scholarly journals Native and invading yellow starthistle (Centaurea solstitialis) microbiomes differ in composition and diversity of bacteria

2017 ◽  
Author(s):  
Patricia Lu-Irving ◽  
Julia Harenčár ◽  
Hailey Sounart ◽  
Shana R Welles ◽  
Sarah M Swope ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Plant Pathogens ◽  
Bacterial Community Composition ◽  
Microbial Interactions ◽  
Invasion Success ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
List Type ◽  
Plant Genotype ◽  
Yellow Starthistle

SUMMARYInvasive species could benefit from introduction to locations with favorable species interactions. Microbiomes are an important source of interactions that vary across regions. We examine whether bacterial communities could explain more favorable microbial interactions in highly invasive populations of yellow starthistle.We sequenced amplicons of prokaryotic 16S rRNA genes to characterize bacterial community composition in the phyllosphere, ectorhizosphere, and endorhizosphere of plants from seven invading populations in California, USA and eight native populations in Europe. We tested for differentiation of microbiomes by geography, plant compartment, and plant genotype.Bacterial communities differed significantly between native and invaded ranges within plant compartments, with consistently lower diversity in plants from the invaded range. Genera containing known plant pathogens also showed lower diversity in invaded range plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbial differences between ranges.Our findings reveal changes in the composition and diversity of bacterial interactions in invading plants, consistent with observations of altered soil interactions in this invasion. These results call for further study of the sources of variation in microbiomes and the potential for bacteria to facilitate invasion success.

scholarly journals Native and Invading Yellow Starthistle (Centaurea solstitialis) Microbiomes Differ in Composition and Diversity of Bacteria

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Patricia Lu-Irving ◽  
Julia G. Harenčár ◽  
Hailey Sounart ◽  
Shana R. Welles ◽  
Sarah M. Swope ◽  
...  
Keyword(s):  
Species Interactions ◽  
Invasive Plant ◽  
Microbial Interactions ◽  
Invasion Success ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Centaurea Solstitialis ◽  
Plant Genotype ◽  
Yellow Starthistle ◽  
Content Type

ABSTRACTInvasive species could benefit from being introduced to locations with more favorable species interactions, including the loss of enemies, the gain of mutualists, or the simplification of complex interaction networks. Microbiomes are an important source of species interactions with strong fitness effects on multicellular organisms, and these interactions are known to vary across regions. The highly invasive plant yellow starthistle (Centaurea solstitialis) has been shown to experience more favorable microbial interactions in its invasions of the Americas, but the microbiome that must contribute to this variation in interactions is unknown. We sequenced amplicons of 16S rRNA genes to characterize bacterial community compositions in the phyllosphere, ectorhizosphere, and endorhizosphere of yellow starthistle plants from seven invading populations in California, USA, and eight native populations in Europe. We tested for the differentiation of microbiomes by geography, plant compartment, and plant genotype. Bacterial communities differed significantly between native and invading plants within plant compartments, with consistently lower diversity in the microbiome of invading plants. The diversity of bacteria in roots was positively correlated with plant genotype diversity within both ranges, but this relationship did not explain microbiome differences between ranges. Our results reveal that these invading plants are experiencing either a simplified microbial environment or simplified microbial interactions as a result of the dominance of a few taxa within their microbiome. Our findings highlight several alternative hypotheses for the sources of variation that we observe in invader microbiomes and the potential for altered bacterial interactions to facilitate invasion success.IMPORTANCEPrevious studies have found that introduced plants commonly experience more favorable microbial interactions in their non-native range, suggesting that changes to the microbiome could be an important contributor to invasion success. Little is known about microbiome variation across native and invading populations, however, and the potential sources of more favorable interactions are undescribed. Here, we report one of the first microbiome comparisons of plants from multiple native and invading populations, in the noxious weed yellow starthistle. We identify clear differences in composition and diversity of microbiome bacteria. Our findings raise new questions about the sources of these differences, and we outline the next generation of research that will be required to connect microbiome variation to its potential role in plant invasions.

