽  
Mohamed Hijri ◽  
Anissa Lounès-Hadj Sahraoui
Keyword(s):  
Community Structure ◽  
Bacterial Diversity ◽  
Contaminated Soil ◽  
Mycorrhizal Fungi ◽  
Agricultural Soils ◽  
Illumina Miseq ◽  
Added Value ◽  
Rrna Gene ◽  
Aromatic Plants ◽  
Mycorrhizal Inoculation

To cope with soil contamination by trace elements (TE), phytomanagement has attracted much attention as being an eco-friendly and cost-effective green approach. In this context, aromatic plants could represent a good option not only to immobilize TE, but also to use their biomass to extract essential oils, resulting in high added-value products suitable for non-food valorization. However, the influence of aromatic plants cultivation on the bacterial community structure and functioning in the rhizosphere microbiota remains unknown. Thus, the present study aims at determining in TE-aged contaminated soil (Pb – 394 ppm, Zn – 443 ppm, and Cd – 7ppm, respectively, 11, 6, and 17 times higher than the ordinary amounts in regional agricultural soils) the effects of perennial clary sage (Salvia sclarea L.) cultivation, during two successive years of growth and inoculated with arbuscular mycorrhizal fungi, on rhizosphere bacterial diversity and community structure. Illumina MiSeq amplicon sequencing targeting bacterial 16S rRNA gene was used to assess bacterial diversity and community structure changes. Bioinformatic analysis of sequencing datasets resulted in 4691 and 2728 bacterial Amplicon Sequence Variants (ASVs) in soil and root biotopes, respectively. Our findings have shown that the cultivation of clary sage displayed a significant year-to-year effect, on both bacterial richness and community structures. We found that the abundance of plant-growth promoting rhizobacteria significantly increased in roots during the second growing season. However, we didn’t observe any significant effect of mycorrhizal inoculation neither on bacterial diversity nor on community structure. Our study brings new evidence in TE-contaminated areas of the effect of a vegetation cover with clary sage cultivation on the microbial soil functioning.

Allelopathic and Medicinal plant. 26. Millettia speciosa

2020 ◽  
Vol 51 (2) ◽  
pp. 125-146
Author(s):  
Nasiruddin Nasiruddin ◽  
Yu Zhangxin ◽  
Ting Zhao Chen Guangying ◽  
Minghui Ji
Keyword(s):  
Community Structure ◽  
Medicinal Plant ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Wiener Index ◽  
Pseudomonas Spp ◽  
Evenness Index ◽  
Gradient Gel Electrophoresis ◽  
Rhizosphere Pseudomonas

We grew cucumber in pots in greenhouse for 9-successive cropping cycles and analyzed the rhizosphere Pseudomonas spp. community structure and abundance by PCR-denaturing gradient gel electrophoresis and quantitative PCR. Results showed that continuous monocropping changed the cucumber rhizosphere Pseudomonas spp. community. The number of DGGE bands, Shannon-Wiener index and Evenness index decreased during the 3rd cropping and thereafter, increased up to the 7th cropping, however, however, afterwards they decreased again. The abundance of Pseudomonas spp. increased up to the 5th successive cropping and then decreased gradually. These findings indicated that the structure and abundance of Pseudomonas spp. community changed with long-term cucumber monocropping, which might be linked to soil sickness caused by its continuous monocropping.

scholarly journals Spatial and Temporal Variation in Microbial Diversity and Community Structure in a Contaminated Mangrove Wetland

2020 ◽  
Vol 10 (17) ◽  
pp. 5850
Author(s):  
Jiaojiao Ma ◽  
Ting Zhou ◽  
Chunyu Xu ◽  
Dawen Shen ◽  
Songjun Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Spatial Variation ◽  
Temporal Variation ◽  
Bacterial Diversity ◽  
Diversity Index ◽  
Total Carbon ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Mangrove Wetland ◽  
Mangrove Soils

Field and laboratory investigations were conducted to characterize bacterial diversity and community structure in a badly contaminated mangrove wetland adjacent to the metropolitan area of a megacity in subtropical China. Next-generation sequencing technique was used for sequencing the V4–V5 region of the 16s rRNA gene on the Illumina system. Collectively, Proteobacteria, Chloroflexi, Planctomycetes, Actinobacteria and Bacteroidetes were the predominant phyla identified in the investigated soils. A significant spatial variation in bacterial diversity and community structure was observed for the investigated mangrove soils. Heavy metal pollution played a key role in reducing the bacterial diversity. The spatial variation in soil-borne heavy metals shaped the spatial variation in bacterial diversity and community structure in the study area. Other environmental factors such as total carbon and total nitrogen in the soils that are affected by seasonal change in temperature could also influence the bacterial abundance, diversity and community structure though the temporal variation was relatively weaker, as compared to spatial variation. The bacterial diversity index was lower in the investigated site than in the comparable reference site with less contaminated status. The community structure in mangrove soils at the current study site was, to a remarkable extent, different from those in the tropical mangrove wetlands around the world.

