Bacterial community structure and denitrifier (nir-gene) abundance in soil water and groundwater beneath agricultural land in tropical North Queensland, Australia

Soil Research ◽  
2011 ◽  
Vol 49 (1) ◽  
pp. 65 ◽  
Author(s):  
Steven A. Wakelin ◽  
Paul N. Nelson ◽  
John D. Armour ◽  
Velupillai Rasiah ◽  
Matthew J. Colloff
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Soil Water ◽  
Water Samples ◽  
Bacterial Community Structure ◽  
Management Practices ◽  
Agricultural Land ◽  
Rrna Gene ◽  
Gene Abundance ◽  
Copy Numbers

We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05), particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P < 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NO-forming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater discharges lower in the GBR catchment zones.

scholarly journals Bacterial Community Structure and Diversity in a Century-Old Manure-Treated Agroecosystem

2004 ◽  
Vol 70 (10) ◽  
pp. 5868-5874 ◽  
Author(s):  
H. Y. Sun ◽  
S. P. Deng ◽  
W. R. Raun
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Management Practices ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
Lime Treatment ◽  
Soil Microbial Community Structure ◽  
Treated Soil

ABSTRACT Changes in soil microbial community structure and diversity may reflect environmental impact. We examined 16S rRNA gene fingerprints of bacterial communities in six agroecosystems by PCR amplification and denaturing gradient gel electrophoresis (PCR-DGGE) separation. These soils were treated with manure for over a century or different fertilizers for over 70 years. Bacterial community structure and diversity were affected by soil management practices, as evidenced by changes in the PCR-DGGE banding patterns. Bacterial community structure in the manure-treated soil was more closely related to the structure in the untreated soil than that in soils treated with inorganic fertilizers. Lime treatment had little effect on bacterial community structure. Soils treated with P and N-P had bacterial community structures more closely related to each other than to those of soils given other treatments. Among the soils tested, a significantly higher number of bacterial ribotypes and a more even distribution of the bacterial community existed in the manure-treated soil. Of the 99 clones obtained from the soil treated with manure for over a century, two (both Pseudomonas spp.) exhibited 100% similarity to sequences in the GenBank database. Two of the clones were possible chimeras. Based on similarity matching, the remaining 97 clones formed six major clusters. Fifty-six out of 97 were assigned taxonomic units which grouped into five major taxa: α-, β-, and γ-Proteobacteria (36 clones), Acidobacteria (16 clones), Bacteroidetes (2 clones), Nitrospirae (1 clone), and Firmicutes (1 clone). Forty-one clones remained unclassified. Results from this study suggested that bacterial community structure was closely related to agroecosystem management practices conducted for over 70 years.

scholarly journals The root endophytic bacterial community of Ricinus communis L. resembles the seeds community more than the rhizosphere bacteria independent of soil water content

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Stephanie E. Hereira-Pacheco ◽  
Yendi E. Navarro-Noya ◽  
Luc Dendooven
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Water Content ◽  
Soil Water ◽  
Soil Water Content ◽  
Plant Development ◽  
Bacterial Community Structure ◽  
Ricinus Communis ◽  
Ricinus Communis L ◽  
Endophytic Bacterial Community

AbstractRhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.

scholarly journals Both Leaf Properties and Microbe-Microbe Interactions Influence Within-Species Variation in Bacterial Population Diversity and Structure in the Lettuce (Lactuca Species) Phyllosphere

2010 ◽  
Vol 76 (24) ◽  
pp. 8117-8125 ◽  
Author(s):  
Paul J. Hunter ◽  
Paul Hand ◽  
David Pink ◽  
John M. Whipps ◽  
Gary D. Bending
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Population Diversity ◽  
Microbial Interactions ◽  
Soluble Carbohydrates ◽  
Rrna Gene ◽  
Species Variation ◽  
Clone Libraries ◽  
Microbe Interactions

ABSTRACT Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.

Characterization of bacterial community structure dynamics in a rat burn wound model using 16S rRNA gene sequencing

2022 ◽  
Author(s):  
Chen Zheng-li ◽  
Peng Yu ◽  
Wu Guo-sheng ◽  
Hong Xu-Dong ◽  
Fan Hao ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Community Structure ◽  
Bacterial Species ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Sprague Dawley ◽  
Rrna Gene Sequencing

Abstract Burns destroy the skin barrier and alter the resident bacterial community, thereby facilitating bacterial infection. To treat a wound infection, it is necessary to understand the changes in the wound bacterial community structure. However, traditional bacterial cultures allow the identification of only readily growing or purposely cultured bacterial species and lack the capacity to detect changes in the bacterial community. In this study, 16S rRNA gene sequencing was used to detect alterations in the bacterial community structure in deep partial-thickness burn wounds on the back of Sprague-Dawley rats. These results were then compared with those obtained from the bacterial culture. Bacterial samples were collected prior to wounding and 1, 7, 14, and 21 days after wounding. The 16S rRNA gene sequence analysis showed that the number of resident bacterial species decreased after the burn. Both resident bacterial richness and diversity, which were significantly reduced after the burn, recovered following wound healing. The dominant resident strains also changed, but the inhibition of bacterial community structure was in a non-volatile equilibrium state, even in the early stage after healing. Furthermore, the correlation between wound and environmental bacteria increased with the occurrence of burns. Hence, the 16S rRNA gene sequence analysis reflected the bacterial condition of the wounds better than the bacterial culture. 16S rRNA sequencing in the Sprague-Dawley rat burn model can provide more information for the prevention and treatment of burn infections in clinical settings and promote further development in this field.

Changes in Bacterial Community Structure of Agricultural Land Due to Long-Term Organic and Chemical Amendments

2012 ◽  
Vol 64 (2) ◽  
pp. 450-460 ◽  
Author(s):  
Vasvi Chaudhry ◽  
Ateequr Rehman ◽  
Aradhana Mishra ◽  
Puneet Singh Chauhan ◽  
Chandra Shekhar Nautiyal
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Agricultural Land
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