Bacterial communities in Antarctic lichens

2016 ◽  
Vol 28 (6) ◽  
pp. 455-461 ◽  
Author(s):  
Chae Haeng Park ◽  
Kyung Mo Kim ◽  
Ok-Sun Kim ◽  
Gajin Jeong ◽  
Soon Gyu Hong
Keyword(s):  
Bacterial Communities ◽  
Growth Form ◽  
Bacterial Community Composition ◽  
Low Frequency ◽  
Distance Matrix ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Unifrac Distance ◽  
Microbial Community Structures ◽  
Crustose Lichens

AbstractTo date, many studies surveying the bacterial communities in lichen thalli from diverse geographical areas have shown that Alphaproteobacteria is the predominant bacterial class in most lichens. In this study, bacterial communities in several Antarctic lichens with different growth form and substrates were analysed. The bacterial community composition in fruticose and foliose lichens, Cladonia, Umbilicaria and Usnea, and crustose lichens, Buelia granulosa, Amandinea coniops and Ochrolechia parella, from King George Island was analysed by pyrosequencing of bacterial 16S rRNA genes. Results showed that Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes were predominant phyla. The predominant bacterial class in most of the samples was Alphaproteobacteria. Acetobacteriaceae of the order Rhodospiralles in Alphaproteobacteria was the most abundant bacterial family in Antarctic lichens. The LAR1 lineage of the order Rhizobiales, a putative N-fixer which has been frequently observed in lichens from temperate areas, was detected only from a few samples at low frequency. It is expected that other bacterial taxa are working as N-fixers in Antarctic lichens. From the PCoA analysis of the Fast UniFrac distance matrix, it was proposed that the microbial community structures in Antarctic lichens were affected by host species, growth form and substrates.

scholarly journals ENDOPHYTES: STRUCTURAL AND FUNCTIONAL DIVERSITY AND BIOTECHNOLOGICAL APPLICATIONS IN CONTROL OF PLANT PATHOGENS

2008 ◽  
Vol 6 (2) ◽  
pp. 17-26 ◽  
Author(s):  
Gabriele Berg ◽  
Henry M?ller ◽  
Christin Zachow ◽  
Katja Opelt ◽  
Katja Scherwinski ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Endophytic Bacteria ◽  
Host Plants ◽  
Plant Pathogens ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Serratia Plymuthica ◽  
In Situ Conditions ◽  
Antagonistic Potential

Endophytes are an interesting group of plant-associated bacteria that live inside plants and show neutral or beneficial interaction with their host plants. The structure of bacterial communities in endophytic microenvironments of important crops (different cultivars of potato, lettuce, and sugar beet) and native plants (different bryophyte species) was analyzed by a multiphasic approach at different field sites in Europe. Interestingly, results of the cultivation-independent approaches using Single-Strand Conformation Polymorphism (SSCP) and/or Terminal Restriction Fragments Length Polymorphism (T-RFLP) of 16S rRNA genes amplified by universal as well as group-specific and functional primers revealed a high diversity and specificity of endophytic bacterial communities. The antagonistic potential of endophytic bacteria, which was determined by screening for in vitro antagonism against different pathogens (bacteria, fungi, protists, and nematodes) ranged from 5 to 43 %. An impressive, phylogenetically diverse spectrum of antagonistic strains was found. The indigenous antagonistic potential of endophytic bacteria was influenced by the plant genotype and developmental stage, the internal microenvironment, and the soil type. A screening strategy for biocontrol strains resulted in the selection of promising candidates. These strains were evaluated in greenhouse and field trials regarding their efficiency to control pathogens under in situ conditions. One product (RhizoStar®) on the basis of serratia plymuthica HRO-C48 to control Verticillium wilt on different host plants was developed. For other promising candidates likePseudomonas trivialis 3Re2-7 (B3) and serratia plymuthica 3Re4-18 (B4) a biological control strategy against the soil-borne pathogen Rhizoctonia solani will be established. These studies were funded by the Deutsche Forschungs-gemeinschaft, the Ministry of Consumer Protection, Food and Agriculture (Germany) and by private industries (KWS SAAT AG, Strawberry farm Rovershagen, and Nor-ddeutsche Pflanzenzucht Hans-Georg Lembke KG, Ho-henlieth, Germany) by grants to G.B.

