Bacterial communities of the rhizosphere and endorhiza associated with field-grown cucumber plants inoculated with a plant growth-promoting rhizobacterium or its genetically modified derivative

1997 ◽  
Vol 43 (4) ◽  
pp. 344-353 ◽  
Author(s):  
W. F. Mahaffee ◽  
J. W. Kloepper
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Genetically Modified ◽  
Acid Methyl Ester ◽  
Wild Type ◽  
Natural Ecosystems ◽  
Genus Level ◽  
Plant Growth Promoting ◽  
The Impact

The future use of genetically modified microorganisms in the environment will be dependent on the ability to assess potential or theoretical risks associated with their introduction into natural ecosystems. To assess potential risks, several ecological parameters must be examined, including the impact of the introduced genetically modified organism on the microbial communities associated with the environment into which the introduction will occur. A 2-year field study was established to examine whether the indigenous bacterial communities of the rhizosphere and endorhiza (internal root tissues) were affected differently by the introduction of an unaltered wild type and its genetically modified derivative. Treatments consisted of the wild-type strain Pseudomonas fluorescens 89B-27 and a bioluminescent derivative GEM-8 (89B-27::Tn4431). Cucumber root or seed samples were taken 0, 7, 14, 21, 35, and 70 days after planting (DAP) in 1994 and 0, 7, 14, 28, 42, and 70 DAP in 1995. Samples were processed to examine the bacterial communities of both the rhizosphere and endorhiza. Over 7200 bacterial colonies were isolated from the rhizosphere and endorhiza and identified using the Sherlock System (Microbial ID, Inc.) for fatty acid methyl ester analysis. Community structure at the genus level was assessed using genera richness and Hill's diversity numbers, N1 and N2. The aerobic–heterotrophic bacterial community structure at the genus level did not significantly vary between treatments but did differ temporally. The data indicate that the introduction of the genetically modified derivative of 89B-27 did not pose a greater environmental risk than its unaltered wild type with respect to aerobic–heterotrophic bacterial community structure.Key words: diversity, ecology, PGPR, Pseudomonas, root colonizaton, GEM.

scholarly journals Biofilm Bacterial Community Structure in Streams Affected by Acid Mine Drainage

2009 ◽  
Vol 75 (11) ◽  
pp. 3455-3460 ◽  
Author(s):  
Gavin Lear ◽  
Dev Niyogi ◽  
Jon Harding ◽  
Yimin Dong ◽  
Gillian Lewis
Keyword(s):  
Community Structure ◽  
Acid Mine Drainage ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Mine Drainage ◽  
Iron Hydroxide ◽  
Acidic Ph ◽  
Dissolved Metals ◽  
Acid Mine ◽  
The Impact

ABSTRACT We examined the bacterial communities of epilithic biofilms in 17 streams which represented a gradient ranging from relatively pristine streams to streams highly impacted by acid mine drainage (AMD). A combination of automated ribosomal intergenic spacer analysis with multivariate analysis and ordination provided a sensitive, high-throughput method to monitor the impact of AMD on stream bacterial communities. Significant differences in community structure were detected among neutral to alkaline (pH 6.7 to 8.3), acidic (pH 3.9 to 5.7), and very acidic (pH 2.8 to 3.5) streams. DNA sequence analysis revealed that the acidic streams were generally dominated by bacteria related to the iron-oxidizing genus Gallionella, while the organisms in very acidic streams were less diverse and included a high proportion of acidophilic eukaryotes, including taxa related to the algal genera Navicula and Klebsormidium. Despite the presence of high concentrations of dissolved metals (e.g., Al and Zn) and deposits of iron hydroxide in some of the streams studied, pH was the most important determinant of the observed differences in bacterial community variability. These findings confirm that any restoration activities in such systems must focus on dealing with pH as the first priority.

scholarly journals Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India

2021 ◽  
Author(s):  
Parvathi Ammini ◽  
Michela R Catena ◽  
Jasna Vijayan ◽  
Nikhil Phadke ◽  
Nikhita Gogate
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Salinity Gradient ◽  
Pearson Correlation ◽  
Temporal Variations ◽  
Spatial And Temporal Variation ◽  
Physico Chemical ◽  
The Impact

Abstract In the present study, we analysed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary, CE), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year, to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Statistical analysis indicated significant variations in bacterial communities between freshwater, mesohaline and euryhaline regions, as well as between the monsoon (wet) and non-monsoon (dry) periods. Non-metric multidimensional scaling (NMDS) analysis demonstrated that the bacterial communities cluster according to different salinity regimes of the estuary. Canonical Correspondence analysis (CCA) showed a clear spatial and temporal variation in the distribution of bacterial communities in the CE. Abundance of Betaproteobacteria was high in the freshwater regions, while Gammaproteobacteria, Alphaproteobacteria and Epsilonproteobactera were more abundant in mesohaline and euryhaline regions of the estuary. Correlagram based on Pearson correlation analysis demonstrated the impact of different physico-chemical variables on the distribution of dominant phyla, class and genera. Spatial and temporal variations in bacterial community structure could be due to regional variations in environmental conditions imparted by allochthonous inputs, monsoonal rainfall, and tidal influence.

