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.

scholarly journals Rhizosphere Community Selection Reveals Bacteria Associated With Reduced Root Disease

2020 ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

scholarly journals Rhizosphere community selection reveals bacteria associated with reduced root disease

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

scholarly journals Vaginal Microbiota of Women with Frequent Vulvovaginal Candidiasis

2009 ◽  
Vol 77 (9) ◽  
pp. 4130-4135 ◽  
Author(s):  
Xia Zhou ◽  
Rachel Westman ◽  
Roxana Hickey ◽  
Melanie A. Hansmann ◽  
Colleen Kennedy ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Vulvovaginal Candidiasis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Novel Bacteria

ABSTRACT Vulvovaginal candidiasis (VVC) is an insidious infection that afflicts a large proportion of women of all ages, and 5 to 8% of affected women experience recurrent VVC (RVVC). The aim of this study was to explore the possible importance of vaginal bacterial communities in reducing the risk of RVVC. The species composition and diversity of microbial communities were evaluated for 42 women with and without frequent VVC based on profiles of terminal restriction fragment polymorphisms of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences from the numerically dominant microbial populations. The data showed that there were no significant differences between the vaginal microbial communities of women in the two groups (likelihood score, 5.948; bootstrap P value, 0.26). Moreover, no novel bacteria were found in the communities of women with frequent VVC. The vaginal communities of most women in both groups (38/42; 90%) were dominated by species of Lactobacillus. The results of this study failed to provide evidence for the existence of altered or unusual vaginal bacterial communities in women who have frequent VVC compared to women who do not have frequent VVC. The findings suggest that commensal vaginal bacterial species may not be able to prevent VVC.

scholarly journals Rhizosphere Microbial Response to Multiple Metal(loid)s in Different Contaminated Arable Soils Indicates Crop-Specific Metal-Microbe Interactions

2018 ◽  
Vol 84 (24) ◽  
Author(s):  
Weimin Sun ◽  
Enzong Xiao ◽  
Valdis Krumins ◽  
Max M. Häggblom ◽  
Yiran Dong ◽  
...  
Keyword(s):  
Bacterial Communities ◽  
Metal Contamination ◽  
Abiotic Factors ◽  
Regression Tree ◽  
Chemical Properties ◽  
Environmental Parameters ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Arable Soils ◽  
Microbe Interactions

ABSTRACTIn this study, we sampled rhizosphere soils from seven different agricultural fields adjacent to mining areas and cultivated with different crops (corn, rice, or soybean), to study the interactions among the innate microbiota, soil chemical properties, plants, and metal contamination. The rhizosphere bacterial communities were characterized by Illumina sequencing of the 16S rRNA genes, and their interactions with the local environments, including biotic and abiotic factors, were analyzed. Overall, these soils were heavily contaminated with multiple metal(loid)s, including V, Cr, Cu, Sb, Pb, Cd, and As. The interactions between environmental parameters and microbial communities were identified using multivariate regression tree analysis, canonical correspondence analysis, and network analysis. Notably, metal-microbe interactions were observed to be crop specific. The rhizosphere communities were strongly correlated with V and Cr levels, although these sites were contaminated from Sb and Zn/Pb mining, suggesting that these two less-addressed metals may play important roles in shaping the rhizosphere microbiota. Members ofGaiellaceaecooccurred with other bacterial taxa (biotic interactions) and several metal(loid)s, suggesting potential metal(loid) resistance or cycling involving this less-well-known taxon.IMPORTANCEThe rhizosphere is the “hub” for plant-microbe interactions and an active region for exchange of nutrients and energy between soil and plants. In arable soils contaminated by mining activities, the rhizosphere may be an important barrier resisting metal uptake. Therefore, the responses of the rhizosphere microbiota to metal contamination involve important biogeochemical processes, which can affect metal bioavailability and thus impact food safety. However, understanding these processes remains a challenge. The current study illustrates that metal-microbe interactions may be crop specific and some less-addressed metals, such as V and Cr, may play important roles in shaping bacterial communities. The current study provides new insights into metal-microbe interactions and contributes to future implementation and monitoring efforts in contaminated arable soils.

scholarly journals Rhizosphere community selection reveals bacteria associated with reduced root disease

2020 ◽  
Author(s):  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
Scot H. Hulbert ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities.Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil.Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

scholarly journals Rhizosphere community selection reveals bacteria associated with reduced root disease 

2020 ◽  
Author(s):  
Timothy Paulitz ◽  
Chuntao Yin ◽  
Juan M. Casa Vargas ◽  
Daniel C. Schlatter ◽  
Christina H. Hagerty ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Plant Growth ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Wheat Root ◽  
Root Disease ◽  
Plant Diseases ◽  
16S Rrna Genes ◽  
Rrna Genes