Impacts of different salinities on bacterial biofilm communities in fresh water

2014 ◽  
Vol 60 (5) ◽  
pp. 319-326 ◽  
Author(s):  
Lei Zhang ◽  
Guang Gao ◽  
Xiangming Tang ◽  
Keqiang Shao
Keyword(s):  
Fresh Water ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Bacterial Biofilm ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Biofilms ◽  
Biofilm Growth ◽  
Metabolic Characteristics ◽  
Attached Bacteria

Natural and anthropogenic salinization continuously impacts inland aquatic ecosystems. Associated bacterial biofilms respond rapidly to environmental conditions and are potential bioindicators for changes in water quality. This study evaluates the effects of different salinity concentrations (0.3‰–10‰) on bacterial biofilms communities grown in fresh water from Lake Bosten. Bacterial communities associated with biofilms were analyzed using terminal restriction fragment length polymorphism and clone library analyses of 16S rRNA genes. Results indicated that the attached bacterial community composition (ABCC) changed over several weeks of biofilm growth, but all followed similar bacterial successional trends in the different salinity groups. Detailed analysis showed the following. (i) ABCC did not differ (P > 0.05) in the low-salinity groups (0.3‰–3.5‰), which may be related to the lower osmotic pressure and the shorter time scale (weeks) of their present habitats. (ii) There were significant differences between the oligosaline (3.5‰) and saline (10‰) groups (P < 0.05). In particular, genus Flavobacterium became dominant in attached bacterial communities in the saline groups. The higher abundance of genus Flavobacterium was possibly due to the biological and metabolic characteristics of the bacteria. (iii) Some bacterial taxa can maintain the higher abundance within attached bacteria in the entire process of biofilms growth, such as the genera Hydrogenophaga and Methyloversatilis in Betaproteobacteria and the family Sphingomonadaceae in Alphaproteobacteria. These data suggested that the bacterial successional trends within biofilms seem almost unaffected by salinity (0.3‰–10‰), but ABCC in saline groups (10‰) are notably changed.

scholarly journals Links between Plant and Rhizoplane Bacterial Communities in Grassland Soils, Characterized Using Molecular Techniques

2005 ◽  
Vol 71 (11) ◽  
pp. 6784-6792 ◽  
Author(s):  
Naoise Nunan ◽  
Timothy J. Daniell ◽  
Brajesh K. Singh ◽  
Artemis Papert ◽  
James W. McNicol ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Plant Species ◽  
Bacterial Communities ◽  
Rhizosphere Soil ◽  
Bacterial Community Composition ◽  
Molecular Techniques ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Grassland Soils

ABSTRACT Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed “bulk” rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

scholarly journals Airborne Bacterial Community Composition According to Their Origin in Tenerife, Canary Islands

2021 ◽  
Vol 12 ◽  
Author(s):  
Cristina González-Martín ◽  
Carlos J. Pérez-González ◽  
Elena González-Toril ◽  
Francisco J. Expósito ◽  
Ángeles Aguilera ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Urban Site ◽  
High Mountain ◽  
Microbial Composition ◽  
Back Trajectories ◽  
Air Masses