scholarly journals Free-living Bacterial Communities Are Mostly Dominated by Oligotrophs

2018 ◽  
Author(s):  
Yingnan Gao ◽  
Martin Wu
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Nutrient Availability ◽  
Bacterial Communities ◽  
Copy Number ◽  
Ecological Strategy ◽  
Natural Habitats ◽  
Free Living ◽  
The Impact ◽  
Copiotrophic Bacteria

AbstractIn response to resource availability, bacteria have evolved two distinct ecological strategies. Copiotrophic bacteria grow fast and are heavily favored by selection where the resource is abundant. In contrast, oligotrophic bacteria grow slowly but more efficiently and are highly adaptive in nutrient-poor environments (Koch, 2001). Although oligotrophs and copiotrophs are ubiquitous, except for a few well-characterized environments like the open ocean and animal gut, the relative abundance of oligotrophic and copiotrophic bacteria and their importance in the global ecosystem are still unclear. In addition, although several studies have demonstrated the impact of nutrient availability on the bacterial community structure under experimental conditions (Klappenbach et al., 2000, Nemergut et al., 2016), the role of nutrients in shaping the structures of bacterial communities in their natural habitats remains largely unknown. Using the ribosomal RNA operon (rrn) copy number to capture the bacterial ecological strategy, we analyzed 44,045 samples from two large bacterial community repositories that cover 78 environmental types. Here we show that animal-associated microbiota are dominated by copiotrophs while plant-associated and free-living bacterial communities are mostly dominated by oligotrophs. Our results suggest that nutrient availability plays an important role in determining the structure and ecological strategy of bacterial communities in nature. We demonstrate that the average and distribution of rrn copy number are simple yet robust predictors of the ecological strategy of bacterial communities that can be applied to all sequence-based microbial surveys to link the community structure and function.

scholarly journals The capacity of wastewater treatment plants drives bacterial community structure and its assembly

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Young Kyung Kim ◽  
Keunje Yoo ◽  
Min Sung Kim ◽  
Il Han ◽  
Minjoo Lee ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Activated Sludge ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Wastewater Treatment Plants ◽  
High Capacity ◽  
Operating Conditions ◽  
Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

scholarly journals Effects of Plastic Debris on the Biofilm Bacterial Communities in Lake Water

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1465
Author(s):  
Chao Shen ◽  
Liuyan Huang ◽  
Guangwu Xie ◽  
Yulai Wang ◽  
Zongkai Ma ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Diversity Index ◽  
Plastic Substrate ◽  
Simpson Index ◽  
Plastic Debris ◽  
Plastic Substrates ◽  
Wiener Diversity Index

Increasing discharge of plastic debris into aquatic ecosystems and the worsening ecological risks have received growing attention. Once released, plastic debris could serve as a new substrate for microbes in waters. The complex relationship between plastics and biofilms has aroused great interest. To confirm the hypothesis that the presence of plastic in water affects the composition of biofilm in natural state, in situ biofilm culture experiments were conducted in a lake for 40 days. The diversity of biofilm attached on natural (cobble stones (CS) and wood) and plastic substrates (Polyethylene terephthalate (PET) and Polymethyl methacrylate (PMMA)) were compared, and the community structure and composition were also analyzed. Results from high-throughput sequencing of 16S rRNA showed that the diversity and species richness of biofilm bacterial communities on natural substrate (observed species of 1353~1945, Simpson index of 0.977~0.989 and Shannon–Wiener diversity index of 7.42~8.60) were much higher than those on plastic substrates (observed species of 900~1146, Simpson index of 0.914~0.975 and Shannon–Wiener diversity index of 5.47~6.99). The NMDS analyses were used to confirm the taxonomic significance between different samples, and Anosim (p = 0.001, R = 0.892) and Adonis (p = 0.001, R = 808, F = 11.19) demonstrated that this classification was statistically rigorous. Different dominant bacterial communities were found on plastic and natural substrates. Alphaproteobacterial, Betaproteobacteria and Synechococcophycideae dominated on the plastic substrate, while Gammaproteobacteria, Phycisphaerae and Planctomycetia played the main role on the natural substrates. The bacterial community structure of the two substrates also showed significant difference which is consistent with previous studies using other polymer types. Our results shed light on the fact that plastic debris can serve as a new habitat for biofilm colonization, unlike natural substrates, pathogens and plastic-degrading microorganisms selectively attached to plastic substrates, which affected the bacterial community structure and composition in aquatic environment. This study provided a new insight into understanding the potential impacts of plastics serving as a new habitat for microbial communities in freshwater environments. Future research should focus on the potential impacts of plastic-attached biofilms in various aquatic environments and the whole life cycle of plastics (i.e., from plastic fragments to microplastics) and also microbial flock characteristics using microbial plastics in the natural environment should also be addressed.