Abstract Background: Microbes benefit plants by increasing nutrient availability, producing plant growth hormones, and protecting against pathogens. However, it is largely unknown how plants change root microbial communities. Results: In this study, we used a multi-cycle selection system and infection by the soilborne fungal pathogen Rhizoctonia solani AG8 (hereafter AG8) to examine how plants impact the rhizosphere bacterial community and recruit beneficial microorganisms to suppress soilborne fungal pathogens and promote plant growth. Successive plantings dramatically enhanced disease suppression on susceptible wheat cultivars to AG8 in the greenhouse. Accordingly, analysis of the rhizosphere soil microbial community using deep sequencing of 16S rRNA genes revealed distinct bacterial community profiles assembled over successive wheat plantings. Moreover, the cluster of bacterial communities formed from the AG8-infected rhizosphere was distinct from those without AG8 infection. Interestingly, the bacterial communities from the rhizosphere with the lowest wheat root disease gradually separated from those with the worst wheat root disease over planting cycles. Successive monocultures and application of AG8 increased the abundance of some bacterial genera which have potential antagonistic activities, such as Chitinophaga, Pseudomonas, Chryseobacterium, and Flavobacterium, and a group of plant growth-promoting (PGP) and nitrogen-fixing microbes, including Pedobacter, Variovorax, and Rhizobium. Furthermore, 47 bacteria isolates belong to 35 species were isolated. Among them, eleven and five exhibited antagonistic activities to AG8 and Rhizoctonia oryzae in vitro, respectively. Notably, Janthinobacterium displayed broad antagonism against the soilborne pathogens Pythium ultimum, AG8, and R. oryzae in vitro, and disease suppressive activity to AG8 in soil. Conclusions: Our results demonstrated that successive wheat plantings and pathogen infection can shape the rhizosphere microbial communities and specifically accumulate a group of beneficial microbes. Our findings suggest that soil community selection may offer the potential for addressing agronomic concerns associated with plant diseases and crop productivity.

scholarly journals Coupling Root Diameter With Rooting Depth to Reveal the Heterogeneous Assembly of Root-Associated Bacterial Communities in Soybean

2021 ◽  
Vol 12 ◽  
Author(s):  
Wen Luo ◽  
Xiaoyu Zai ◽  
Jieyu Sun ◽  
Da Li ◽  
Yuanli Li ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Plant Root ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Root Diameter ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rooting Depth

Root diameter and rooting depth lead to morphological and architectural heterogeneity of plant roots; however, little is known about their effects on root-associated microbial communities. Bacterial community assembly was explored across 156 samples from three rhizocompartments (the rhizosphere, rhizoplane, and endosphere) for different diameters (0.0–0.5 mm, 0.5–1.0 mm, 1.0–2.0 mm, and>2.0 mm) and depths (0–5 cm, 5–10 cm, 10–15 cm, and 15–20 cm) of soybean [Glycine max (L.) Merrill] root systems. The microbial communities of all samples were analyzed using amplicon sequencing of bacterial 16S rRNA genes. The results showed that root diameter significantly affected the rhizosphere and endosphere bacterial communities, while rooting depth significantly influenced the rhizosphere and rhizoplane bacterial communities. The bacterial alpha diversity decreased with increasing root diameter in all three rhizocompartments, and the diversity increased with increasing rooting depth only in the rhizoplane. Clearly, the hierarchical enrichment process of the bacterial community showed a change from the rhizosphere to the rhizoplane to the endosphere, and the bacterial enrichment was higher in thinner or deeper roots (except for the roots at a depth of 15–20 cm). Network analysis indicated that thinner or deeper roots led to higher bacterial network complexity. The core and keystone taxa associated with the specific root diameter class and rooting depth class harbored specific adaptation or selection strategies. Root diameter and rooting depth together affected the root-associated bacterial assembly and network complexity in the root system. Linking root traits to microbiota may enhance our understanding of plant root-microbe interactions and their role in developing environmentally resilient root ecosystems.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

scholarly journals Variability of the Sheep Lung Microbiota

2016 ◽  
Vol 82 (11) ◽  
pp. 3225-3238 ◽  
Author(s):  
Laura Glendinning ◽  
Steven Wright ◽  
Jolinda Pollock ◽  
Peter Tennant ◽  
David Collie ◽  
...  
Keyword(s):  
Spatial Variability ◽  
Dna Sequences ◽  
Bacterial Communities ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Large Animal ◽  
Local Factors ◽  
Adult Sheep ◽  
Sequencing Technologies ◽  
Host Influence

ABSTRACTSequencing technologies have recently facilitated the characterization of bacterial communities present in lungs during health and disease. However, there is currently a dearth of information concerning the variability of such data in health both between and within subjects. This study seeks to examine such variability using healthy adult sheep as our model system. Protected specimen brush samples were collected from three spatially disparate segmental bronchi of six adult sheep (age, 20 months) on three occasions (day 0, 1 month, and 3 months). To further explore the spatial variability of the microbiotas, more-extensive brushing samples (n= 16) and a throat swab were taken from a separate sheep. The V2 and V3 hypervariable regions of the bacterial 16S rRNA genes were amplified and sequenced via Illumina MiSeq. DNA sequences were analyzed using the mothur software package. Quantitative PCR was performed to quantify total bacterial DNA. Some sheep lungs contained dramatically different bacterial communities at different sampling sites, whereas in others, airway microbiotas appeared similar across the lung. In our spatial variability study, we observed clustering related to the depth within the lung from which samples were taken. Lung depth refers to increasing distance from the glottis, progressing in a caudal direction. We conclude that both host influence and local factors have impacts on the composition of the sheep lung microbiota.IMPORTANCEUntil recently, it was assumed that the lungs were a sterile environment which was colonized by microbes only during disease. However, recent studies using sequencing technologies have found that there is a small population of bacteria which exists in the lung during health, referred to as the “lung microbiota.” In this study, we characterize the variability of the lung microbiotas of healthy sheep. Sheep not only are economically important animals but also are often used as large animal models of human respiratory disease. We conclude that, while host influence does play a role in dictating the types of microbes which colonize the airways, it is clear that local factors also play an important role in this regard. Understanding the nature and influence of these factors will be key to understanding the variability in, and functional relevance of, the lung microbiota.

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