Microorganisms are ubiquitous in the environment, and the atmosphere is no exception. However, airborne bacterial communities are some of the least studied. Increasing our knowledge about these communities and how environmental factors shape them is key to understanding disease outbreaks and transmission routes. We describe airborne bacterial communities at two different sites in Tenerife, La Laguna (urban, 600 m.a.s.l.) and Izaña (high mountain, 2,400 m.a.s.l.), and how they change throughout the year. Illumina MiSeq sequencing was used to target 16S rRNA genes in 293 samples. Results indicated a predominance of Proteobacteria at both sites (&gt;65%), followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria were the most frequent within the Proteobacteria phylum during spring and winter, while Alphaproteobacteria dominated in the fall and summer. Within the 519 genera identified, Cellvibrio was the most frequent during spring (35.75%) and winter (30.73%); Limnobacter (24.49%) and Blastomonas (19.88%) dominated in the summer; and Sediminibacterium represented 10.26 and 12.41% of fall and winter samples, respectively. Sphingomonas was also identified in 17.15% of the fall samples. These five genera were more abundant at the high mountain site, while other common airborne bacteria were more frequent at the urban site (Kocuria, Delftia, Mesorhizobium, and Methylobacterium). Diversity values showed different patterns for both sites, with higher values during the cooler seasons in Izaña, whereas the opposite was observed in La Laguna. Regarding wind back trajectories, Tropical air masses were significantly different from African ones at both sites, showing the highest diversity and characterized by genera regularly associated with humans (Pseudomonas, Sphingomonas, and Cloacibacterium), as well as others related to extreme conditions (Alicyclobacillus) or typically associated with animals (Lachnospiraceae). Marine and African air masses were consistent and very similar in their microbial composition. By contrast, European trajectories were dominated by Cellvibrio, Pseudomonas, Pseudoxanthomonas, and Sediminibacterium. These data contribute to our current state of knowledge in the field of atmospheric microbiology. However, future studies are needed to increase our understanding of the influence of different environmental factors on atmospheric microbial dispersion and the potential impact of airborne microorganisms on ecosystems and public health.

scholarly journals Partitioning of Bacterial Communities between Seawater and Healthy, Black Band Diseased, and Dead Coral Surfaces

2002 ◽  
Vol 68 (5) ◽  
pp. 2214-2228 ◽  
Author(s):  
Jorge Frias-Lopez ◽  
Aubrey L. Zerkle ◽  
George T. Bonheyo ◽  
Bruce W. Fouke
Keyword(s):  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Coral Tissue ◽  
Dead Coral ◽  
Netherlands Antilles ◽  
Southern Caribbean ◽  
Black Band

ABSTRACT Distinct partitioning has been observed in the composition and diversity of bacterial communities inhabiting the surface and overlying seawater of three coral species infected with black band disease (BBD) on the southern Caribbean island of Curaçao, Netherlands Antilles. PCR amplification and sequencing of bacterial 16S rRNA genes (rDNA) with universally conserved primers have identified over 524 unique bacterial sequences affiliated with 12 bacterial divisions. The molecular sequences exhibited less than 5% similarity in bacterial community composition between seawater and the healthy, black band diseased, and dead coral surfaces. The BBD bacterial mat rapidly migrates across and kills the coral tissue. Clone libraries constructed from the BBD mat were comprised of eight bacterial divisions and 13% unknowns. Several sequences representing bacteria previously found in other marine and terrestrial organisms (including humans) were isolated from the infected coral surfaces, including Clostridium spp., Arcobacter spp., Campylobacter spp., Cytophaga fermentans, Cytophaga columnaris, and Trichodesmium tenue.

scholarly journals Secretory Antibodies Do Not Affect the Composition of the Bacterial Microbiota in the Terminal Ileum of 10-Week-Old Mice

2003 ◽  
Vol 69 (4) ◽  
pp. 2100-2109 ◽  
Author(s):  
Leanne Sait ◽  
Maja Galic ◽  
Richard A. Strugnell ◽  
Peter H. Janssen
Keyword(s):  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Small Animal ◽  
Rflp Analysis ◽  
Similarity Coefficient ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pairwise Similarity ◽  
Gastrointestinal Microbiota ◽  
Secretory Antibodies

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis was conducted on the 16S rRNA genes of the bacterial communities colonizing the epithelial surfaces of the terminal ilea of open conventionally housed mice in an institutional small-animal facility. Polymeric-immunoglobulin-receptor-deficient (pIgR−/−) mice that were unable to secrete antibodies across mucosal surfaces were cohoused with normal and otherwise genetically identical wild-type (C57BL/6) mice for 4 weeks. If secretory antibodies played a role in modeling the gastrointestinal microbiota, C57BL/6 mice would have had a more distinct and uniform microbiota than their pIgR−/− cage mates. The T-RFLP profiles of the bacterial communities were compared by using Sorensen's pairwise similarity coefficient, a newly developed weighted pairwise similarity coefficient, and on the basis of Shannon's and Simpson's diversity indices. No systematic differences were observed between the dominant components of the mucosa-associated bacterial communities of the terminal ileal walls of the two types of mice, indicating that secretory antibodies do not control the composition of this microbiota. Similar analyses of experiments conducted at two different times, between which the bacterial community composition of the mouse colony in the small-animal facility appeared to have changed, showed that differences could have been detected, had they existed.