Tu1716 Evaluation of the Impact of Different Commercially Available DNA Extraction Kits and Laboratories for Assessing Bacterial Community Structure in Fecal Samples - Implications for IBD Research

2013 ◽  
Vol 144 (5) ◽  
pp. S-829
Author(s):  
Nicholas A. Kennedy ◽  
Alan Walker ◽  
UK IBD Microbiota Consortia ◽  
UK IBD Genetics Consortia ◽  
Susan H. Berry ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Dna Extraction ◽  
Bacterial Community Structure ◽  
Fecal Samples ◽  
The Impact

scholarly journals Significant Differences in the Gut Bacterial Communities of Hooded Crane (Grus monacha) in Different Seasons at a Stopover Site on the Flyway

Animals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 701 ◽  
Author(s):  
Fengling Zhang ◽  
Xingjia Xiang ◽  
Yuanqiu Dong ◽  
Shaofei Yan ◽  
Yunwei Song ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Bacterial Community Composition ◽  
Stopover Site ◽  
Intestinal Bacterial Community ◽  
Hooded Crane ◽  
Grus Monacha

Intestinal bacterial communities form an integral component of the organism. Many factors influence gut bacterial community composition and diversity, including diet, environment and seasonality. During seasonal migration, birds use many habitats and food resources, which may influence their intestinal bacterial community structure. Hooded crane (Grus monacha) is a migrant waterbird that traverses long distances and occupies varied habitats. In this study, we investigated the diversity and differences in intestinal bacterial communities of hooded cranes over the migratory seasons. Fecal samples from hooded cranes were collected at a stopover site in two seasons (spring and fall) in Lindian, China, and at a wintering ground in Shengjin Lake, China. We analyzed bacterial communities from the fecal samples using high throughput sequencing (Illumina Mi-seq). Firmicutes, Proteobacteria, Tenericutes, Cyanobacteria, and Actinobacteria were the dominant phyla across all samples. The intestinal bacterial alpha-diversity of hooded cranes in winter was significantly higher than in fall and spring. The bacterial community composition significantly differed across the three seasons (ANOSIM, P = 0.001), suggesting that seasonal fluctuations may regulate the gut bacterial community composition of migratory birds. This study provides baseline information on the seasonal dynamics of intestinal bacterial community structure in migratory hooded cranes.

scholarly journals Regulating soil bacterial diversity, community structure and enzyme activity using residues from golden apple snails

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jiaxin Wang ◽  
Xuening Lu ◽  
Jiaen Zhang ◽  
Guangchang Wei ◽  
Yue Xiong
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Soil Nutrients ◽  
Pomacea Canaliculata ◽  
Soil Bacterial Diversity ◽  
Amended Soils ◽  
Soil Bacterial ◽  
The Impact ◽  
Amended Soil

Abstract It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28–7.75) and nutrient-enriched soil, with amendment of 2.5–100 g kg−1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132–912%), and some soil exocellular enzyme activities were enhanced (by 2–98%) in GAS residue amended soil, with amendment of 1.0–100 g kg−1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg−1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg−1 of GAS residue and 50 g kg−1 of lime amended soils, respectively. Firmicutes (15–35%) was the most abundant phylum while Bacterioidetes (1–6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.

scholarly journals Comparative analysis of the composition of bacterial communities from two constructed wetlands for municipal and swine wastewater treatment

2009 ◽  
Vol 8 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Paula Arroyo ◽  
Gemma Ansola ◽  
Ivan Blanco ◽  
Patricia Molleda ◽  
Estanislao de Luis Calabuig ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Bacterial Community Structure ◽  
Typha Latifolia ◽  
Treatment System ◽  
Swine Wastewater ◽  
Wastewater Treatment System ◽  
Wastewater Treatment Systems

This work provides information about bacterial community structure in natural wastewater treatment systems treating different types of wastewater. The diversity and composition of bacterial communities associated with the rhizosphere of Typha latifolia and Salix atrocinerea were studied and compared among two different natural wastewater treatment systems, using the direct sequencing of the 16S ribosomal RNA codifying genes. Phylogenetic affiliations of the bacteria detected allowed us to define the main groups present in these particular ecosystems. Moreover, bacterial community structure was studied through two diversity indices. Ten identified and five non-identified phyla were found in the samples; the phylum Proteobacteria was the predominant group in the four ecosystems. The results showed a bacterial community dominated by beta-proteobacteria and a lower diversity value in the swine wastewater treatment system. The municipal wastewater treatment system presented a high diverse community in both macrophytes (Typha latifolia and Salix atrocinerea), with gamma-proteobacteria and alpha-proteobacteria, respectively, as the most abundant groups.

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