Temporal and spatial variability in the community structure of the fauna of four sandy beaches in south-eastern New South Wales.

1984 ◽  
Vol 35 (6) ◽  
pp. 663 ◽  
Author(s):  
DM Dexter
Keyword(s):  
Community Structure ◽  
Diversity Index ◽  
Abundant Species ◽  
Sandy Beaches ◽  
Sampling Procedure ◽  
Wave Action ◽  
Physical Factors ◽  
Faunal Composition ◽  
South Wales ◽  
Temporal And Spatial

Four intertidal sandy beaches with different exposures, La Perouse, Ocean Beach, Dolls Point, and Towra Point, were studied for temporal and spatial changes in faunal composition and community structure. Each of these beaches was sampled from 6 to 12 times between July 1980 and July 1981 using a 500 �m sieve. A stratified random sampling procedure across the intertidal zone isolated 40 660 individuals representing 85 species. Distribution and abundance of species were strongly influenced by tidal level. Densities changed during the year but no seasonal changes in intertidal zonation patterns were found. Changes in density were correlated with the reproductive activities of the abundant species, especially Pseudolana concinna and Exoediceros maculosus at La Perouse, and Spio pacifica at Dolls Point and Towra Point. The number of species increased from high to low tide, and also increased with decreasing exposure to wave action. Crustaceans dominated the fauna in the most exposed site and decreased in abundance with increasing protection. Ocean Beach experienced the least fluctuation in physical factors such as wave action, salinity, and temperature, and its fauna exhibited the highest diversity index (H') and evenness (J'), the most stable density, and the greatest stability in faunal composition through time. The highest densities and the most species were found at Towra Point, which also was the most protected site.

Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

2016 ◽  
Vol 66 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Weining Sun ◽  
Huazhi Xiao ◽  
Qian Peng ◽  
Qiaoge Zhang ◽  
Xingxing Li ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Different Seasons

scholarly journals Interaction between typical sulfonamides and bacterial diversity in drinking water

2018 ◽  
Vol 16 (6) ◽  
pp. 914-920 ◽  
Author(s):  
Qing Wu ◽  
Shuqun Li ◽  
Xiaofei Zhao ◽  
Xinhua Zhao
Keyword(s):  
Drinking Water ◽  
Community Structure ◽  
Microbial Community ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Microbial Community Structure ◽  
Antibiotic Use ◽  
Community Diversity ◽  
Wide Range ◽  
Growth Of Bacteria

Abstract The abuse of antibiotics is becoming more serious as antibiotic use has increased. The sulfa antibiotics, sulfamerazine (SM1) and sulfamethoxazole (SMZ), are frequently detected in a wide range of environments. The interaction between SM1/SMZ and bacterial diversity in drinking water was investigated in this study. The results showed that after treatment with SM1 or SMZ at four different concentrations, the microbial community structure of the drinking water changed statistically significantly compared to the blank sample. At the genus level, the proportions of the different bacteria in drinking water may affect the degradation of the SM1/SMZ. The growth of bacteria in drinking water can be inhibited after the addition of SM1/SMZ, and bacterial community diversity in drinking water declined in this study. Furthermore, the resistance gene sul2 was induced by SM1 in the drinking water.

scholarly journals Contrasting recruitment seasonality of sea urchin species in Gran Canaria, Canary Islands (eastern Atlantic)

2014 ◽  
Vol 15 (3) ◽  
pp. 475 ◽  
Author(s):  
S. GARCIA-SANZ ◽  
P. G. NAVARRO ◽  
F. TUYA
Keyword(s):  
Community Structure ◽  
Seasonal Variation ◽  
Sea Urchin ◽  
Sea Urchins ◽  
Late Summer ◽  
Paracentrotus Lividus ◽  
Abundant Species ◽  
Late Winter ◽  
Gran Canaria ◽  
Arbacia Lixula

Despite sea-urchins can play an important role affecting the community structure of subtidal bottoms, factors controlling the dynamics of sea-urchin populations are still poorly understood. We assessed the seasonal variation in recruitment of three sea-urchin species (Diadema africanum, Paracentrotus lividus and Arbacia lixula) at Gran Canaria Island (eastern Atlantic) via monthly deployment of artificial collectors throughout an entire annual cycle on each of four adjacent habitat patches (seagrasses, sandy patches, ‘urchin-grazed’ barrens and macroalgal-dominated beds) within a shallow coastal landscape. Paracentrotus lividus and A. lixula had exclusively one main recruitment peak in late winter-spring. Diadema africanum recruitment was also seasonal, but recruits appeared in late summer-autumn, particularly on ‘urchin-grazed’ barrens with large abundances of adult conspecifics. In conclusion, this study has demonstrated non-overlapping seasonal recruitment patterns of the less abundant species (P. lividus and A. lixula) with the most conspicuous species (D. africanum) in the study area.

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