scholarly journals Wastewater Treatment Effluent Reduces the Abundance and Diversity of Benthic Bacterial Communities in Urban and Suburban Rivers

2013 ◽  
Vol 79 (6) ◽  
pp. 1897-1905 ◽  
Author(s):  
Bradley Drury ◽  
Emma Rosi-Marshall ◽  
John J. Kelly
Keyword(s):  
Wastewater Treatment ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Treatment Plant ◽  
Freshwater Ecosystems ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Content Type ◽  
Wwtp Effluent ◽  
Sediment Bacterial Communities

ABSTRACTIn highly urbanized areas, wastewater treatment plant (WWTP) effluent can represent a significant component of freshwater ecosystems. As it is impossible for the composition of WWTP effluent to match the composition of the receiving system, the potential exists for effluent to significantly impact the chemical and biological characteristics of the receiving ecosystem. We assessed the impacts of WWTP effluent on the size, activity, and composition of benthic microbial communities by comparing two distinct field sites in the Chicago metropolitan region: a highly urbanized river receiving effluent from a large WWTP and a suburban river receiving effluent from a much smaller WWTP. At sites upstream of effluent input, the urban and suburban rivers differed significantly in chemical characteristics and in the composition of their sediment bacterial communities. Although effluent resulted in significant increases in inorganic nutrients in both rivers, surprisingly, it also resulted in significant decreases in the population size and diversity of sediment bacterial communities. Tag pyrosequencing of bacterial 16S rRNA genes revealed significant effects of effluent on sediment bacterial community composition in both rivers, including decreases in abundances ofDeltaproteobacteria,Desulfococcus,Dechloromonas, andChloroflexisequences and increases in abundances ofNitrospiraeandSphingobacterialessequences. The overall effect of the WWTP inputs was that the two rivers, which were distinct in chemical and biological properties upstream of the WWTPs, were almost indistinguishable downstream. These results suggest that WWTP effluent has the potential to reduce the natural variability that exists among river ecosystems and indicate that WWTP effluent may contribute to biotic homogenization.

scholarly journals Diversity and Dynamics of Seaweed Associated Microbial Communities Inhabiting the Lagoon of Venice

2020 ◽  
Vol 8 (11) ◽  
pp. 1657
Author(s):  
Abdul-Salam Juhmani ◽  
Alessandro Vezzi ◽  
Mohammad Wahsha ◽  
Alessandro Buosi ◽  
Fabio De Pascale ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Bacterial Communities ◽  
Host Response ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nutrient Concentrations ◽  
Lagoon Of Venice ◽  
Anthropogenic Stressors ◽  
Rich Diversity

Seaweeds are a group of essential photosynthetic organisms that harbor a rich diversity of associated microbial communities with substantial functions related to host health and defense. Environmental and anthropogenic stressors may disrupt the microbial communities and their metabolic activity, leading to host physiological alterations that negatively affect seaweeds’ performance and survival. Here, the bacterial communities associated with one of the most common seaweed, Ulva laetevirens Areshough, were sampled over a year at three sites of the lagoon of Venice affected by different environmental and anthropogenic stressors. Bacterial communities were characterized through Illumina sequencing of the V4 hypervariable region of 16S rRNA genes. The study demonstrated that the seaweed associated bacterial communities at sites impacted by environmental stressors were host-specific and differed significantly from the less affected site. Furthermore, these communities were significantly distinct from those of the surrounding seawater. The bacterial communities’ composition was significantly correlated with environmental parameters (nutrient concentrations, dissolved oxygen saturation, and pH) across sites. This study showed that several more abundant bacteria on U. laetevirens at stressed sites belonged to taxa related to the host response to the stressors. Overall, environmental parameters and anthropogenic stressors were shown to substantially affect seaweed associated bacterial communities, which reflect the host response to environmental variations.

Sign in / Sign up

Export Citation Format

Share Document